Sample	POS	FILTER	REF	ALT	DP	AF	SB	DP4	IMPACT	FUNCLASS	EFFECT	GENE	CODON	AA	TRID	min(AF)	max(AF)	countunique(change)	countunique(FUNCLASS)	change
ERR5749096	241	PASS	C	T	12154	0.856014	0	0,0,6050,6037	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749096	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	7364	0.001086	0	7358,0,8,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749096	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	7364	0.002173	0	7324,0,16,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749096	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	7364	0.003123	0	7324,0,23,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749096	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	7353	0.002584	0	6774,0,523,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749096	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	7353	0.001224	0	7344,0,9,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749096	657	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7375	0.00339	0	0,7347,0,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A131V	leader	0.001202	0.365979	3	1	C>T
ERR5749096	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	31296	7.03E-4	23	23899,7375,22,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749096	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	31296	0.001502	52	23874,7375,47,0	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749096	843	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	47710	7.76E-4	4	23852,23783,26,33	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cAt	P13H	nsp2	0.000301	0.050923	4	2	C>A
ERR5749096	913	PASS	C	T	23906	0.917761	0	0,14,0,23849	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749096	2293	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	10437	0.001437	0	10416,0,21,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caG/caT	Q496H	nsp2	0.001437	0.968398	1	1	G>T
ERR5749096	2305	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTAAATAAATTTTTGGCTTTGTGTGCTGACTCTATCATTATTGGTGGAGCTAAACTTAAAGC	G	10437	0.001533	0	10421,0,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtaaataaatttttggctttgtgtgctgactctatcattattggtggagctaaacttaaagccttg/	VNKFLALCADSIIIGGAKLKAL502	nsp2	0.000443	0.070409	4	3	GCTTGTAAATAAATTTTTGGCTTTGTGTGCTGACTCTATCATTATTGGTGGAGCTAAACTTAAAGC>G
ERR5749096	2862	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	7435	0.001345	0	7346,79,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gaa/	E49	nsp3	0.000547	0.850688	4	2	CAG>C
ERR5749096	3037	PASS	C	T	14618	0.826105	45	0,15,7302,7197	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749096	3177	PASS	C	T	29608	0.923095	4	4,3,22242,7333	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P153L	nsp3	0.000773	0.96008	3	2	C>T
ERR5749096	3267	PASS	C	T	22248	0.968312	2147483647	0,0,22234,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749096	4423	PASS	C	T	14977	0.953796	310	1,9,14956,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	cgC/cgT	R568	nsp3	0.00063	0.953796	2	2	C>T
ERR5749096	4861	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	15065	6.64E-4	0	0,15055,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	agt/	S716	nsp3	0.000632	0.115789	2	1	TA>T
ERR5749096	5002	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	14353	0.001115	0	14331,6,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acg/	T763	nsp3	0.001115	0.976835	3	2	CCA>C
ERR5749096	5170	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	14326	0.001745	0	0,14301,0,25	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T819	nsp3	0.000565	0.894036	2	2	CCA>C
ERR5749096	5388	PASS	C	A	3731	0.958724	2147483647	0,0,3730,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749096	5605	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	26924	4.09E-4	0	23181,3732,10,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K963	nsp3	0.000409	0.095477	2	2	GA>G
ERR5749096	5628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	23190	5.61E-4	0	23177,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acg/	T970	nsp3	0.000561	0.973644	3	2	CG>C
ERR5749096	5986	PASS	C	T	9398	0.975101	0	1,0,9389,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749096	6414	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAGT	A	25260	0.001227	0	0,25229,0,31	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gtagtg/gtg	VV1233V	nsp3	0.000549	0.930413	2	2	AAGT>A
ERR5749096	6954	PASS	T	C	20119	0.820319	0	0,1,0,20018	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749096	7070	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	26668	0.00915	1526	6231,20177,246,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggc/Cgc	G1451R	nsp3	0.000698	0.101434	3	1	G>C
ERR5749096	8092	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	23546	8.92E-4	0	23525,0,21,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T1793	nsp3	0.000539	0.063953	3	2	CA>C
ERR5749096	8964	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	14541	8.25E-4	0	14526,3,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K138	nsp4	0.000553	0.981649	4	2	CA>C
ERR5749096	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	24334	0.001931	115	13742,10545,47,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749096	10193	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	18078	7.74E-4	0	18064,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gaa/	E47	3Cpro	0.000774	0.869819	2	2	GA>G
ERR5749096	10323	PASS	A	G	18055	0.961119	0	0,1,0,18041	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749096	11095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTT	C	27925	6.09E-4	0	27896,0,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L43	nsp6	0.000515	0.887707	7	2	CTT>C
ERR5749096	11185	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	54500	7.52E-4	6	27743,26646,28,19	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttG/ttA	L71	nsp6	0.000356	0.883658	3	3	G>A
ERR5749096	11287	PASS	GTCTGGTTTT	G	27929	0.996849	0	0,88,0,27841	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749096	11355	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	36255	6.9E-4	0	8311,27919,5,20	HIGH	NONE	FRAME_SHIFT	ORF1ab	aga/	R129	nsp6	0.000455	0.982262	3	2	CA>C
ERR5749096	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	31552	0.001426	17	23177,8307,46,6	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749096	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	19460	0.00185	0	19393,0,37,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749096	12513	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19458	0.001028	0	19426,0,21,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aTg	T141M	nsp8	0.000794	0.984064	2	2	C>T
ERR5749096	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	42817	0.001588	0	21372,21327,39,38	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749096	13994	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	18014	7.22E-4	0	18001,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L186	RdRp	0.000427	0.114441	3	2	CT>C
ERR5749096	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	17873	0.004252	2147483647	17427,138,12,289	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749096	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	34724	4.03E-4	0	17418,17320,7,7	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749096	14408	PASS	C	T	34724	0.841349	9	1,5,17329,17127	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749096	14676	PASS	C	T	16516	0.799891	0	16,0,16445,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749096	15240	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21905	0.003104	0	21803,20,72,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N600	RdRp	0.000934	0.931284	2	2	C>T
ERR5749096	15279	PASS	C	T	21883	0.883151	0	2,0,21854,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749096	15983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	15217	7.89E-4	0	15200,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T850	RdRp	0.000701	0.338235	2	1	TA>T
ERR5749096	16176	PASS	T	C	22034	0.98112	0	0,0,6792,15235	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749096	16508	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	28110	0.00121	0	28049,8,52,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGt/gTt	G91V	helicase	0.000561	0.074909	2	2	G>T
ERR5749096	17502	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	16355	6.11E-4	0	16345,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N423	helicase	0.000611	0.9865	2	2	CA>C
ERR5749096	17678	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16356	0.001162	0	3,16326,0,19	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aTg	T481M	helicase	0.001162	0.968704	2	1	C>T
ERR5749096	17766	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	16931	7.68E-4	0	16918,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F511	helicase	0.000768	0.920632	2	2	CT>C
ERR5749096	17781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	16931	6.5E-4	0	16920,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N516	helicase	0.00065	0.986978	2	2	TA>T
ERR5749096	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	23675	0.001014	0	23651,0,24,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749096	18747	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	23675	4.65E-4	0	23664,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tataat/	YN237	ExoN	0.000375	0.982946	4	2	CTA>C
ERR5749096	18756	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	23672	7.18E-4	0	23656,0,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F240	ExoN	0.000392	0.942688	3	2	GT>G
ERR5749096	19343	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	14965	8.69E-4	0	14952,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F436	ExoN	0.000519	0.192257	7	2	CT>C
ERR5749096	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15859	0.001135	0	15831,0,18,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749096	20951	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	27815	4.31E-4	0	27802,1,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gat/	D99	MethTr	0.000431	0.138667	3	3	CAG>C
ERR5749096	20987	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	55502	6.13E-4	0	27766,27704,17,17	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L111	MethTr	0.000276	0.056129	4	2	CT>C
ERR5749096	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	27816	6.11E-4	0	0,27799,0,17	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TA>T
ERR5749096	21762	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTATACA	C	13208	0.001741	0	13185,0,23,0	MODERATE	NONE	CODON_DELETION	S	atacat/	IH68	S	0.001297	0.875707	2	2	CTATACA>C
ERR5749096	21764	PASS	ATACATG	A	13208	0.995987	0	53,0,13155,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749096	21990	PASS	TTTA	T	13211	0.998259	0	0,23,0,13188	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749096	22293	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	36938	4.33E-4	23	11188,25734,0,16	HIGH	NONE	FRAME_SHIFT	S	tta/	L244	S	0.000308	0.160511	4	1	TA>T
ERR5749096	22384	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	11189	0.001609	0	11162,0,19,0	LOW	SILENT	SYNONYMOUS_CODING	S	acT/acC	T274	S	0.001609	0.118834	1	1	T>C
ERR5749096	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	21048	0.001473	0	0,21003,0,35	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749096	23063	PASS	A	T	12774	0.862768	0	0,1,0,12734	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749096	23271	PASS	C	A	30338	0.921287	0	3,0,30312,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749096	23403	PASS	A	G	30341	0.971392	0	0,5,0,30318	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749096	23426	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTT	G	30352	4.28E-4	0	0,30339,0,13	HIGH	NONE	FRAME_SHIFT	S	gtt/	V622	S	0.000428	0.916192	4	2	GTT>G
ERR5749096	23604	PASS	C	A	13906	0.939451	0	8,0,13889,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749096	23709	PASS	C	T	13890	0.938733	0	0,5,0,13861	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749096	23817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	27492	9.09E-4	1	13561,13888,12,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTt/cCt	L752P	S	0.000646	0.066832	1	1	T>C
ERR5749096	24506	PASS	T	G	20551	0.974308	0	27,0,20521,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749096	24914	PASS	G	C	43218	0.959484	0	0,0,21530,21631	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749096	25482	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	43770	3.2E-4	0	21900,21857,7,7	HIGH	NONE	FRAME_SHIFT	ORF3a	gct/	A31	orf3a	0.00032	0.83761	2	2	CG>C
ERR5749096	25496	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	43750	6.4E-4	11	21635,21598,216,255	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aTa/aGa	I35R	orf3a	0.000369	0.96555	3	2	T>G
ERR5749096	25555	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	21924	0.001186	0	0,21898,0,26	HIGH	NONE	FRAME_SHIFT	ORF3a	ttt/	F56	orf3a	0.000552	0.900573	5	2	GT>G
ERR5749096	25587	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	21928	7.75E-4	0	0,21911,0,17	HIGH	NONE	FRAME_SHIFT	ORF3a	aag/	K67	orf3a	0.000598	0.813206	6	2	CA>C
ERR5749096	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	11429	0.003587	352	11340,28,24,19	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749096	27513	PASS	C	T	27216	0.981739	0	3,0,27178,1	LOW	SILENT	SYNONYMOUS_CODING	ORF7a	taC/taT	Y40	orf7a	0.001863	0.982462	2	2	C>T
ERR5749096	27972	PASS	C	T	8672	0.905789	0	0,0,8590,57	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749096	28048	PASS	G	T	8613	0.929409	0	0,3,0,8605	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749096	28111	PASS	A	G	36652	0.979237	1	10,2,28012,8617	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749096	28270	PASS	TA	T	54410	0.995663	632	242,4,27692,26482	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749096	28280	PASS	G	C	54306	0.934519	26	10,0,27748,26459	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749096	28281	PASS	A	T	54306	0.912809	40	32,7,27728,26458	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749096	28282	PASS	T	A	54310	0.908451	45	34,7,27640,26480	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749096	28292	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	55780	0.001273	0	27785,27924,34,37	HIGH	NONE	FRAME_SHIFT	N	aat/	N8	N	0.000304	0.055324	4	2	CA>C
ERR5749096	28881	PASS	G	A	20958	0.774311	21	11,1,10397,10295	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749096	28882	PASS	G	A	20957	0.830987	9	6,1,10492,10257	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749096	28883	PASS	G	C	20957	0.944839	6	0,2,10511,10427	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749096	28977	PASS	C	T	10652	0.914664	0	0,1,0,10633	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749096	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	60446	0.001125	0	30347,29993,41,41	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749096	29253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	30433	3.61E-4	0	0,30422,0,11	HIGH	NONE	FRAME_SHIFT	N	gga/	G328	N	0.000361	0.053998	4	2	CG>C
ERR5749096	29743	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7783	0.003469	0	0,7749,0,29	.	.	.	.	.	.	.	0.001027	0.859785	2	1	C>T
ERR5749097	241	PASS	C	T	12978	0.859532	0	1,1,6436,6486	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749097	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	14817	0.0027	0	14779,2,40,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749097	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	14819	6.75E-4	0	14752,4,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749097	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	14819	0.003037	0	14752,4,45,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749097	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	14808	0.001621	0	14084,8,586,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749097	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	14808	0.001756	0	14774,8,26,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749097	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	36461	8.23E-4	20	21599,14821,25,5	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749097	913	PASS	C	T	21618	0.910954	0	0,15,0,21567	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749097	1510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	22441	0.003476	0	0,22147,0,87	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G235	nsp2	0.002159	0.937304	1	1	T>C
ERR5749097	1813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	20048	0.001147	0	0,20005,0,27	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcA	A336	nsp2	0.001022	0.152738	4	2	T>A
ERR5749097	1820	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	20058	0.00329	0	0,19958,0,68	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggt/Agt	G339S	nsp2	0.001189	0.949024	2	2	G>A
ERR5749097	2855	PASS	C	T	12659	0.926613	0	2,0,12573,79	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L46F	nsp3	0.000497	0.926613	2	2	C>T
ERR5749097	3037	PASS	C	T	24987	0.816865	82	1,31,12498,12264	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749097	3177	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	33692	8.61E-4	39	21076,12574,34,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cAt	P153H	nsp3	0.000773	0.96008	3	2	C>A
ERR5749097	3267	PASS	C	T	21108	0.971101	0	3,0,21096,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749097	5388	PASS	C	A	8376	0.961318	2147483647	0,0,8371,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749097	5497	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	8373	0.001075	0	0,8362,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaaaga/	KR927	nsp3	0.000964	0.897745	3	2	CAA>C
ERR5749097	5986	PASS	C	T	15629	0.975686	0	4,0,15615,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749097	6762	PASS	C	T	39244	0.964683	12	2,6,24572,14642	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T1348I	nsp3	0.001474	0.966761	2	1	C>T
ERR5749097	6954	PASS	T	C	24485	0.816459	0	0,4,0,24339	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749097	8664	PASS	C	T	26560	0.957492	0	5,0,26535,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T37I	nsp4	0.003182	0.985915	1	1	C>T
ERR5749097	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	34589	5.78E-4	49	19186,15383,20,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749097	10323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	20291	0.001528	0	0,20201,0,32	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749097	11287	PASS	GTCTGGTTTT	G	19103	0.998377	0	0,31,0,19072	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749097	12162	PASS	A	G	43486	0.969025	16	7,0,24253,19206	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cAg/cGg	Q24R	nsp8	0.000894	0.982497	1	1	A>G
ERR5749097	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	32894	0.001611	0	16413,16374,31,32	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749097	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	11383	0.00448	2147483647	11091,100,5,180	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749097	14408	PASS	C	T	22101	0.841817	9	0,3,11034,10910	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749097	14676	PASS	C	T	13417	0.748528	0	3,0,13373,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749097	15279	PASS	C	T	22606	0.91082	0	3,0,22576,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749097	16176	PASS	T	C	23023	0.978847	5	3,0,12201,10807	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749097	16939	PASS	T	C	22306	0.957276	0	0,0,22285,3	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Tta/Cta	L235	helicase	0.000959	0.959205	2	2	T>C
ERR5749097	17615	PASS	A	G	18898	0.893163	0	0,2,2,18837	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749097	18246	PASS	C	T	14784	0.961107	0	0,3,0,14769	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y69	ExoN	0.960724	0.984848	1	1	C>T
ERR5749097	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	27572	5.44E-4	0	27557,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749097	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	36811	0.002119	0	36707,0,83,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749097	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34240	9.93E-4	0	34161,0,35,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749097	21762	PASS	C	T	15737	0.875707	0	1,0,15686,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gTt	A67V	S	0.001297	0.875707	2	2	C>T
ERR5749097	21764	PASS	ATACATG	A	15737	0.998157	0	29,0,15708,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749097	21990	PASS	TTTA	T	15741	0.998031	0	0,31,3,15707	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749097	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16032	0.001185	0	97,15911,0,20	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749097	23063	PASS	A	T	95	0.863158	2147483647	0,0,0,95	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749097	23271	PASS	C	A	22368	0.922523	0	4,0,22341,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749097	23403	PASS	A	G	22365	0.966957	0	0,1,0,22348	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749097	23604	PASS	C	A	18901	0.937887	0	21,0,18871,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749097	23709	PASS	C	T	18879	0.94131	0	0,7,2,18841	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749097	24506	PASS	T	G	18368	0.977134	0	11,0,18352,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749097	24914	PASS	G	C	41683	0.959096	0	0,0,20771,20885	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749097	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	28483	0.002598	107	20262,8130,84,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749097	25571	PASS	C	T	20611	0.909223	0	0,4,0,20572	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	tCc/tTc	S60F	orf3a	0.001558	0.922217	1	1	C>T
ERR5749097	25587	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	20621	6.79E-4	0	1,20604,0,14	HIGH	NONE	FRAME_SHIFT	ORF3a	aag/	K67	orf3a	0.000598	0.813206	6	2	CA>C
ERR5749097	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	25123	0.001473	550	25025,16,16,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749097	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	25085	6.38E-4	0	25069,0,16,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749097	25855	PASS	G	T	25051	0.892619	0	0,62,5,24967	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gac/Tac	D155Y	orf3a	0.001326	0.969697	1	1	G>T
ERR5749097	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	14499	0.002414	0	6,14457,0,35	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749097	27972	PASS	C	T	14329	0.900412	56	3,3,14204,68	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749097	28048	PASS	G	T	14268	0.920592	0	0,22,0,14236	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749097	28111	PASS	A	G	33222	0.977485	0	4,3,18936,14268	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749097	28270	PASS	TA	T	36601	0.994536	550	204,2,18669,17732	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749097	28280	PASS	G	C	36522	0.936696	46	20,1,18711,17712	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749097	28281	PASS	A	T	36522	0.916434	72	33,2,18703,17710	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749097	28282	PASS	T	A	36523	0.909181	26	36,13,18661,17718	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749097	28881	PASS	G	A	17584	0.733223	14	12,3,8615,8623	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749097	28882	PASS	G	A	17584	0.824613	12	5,0,8800,8610	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749097	28883	PASS	G	C	17584	0.935965	0	0,0,8819,8750	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749097	28977	PASS	C	T	8967	0.929185	0	0,1,1,8941	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749097	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	40467	0.001013	95	31448,8936,14,29	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749097	29096	PASS	G	T	31483	0.051234	0	29776,0,1687,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Ggc/Tgc	G275C	N	0.003164	0.051234	2	1	G>T
ERR5749097	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	62502	7.84E-4	0	31383,31025,32,29	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749098	219	PASS	G	T	29008	0.789851	4	84,73,14393,14416	.	.	.	.	.	.	.	0.001608	0.789851	2	1	G>T
ERR5749098	241	PASS	C	T	29003	0.845533	3	2,4,14441,14407	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749098	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	10780	7.42E-4	0	10769,1,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749098	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	40660	4.92E-4	14	29841,10797,19,1	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749098	913	PASS	C	T	29853	0.912706	0	0,18,0,29799	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749098	2702	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	52237	6.89E-4	2650	51895,40,69,115	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F633V	nsp2	0.000632	0.333333	1	1	T>G
ERR5749098	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	103688	0.001167	2147483647	51722,48559,103,3006	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749098	3037	PASS	C	T	30422	0.821609	70	0,23,15203,14958	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749098	3267	PASS	C	T	28476	0.969729	0	3,0,28462,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749098	3671	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	36247	9.38E-4	0	18074,17920,19,19	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E318K	nsp3	0.000351	0.0625	6	2	G>A
ERR5749098	4764	PASS	A	G	19163	0.93404	0	3,0,19133,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cAt/cGt	H682R	nsp3	0.000673	0.93404	4	2	A>G
ERR5749098	5388	PASS	C	A	8444	0.957603	0	1,0,8440,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749098	5986	PASS	C	T	19790	0.97524	0	1,0,19771,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749098	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18407	0.00125	0	2,18174,0,32	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749098	6954	PASS	T	C	32897	0.818099	0	0,9,0,32733	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749098	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	43498	6.67E-4	96	20195,23274,29,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749098	11287	PASS	GTCTGGTTTT	G	23355	0.998501	0	0,35,0,23320	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749098	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	41993	0.001238	1	20966,20922,26,28	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749098	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	15807	0.003606	2147483647	15445,123,6,223	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749098	14408	PASS	C	T	30745	0.839616	5	4,8,15355,15167	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749098	14676	PASS	C	T	17010	0.809465	0	2,0,16970,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749098	15279	PASS	C	T	29860	0.895814	0	1,0,29824,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749098	16176	PASS	T	C	25153	0.98032	0	0,0,11122,14024	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749098	17747	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19017	0.001052	0	18989,1,20,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P504L	helicase	0.000839	0.968462	2	2	C>T
ERR5749098	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	33611	4.17E-4	0	0,33597,0,14	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749098	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	42581	0.002325	0	42448,2,104,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749098	21764	PASS	ATACATG	A	19218	0.996618	0	65,0,19153,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749098	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	19219	5.72E-4	0	19207,1,11,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749098	21990	PASS	TTTA	T	19225	0.999324	0	0,13,8,19204	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749098	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	38587	9.33E-4	2	16409,22124,18,19	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749098	23063	PASS	A	T	16400	0.872073	0	0,2,0,16336	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749098	23271	PASS	C	A	28952	0.912061	0	4,0,28925,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749098	23403	PASS	A	G	28942	0.970424	0	0,6,0,28918	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749098	23604	PASS	C	A	21758	0.936207	0	13,0,21731,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749098	23709	PASS	C	T	21732	0.939582	0	0,9,0,21697	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749098	23817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	47563	7.78E-4	2	25764,21737,22,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTt/cCt	L752P	S	0.000646	0.066832	1	1	T>C
ERR5749098	24506	PASS	T	G	22919	0.973428	0	9,0,22900,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749098	24914	PASS	G	C	40723	0.961791	3	1,0,20284,20412	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749098	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	33723	0.001245	58	23924,9736,56,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749098	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	37920	0.001556	786	37784,31,28,33	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749098	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	37853	6.87E-4	0	37827,0,26,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749098	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	38088	0.001234	2031	37481,202,220,143	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749098	26395	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	32546	7.07E-4	2837	16376,15160,9,972	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	Ctt/Att	L51I	E	0.000707	0.745829	2	1	C>A
ERR5749098	27391	PASS	A	C	25588	0.938682	0	0,28,6,25550	.	.	.	.	.	.	.	0.000702	0.938682	3	1	A>C
ERR5749098	27972	PASS	C	T	17005	0.899206	20	1,1,16872,72	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749098	28048	PASS	G	T	16935	0.924771	0	0,25,0,16902	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749098	28111	PASS	A	G	44489	0.978736	0	6,3,27515,16948	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749098	28250	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TCTG	27468	8.01E-4	0	27396,0,22,0	MODERATE	NONE	CODON_INSERTION	ORF8	ttc/CTGttc	F120LF	orf8	0.000494	0.993968	5	3	T>TCTG
ERR5749098	28250	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TG	27468	0.00233	0	27396,0,64,0	HIGH	NONE	FRAME_SHIFT	ORF8	ttc/Gttc	F120V?	orf8	0.000494	0.993968	5	3	T>TG
ERR5749098	28253	PASS	C	T	27430	0.942545	24	102,1,27299,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749098	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	27430	0.003573	24	27332,0,97,1	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749098	28254	PASS	A	C	27430	0.90051	0	63,0,27252,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	Atc/Ctc	I121L	orf8	0.000541	0.914398	3	2	A>C
ERR5749098	28270	PASS	TA	T	53520	0.9946	752	283,4,27124,26107	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749098	28271	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AA	A	53515	0.001233	191	27336,26116,66,0	.	.	.	.	.	.	.	0.000482	0.924941	3	2	AA>A
ERR5749098	28280	PASS	G	C	53427	0.937897	5	10,5,27237,26082	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749098	28281	PASS	A	T	53427	0.915586	24	29,10,27227,26080	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749098	28282	PASS	T	A	53429	0.911378	3	21,15,27154,26102	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749098	28881	PASS	G	A	24739	0.753224	26	15,2,12190,12162	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749098	28882	PASS	G	A	24738	0.829008	7	10,4,12371,12144	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749098	28883	PASS	G	C	24738	0.944862	0	0,0,12395,12328	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749098	28977	PASS	C	T	12579	0.92885	0	0,1,3,12567	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749098	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	69932	9.44E-4	0	35145,34686,38,38	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749099	241	PASS	C	T	14912	0.863063	0	0,0,7419,7443	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749099	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	12600	7.14E-4	0	12597,0,9,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749099	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	12600	0.002302	0	12566,0,29,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749099	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12585	0.002384	0	11499,0,1027,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749099	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	12585	7.15E-4	0	12576,0,9,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749099	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	30562	6.22E-4	23	17916,12620,17,2	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749099	913	PASS	C	T	17930	0.918516	0	0,9,0,17907	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749099	3037	PASS	C	T	17538	0.822215	30	0,10,8763,8648	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749099	3267	PASS	C	T	18328	0.969718	0	3,0,18315,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749099	4237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTA	T	36305	4.41E-4	0	18168,18121,8,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	ata/	I508	nsp3	0.000302	0.918634	2	2	TTA>T
ERR5749099	5388	PASS	C	A	6052	0.9539	0	1,0,6047,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749099	5986	PASS	C	T	12610	0.972165	2147483647	0,0,12606,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749099	6762	PASS	C	T	31778	0.962647	11	1,4,19980,11769	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T1348I	nsp3	0.001474	0.966761	2	1	C>T
ERR5749099	6954	PASS	T	C	19925	0.824592	0	0,2,0,19846	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749099	8664	PASS	C	T	18098	0.95668	2147483647	0,0,18083,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T37I	nsp4	0.003182	0.985915	1	1	C>T
ERR5749099	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	28320	0.002048	136	16394,11868,58,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749099	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	19233	0.001352	0	19174,1,45,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749099	11287	PASS	GTCTGGTTTT	G	19228	0.998076	0	0,37,1,19190	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749099	12125	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	17162	0.001049	0	6,17095,0,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y12H	nsp8	0.000847	0.113436	1	1	T>C
ERR5749099	12162	PASS	A	G	38715	0.977296	7	1,4,21535,17149	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cAg/cGg	Q24R	nsp8	0.000894	0.982497	1	1	A>G
ERR5749099	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29991	0.0012	1	14979,14937,21,23	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749099	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12171	0.002301	2130	11960,83,7,115	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749099	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	23814	4.62E-4	0	11948,11864,6,5	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749099	14408	PASS	C	T	23814	0.845385	9	2,7,11886,11741	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749099	14676	PASS	C	T	11740	0.84293	0	7,0,11710,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749099	15279	PASS	C	T	18942	0.88998	0	3,0,18911,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749099	16176	PASS	T	C	20028	0.981875	0	0,0,10135,9885	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749099	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	19625	0.001019	0	19603,1,20,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749099	16939	PASS	T	C	19605	0.953277	0	0,0,19580,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Tta/Cta	L235	helicase	0.000959	0.959205	2	2	T>C
ERR5749099	17615	PASS	A	G	15698	0.907759	0	0,4,2,15656	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749099	18246	PASS	C	T	12272	0.960724	0	0,4,0,12260	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y69	ExoN	0.960724	0.984848	1	1	C>T
ERR5749099	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	24829	8.46E-4	0	24808,0,21,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749099	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24419	0.002334	0	24344,0,65,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749099	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23148	0.001469	0	23083,0,37,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749099	21764	PASS	ATACATG	A	12360	0.994175	0	71,0,12288,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749099	21990	PASS	TTTA	T	12362	0.998059	0	0,24,2,12336	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749099	23063	PASS	A	T	14349	0.867238	0	0,4,0,14284	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749099	23271	PASS	C	A	19224	0.923221	0	1,0,19204,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749099	23403	PASS	A	G	19217	0.979289	0	0,2,1,19203	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749099	23604	PASS	C	A	15625	0.942464	0	12,0,15607,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749099	23709	PASS	C	T	15613	0.945878	0	0,4,1,15591	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749099	24506	PASS	T	G	16614	0.975563	0	15,0,16593,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749099	24914	PASS	G	C	37682	0.962449	2	2,1,18776,18879	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749099	25571	PASS	C	T	17700	0.915819	0	0,12,0,17673	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	tCc/tTc	S60F	orf3a	0.001558	0.922217	1	1	C>T
ERR5749099	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	18313	6.01E-4	0	18302,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749099	25782	PASS	C	T	18297	0.955348	0	2,0,18271,0	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	tgC/tgT	C130	orf3a	0.000916	0.955348	1	1	C>T
ERR5749099	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	18494	0.001298	1210	18206,138,56,79	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749099	25855	PASS	G	T	18287	0.901788	0	0,45,0,18232	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gac/Tac	D155Y	orf3a	0.001326	0.969697	1	1	G>T
ERR5749099	26526	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	11034	0.001541	0	3,11004,0,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Gca/Aca	A2T	M	0.001224	0.951192	3	1	G>A
ERR5749099	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	13027	0.001228	0	2,13008,0,16	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749099	27972	PASS	C	T	10825	0.907621	39	1,2,10723,61	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749099	28048	PASS	G	T	10771	0.931668	0	0,14,0,10752	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749099	28111	PASS	A	G	30028	0.977354	1	4,3,19244,10771	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749099	28270	PASS	TA	T	37395	0.995481	427	169,4,19024,18202	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749099	28280	PASS	G	C	37330	0.943665	21	8,0,19065,18193	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749099	28281	PASS	A	T	37330	0.923359	20	22,7,19053,18188	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749099	28282	PASS	T	A	37334	0.913082	6	19,11,19022,18200	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749099	28881	PASS	G	A	15635	0.781964	12	5,0,7734,7691	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749099	28882	PASS	G	A	15635	0.832875	0	1,0,7829,7677	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749099	28883	PASS	G	C	15635	0.94685	0	0,0,7834,7788	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749099	28977	PASS	C	T	7945	0.93304	0	0,1,0,7917	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749099	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	54975	0.001	0	27591,27279,37,36	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749100	241	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8	0.75	0	0,0,4,4	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749100	913	PASS	C	T	154	0.88961	2147483647	0,0,0,154	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749100	1021	PASS	G	T	331	0.054381	0	313,0,18,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caG/caT	Q72H	nsp2	0.003544	0.054381	1	1	G>T
ERR5749100	1247	PASS	G	T	254	0.098425	0	0,228,0,26	HIGH	NONSENSE	STOP_GAINED	ORF1ab	Gaa/Taa	E148*	nsp2	0.001076	0.098425	2	2	G>T
ERR5749100	1357	PASS	TG	T	295	0.077966	0	272,0,23,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/	V185	nsp2	0.000493	0.077966	3	2	TG>T
ERR5749100	1874	PASS	G	T	151	0.344371	0	0,98,0,53	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gca/Tca	A357S	nsp2	0.001611	0.344371	2	1	G>T
ERR5749100	3037	PASS	C	T	38	0.842105	0	0,0,19,19	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749100	3267	PASS	C	T	97	1.0	2147483647	0,0,97,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749100	3832	PASS	C	T	55	0.327273	0	35,0,20,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	agC/agT	S371	nsp3	0.000689	0.327273	4	2	C>T
ERR5749100	4133	PASS	G	GA	90	0.155556	55	26,50,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/gAtt	V472D?	nsp3	0.000771	0.155556	2	1	G>GA
ERR5749100	4136	PASS	G	T	90	0.155556	55	26,50,14,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Ttt	V473F	nsp3	0.00075	0.974623	4	2	G>T
ERR5749100	4529	PASS	TTTTACTTTTACACCAGTAAAACAACTG	T	72	0.402778	0	0,43,0,29	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ttttacttttacaccagtaaaacaactgta/tta	FYFYTSKTTV604L	nsp3	0.000527	0.402778	3	1	TTTTACTTTTACACCAGTAAAACAACTG>T
ERR5749100	4687	PASS	A	G	71	0.126761	0	61,0,10,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acA/acG	T656	nsp3	0.126761	0.126761	1	1	A>G
ERR5749100	5388	PASS	C	A	14	0.928571	2147483647	0,0,14,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749100	5605	PASS	G	A	199	0.095477	4	166,14,19,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaG/aaA	K962	nsp3	0.000409	0.095477	2	2	G>A
ERR5749100	5986	PASS	C	T	60	1.0	2147483647	0,0,60,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749100	6408	PASS	C	T	132	0.166667	0	0,107,0,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S1230F	nsp3	0.166667	0.166667	1	1	C>T
ERR5749100	6741	PASS	G	T	194	0.056701	0	0,183,0,11	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cGg/cTg	R1341L	nsp3	0.001093	0.204082	3	2	G>T
ERR5749100	6954	PASS	T	C	574	0.804878	2147483647	0,0,0,571	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749100	6982	PASS	C	T	576	0.899306	2147483647	0,0,0,576	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C1421	nsp3	0.001915	0.911934	1	1	C>T
ERR5749100	8151	PASS	T	C	50	0.34	0	14,15,10,10	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gTc/gCc	V1811A	nsp3	0.00055	0.34	2	1	T>C
ERR5749100	8254	PASS	A	G	29	0.862069	0	0,4,0,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atA/atG	I1845M	nsp3	0.000412	0.959563	2	2	A>G
ERR5749100	8669	PASS	T	C	49	0.22449	0	38,0,11,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F39L	nsp4	0.000973	0.22449	1	1	T>C
ERR5749100	9202	PASS	TG	T	135	0.155556	0	0,114,0,21	HIGH	NONE	FRAME_SHIFT	ORF1ab	gat/	D217	nsp4	0.002572	0.155556	1	1	TG>T
ERR5749100	9473	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	6	1.0	2147483647	0,0,0,6	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gct/Act	A307T	nsp4	0.888889	1	1	1	G>A
ERR5749100	10263	PASS	C	T	2088	0.192529	0	820,818,225,223	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A70V	3Cpro	0.000593	0.192529	3	2	C>T
ERR5749100	10386	PASS	C	CT	1172	0.070819	948	43,1046,83,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tca/tTca	S113F?	3Cpro	0.000642	0.160456	4	2	C>CT
ERR5749100	11287	PASS	GTCTGGTTTT	G	1125	0.996444	0	0,4,0,1121	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749100	12067	PASS	G	T	3121	0.086511	0	1404,1404,158,153	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atT	M75I	nsp7	0.001146	0.086511	2	1	G>T
ERR5749100	13506	PASS	C	T	268	0.074627	0	122,123,11,11	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749100	14087	PASS	G	T	321	0.130841	0	274,0,47,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tGg/tTg	W216L	RdRp	0.001684	0.130841	2	1	G>T
ERR5749100	14408	PASS	C	T	10	0.9	0	0,0,5,5	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749100	14676	PASS	C	T	29	0.793103	2147483647	0,0,28,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749100	15279	PASS	C	T	83	0.915663	2147483647	0,0,83,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749100	16117	PASS	G	C	49	0.244898	0	0,37,0,12	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gat/Cat	D893H	RdRp	0.001841	0.244898	3	1	G>C
ERR5749100	16176	PASS	T	C	72	0.986111	0	0,0,23,49	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749100	16439	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	303	0.026403	0	0,295,0,8	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTg/aAg	M68K	helicase	0.016667	0.054348	1	1	T>A
ERR5749100	16573	PASS	G	T	965	0.156477	7	809,0,155,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gac/Tac	D113Y	helicase	0.000597	0.156477	4	2	G>T
ERR5749100	17081	PASS	G	T	266	0.120301	0	0,231,0,35	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGa/gTa	G282V	helicase	0.001926	0.120301	3	2	G>T
ERR5749100	18658	PASS	TG	T	1728	0.115741	0	1528,0,200,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tgt/	C207	ExoN	0.000507	0.115741	3	2	TG>T
ERR5749100	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	1704	0.002934	0	1699,0,5,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749100	19396	PASS	G	T	255	0.078431	0	234,0,21,0	HIGH	NONSENSE	STOP_GAINED	ORF1ab	Gag/Tag	E453*	ExoN	0.002594	0.078431	2	2	G>T
ERR5749100	19483	PASS	G	C	256	0.089844	0	0,232,0,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gct/Cct	A482P	ExoN	0.001112	0.089844	3	1	G>C
ERR5749100	19656	PASS	G	T	211	0.189573	0	170,0,41,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaG/aaT	K12N	endoR	0.001929	0.189573	1	1	G>T
ERR5749100	20544	PASS	C	T	359	0.13649	0	310,0,49,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S308	endoR	0.000834	0.975334	2	1	C>T
ERR5749100	20951	PASS	C	T	375	0.138667	0	319,0,56,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCa/tTa	S98L	MethTr	0.000431	0.138667	3	3	C>T
ERR5749100	21764	PASS	ATACATG	A	83	1.0	2147483647	0,0,83,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749100	21990	PASS	TTTA	T	92	0.902174	0	0,19,0,83	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749100	22620	PASS	G	T	1994	0.059178	39	1725,148,120,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tGg/tTg	W353L	S	0.002272	0.059178	2	2	G>T
ERR5749100	23063	PASS	A	T	152	0.855263	2147483647	0,0,0,150	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749100	23271	PASS	C	A	302	0.92053	2147483647	0,0,302,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749100	23294	PASS	G	C	302	0.102649	0	268,0,34,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gat/Cat	D578H	S	0.001754	0.102649	2	1	G>C
ERR5749100	23403	PASS	A	G	302	0.980132	2147483647	0,0,0,302	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749100	23426	PASS	G	T	302	0.102649	0	0,268,0,34	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gtt/Ttt	V622F	S	0.000428	0.916192	4	2	G>T
ERR5749100	23604	PASS	C	A	188	0.957447	2147483647	0,0,188,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749100	23689	PASS	T	C	187	0.197861	0	0,150,0,37	LOW	SILENT	SYNONYMOUS_CODING	S	aaT/aaC	N709	S	0.008146	0.197861	1	1	T>C
ERR5749100	23709	PASS	C	T	187	0.957219	2147483647	0,0,0,187	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749100	24506	PASS	T	G	93	0.978495	2147483647	0,0,93,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749100	24914	PASS	G	C	484	0.977273	0	0,0,241,242	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749100	25135	PASS	G	T	35	0.4	0	21,0,14,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aaG/aaT	K1191N	S	0.003281	0.884331	3	2	G>T
ERR5749100	25391	PASS	TTA	T	780	0.191026	0	631,0,149,0	HIGH	NONE	FRAME_SHIFT+START_LOST	ORF3a	atg/	M1	orf3a	0.000585	0.191026	1	1	TTA>T
ERR5749100	25626	PASS	C	T	806	0.915633	0	0,0,26,780	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	caC/caT	H78	orf3a	0.000403	0.915633	3	2	C>T
ERR5749100	26717	PASS	TG	T	158	0.063291	0	74,74,5,5	HIGH	NONE	FRAME_SHIFT	M	gtg/	V66	M	0.001602	0.063291	2	2	TG>T
ERR5749100	26718	PASS	G	T	158	0.075949	0	66,66,8,8	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Gtg/Ttg	V66L	M	0.001439	0.075949	1	1	G>T
ERR5749100	27065	PASS	G	T	1293	0.057231	0	0,1197,0,95	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	ttG/ttT	L181F	M	0.001008	0.897124	3	2	G>T
ERR5749100	27745	PASS	A	G	846	0.082742	0	0,763,0,83	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Aga/Gga	R118G	orf7a	0.000941	0.082742	2	2	A>G
ERR5749100	27972	PASS	C	T	26	0.884615	2147483647	0,0,26,0	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749100	28048	PASS	G	T	26	0.923077	2147483647	0,0,0,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749100	28111	PASS	A	G	1420	0.979577	0	0,0,1393,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749100	28270	PASS	TA	T	4619	0.997186	44	16,0,2384,2222	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749100	28280	PASS	G	C	4611	0.944697	3	0,1,2384,2218	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749100	28281	PASS	A	T	4611	0.934071	6	3,0,2383,2218	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749100	28282	PASS	T	A	4612	0.924111	0	3,3,2380,2220	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749100	28292	PASS	C	CA	4790	0.055324	0	2259,2266,132,133	HIGH	NONE	FRAME_SHIFT	N	aat/aaAt	N8K?	N	0.000304	0.055324	4	2	C>CA
ERR5749100	28881	PASS	G	A	19	0.947368	0	0,0,10,9	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749100	28882	PASS	G	A	19	0.842105	0	0,0,10,9	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749100	28883	PASS	G	C	19	0.947368	0	0,0,10,9	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749100	28977	PASS	C	T	10	1.0	2147483647	0,0,0,10	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749101	241	PASS	C	T	15869	0.851156	0	1,1,7839,7947	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749101	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	13306	0.00248	0	13273,0,33,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749101	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	13305	0.001278	0	13218,0,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749101	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	13305	9.02E-4	0	13218,0,12,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749101	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	13305	0.004134	0	13218,0,55,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749101	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	13292	0.002407	0	12177,4,956,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749101	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	13292	0.00173	0	13265,4,23,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749101	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	13293	7.52E-4	0	13276,6,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749101	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	13295	0.001279	0	13258,10,17,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749101	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATGGTTG	T	13295	6.77E-4	0	13258,10,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	atggttgag/	MVE85	leader	0.000587	0.476744	4	1	TATGGTTG>T
ERR5749101	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	36476	6.03E-4	15	23132,13321,19,3	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749101	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	36474	4.39E-4	3	23078,13301,12,4	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749101	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	36474	0.001974	10	23078,13301,53,19	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749101	913	PASS	C	T	23135	0.907716	0	0,15,0,23082	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749101	3037	PASS	C	T	22390	0.82787	61	2,27,11200,11030	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749101	3267	PASS	C	T	21213	0.972611	0	4,0,21198,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749101	5388	PASS	C	A	7506	0.956302	2147483647	0,0,7504,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749101	5986	PASS	C	T	13670	0.975786	2147483647	0,0,13659,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749101	6954	PASS	T	C	25249	0.819478	0	0,5,4,25120	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749101	7860	PASS	C	T	22093	0.666818	0	0,29,3,21841	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T1714I	nsp3	0.000611	0.666818	2	2	C>T
ERR5749101	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	36199	0.001216	146	16770,19385,44,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749101	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	18678	0.001553	0	18622,0,41,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749101	11287	PASS	GTCTGGTTTT	G	18679	0.996841	0	0,59,1,18619	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749101	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	37211	0.00129	0	18570,18527,27,27	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749101	14401	PASS	T	G	387	0.204134	18	4,128,0,255	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749101	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	14822	0.001147	0	4,14801,0,17	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749101	14408	PASS	C	T	14822	0.781339	0	0,7,4,14647	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749101	14599	PASS	C	T	14864	0.922766	65	6,2,14835,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L387	RdRp	0.000639	0.922766	3	2	C>T
ERR5749101	14676	PASS	C	T	14858	0.716045	0	8,0,14763,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749101	15279	PASS	C	T	25095	0.925483	0	7,0,25067,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749101	16176	PASS	T	C	22802	0.980396	0	1,1,11267,11525	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749101	16523	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22883	0.005331	0	22739,0,130,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T96I	helicase	0.001196	0.056848	2	1	C>T
ERR5749101	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	19162	0.001409	0	19135,0,27,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749101	18687	PASS	C	T	25085	0.980905	0	2,0,25047,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C216	ExoN	0.000374	0.981963	3	2	C>T
ERR5749101	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	32815	0.002743	0	32689,4,96,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749101	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	22138	5.42E-4	0	0,22125,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TA>T
ERR5749101	21304	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	31898	0.002289	0	6,31786,0,94	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgc/Agc	R216S	MethTr	0.000411	0.605296	3	2	C>A
ERR5749101	21305	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	31898	0.002289	0	6,31754,0,92	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cGc/cAc	R216H	MethTr	0.000727	0.703943	1	1	G>A
ERR5749101	21462	PASS	T	C	16720	0.957177	2147483647	0,0,16705,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaT/aaC	N268	MethTr	0.00078	0.959051	2	2	T>C
ERR5749101	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	33206	6.93E-4	0	16290,16599,13,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749101	21764	PASS	ATACATG	A	13110	0.994813	0	67,0,13042,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749101	21990	PASS	TTTA	T	13115	0.998246	0	0,23,3,13089	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749101	22264	PASS	C	T	22929	0.963496	66	2,9,0,22909	LOW	SILENT	SYNONYMOUS_CODING	S	aaC/aaT	N234	S	0.001131	0.963496	2	2	C>T
ERR5749101	23063	PASS	A	T	12476	0.86446	0	0,2,0,12408	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749101	23271	PASS	C	A	22888	0.921618	2147483647	0,0,22867,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749101	23403	PASS	A	G	22885	0.96548	0	0,7,0,22867	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749101	23604	PASS	C	A	16215	0.947333	0	16,0,16193,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749101	23709	PASS	C	T	16194	0.935223	0	0,4,4,16151	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749101	24506	PASS	T	G	20698	0.975891	0	9,0,20684,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749101	24914	PASS	G	C	34463	0.957752	0	0,1,17179,17259	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749101	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	26533	0.001131	50	17310,9171,34,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749101	25413	PASS	C	T	17461	0.968329	0	3,0,17444,0	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	atC/atT	I7	orf3a	0.00145	0.968329	2	1	C>T
ERR5749101	25587	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	17463	7.44E-4	0	3,17445,0,13	HIGH	NONE	FRAME_SHIFT	ORF3a	aag/	K67	orf3a	0.000598	0.813206	6	2	CA>C
ERR5749101	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	53924	3.15E-4	0	2,53903,0,17	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749101	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	11850	9.28E-4	0	1,11831,0,11	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749101	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	11850	6.75E-4	0	1,11840,0,8	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749101	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	11850	0.004051	0	1,11799,0,48	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749101	27972	PASS	C	T	11541	0.905294	37	1,2,11406,86	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749101	28048	PASS	G	T	11456	0.916376	0	0,19,0,11434	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749101	28095	PASS	A	T	11465	0.954296	68	2,3,0,11440	HIGH	NONSENSE	STOP_GAINED	ORF8	Aaa/Taa	K68*	orf8	0.002672	0.967672	2	2	A>T
ERR5749101	28111	PASS	A	G	28482	0.978021	3	5,1,17006,11459	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749101	28250	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TCTG	17000	0.002	0	16968,0,34,0	MODERATE	NONE	CODON_INSERTION	ORF8	ttc/CTGttc	F120LF	orf8	0.000494	0.993968	5	3	T>TCTG
ERR5749101	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	16990	0.002119	0	16961,0,36,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749101	28270	PASS	TA	T	32932	0.99502	337	157,9,16780,15988	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749101	28280	PASS	G	C	32872	0.934869	30	19,3,16810,15972	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749101	28281	PASS	A	T	32872	0.898485	38	27,5,16791,15968	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749101	28282	PASS	T	A	32872	0.920054	0	17,16,16778,15978	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749101	28881	PASS	G	A	16762	0.766615	19	10,1,8305,8255	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749101	28882	PASS	G	A	16762	0.824305	18	7,0,8388,8194	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749101	28883	PASS	G	C	16762	0.944517	6	0,2,8413,8336	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749101	28977	PASS	C	T	8545	0.929315	0	0,3,1,8528	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749101	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	31272	8.95E-4	130	22714,8489,3,29	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749101	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	45110	0.001086	0	22653,22375,29,29	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749101	29835	PASS	C	T	9433	0.969363	2147483647	0,0,0,9432	.	.	.	.	.	.	.	0.125879	0.969363	1	1	C>T
ERR5749102	241	PASS	C	T	34812	0.862059	5	2,6,17312,17358	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749102	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	16378	0.001832	0	16351,2,30,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749102	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	16378	5.5E-4	0	16299,2,9,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749102	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	16378	0.003602	0	16299,2,59,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749102	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	16377	0.002259	0	15142,10,1101,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749102	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	49898	3.81E-4	21	33478,16401,18,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749102	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	49898	9.02E-4	8	33446,16392,35,10	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749102	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	33468	8.96E-4	0	0,33390,0,38	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749102	913	PASS	C	T	33470	0.902241	0	0,26,0,33392	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749102	1027	PASS	T	C	76	0.276316	66	34,21,0,21	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccT/ccC	P74	nsp2	0.001454	0.276316	1	1	T>C
ERR5749102	1337	PASS	G	T	17	0.588235	0	0,7,0,10	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggt/Tgt	G178C	nsp2	0.588235	0.588235	1	1	G>T
ERR5749102	1573	PASS	A	G	16	0.75	2147483647	0,0,12,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acA/acG	T256	nsp2	0.001231	0.75	1	1	A>G
ERR5749102	2702	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	65202	6.75E-4	2147483647	64719,48,97,180	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F633V	nsp2	0.000632	0.333333	1	1	T>G
ERR5749102	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	129304	0.001895	2147483647	64531,60011,145,4254	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749102	3037	PASS	C	T	37623	0.809106	72	3,34,18788,18511	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749102	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	18995	0.001369	650	14,18942,25,7	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749102	3177	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	55600	7.73E-4	75	36589,18949,56,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cAt	P153H	nsp3	0.000773	0.96008	3	2	C>A
ERR5749102	3267	PASS	C	T	36645	0.967854	0	1,0,36623,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749102	3671	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	47130	6.79E-4	0	23529,23356,17,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E318K	nsp3	0.000351	0.0625	6	2	G>A
ERR5749102	3877	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	45938	5.88E-4	0	43540,0,2381,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcG	A386	nsp3	0.000588	0.960227	2	1	T>G
ERR5749102	4237	PASS	T	C	62887	0.910204	4	1,3,31509,31214	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaT/aaC	N506	nsp3	0.000302	0.918634	2	2	T>C
ERR5749102	4255	PASS	G	A	63001	0.794956	88	52,7,31278,31080	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccG/ccA	P512	nsp3	0.001102	0.871853	2	1	G>A
ERR5749102	5388	PASS	C	A	11937	0.956019	2147483647	0,0,11929,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749102	5575	PASS	C	T	11952	0.942855	353	11,2,0,11935	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y952	nsp3	0.01018	0.961493	1	1	C>T
ERR5749102	5986	PASS	C	T	24668	0.974339	0	2,0,24645,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749102	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23389	0.001069	0	2,23113,0,43	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749102	6954	PASS	T	C	41981	0.816536	0	0,4,1,41759	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749102	7070	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	77133	8.04E-4	174	34920,42119,62,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggc/Agc	G1451S	nsp3	0.000698	0.101434	3	1	G>A
ERR5749102	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	55287	6.51E-4	105	27686,27565,36,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749102	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	35122	0.001879	0	34033,3,66,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749102	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	35106	0.001424	0	35007,0,82,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749102	11287	PASS	GTCTGGTTTT	G	35098	0.997094	0	0,102,0,34996	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749102	11507	PASS	G	A	51413	0.898197	16	11,2,25683,25546	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Att	V179I	nsp6	0.007744	0.914418	2	2	G>A
ERR5749102	12125	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	29515	8.47E-4	0	16,29383,0,31	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y12H	nsp8	0.000847	0.113436	1	1	T>C
ERR5749102	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	55182	0.00116	0	27561,27480,36,37	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749102	14408	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9	0.888889	0	0,0,5,4	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749102	14676	PASS	C	T	15	0.733333	2147483647	0,0,15,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749102	15246	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	23750	0.001432	910	23690,8,5,32	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttA/ttT	L602F	RdRp	0.001432	0.633333	1	1	A>T
ERR5749102	15279	PASS	C	T	23709	0.886035	0	6,0,23656,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749102	15420	PASS	T	G	23652	0.922924	0	0,61,0,23580	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcG	A660	RdRp	0.908883	0.934773	1	1	T>G
ERR5749102	16176	PASS	T	C	35364	0.97998	0	3,3,16606,18738	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749102	17502	PASS	C	T	28988	0.981682	0	2,0,28960,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F422	helicase	0.000611	0.9865	2	2	C>T
ERR5749102	18501	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	53712	0.001676	0	4,53452,0,110	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y154	ExoN	0.000336	0.857143	4	2	C>T
ERR5749102	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	39875	7.52E-4	0	39845,0,30,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749102	19011	PASS	C	T	44141	0.968329	0	4,0,44112,2	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D324	ExoN	0.000408	0.975746	4	2	C>T
ERR5749102	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	44081	4.08E-4	0	0,44063,0,18	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749102	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	55526	0.002053	0	55376,0,117,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749102	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	55004	8.18E-4	0	54872,1,48,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749102	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	62525	7.2E-4	1	30544,31266,24,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749102	21764	PASS	ATACATG	A	24599	0.997398	0	66,0,24535,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749102	21990	PASS	TTTA	T	24611	0.997887	0	0,52,6,24553	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749102	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	28180	0.001278	0	3,28130,0,36	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749102	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	52505	9.14E-4	5	24285,28149,27,22	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749102	23063	PASS	A	T	24289	0.854049	0	0,4,3,24136	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749102	23271	PASS	C	A	39432	0.917351	0	5,0,39382,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749102	23403	PASS	A	G	39422	0.965704	0	0,5,1,39391	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749102	23604	PASS	C	A	28798	0.933468	0	30,0,28741,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749102	23709	PASS	C	T	28763	0.934673	0	0,7,4,28705	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749102	23817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	61210	7.35E-4	1	32365,28774,26,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTt/cCt	L752P	S	0.000646	0.066832	1	1	T>C
ERR5749102	24506	PASS	T	G	32911	0.971772	0	15,0,32886,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749102	24914	PASS	G	C	59138	0.958859	0	0,0,29465,29636	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749102	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	45191	0.001969	136	31596,13487,100,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749102	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	41158	7.29E-4	0	41128,0,30,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749102	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	41524	0.001975	2147483647	40763,237,242,226	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749102	26748	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	22728	0.001056	0	18,22260,0,426	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Atc/Ctc	I76L	M	0.001056	0.926238	2	1	A>C
ERR5749102	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	22765	4.83E-4	0	1,22746,0,11	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749102	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	22765	4.83E-4	0	1,22753,0,11	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749102	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	22767	0.001757	0	1,22722,0,40	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749102	27765	PASS	C	T	38205	0.96257	0	0,5,0,38181	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7b	Ctt/Ttt	L4F	orf7b	0.00109	0.970449	1	1	C>T
ERR5749102	27972	PASS	C	T	22228	0.897427	17	3,1,22048,106	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749102	28001	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	44192	9.96E-4	0	22041,22061,26,25	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ccG/ccA	P36	orf8	0.00085	0.830607	2	1	G>A
ERR5749102	28048	PASS	G	T	22149	0.907806	0	0,26,0,22109	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749102	28111	PASS	A	G	58592	0.979093	0	5,3,36402,22161	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749102	28239	PASS	GTTGTT	G	36319	0.982323	0	649,0,35677,0	HIGH	NONE	FRAME_SHIFT	ORF8	gtttta/	VL117	orf8	0.000417	0.984998	9	2	GTTGTT>G
ERR5749102	28249	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	ATC	35811	0.001089	0	35764,0,39,0	HIGH	NONE	FRAME_SHIFT	ORF8	ttc/CTttc	F120L?	orf8	0.000443	0.063605	3	2	A>ATC
ERR5749102	28250	PASS	T	TCTG	35811	0.992405	0	236,0,35539,0	MODERATE	NONE	CODON_INSERTION	ORF8	ttc/CTGttc	F120LF	orf8	0.000494	0.993968	5	3	T>TCTG
ERR5749102	28250	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TATG	35811	7.26E-4	0	236,0,26,0	MODERATE	NONE	CODON_INSERTION	ORF8	ttc/ATGttc	F120MF	orf8	0.000494	0.993968	5	3	T>TATG
ERR5749102	28253	PASS	CA	C	35811	0.993689	0	226,0,35585,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749102	28254	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	ATC	35811	7.26E-4	0	35781,0,26,0	HIGH	NONE	FRAME_SHIFT+STOP_LOST+SPLICE_SITE_REGION	ORF8	taa/tCTaa	*122S?	orf8	0.000541	0.914398	3	2	A>ATC
ERR5749102	28270	PASS	TA	T	68883	0.996167	387	235,27,35573,33046	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749102	28271	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AA	A	68883	0.001379	250	35711,33072,94,1	.	.	.	.	.	.	.	0.000482	0.924941	3	2	AA>A
ERR5749102	28280	PASS	G	C	68882	0.944456	29	23,5,35701,33027	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749102	28281	PASS	A	T	68882	0.93245	25	40,15,35698,33024	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749102	28282	PASS	T	A	68887	0.903088	14	31,15,35635,33043	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749102	28881	PASS	G	A	25649	0.734493	46	20,1,12665,12513	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749102	28882	PASS	G	A	25645	0.813843	45	16,0,12843,12513	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749102	28883	PASS	G	C	25647	0.942488	6	3,0,12871,12746	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749102	28977	PASS	C	T	13128	0.906155	0	0,4,2,13086	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749102	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	101742	0.001288	2	51093,50463,83,74	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749103	241	PASS	C	T	2332	0.873499	0	0,0,1158,1160	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749103	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	5034	0.001986	0	5026,0,10,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749103	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	5034	0.001986	0	5021,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749103	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	5028	0.002983	0	4660,0,342,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749103	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	5028	0.001989	0	5018,0,10,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749103	657	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5043	0.003569	0	0,5017,0,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A131V	leader	0.001202	0.365979	3	1	C>T
ERR5749103	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	13768	0.001453	1	8711,5037,14,6	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749103	913	PASS	C	T	8720	0.917661	0	0,6,0,8706	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749103	1573	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	391	0.028133	208	0,376,11,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acA/acG	T256	nsp2	0.001231	0.75	1	1	A>G
ERR5749103	1636	PASS	G	T	13958	0.958805	2147483647	0,0,13956,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gaG/gaT	E277D	nsp2	0.00204	0.963192	2	2	G>T
ERR5749103	2305	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	9114	0.003401	0	9065,0,34,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaG/aaC	K500N	nsp2	0.000443	0.070409	4	3	G>C
ERR5749103	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	32544	0.001291	2327	16225,15276,32,919	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749103	2862	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21255	0.001176	0	4896,16329,6,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T48I	nsp3	0.000547	0.850688	4	2	C>T
ERR5749103	3037	PASS	C	T	9750	0.826154	24	0,8,4865,4814	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749103	3267	PASS	C	T	10984	0.967316	0	2,0,10972,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749103	4237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTA	T	21135	9.94E-4	0	10563,10551,11,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	ata/	I508	nsp3	0.000302	0.918634	2	2	TTA>T
ERR5749103	4999	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8273	0.001692	0	8250,3,14,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N760	nsp3	0.001692	0.947468	1	1	C>T
ERR5749103	5100	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8268	0.001693	0	8246,0,15,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCa/tTa	S794L	nsp3	0.001443	0.071429	2	2	C>T
ERR5749103	5388	PASS	C	A	3350	0.963582	2147483647	0,0,3349,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749103	5628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CGT	C	9757	0.001025	0	9747,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tgtggt/	CG971	nsp3	0.000561	0.973644	3	2	CGT>C
ERR5749103	5730	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9756	0.00164	0	9736,0,16,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T1004I	nsp3	0.001601	0.721782	1	1	C>T
ERR5749103	5986	PASS	C	T	8658	0.9769	2147483647	0,0,8651,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749103	6606	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8843	0.002262	0	8816,0,20,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S1296F	nsp3	0.002262	0.945412	1	1	C>T
ERR5749103	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	8818	0.004763	0	3,8773,0,42	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L1328S?	nsp3	0.000731	0.14377	4	2	C>CT
ERR5749103	6954	PASS	T	C	14284	0.814268	0	0,4,0,14200	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749103	6990	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	14318	0.002025	0	0,14289,0,29	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L1425	nsp3	0.000504	0.101156	4	2	CT>C
ERR5749103	7544	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	10477	0.001623	0	0,10445,0,32	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Ttt	V1609F	nsp3	0.001623	0.875709	2	1	G>T
ERR5749103	8950	PASS	C	T	17983	0.979536	0	3,1,11764,6210	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I132	nsp4	0.002808	0.982604	1	1	C>T
ERR5749103	9170	PASS	C	T	11768	0.82019	0	0,10,0,11733	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Ttt	L206F	nsp4	0.82019	0.841764	1	1	C>T
ERR5749103	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	11567	0.00121	6	9913,1640,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749103	9694	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTA	T	19744	5.06E-4	30	9883,9855,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	atc/	I382	nsp4	0.000506	0.057471	1	1	TTA>T
ERR5749103	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	18114	0.001215	0	18066,0,38,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749103	11287	PASS	GTCTGGTTTT	G	18108	0.998896	0	0,20,0,18088	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749103	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	12231	0.001063	0	12218,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749103	13384	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	10896	0.001285	0	10882,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggt/	G121	nsp10	0.000578	0.056161	3	3	CG>C
ERR5749103	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21761	0.001057	0	10869,10838,12,13	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749103	14097	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11096	0.002433	0	11045,13,27,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F219	RdRp	0.000613	0.981481	2	2	C>T
ERR5749103	14098	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	11175	0.001879	0	11035,92,22,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggt/Cgt	G220R	RdRp	0.000806	0.065317	4	2	G>C
ERR5749103	14408	PASS	C	T	2745	0.84408	3	0,1,1370,1353	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749103	14676	PASS	C	T	6965	0.814645	0	3,0,6954,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749103	15240	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10093	0.001882	0	10064,4,19,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N600	RdRp	0.000934	0.931284	2	2	C>T
ERR5749103	15279	PASS	C	T	10089	0.8876	2147483647	0,0,10066,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749103	15983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	6860	0.002624	0	6843,0,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T850	RdRp	0.000701	0.338235	2	1	TA>T
ERR5749103	16176	PASS	T	C	11010	0.983379	0	0,1,4135,6872	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749103	16792	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CGT	C	32837	3.35E-4	36	15386,17440,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gta/	V187	helicase	0.000335	0.072562	5	2	CGT>C
ERR5749103	16974	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	15355	5.86E-4	0	0,15346,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/	V247	helicase	0.000586	0.055482	2	2	TG>T
ERR5749103	17167	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8100	0.001728	0	8081,0,14,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cat/Tat	H311Y	helicase	0.001728	0.238095	1	1	C>T
ERR5749103	17181	PASS	T	C	8098	0.98691	0	7,0,8089,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaT/gaC	D315	helicase	0.986595	0.991193	1	1	T>C
ERR5749103	17442	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	12397	8.87E-4	0	12387,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gct/	A403	helicase	0.000887	0.972741	2	2	TG>T
ERR5749103	18457	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14223	0.001406	0	14180,0,22,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cca/Tca	P140S	ExoN	0.001253	0.951352	2	1	C>T
ERR5749103	18576	PASS	C	T	14246	0.866138	0	0,7,0,14196	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D179	ExoN	0.005404	0.876866	2	2	C>T
ERR5749103	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	23251	8.6E-4	0	23231,0,20,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749103	19113	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	26454	5.29E-4	39	13229,13227,0,14	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K359	ExoN	0.000461	0.125	4	3	CA>C
ERR5749103	19296	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTA	G	13650	5.86E-4	0	13641,1,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/	Y420	ExoN	0.000586	0.977017	2	2	GTA>G
ERR5749103	19524	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13649	0.001246	0	0,13624,0,18	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ctC/ctT	L495	ExoN	0.000745	0.953697	2	2	C>T
ERR5749103	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8865	0.002707	0	8831,0,24,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749103	20091	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	8852	0.001356	0	0,8840,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	caa/Acaa	Q159T?	endoR	0.000368	0.051583	1	1	C>CA
ERR5749103	20179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8877	0.001915	0	12,8835,0,17	HIGH	NONSENSE	STOP_GAINED	ORF1ab	Caa/Taa	Q187*	endoR	0.001915	0.20339	1	1	C>T
ERR5749103	20235	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAGG	C	25172	5.96E-4	0	25155,2,15,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	aggagt/agt	RS206S	endoR	0.000596	0.925795	3	2	CAGG>C
ERR5749103	20930	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15776	0.001141	0	15744,0,21,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aTg	T91M	MethTr	0.000902	0.95585	2	2	C>T
ERR5749103	21032	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATC	A	15759	8.25E-4	0	1,15745,0,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctc/	L126	MethTr	0.000568	0.088561	2	2	ATC>A
ERR5749103	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	15771	0.002727	0	0,15700,0,43	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TA>T
ERR5749103	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAA	T	15771	0.001775	0	0,15700,0,28	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TAA>T
ERR5749103	21234	PASS	C	T	22483	0.548103	0	13,0,21987,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A192	MethTr	0.000472	0.857572	5	2	C>T
ERR5749103	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19487	0.001232	0	9564,9731,13,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749103	21733	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	10228	0.001662	0	10168,7,17,0	LOW	SILENT	SYNONYMOUS_CODING	S	ccT/ccC	P57	S	0.001662	0.065814	2	1	T>C
ERR5749103	21733	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10228	0.002542	0	10168,7,32,0	LOW	SILENT	SYNONYMOUS_CODING	S	ccT/ccG	P57	S	0.001662	0.065814	2	1	T>G
ERR5749103	21736	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	10228	0.00176	0	10203,7,18,0	HIGH	NONE	FRAME_SHIFT	S	tcc/	S60	S	0.001596	0.804427	3	2	CT>C
ERR5749103	21764	PASS	ATACATG	A	10221	0.997456	0	26,0,10195,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749103	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	10221	8.81E-4	0	10212,0,9,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749103	21990	PASS	TTTA	T	10222	0.998141	0	0,19,1,10202	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749103	22016	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	17004	9.41E-4	0	16983,5,16,0	HIGH	NONE	FRAME_SHIFT	S	tgg/	W152	S	0.000941	0.94646	2	2	TG>T
ERR5749103	22290	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	17001	0.001588	0	2,16972,0,27	HIGH	NONE	FRAME_SHIFT	S	tta/	L244	S	0.000389	0.578006	2	2	CT>C
ERR5749103	22690	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	15447	0.002007	0	15174,0,33,0	LOW	SILENT	SYNONYMOUS_CODING	S	acT/acC	T376	S	0.000815	0.051311	2	1	T>C
ERR5749103	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	15486	0.001227	0	0,15463,0,20	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749103	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26858	9.68E-4	0	11356,15468,10,16	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749103	23063	PASS	A	T	11354	0.872468	0	0,1,0,11294	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749103	23271	PASS	C	A	11291	0.926224	0	1,0,11273,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749103	23403	PASS	A	G	11285	0.968454	0	0,2,0,11277	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749103	23604	PASS	C	A	11065	0.941347	0	7,0,11050,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749103	23635	PASS	C	T	11042	0.951277	2147483647	0,0,11026,0	LOW	SILENT	SYNONYMOUS_CODING	S	tcC/tcT	S691	S	0.002385	0.958978	1	1	C>T
ERR5749103	23709	PASS	C	T	11048	0.940623	0	0,7,0,11028	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749103	23802	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11070	0.001987	0	4,11034,0,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCt/aTt	T747I	S	0.001717	0.977181	3	2	C>T
ERR5749103	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	17844	5.6E-4	0	6774,11060,4,6	HIGH	NONE	FRAME_SHIFT	S	ttg/	L753	S	0.000334	0.080808	2	2	CT>C
ERR5749103	24237	PASS	C	T	8498	0.889739	2147483647	0,0,8478,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gTt	A892V	S	0.001242	0.889739	1	1	C>T
ERR5749103	24506	PASS	T	G	13112	0.973688	0	5,0,13104,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749103	24914	PASS	G	C	32718	0.96207	0	0,0,16291,16406	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749103	25350	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	18022	0.00111	0	17997,1,23,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCa/cAa	P1263Q	S	0.000626	0.97904	4	2	C>A
ERR5749103	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	4319	0.004168	375	4279,14,1,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749103	25769	PASS	G	T	4283	0.929022	0	7,0,4274,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aGg/aTg	R126M	orf3a	0.929022	0.929022	1	1	G>T
ERR5749103	25844	PASS	C	T	4278	0.924731	2147483647	0,0,0,4271	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aCt/aTt	T151I	orf3a	0.001226	0.938776	1	1	C>T
ERR5749103	26208	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23936	0.001755	0	8,23865,0,46	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	agC/agT	S272	orf3a	0.000315	0.922222	2	2	C>T
ERR5749103	26208	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	23936	6.27E-4	0	8,23913,0,15	HIGH	NONE	FRAME_SHIFT	ORF3a	gtg/	V273	orf3a	0.000315	0.922222	2	2	CG>C
ERR5749103	26510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	8910	0.001796	0	0,8881,0,17	.	.	.	.	.	.	.	0.001235	0.933642	2	1	T>C
ERR5749103	26681	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9481	0.002004	0	9433,18,19,0	LOW	SILENT	SYNONYMOUS_CODING	M	ttC/ttT	F53	M	0.001297	0.074505	1	1	C>T
ERR5749103	26710	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTTG	C	9445	0.001059	0	9408,30,10,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtttt/ttt	CF64F	M	0.000649	0.102857	1	1	CTTG>C
ERR5749103	27493	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34019	7.94E-4	81	17060,16923,0,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Cct/Tct	P34S	orf7a	0.000794	0.971493	2	1	C>T
ERR5749103	27577	PASS	C	T	17064	0.852028	0	3,0,17022,0	HIGH	NONSENSE	STOP_GAINED	ORF7a	Caa/Taa	Q62*	orf7a	0.000614	0.952205	4	2	C>T
ERR5749103	27746	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	17060	5.28E-4	0	0,17051,0,9	HIGH	NONE	FRAME_SHIFT	ORF7a	aag/	K119	orf7a	0.000528	0.94095	3	2	GA>G
ERR5749103	27972	PASS	C	T	5875	0.900596	36	2,2,5819,34	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749103	28048	PASS	G	T	5845	0.920616	0	0,6,0,5835	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749103	28111	PASS	A	G	25279	0.978599	6	14,1,19405,5844	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749103	28195	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	19433	0.001081	0	19387,0,34,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	cGt/cTt	R101L	orf8	0.000851	0.926081	3	2	G>T
ERR5749103	28249	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	19425	5.15E-4	0	19416,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF8	ttc/	F120	orf8	0.000443	0.063605	3	2	AT>A
ERR5749103	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19421	0.001751	0	19332,1,35,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749103	28270	PASS	TA	T	37592	0.994653	419	191,10,19162,18229	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749103	28280	PASS	G	C	37504	0.935047	18	12,2,19196,18219	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749103	28281	PASS	A	T	37504	0.916516	49	21,1,19194,18225	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749103	28282	PASS	T	A	37507	0.90951	11	24,12,19149,18232	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749103	28651	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	19077	9.96E-4	0	0,19058,0,19	HIGH	NONE	FRAME_SHIFT	N	aaa/	K127	N	0.000502	0.918117	3	2	CA>C
ERR5749103	28881	PASS	G	A	7237	0.778499	0	1,0,3580,3568	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749103	28882	PASS	G	A	7237	0.836811	0	0,0,3621,3550	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749103	28883	PASS	G	C	7237	0.943761	3	0,1,3625,3600	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749103	28977	PASS	C	T	3678	0.933931	2147483647	0,0,0,3673	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749103	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	22947	0.004358	733	19246,3554,7,104	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749103	29095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19268	0.002128	0	19213,0,42,0	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F274	N	0.000792	0.961279	2	2	C>T
ERR5749103	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	38265	0.001124	0	19216,18986,26,26	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749103	29743	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	6817	0.001027	0	0,6810,0,7	.	.	.	.	.	.	.	0.001027	0.859785	2	1	CG>C
ERR5749104	210	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	17909	0.001452	4	9011,8863,18,12	.	.	.	.	.	.	.	0.001452	1	2	1	G>A
ERR5749104	241	PASS	C	T	17985	0.843369	6	0,3,8944,8948	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749104	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	11762	0.004761	0	11705,4,56,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749104	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	11771	6.8E-4	0	11654,14,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749104	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	11771	0.002124	0	11654,14,25,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749104	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	11771	0.005607	0	11654,14,66,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749104	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	11761	0.001871	2	10683,14,863,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749104	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	11761	0.001956	0	11724,14,23,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749104	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	11762	0.001105	0	11732,15,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749104	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	11761	0.00102	0	11731,16,12,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749104	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	38012	3.95E-4	20	26226,11768,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749104	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	38015	5.52E-4	21	26150,11747,20,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749104	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	38015	0.002315	9	26150,11747,68,20	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749104	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26232	9.15E-4	0	0,26180,0,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749104	913	PASS	C	T	26232	0.917162	0	0,15,0,26173	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749104	2706	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	91346	5.91E-4	0	45848,45393,34,31	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T634I	nsp2	0.000591	0.821437	1	1	C>T
ERR5749104	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	91402	0.001335	2147483647	45687,42702,62,2750	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749104	3037	PASS	C	T	16403	0.829848	35	1,15,8189,8092	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749104	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	8294	0.002411	505	4,8252,20,6	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749104	3267	PASS	C	T	26028	0.967266	0	4,0,26011,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749104	4237	PASS	T	C	35167	0.915347	4	1,3,17602,17476	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaT/aaC	N506	nsp3	0.000302	0.918634	2	2	T>C
ERR5749104	4255	PASS	G	A	35215	0.848104	57	27,2,17503,17498	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccG/ccA	P512	nsp3	0.001102	0.871853	2	1	G>A
ERR5749104	5388	PASS	C	A	5411	0.960636	2147483647	0,0,5409,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749104	5575	PASS	C	T	5421	0.952038	280	9,0,0,5410	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y952	nsp3	0.01018	0.961493	1	1	C>T
ERR5749104	5986	PASS	C	T	11670	0.974036	2147483647	0,0,11662,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749104	6954	PASS	T	C	30735	0.829868	0	0,2,3,30567	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749104	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	30435	3.61E-4	35	14519,15905,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749104	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	26333	0.002127	0	25553,3,56,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749104	11287	PASS	GTCTGGTTTT	G	26318	0.995934	0	0,107,0,26211	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749104	11355	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	39976	8.25E-4	0	13630,26305,13,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCa/gTa	A128V	nsp6	0.000455	0.982262	3	2	C>T
ERR5749104	11507	PASS	G	A	27138	0.908431	9	8,2,13557,13474	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Att	V179I	nsp6	0.007744	0.914418	2	2	G>A
ERR5749104	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	17657	0.001076	0	17613,0,19,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749104	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	41150	0.001337	0	20551,20503,28,28	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749104	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	6333	0.005685	1701	6163,64,3,100	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749104	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	12275	0.001629	0	6150,6114,10,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749104	14408	PASS	C	T	12275	0.840815	0	0,0,6125,6052	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749104	14676	PASS	C	T	17266	0.81397	0	6,0,17210,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749104	15277	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27425	0.006345	0	27217,0,188,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cac/Tac	H613Y	RdRp	0.006345	0.326816	1	1	C>T
ERR5749104	15279	PASS	C	T	27425	0.911613	0	1,0,27381,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749104	15420	PASS	T	G	27389	0.928329	0	0,38,0,27319	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcG	A660	RdRp	0.908883	0.934773	1	1	T>G
ERR5749104	16176	PASS	T	C	23424	0.982838	0	0,1,9070,14343	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749104	17502	PASS	C	T	14046	0.982771	2147483647	0,0,14028,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F422	helicase	0.000611	0.9865	2	2	C>T
ERR5749104	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	24124	7.46E-4	0	24106,0,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749104	19011	PASS	C	T	31464	0.971968	0	4,0,31448,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D324	ExoN	0.000408	0.975746	4	2	C>T
ERR5749104	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26523	0.001885	0	26456,0,51,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749104	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	44518	7.64E-4	3	21816,22224,17,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749104	21764	PASS	ATACATG	A	11159	0.997401	0	27,0,11130,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749104	21990	PASS	TTTA	T	11168	0.996418	0	0,40,8,11120	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749104	23271	PASS	C	A	28006	0.914161	0	1,0,27976,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749104	23403	PASS	A	G	27997	0.97189	0	0,6,1,27978	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749104	23604	PASS	C	A	14765	0.929631	0	15,0,14738,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749104	23709	PASS	C	T	14759	0.944779	0	0,3,6,14742	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749104	24010	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATTTATTGAAGATCTAC	A	21975	4.55E-4	0	189,21779,0,10	HIGH	NONE	FRAME_SHIFT	S	attgaagatctacttttc/	IEDLLF818	S	0.000455	0.926398	4	2	ATTTATTGAAGATCTAC>A
ERR5749104	24237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11351	0.001498	0	11316,0,19,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gTt	A892V	S	0.001242	0.889739	1	1	C>T
ERR5749104	24506	PASS	T	G	24006	0.974965	0	10,0,23992,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749104	24914	PASS	G	C	36309	0.962158	0	1,1,18092,18192	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749104	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	27604	9.78E-4	60	16665,10895,38,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749104	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	24475	0.001185	354	24366,24,14,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749104	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	24436	7.37E-4	0	24418,0,18,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749104	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	41161	4.86E-4	0	4,41133,0,20	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749104	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	11227	7.13E-4	0	0,11212,0,8	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749104	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	11227	8.91E-4	0	0,11216,0,10	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749104	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	11229	0.003384	0	0,11185,0,38	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749104	27765	PASS	C	T	28180	0.966146	0	0,5,3,28157	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7b	Ctt/Ttt	L4F	orf7b	0.00109	0.970449	1	1	C>T
ERR5749104	27972	PASS	C	T	9467	0.90525	17	2,1,9382,56	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749104	28048	PASS	G	T	9425	0.92382	0	0,13,0,9407	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749104	28111	PASS	A	G	37586	0.980658	1	4,2,28140,9426	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749104	28239	PASS	GTTGTT	G	28095	0.983769	0	459,0,27639,0	HIGH	NONE	FRAME_SHIFT	ORF8	gtttta/	VL117	orf8	0.000417	0.984998	9	2	GTTGTT>G
ERR5749104	28249	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	ATC	27738	8.65E-4	0	27712,0,24,0	HIGH	NONE	FRAME_SHIFT	ORF8	ttc/CTttc	F120L?	orf8	0.000443	0.063605	3	2	A>ATC
ERR5749104	28250	PASS	T	TCTG	27738	0.992141	0	172,0,27520,0	MODERATE	NONE	CODON_INSERTION	ORF8	ttc/CTGttc	F120LF	orf8	0.000494	0.993968	5	3	T>TCTG
ERR5749104	28250	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TATG	27738	7.93E-4	0	172,0,22,0	MODERATE	NONE	CODON_INSERTION	ORF8	ttc/ATGttc	F120MF	orf8	0.000494	0.993968	5	3	T>TATG
ERR5749104	28253	PASS	CA	C	27738	0.993979	0	167,0,27571,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749104	28254	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	ATC	27738	5.41E-4	0	27722,0,15,0	HIGH	NONE	FRAME_SHIFT+STOP_LOST+SPLICE_SITE_REGION	ORF8	taa/tCTaa	*122S?	orf8	0.000541	0.914398	3	2	A>ATC
ERR5749104	28270	PASS	TA	T	53806	0.995967	438	196,9,27535,26054	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749104	28271	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AA	A	53806	0.00145	222	27660,26068,78,0	.	.	.	.	.	.	.	0.000482	0.924941	3	2	AA>A
ERR5749104	28280	PASS	G	C	53805	0.947514	23	16,3,27676,26039	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749104	28281	PASS	A	T	53805	0.931196	16	20,7,27671,26038	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749104	28282	PASS	T	A	53808	0.908248	16	23,9,27626,26043	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749104	28881	PASS	G	A	21135	0.775491	14	8,1,10504,10374	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749104	28882	PASS	G	A	21135	0.828815	1	5,3,10584,10348	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749104	28883	PASS	G	C	21135	0.945777	0	0,0,10603,10520	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749104	28977	PASS	C	T	10782	0.914673	2147483647	0,0,0,10760	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749104	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	37937	0.001845	318	27127,10689,4,68	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749104	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	53901	0.001447	0	27059,26730,50,47	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749105	193	PASS	C	T	704	0.866477	0	1,0,701,0	.	.	.	.	.	.	.	0.823815	0.866477	1	1	C>T
ERR5749105	239	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	1407	0.005686	8	690,699,11,5	.	.	.	.	.	.	.	0.000495	0.25	4	1	T>G
ERR5749105	241	PASS	C	T	1407	0.851457	0	0,0,700,701	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749105	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	2427	0.004532	0	2416,0,11,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749105	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	2427	0.003708	0	2416,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749105	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	2425	0.003711	0	2201,0,200,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749105	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTAAAGTCATTT	C	8243	0.002184	25	5795,2430,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctaaagtcattt/	LKSF140	leader	0.000316	0.135802	3	2	CTAAAGTCATTT>C
ERR5749105	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	8243	8.49E-4	1	5807,2427,6,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749105	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	5808	0.002755	0	0,5792,0,16	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTg	L35F?	nsp2	0.000551	0.081967	3	2	C>CT
ERR5749105	913	PASS	C	T	5809	0.904459	0	0,1,0,5800	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749105	2695	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14441	0.0018	0	14384,2,30,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N630	nsp2	0.0018	0.142556	1	1	C>T
ERR5749105	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	28744	0.001531	2474	14360,13377,21,918	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749105	3037	PASS	C	T	8000	0.844125	2	4,6,3989,3953	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749105	3267	PASS	C	T	8081	0.968939	0	1,0,8077,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749105	3832	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	7848	0.001529	0	7836,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L373	nsp3	0.000689	0.327273	4	2	CT>C
ERR5749105	3877	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	7848	0.002294	0	7034,0,811,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcG	A386	nsp3	0.000588	0.960227	2	1	T>G
ERR5749105	4529	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTTTAC	T	5793	0.001554	0	0,5784,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	tacttt/	YF605	nsp3	0.000527	0.402778	3	1	TTTTAC>T
ERR5749105	5388	PASS	C	A	2636	0.959788	2147483647	0,0,2636,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749105	5986	PASS	C	T	8111	0.972383	2147483647	0,0,8106,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749105	6337	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	9720	0.001029	0	9710,0,10,0	HIGH	NONE	FRAME_SHIFT+STOP_GAINED	ORF1ab	gat/Tgat	D1208*?	nsp3	0.000579	0.91624	3	2	G>GT
ERR5749105	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7677	0.002735	0	0,7595,0,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749105	7564	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	8311	9.63E-4	0	0,8303,0,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/	Y1617	nsp3	0.000586	0.056194	4	2	CT>C
ERR5749105	7735	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15204	0.001842	0	15158,0,34,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I1672	nsp3	0.000658	0.954659	3	2	C>T
ERR5749105	7764	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15204	0.001776	0	15169,0,28,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCc/tTc	S1682F	nsp3	0.001052	0.964731	1	1	C>T
ERR5749105	7926	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	15205	0.001447	0	0,15183,0,22	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1737	nsp3	0.000531	0.97019	5	2	CA>C
ERR5749105	7945	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15207	0.002433	0	2,15155,0,44	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y1742	nsp3	0.001244	0.950558	2	2	C>T
ERR5749105	8327	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6894	0.006672	0	6837,5,48,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Ttt	L1870F	nsp3	0.001407	0.90398	1	1	C>T
ERR5749105	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	9842	0.001219	2	9041,789,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749105	11071	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	20901	0.001292	0	20842,0,30,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttG/ttA	L33	nsp6	0.001292	0.087481	5	3	G>A
ERR5749105	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	20901	0.002153	0	20321,0,45,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749105	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	20894	0.00201	0	20834,0,55,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749105	11095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTTTTTACCTTTTGCTATGGGTATTATTGCTATGTCTGCTT	C	20893	0.001005	0	20868,0,21,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tttttaccttttgctatgggtattattgctatgtctgctttt/	FLPFAMGIIAMSAF42	nsp6	0.000515	0.887707	7	2	CTTTTTACCTTTTGCTATGGGTATTATTGCTATGTCTGCTT>C
ERR5749105	11110	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	20893	9.57E-4	0	20793,0,25,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcC	A46	nsp6	0.000477	0.803913	2	2	T>C
ERR5749105	11287	PASS	GTCTGGTTTT	G	20891	0.998564	0	0,30,0,20861	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749105	11750	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17970	0.003895	0	9109,8716,57,52	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L260F	nsp6	0.001019	0.70989	2	1	C>T
ERR5749105	12273	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	15138	0.001519	0	15094,0,26,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K61R	nsp8	0.000778	0.2	3	2	A>G
ERR5749105	13498	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	16716	0.001974	1	8332,8292,20,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Aca/Gca	T20A	RdRp	0.001341	0.952048	1	1	A>G
ERR5749105	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16722	0.001914	0	8346,8331,16,16	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749105	14408	PASS	C	T	1280	0.852344	0	0,0,640,629	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749105	14676	PASS	C	T	4081	0.824553	2147483647	0,0,4068,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749105	15279	PASS	C	T	7907	0.907803	2147483647	0,0,7899,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749105	15371	PASS	C	T	15720	0.786959	1	3,4,7835,7741	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aTg	T644M	RdRp	0.00056	0.786959	4	2	C>T
ERR5749105	15983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	4655	0.002578	0	4644,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T850	RdRp	0.000701	0.338235	2	1	TA>T
ERR5749105	16176	PASS	T	C	7447	0.980932	0	0,0,2784,4662	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749105	16508	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	18162	0.001046	0	18130,2,30,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGt/gTt	G91V	helicase	0.000561	0.074909	2	2	G>T
ERR5749105	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	15207	0.00171	0	15181,0,26,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749105	17615	PASS	A	G	8987	0.902748	2147483647	0,0,0,8955	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749105	17747	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12450	0.001606	0	12426,0,20,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P504L	helicase	0.000839	0.968462	2	2	C>T
ERR5749105	18501	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	12667	0.001263	0	0,12651,0,16	HIGH	NONE	FRAME_SHIFT	ORF1ab	gga/Agga	G156R?	ExoN	0.000336	0.857143	4	2	C>CA
ERR5749105	18501	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12667	0.001658	0	0,12599,0,25	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y154	ExoN	0.000336	0.857143	4	2	C>T
ERR5749105	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	20699	7.73E-4	0	20683,0,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749105	18761	PASS	T	C	20688	0.251353	0	15176,0,5501,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTg/aCg	M241T	ExoN	0.001048	0.251353	3	1	T>C
ERR5749105	19524	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13700	0.001314	0	0,13673,0,19	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ctC/ctT	L495	ExoN	0.000745	0.953697	2	2	C>T
ERR5749105	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7438	0.004706	0	7401,0,36,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749105	20825	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19811	0.001312	25	12543,7234,26,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T56I	MethTr	0.001237	0.202489	2	1	C>T
ERR5749105	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21930	0.001961	0	10708,10935,25,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749105	21764	PASS	ATACATG	A	10655	0.998029	0	21,0,10634,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749105	21867	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	21269	0.002633	231	10442,10589,190,42	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aGa/aTa	R102I	S	0.000625	0.861881	2	2	G>T
ERR5749105	21990	PASS	TTTA	T	10661	0.995873	0	0,44,4,10613	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749105	22280	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ACTTTACTTG	A	18167	7.71E-4	0	2,18151,0,14	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	cttgctttacat/cat	LALH242H	S	0.00046	0.997799	1	1	ACTTTACTTG>A
ERR5749105	22690	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	20979	0.001287	0	20611,23,31,0	LOW	SILENT	SYNONYMOUS_CODING	S	acT/acC	T376	S	0.000815	0.051311	2	1	T>C
ERR5749105	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	21007	0.00119	0	0,20976,0,27	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749105	23063	PASS	A	T	9002	0.858587	0	0,3,0,8967	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749105	23271	PASS	C	A	6547	0.920422	0	1,0,6535,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749105	23403	PASS	A	G	6544	0.976773	2147483647	0,0,0,6540	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749105	23604	PASS	C	A	10088	0.942209	0	9,0,10074,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749105	23664	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20001	0.00145	0	9928,10009,15,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCa/gTa	A701V	S	0.000837	0.918	2	2	C>T
ERR5749105	23709	PASS	C	T	10075	0.934988	0	0,2,3,10051	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749105	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	15966	0.001002	69	5859,10091,16,0	HIGH	NONE	FRAME_SHIFT	S	ttg/	L753	S	0.000334	0.080808	2	2	CT>C
ERR5749105	24010	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	5937	0.001179	0	70,5861,0,7	HIGH	NONE	FRAME_SHIFT	S	ttt/	F817	S	0.000455	0.926398	4	2	AT>A
ERR5749105	24320	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6468	0.00402	0	0,6427,0,28	HIGH	NONSENSE	STOP_GAINED	S	Caa/Taa	Q920*	S	0.000763	0.138365	4	2	C>T
ERR5749105	24506	PASS	T	G	11414	0.974768	0	9,0,11401,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749105	24914	PASS	G	C	22786	0.957825	3	1,0,11343,11417	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749105	25626	PASS	C	T	23156	0.841898	5	2,3,4738,18372	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	caC/caT	H78	orf3a	0.000403	0.915633	3	2	C>T
ERR5749105	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	4789	0.005847	205	4733,15,17,12	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749105	26013	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27506	0.001054	0	27458,0,30,0	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	ttC/ttT	F207	orf3a	0.000839	0.974528	1	1	C>T
ERR5749105	26158	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	27453	4.74E-4	0	0,27439,0,13	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF3a	gttaat/gat	VN256D	orf3a	0.000297	0.905181	6	2	GTTA>G
ERR5749105	26159	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTAATCCAG	T	27453	0.001129	0	0,27422,0,31	HIGH	NONE	FRAME_SHIFT	ORF3a	ccagtaatg/	PVM258	orf3a	0.000311	0.053032	2	2	TTAATCCAG>T
ERR5749105	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	7724	0.001295	0	0,7714,0,10	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749105	27459	PASS	G	T	17833	0.943812	34	1,6,0,17823	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	gaG/gaT	E22D	orf7a	0.002024	0.943812	1	1	G>T
ERR5749105	27476	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17833	0.001122	0	0,17804,0,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	aCa/aTa	T28I	orf7a	0.000547	0.22827	4	2	C>T
ERR5749105	27972	PASS	C	T	3591	0.896408	18	1,1,3553,23	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749105	28048	PASS	G	T	3571	0.91543	0	0,5,0,3566	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749105	28093	PASS	C	T	3579	0.962001	30	1,2,0,3571	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tCt/tTt	S67F	orf8	0.001515	0.967675	1	1	C>T
ERR5749105	28111	PASS	A	G	14121	0.97656	0	2,0,10539,3578	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749105	28250	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TCTG	10529	0.016716	0	10355,0,176,0	MODERATE	NONE	CODON_INSERTION	ORF8	ttc/CTGttc	F120LF	orf8	0.000494	0.993968	5	3	T>TCTG
ERR5749105	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10530	0.004653	0	10449,1,52,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749105	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	10525	0.016817	0	10352,1,177,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749105	28270	PASS	TA	T	20418	0.994857	243	103,4,10391,9922	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749105	28280	PASS	G	C	20373	0.937368	26	10,0,10417,9914	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749105	28281	PASS	A	T	20373	0.915869	33	18,2,10409,9915	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749105	28282	PASS	T	A	20376	0.911808	15	14,4,10379,9921	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749105	28881	PASS	G	A	2892	0.761065	2	3,1,1431,1412	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749105	28882	PASS	G	A	2891	0.83293	0	1,0,1449,1410	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749105	28883	PASS	G	C	2891	0.945694	0	0,0,1450,1439	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749105	28977	PASS	C	T	1473	0.928717	2147483647	0,0,0,1470	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749105	29095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20363	0.001129	0	20319,0,23,0	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F274	N	0.000792	0.961279	2	2	C>T
ERR5749105	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	40410	0.001658	0	20291,20019,40,40	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749105	29386	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	9015	8.87E-4	0	9007,0,8,0	HIGH	NONE	FRAME_SHIFT	N	aag/aaAg	K373K?	N	0.000887	0.899197	4	2	C>CA
ERR5749105	29749	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ACGATCGAGTG	A	5512	0.002721	0	1,5496,0,15	.	.	.	.	.	.	.	0.00126	0.997197	2	1	ACGATCGAGTG>A
ERR5749106	71	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4299	0.00442	0	4274,0,20,0	.	.	.	.	.	.	.	0.002088	0.926791	2	1	C>T
ERR5749106	241	PASS	C	T	7224	0.852159	0	0,1,3592,3593	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749106	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	11359	0.003962	0	11307,15,45,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749106	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	11361	8.8E-4	0	11242,17,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749106	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	11361	0.004225	0	11242,17,48,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749106	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	11361	0.003257	0	11242,17,37,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749106	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	11357	0.002201	5	10341,26,817,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749106	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	11357	0.001849	0	11310,26,21,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749106	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	11357	7.04E-4	0	11311,28,8,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttatg/gtg	VM84V	leader	0.000554	0.991848	4	1	GTTA>G
ERR5749106	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	11357	0.001057	0	11311,28,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749106	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	11360	9.68E-4	0	11315,31,11,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749106	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	36845	0.00209	4	25423,11333,57,20	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749106	913	PASS	C	T	25473	0.911004	0	0,16,0,25420	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749106	2702	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	42144	7.12E-4	2506	41859,53,52,113	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F633V	nsp2	0.000632	0.333333	1	1	T>G
ERR5749106	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	83568	0.001256	2147483647	41709,39192,71,2369	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749106	3037	PASS	C	T	17840	0.804428	67	1,26,8910,8758	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749106	3177	PASS	C	T	33932	0.881027	3	9,1,24886,8979	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P153L	nsp3	0.000773	0.96008	3	2	C>T
ERR5749106	3267	PASS	C	T	24922	0.970468	2147483647	0,0,24904,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749106	4021	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21894	0.018041	0	0,21385,0,477	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N434	nsp3	0.018041	0.439223	1	1	C>T
ERR5749106	4237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTA	T	43580	3.67E-4	0	21802,21762,8,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	ata/	I508	nsp3	0.000302	0.918634	2	2	TTA>T
ERR5749106	4529	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTTTAC	T	18397	5.44E-4	0	2,18382,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	tacttt/	YF605	nsp3	0.000527	0.402778	3	1	TTTTAC>T
ERR5749106	5388	PASS	C	A	6888	0.958333	2147483647	0,0,6884,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749106	5986	PASS	C	T	15004	0.97374	0	4,0,14990,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749106	6310	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29289	9.9E-4	0	29217,0,30,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	agC/agT	S1197	nsp3	0.00099	0.94715	2	2	C>T
ERR5749106	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13958	0.001361	0	8,13791,0,28	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749106	6936	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	56097	5.53E-4	4	27717,27640,18,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S1406F	nsp3	0.000553	0.91447	2	2	C>T
ERR5749106	6954	PASS	T	C	28169	0.811388	0	0,6,0,27988	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749106	8964	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	20035	6.49E-4	0	20013,7,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K138	nsp4	0.000553	0.981649	4	2	CA>C
ERR5749106	9532	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28354	0.002257	12	18901,9377,53,15	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F326	nsp4	0.000899	0.966959	1	1	C>T
ERR5749106	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	28354	9.88E-4	47	18932,9394,28,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749106	10323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	22573	0.002747	0	0,22459,0,63	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749106	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	28330	0.0018	0	28240,0,80,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749106	11287	PASS	GTCTGGTTTT	G	28324	0.996752	0	0,92,0,28232	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749106	12513	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23335	9.43E-4	0	23304,0,22,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aTg	T141M	nsp8	0.000794	0.984064	2	2	C>T
ERR5749106	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	17433	6.31E-4	0	17422,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749106	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	45554	0.00112	0	22747,22697,29,29	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749106	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	4069	0.005407	987	3954,52,2,60	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749106	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	7865	0.001399	1	3943,3919,5,6	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749106	14408	PASS	C	T	7865	0.833312	0	1,1,3916,3872	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749106	14676	PASS	C	T	16789	0.794389	0	3,0,16740,2	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749106	14688	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16789	0.00953	0	16611,2,162,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N416	RdRp	0.000534	0.979772	2	2	C>T
ERR5749106	15026	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAT	C	19410	5.15E-4	0	19403,1,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tataca/	YT530	RdRp	0.000503	0.869455	2	2	CAT>C
ERR5749106	15240	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26043	0.001114	0	25990,15,30,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N600	RdRp	0.000934	0.931284	2	2	C>T
ERR5749106	15279	PASS	C	T	26026	0.879697	2147483647	0,0,25974,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749106	16176	PASS	T	C	25046	0.980476	0	0,1,10044,14988	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749106	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAA	G	24299	5.35E-4	0	24242,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GAA>G
ERR5749106	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	31928	7.52E-4	0	31904,0,24,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749106	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	33003	6.36E-4	0	0,32982,0,21	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749106	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25956	0.002235	0	25871,2,59,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749106	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28221	0.001028	0	28165,0,30,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749106	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	38282	7.31E-4	8	18740,19086,14,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749106	21764	PASS	ATACATG	A	15712	0.997391	0	41,0,15671,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749106	21990	PASS	TTTA	T	15709	0.996817	0	0,50,10,15649	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749106	23063	PASS	A	T	16881	0.865352	0	0,5,0,16805	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749106	23271	PASS	C	A	28626	0.918221	0	8,0,28577,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749106	23403	PASS	A	G	28617	0.964392	0	0,3,0,28595	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749106	23604	PASS	C	A	18541	0.941643	0	18,0,18514,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749106	23709	PASS	C	T	18526	0.945968	0	0,4,8,18492	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749106	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	37914	3.96E-4	29	19352,18547,14,1	HIGH	NONE	FRAME_SHIFT	S	ttg/	L753	S	0.000334	0.080808	2	2	CT>C
ERR5749106	24010	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATTTATTGAAGATCTAC	A	19504	6.67E-4	0	182,19309,0,13	HIGH	NONE	FRAME_SHIFT	S	attgaagatctacttttc/	IEDLLF818	S	0.000455	0.926398	4	2	ATTTATTGAAGATCTAC>A
ERR5749106	24127	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TTTG	34363	4.95E-4	41	15019,19344,0,17	MODERATE	NONE	CODON_INSERTION	S	aac/TTGaac	N856LN	S	0.000324	0.111888	4	1	T>TTTG
ERR5749106	24506	PASS	T	G	25116	0.973523	0	14,0,25096,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749106	24914	PASS	G	C	47001	0.961256	0	1,1,23419,23556	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749106	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	33882	0.00121	63	23018,10810,46,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749106	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	18803	0.00117	480	18727,12,6,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749106	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	18985	5.79E-4	0	18974,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749106	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	50144	3.39E-4	0	2,50118,0,17	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749106	26730	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	32379	3.71E-4	0	16168,16244,6,6	HIGH	NONE	FRAME_SHIFT	M	tac/	Y71	M	0.000371	0.919543	3	2	GT>G
ERR5749106	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	16304	7.36E-4	0	5,16282,0,12	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749106	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	16304	8.59E-4	0	5,16283,0,14	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749106	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	16305	0.002637	0	4,16250,0,43	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749106	27209	PASS	A	T	24985	0.954973	0	1,0,24901,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF6	cAt/cTt	H3L	orf6	0.00088	0.957103	3	2	A>T
ERR5749106	27493	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	54237	0.001641	11	29172,24950,59,34	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Cct/Tct	P34S	orf7a	0.000794	0.971493	2	1	C>T
ERR5749106	27972	PASS	C	T	11676	0.904162	0	0,0,11565,74	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749106	28048	PASS	G	T	11614	0.929998	0	0,17,0,11594	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749106	28111	PASS	A	G	37350	0.979572	4	3,3,25718,11614	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749106	28270	PASS	TA	T	49816	0.995042	558	246,11,25363,24206	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749106	28280	PASS	G	C	49707	0.938902	6	11,5,25432,24176	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749106	28281	PASS	A	T	49707	0.914982	16	30,13,25390,24169	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749106	28282	PASS	T	A	49710	0.912231	1	18,21,25348,24190	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749106	28603	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	47408	0.001076	1	23659,23480,28,30	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F110	N	0.000427	0.883357	2	2	C>T
ERR5749106	28881	PASS	G	A	20013	0.764753	19	10,1,9877,9860	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749106	28882	PASS	G	A	20012	0.830452	6	3,0,9994,9830	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749106	28883	PASS	G	C	20012	0.942035	5	2,5,10010,9969	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749106	28977	PASS	C	T	10223	0.94258	2147483647	0,0,0,10207	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749106	29095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	38298	8.09E-4	0	38247,0,32,0	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F274	N	0.000792	0.961279	2	2	C>T
ERR5749106	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	76044	8.42E-4	0	38180,37750,45,43	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749106	29733	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10984	0.001821	0	0,10956,0,22	.	.	.	.	.	.	.	0.001821	0.915943	2	1	C>T
ERR5749107	241	PASS	C	T	12552	0.867431	5	2,6,6208,6289	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749107	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	11805	0.001525	0	11786,2,18,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749107	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	11806	0.00144	0	11732,2,17,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749107	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	11806	0.004066	19	11732,2,47,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749107	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	11795	0.002459	0	10733,5,935,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749107	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	11795	0.001357	0	11773,6,16,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749107	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	11793	7.63E-4	0	11771,6,9,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttatg/gtg	VM84V	leader	0.000554	0.991848	4	1	GTTA>G
ERR5749107	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	11793	6.78E-4	0	11771,6,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749107	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	26576	4.14E-4	27	14740,11823,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749107	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	26582	0.00173	6	14715,11811,30,16	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749107	913	PASS	C	T	14737	0.91104	0	0,7,0,14698	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749107	1510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	16690	0.004494	0	0,16418,0,77	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G235	nsp2	0.002159	0.937304	1	1	T>C
ERR5749107	2695	PASS	C	T	29427	0.142556	0	24499,2,4874,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N630	nsp2	0.0018	0.142556	1	1	C>T
ERR5749107	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	58542	0.001572	2147483647	29260,27255,49,1842	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749107	3037	PASS	C	T	19321	0.811138	60	0,20,9658,9511	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749107	3267	PASS	C	T	15483	0.970807	0	3,0,15473,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749107	4237	PASS	T	C	37095	0.91298	0	0,0,18610,18389	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaT/aaC	N506	nsp3	0.000302	0.918634	2	2	T>C
ERR5749107	4255	PASS	G	A	37204	0.823352	75	30,1,18483,18404	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccG/ccA	P512	nsp3	0.001102	0.871853	2	1	G>A
ERR5749107	5388	PASS	C	A	6503	0.963863	2147483647	0,0,6500,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749107	5575	PASS	C	T	6511	0.944709	258	8,0,0,6497	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y952	nsp3	0.01018	0.961493	1	1	C>T
ERR5749107	5986	PASS	C	T	13339	0.974286	0	4,0,13323,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749107	6954	PASS	T	C	18668	0.820549	0	0,3,2,18557	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749107	7834	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	44917	0.002649	0	22311,22340,66,64	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N1705	nsp3	0.000523	0.86555	3	2	C>T
ERR5749107	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	27215	4.78E-4	29	16025,11177,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749107	11287	PASS	GTCTGGTTTT	G	14495	0.996137	0	0,56,0,14439	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749107	11507	PASS	G	A	29290	0.903448	2	6,3,14638,14517	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Att	V179I	nsp6	0.007744	0.914418	2	2	G>A
ERR5749107	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26606	0.001128	0	13284,13261,17,18	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749107	13667	PASS	C	A	20179	0.116606	0	17786,0,2386,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aAt	T76N	RdRp	0.02682	0.116606	2	1	C>A
ERR5749107	13669	PASS	T	G	20179	0.114178	0	17779,0,2390,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F77V	RdRp	0.114178	0.114178	1	1	T>G
ERR5749107	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	11077	0.004514	2982	10778,109,9,178	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749107	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	21445	0.002611	0	10743,10658,28,28	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749107	14408	PASS	C	T	21445	0.838051	0	3,3,10682,10533	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749107	14676	PASS	C	T	9410	0.780234	0	2,0,9381,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749107	15279	PASS	C	T	15820	0.887863	0	2,0,15797,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749107	15420	PASS	T	G	15781	0.923009	0	0,38,0,15739	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcG	A660	RdRp	0.908883	0.934773	1	1	T>G
ERR5749107	16176	PASS	T	C	17785	0.980883	3	0,1,10048,7727	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749107	17502	PASS	C	T	14821	0.981985	0	1,0,14804,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F422	helicase	0.000611	0.9865	2	2	C>T
ERR5749107	17678	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14821	0.007827	0	1,14692,0,120	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aTg	T481M	helicase	0.001162	0.968704	2	1	C>T
ERR5749107	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	23030	6.51E-4	0	23015,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749107	19011	PASS	C	T	17993	0.970711	0	2,0,17972,2	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D324	ExoN	0.000408	0.975746	4	2	C>T
ERR5749107	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30993	0.001904	0	30907,1,64,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749107	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	16103	7.45E-4	0	0,16089,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TA>T
ERR5749107	21764	PASS	ATACATG	A	13085	0.997554	26	31,1,13053,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749107	21990	PASS	TTTA	T	13091	0.997556	0	0,32,4,13055	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749107	23063	PASS	A	T	12949	0.857286	0	0,3,0,12880	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749107	23271	PASS	C	A	15489	0.916328	0	1,0,15473,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749107	23403	PASS	A	G	15475	0.968207	2147483647	0,0,0,15465	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749107	23604	PASS	C	A	16393	0.938449	0	20,0,16361,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749107	23709	PASS	C	T	16369	0.940558	0	0,3,9,16339	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749107	24127	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	26120	4.21E-4	2	12855,13260,4,7	HIGH	NONE	FRAME_SHIFT	S	aac/	N856	S	0.000324	0.111888	4	1	TA>T
ERR5749107	24506	PASS	T	G	13569	0.974722	0	5,0,13559,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749107	24914	PASS	G	C	36083	0.961145	0	0,0,17968,18086	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749107	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	22642	0.002517	85	17144,5419,73,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749107	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	18486	9.2E-4	0	18469,0,17,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749107	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	11917	9.23E-4	0	4,11892,0,11	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749107	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	11917	0.001343	0	4,11897,0,16	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749107	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	11918	0.00151	0	4,11895,0,18	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749107	27765	PASS	C	T	16845	0.968359	0	0,4,1,16826	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7b	Ctt/Ttt	L4F	orf7b	0.00109	0.970449	1	1	C>T
ERR5749107	27972	PASS	C	T	11648	0.904104	19	1,1,11537,69	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749107	28048	PASS	G	T	11576	0.913528	0	0,14,1,11555	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749107	28111	PASS	A	G	26060	0.978319	5	2,5,14457,11584	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749107	28239	PASS	GTTGTT	G	14436	0.984137	36	226,2,14207,0	HIGH	NONE	FRAME_SHIFT	ORF8	gtttta/	VL117	orf8	0.000417	0.984998	9	2	GTTGTT>G
ERR5749107	28250	PASS	T	TCTG	14258	0.993968	0	69,0,14172,0	MODERATE	NONE	CODON_INSERTION	ORF8	ttc/CTGttc	F120LF	orf8	0.000494	0.993968	5	3	T>TCTG
ERR5749107	28253	PASS	CA	C	14258	0.995511	0	64,0,14194,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749107	28270	PASS	TA	T	27158	0.995986	144	96,13,14162,12887	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749107	28271	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AA	A	27158	0.00162	121	14212,12900,44,0	.	.	.	.	.	.	.	0.000482	0.924941	3	2	AA>A
ERR5749107	28280	PASS	G	C	27160	0.941348	32	12,0,14226,12886	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749107	28281	PASS	A	T	27160	0.930449	0	5,5,14240,12880	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749107	28282	PASS	T	A	27163	0.892685	4	14,8,14191,12883	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749107	28881	PASS	G	A	12723	0.782284	9	4,0,6321,6244	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749107	28882	PASS	G	A	12721	0.830202	0	1,0,6371,6230	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749107	28883	PASS	G	C	12721	0.943479	0	1,0,6383,6320	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749107	28977	PASS	C	T	6476	0.933138	0	0,1,0,6461	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749107	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	52375	0.001107	0	26298,25980,38,37	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749108	241	PASS	C	T	15539	0.863312	0	1,2,7713,7773	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749108	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	14175	0.001058	0	14162,4,15,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749108	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	14175	7.05E-4	0	14138,4,10,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749108	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	14175	0.001199	0	14138,4,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749108	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	14164	0.001977	0	13014,6,1079,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749108	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	14164	7.06E-4	0	14148,6,10,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749108	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATGGTTG	T	14162	7.06E-4	82	14143,3,7,3	HIGH	NONE	FRAME_SHIFT	ORF1ab	atggttgag/	MVE85	leader	0.000587	0.476744	4	1	TATGGTTG>T
ERR5749108	680	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	38678	8.53E-4	9	24455,14173,17,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gat/Aat	D139N	leader	0.000661	0.166667	3	2	G>A
ERR5749108	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	38678	3.36E-4	13	24460,14202,12,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749108	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	38678	8.53E-4	11	24446,14196,26,7	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749108	913	PASS	C	T	24463	0.92319	0	0,13,0,24418	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749108	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	85473	0.001381	2147483647	42658,40046,73,2475	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749108	3037	PASS	C	T	19903	0.81028	54	0,18,9940,9817	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749108	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10053	0.002089	538	11,10013,21,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749108	3267	PASS	C	T	23978	0.97039	0	5,0,23957,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749108	5388	PASS	C	A	6078	0.956236	2147483647	0,0,6075,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749108	5986	PASS	C	T	13010	0.97648	0	1,0,13002,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749108	6662	PASS	G	A	12441	0.242665	0	9015,0,3398,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtc/Atc	V1315I	nsp3	0.242665	0.242665	1	1	G>A
ERR5749108	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12433	0.001689	0	0,12284,0,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749108	6954	PASS	T	C	26978	0.821632	0	0,3,3,26823	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749108	8664	PASS	C	T	28632	0.958822	0	5,0,28605,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T37I	nsp4	0.003182	0.985915	1	1	C>T
ERR5749108	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	34275	5.25E-4	51	17179,17078,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749108	10615	PASS	C	T	20677	0.865067	0	0,2,1,20603	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D187	3Cpro	0.001623	0.865067	1	1	C>T
ERR5749108	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	23388	0.001924	0	23314,0,65,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749108	11287	PASS	GTCTGGTTTT	G	23384	0.998289	0	0,40,0,23344	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749108	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	41195	8.5E-4	0	25724,15402,24,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749108	12125	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	16991	0.001059	0	1,16924,0,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y12H	nsp8	0.000847	0.113436	1	1	T>C
ERR5749108	12162	PASS	A	G	44159	0.972825	1	161,96,26980,16909	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cAg/cGg	Q24R	nsp8	0.000894	0.982497	1	1	A>G
ERR5749108	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	43554	0.001355	0	21749,21680,33,35	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749108	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10737	0.005122	2796	10496,79,5,156	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749108	14408	PASS	C	T	20915	0.852737	12	0,4,10453,10341	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749108	14676	PASS	C	T	15679	0.800816	0	7,0,15630,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749108	15279	PASS	C	T	26233	0.889109	0	4,0,26191,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749108	16176	PASS	T	C	22812	0.981369	0	2,2,10584,12216	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749108	16939	PASS	T	C	20265	0.951986	0	0,0,20246,2	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Tta/Cta	L235	helicase	0.000959	0.959205	2	2	T>C
ERR5749108	17615	PASS	A	G	16045	0.915114	2147483647	0,0,0,16004	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749108	18246	PASS	C	T	12584	0.961618	0	0,3,0,12567	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y69	ExoN	0.960724	0.984848	1	1	C>T
ERR5749108	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	26785	0.001008	0	26757,0,27,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749108	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	31193	0.002084	0	31109,0,67,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749108	20930	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24338	0.001644	0	24279,0,43,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aTg	T91M	MethTr	0.000902	0.95585	2	2	C>T
ERR5749108	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	29817	5.7E-4	2	14871,14936,7,10	HIGH	NONE	FRAME_SHIFT	S	ctt/Tctt	L5S?	S	0.000394	0.091869	4	1	G>GT
ERR5749108	21727	PASS	C	T	12700	0.869055	364	1,11,12672,0	LOW	SILENT	SYNONYMOUS_CODING	S	ttC/ttT	F55	S	0.000896	0.878141	2	2	C>T
ERR5749108	21764	PASS	ATACATG	A	12689	0.997005	0	37,0,12651,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749108	21990	PASS	TTTA	T	12694	0.998031	0	0,25,6,12663	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749108	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	31720	8.83E-4	3	14153,17518,10,18	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749108	22898	PASS	G	A	14186	0.062244	0	13267,7,906,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ggt/Agt	G446S	S	0.062244	0.981998	1	1	G>A
ERR5749108	22904	PASS	A	G	14186	0.057169	0	13330,2,818,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Gat	N448D	S	0.057169	0.057169	1	1	A>G
ERR5749108	23063	PASS	A	T	14152	0.873516	0	0,5,0,14077	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749108	23271	PASS	C	A	25414	0.924884	0	3,0,25380,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749108	23403	PASS	A	G	25410	0.97198	0	0,2,0,25397	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749108	23604	PASS	C	A	16634	0.942828	0	16,0,16611,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749108	23709	PASS	C	T	16613	0.938482	0	0,4,1,16588	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749108	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	37758	3.71E-4	7	21117,16627,5,9	HIGH	NONE	FRAME_SHIFT	S	ttg/	L753	S	0.000334	0.080808	2	2	CT>C
ERR5749108	24506	PASS	T	G	21854	0.974741	0	9,0,21838,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749108	24914	PASS	G	C	39282	0.960745	0	0,0,19570,19688	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749108	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	25469	0.00106	46	16250,9175,35,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749108	25571	PASS	C	T	16385	0.920537	0	0,5,5,16359	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	tCc/tTc	S60F	orf3a	0.001558	0.922217	1	1	C>T
ERR5749108	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	26273	7.23E-4	0	26254,0,19,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749108	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	26436	0.00121	926	26011,152,168,72	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749108	25854	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26257	8.76E-4	0	5,26187,0,26	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	taC/taT	Y154	orf3a	0.000876	0.939185	1	1	C>T
ERR5749108	25909	PASS	G	A	26291	0.964132	627	20,7,1,26248	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gat/Aat	D173N	orf3a	0.963447	0.964132	1	1	G>A
ERR5749108	26270	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	60871	7.89E-4	0	12740,48067,10,41	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	aCa/aTa	T9I	E	0.000586	0.930791	3	2	C>T
ERR5749108	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	13175	9.87E-4	0	6,13155,0,13	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749108	27509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	45927	0.004028	0	26628,19099,112,79	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	aCa/aTa	T39I	orf7a	0.000843	0.067888	1	1	C>T
ERR5749108	27676	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	26640	9.01E-4	0	16,26388,0,215	HIGH	NONSENSE	STOP_GAINED	ORF7a	Gaa/Taa	E95*	orf7a	0.000609	0.877803	2	2	G>T
ERR5749108	27972	PASS	C	T	11643	0.91205	0	0,0,11563,45	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749108	28048	PASS	G	T	11606	0.918663	0	0,9,0,11593	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749108	28111	PASS	A	G	32801	0.980153	3	4,4,21166,11616	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749108	28270	PASS	TA	T	41125	0.995477	448	181,5,20933,20006	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749108	28280	PASS	G	C	41051	0.939076	16	9,1,20959,19983	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749108	28281	PASS	A	T	41051	0.917834	29	30,9,20955,19996	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749108	28282	PASS	T	A	41054	0.909095	2	21,16,20918,20000	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749108	28881	PASS	G	A	20874	0.782361	15	6,0,10371,10269	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749108	28882	PASS	G	A	20873	0.832655	2	3,1,10439,10241	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749108	28883	PASS	G	C	20873	0.946486	6	0,2,10470,10384	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749108	28977	PASS	C	T	10631	0.935001	2147483647	0,0,0,10613	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749108	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	53928	0.001446	0	27062,26753,48,45	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749108	29348	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	38171	8.65E-4	0	10982,27131,10,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gca/Aca	A359T	N	0.000865	0.968413	2	1	G>A
ERR5749109	241	PASS	C	T	12894	0.861951	0	0,0,6419,6432	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749109	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	9371	0.002348	0	8712,1,630,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749109	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	30808	4.22E-4	1	21394,9396,10,3	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749109	913	PASS	C	T	21393	0.920348	0	0,8,0,21352	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749109	3037	PASS	C	T	18061	0.825203	33	1,14,9024,8901	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749109	3177	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	31009	9.03E-4	53	21891,9079,37,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cAt	P153H	nsp3	0.000773	0.96008	3	2	C>A
ERR5749109	3267	PASS	C	T	21930	0.968855	2147483647	0,0,21916,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749109	4237	PASS	T	C	34179	0.918634	0	5,5,17089,16984	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaT/aaC	N506	nsp3	0.000302	0.918634	2	2	T>C
ERR5749109	4255	PASS	G	A	34216	0.813771	38	22,3,16993,16949	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccG/ccA	P512	nsp3	0.001102	0.871853	2	1	G>A
ERR5749109	5388	PASS	C	A	5191	0.959353	2147483647	0,0,5190,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749109	5575	PASS	C	T	5201	0.946741	278	9,0,0,5191	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y952	nsp3	0.01018	0.961493	1	1	C>T
ERR5749109	5986	PASS	C	T	13483	0.973448	0	1,0,13467,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749109	6954	PASS	T	C	24314	0.827466	0	0,6,0,24191	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749109	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	21068	0.002468	0	20505,1,52,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749109	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	21060	0.001092	0	21014,0,35,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749109	11287	PASS	GTCTGGTTTT	G	21051	0.99867	0	0,28,0,21023	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749109	11507	PASS	G	A	28491	0.912534	5	6,2,14243,14167	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Att	V179I	nsp6	0.007744	0.914418	2	2	G>A
ERR5749109	12125	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	17178	0.001339	0	2,17110,0,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y12H	nsp8	0.000847	0.113436	1	1	T>C
ERR5749109	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	36397	9.89E-4	0	18182,18132,20,20	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749109	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	6487	0.003237	1755	6343,41,4,97	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749109	14408	PASS	C	T	12627	0.848262	6	0,2,6313,6233	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749109	14676	PASS	C	T	13417	0.805023	0	1,0,13364,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749109	15279	PASS	C	T	20494	0.90485	0	5,0,20462,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749109	15420	PASS	T	G	20463	0.926648	0	0,31,0,20426	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcG	A660	RdRp	0.908883	0.934773	1	1	T>G
ERR5749109	16176	PASS	T	C	19157	0.981469	3	1,0,8455,10690	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749109	17502	PASS	C	T	16258	0.982286	2147483647	0,0,16250,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F422	helicase	0.000611	0.9865	2	2	C>T
ERR5749109	19011	PASS	C	T	26717	0.975184	0	9,0,26700,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D324	ExoN	0.000408	0.975746	4	2	C>T
ERR5749109	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30986	0.001807	0	30909,0,56,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749109	21134	PASS	A	G	55797	0.689661	0	9631,6582,23477,16078	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cAa/cGa	Q159R	MethTr	0.001194	0.689661	1	1	A>G
ERR5749109	21764	PASS	ATACATG	A	13707	0.997009	0	41,0,13666,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749109	21990	PASS	TTTA	T	13711	0.998177	0	0,25,1,13685	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749109	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30680	9.78E-4	13	13642,16995,19,11	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749109	23063	PASS	A	T	13651	0.876566	0	0,2,0,13591	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749109	23271	PASS	C	A	22002	0.922643	0	2,0,21975,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749109	23403	PASS	A	G	21997	0.973087	0	0,1,0,21988	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749109	23604	PASS	C	A	15973	0.941526	0	8,0,15952,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749109	23709	PASS	C	T	15961	0.94662	0	0,5,2,15930	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749109	24506	PASS	T	G	17824	0.976605	0	12,0,17807,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749109	24914	PASS	G	C	36330	0.961134	3	1,0,18091,18211	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749109	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	24695	0.001498	39	18038,6603,46,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749109	25702	PASS	C	T	21726	0.647933	0	6087,0,15615,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Cct/Tct	P104S	orf3a	0.557756	0.647933	1	1	C>T
ERR5749109	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	21881	0.001371	1623	21585,116,60,97	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749109	27765	PASS	C	T	22024	0.9664	0	0,2,0,21998	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7b	Ctt/Ttt	L4F	orf7b	0.00109	0.970449	1	1	C>T
ERR5749109	27972	PASS	C	T	11197	0.907207	20	1,1,11103,53	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749109	28048	PASS	G	T	11149	0.925195	0	0,15,0,11126	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749109	28111	PASS	A	G	31940	0.979712	0	4,2,20770,11153	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749109	28239	PASS	GTTGTT	G	20730	0.984998	0	313,0,20417,2	HIGH	NONE	FRAME_SHIFT	ORF8	gtttta/	VL117	orf8	0.000417	0.984998	9	2	GTTGTT>G
ERR5749109	28249	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	ATC	20474	9.28E-4	0	20452,2,19,0	HIGH	NONE	FRAME_SHIFT	ORF8	ttc/CTttc	F120L?	orf8	0.000443	0.063605	3	2	A>ATC
ERR5749109	28250	PASS	T	TCTG	20474	0.993699	0	104,0,20343,2	MODERATE	NONE	CODON_INSERTION	ORF8	ttc/CTGttc	F120LF	orf8	0.000494	0.993968	5	3	T>TCTG
ERR5749109	28253	PASS	CA	C	20474	0.995018	0	102,0,20370,2	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749109	28254	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	ATC	20474	9.28E-4	0	20450,2,19,0	HIGH	NONE	FRAME_SHIFT+STOP_LOST+SPLICE_SITE_REGION	ORF8	taa/tCTaa	*122S?	orf8	0.000541	0.914398	3	2	A>ATC
ERR5749109	28270	PASS	TA	T	39838	0.996486	285	130,7,20340,19358	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749109	28271	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AA	A	39838	0.001406	161	20415,19366,56,0	.	.	.	.	.	.	.	0.000482	0.924941	3	2	AA>A
ERR5749109	28280	PASS	G	C	39839	0.943297	23	14,2,20413,19354	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749109	28281	PASS	A	T	39839	0.941339	24	24,7,20409,19346	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749109	28282	PASS	T	A	39843	0.911678	21	30,11,20361,19357	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749109	28881	PASS	G	A	16707	0.773807	21	8,0,8257,8231	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749109	28882	PASS	G	A	16705	0.843759	0	0,0,8342,8223	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749109	28883	PASS	G	C	16705	0.942832	4	1,3,8355,8328	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749109	28977	PASS	C	T	8487	0.937316	0	0,1,0,8470	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749109	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	61919	0.001502	0	31050,30718,59,56	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749110	241	PASS	C	T	24993	0.853999	1	4,6,12405,12490	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749110	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	17324	9.81E-4	0	17308,2,17,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749110	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	17324	0.003002	0	17253,2,52,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749110	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	17311	0.002831	0	15945,4,1243,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749110	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	17311	6.93E-4	0	17294,5,12,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749110	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	17308	8.67E-4	0	17282,6,15,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749110	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	44071	9.76E-4	10	26685,17332,32,11	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749110	913	PASS	C	T	26701	0.922887	0	0,19,0,26644	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749110	2702	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	52233	6.51E-4	2710	51900,48,61,118	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F633V	nsp2	0.000632	0.333333	1	1	T>G
ERR5749110	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	103669	0.001293	2147483647	51743,48610,99,2979	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749110	3037	PASS	C	T	26379	0.835324	55	2,25,13164,13027	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749110	3267	PASS	C	T	23585	0.972398	0	3,0,23569,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749110	5388	PASS	C	A	7980	0.959524	0	1,0,7974,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749110	5467	PASS	C	T	15905	0.860673	6	1,5,7923,7920	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y916	nsp3	0.025478	0.860673	1	1	C>T
ERR5749110	5986	PASS	C	T	16131	0.974459	0	3,0,16118,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749110	6954	PASS	T	C	30165	0.833681	0	0,7,0,30021	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749110	8950	PASS	C	T	52095	0.980824	12	4,1,17967,34108	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I132	nsp4	0.002808	0.982604	1	1	C>T
ERR5749110	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	42004	9.05E-4	129	19146,22820,38,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749110	11082	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	19872	7.05E-4	0	19863,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000427	0.179468	2	1	TG>T
ERR5749110	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	19872	0.003321	0	19763,0,90,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749110	11287	PASS	GTCTGGTTTT	G	19871	0.998188	0	0,33,0,19835	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749110	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	41881	8.36E-4	2	25984,15822,21,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749110	11750	PASS	C	T	50612	0.68466	44	6,27,25860,22348	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L260F	nsp6	0.001019	0.70989	2	1	C>T
ERR5749110	11750	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	G	50612	0.002687	30	6,27,79,2251	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Gtc	L260V	nsp6	0.001019	0.70989	2	1	C>G
ERR5749110	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	18677	0.001981	0	18599,0,37,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749110	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	43654	0.001443	0	21779,21736,36,38	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749110	13712	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	21739	0.001978	0	21682,0,47,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K91R	RdRp	0.001252	0.300156	1	1	A>G
ERR5749110	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	17754	0.003999	2147483647	17355,131,3,252	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749110	14408	PASS	C	T	34576	0.842926	4	3,6,17248,17079	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749110	14676	PASS	C	T	17619	0.797548	0	7,0,17555,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749110	15279	PASS	C	T	30997	0.878053	0	3,0,30952,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749110	16176	PASS	T	C	26802	0.981979	3	1,0,12809,13977	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749110	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	21631	6.93E-4	0	21614,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749110	17181	PASS	T	C	21361	0.987547	0	15,0,21337,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaT/gaC	D315	helicase	0.986595	0.991193	1	1	T>C
ERR5749110	18576	PASS	C	T	34687	0.858794	0	0,4,0,34583	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D179	ExoN	0.005404	0.876866	2	2	C>T
ERR5749110	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	29086	4.47E-4	0	29073,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749110	19299	PASS	T	C	23665	0.987492	0	4,0,23655,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taT/taC	Y420	ExoN	0.001065	0.987656	2	2	T>C
ERR5749110	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34750	0.002475	0	34631,0,90,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749110	20786	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	814	0.017199	285	0,798,14,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAt/aTt	N43I	MethTr	0.001392	1	1	1	A>T
ERR5749110	21234	PASS	C	T	34852	0.630294	0	26,0,34252,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A192	MethTr	0.000472	0.857572	5	2	C>T
ERR5749110	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	39258	9.93E-4	0	19179,19624,25,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749110	21764	PASS	ATACATG	A	16159	0.996349	0	59,0,16100,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749110	21990	PASS	TTTA	T	16168	0.998268	0	0,28,9,16131	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749110	22295	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	37308	0.001903	1	11034,26178,24,52	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Cat/Tat	H245Y	S	0.000662	0.930915	2	2	C>T
ERR5749110	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	17274	0.001389	0	1,17235,0,24	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749110	23063	PASS	A	T	11649	0.86883	0	0,1,0,11599	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749110	23271	PASS	C	A	28317	0.908182	0	1,0,28280,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749110	23403	PASS	A	G	28313	0.977113	0	0,7,0,28284	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749110	23604	PASS	C	A	18593	0.929059	0	19,0,18565,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749110	23709	PASS	C	T	18577	0.949777	0	0,7,2,18549	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749110	24506	PASS	T	G	25869	0.973791	0	15,0,25850,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749110	24914	PASS	G	C	40630	0.960423	0	1,1,20238,20362	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749110	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	34179	9.36E-4	351	34066,17,19,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749110	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	34402	0.001163	1140	33854,243,163,88	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749110	25844	PASS	C	T	34098	0.930055	0	0,5,1,34054	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aCt/aTt	T151I	orf3a	0.001226	0.938776	1	1	C>T
ERR5749110	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	13550	0.00155	0	0,13526,0,21	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749110	27577	PASS	C	T	29321	0.791003	0	5,0,29150,2	HIGH	NONSENSE	STOP_GAINED	ORF7a	Caa/Taa	Q62*	orf7a	0.000614	0.952205	4	2	C>T
ERR5749110	27972	PASS	C	T	13017	0.890374	20	2,1,12927,39	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749110	28048	PASS	G	T	12985	0.921294	0	0,10,0,12970	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749110	28111	PASS	A	G	35025	0.978358	0	6,3,22018,12990	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749110	28270	PASS	TA	T	42908	0.995362	511	198,4,21754,20955	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749110	28280	PASS	G	C	42827	0.94242	35	13,0,21797,20934	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749110	28281	PASS	A	T	42827	0.916641	45	25,3,21780,20935	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749110	28282	PASS	T	A	42829	0.915898	6	24,15,21747,20946	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749110	28881	PASS	G	A	18036	0.750776	28	17,3,8863,8885	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749110	28882	PASS	G	A	18035	0.836096	16	11,2,9005,8842	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749110	28883	PASS	G	C	18035	0.946715	3	2,0,9024,8995	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749110	28977	PASS	C	T	9191	0.931346	0	0,2,0,9177	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749110	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	51117	0.001076	0	25679,25346,35,32	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749111	241	PASS	C	T	18253	0.872843	3	0,2,9090,9088	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749111	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	15921	0.002198	0	15880,4,35,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749111	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	15923	0.001507	0	15818,6,24,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749111	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	15923	0.004082	0	15818,6,65,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749111	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	15925	9.42E-4	0	15031,12,716,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749111	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	15925	0.002009	0	15881,12,32,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749111	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	15920	8.17E-4	0	15891,11,13,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749111	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	42300	5.2E-4	32	26343,15932,21,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749111	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	42300	0.001773	1	26307,15905,49,26	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749111	913	PASS	C	T	26350	0.90945	0	0,17,2,26294	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749111	1027	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	16682	0.001858	315	16610,28,16,15	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccT/ccC	P74	nsp2	0.001454	0.276316	1	1	T>C
ERR5749111	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	90740	0.001918	2147483647	45382,41697,77,3359	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749111	3037	PASS	C	T	23965	0.803797	61	2,27,11999,11768	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749111	3267	PASS	C	T	25339	0.971783	0	1,0,25323,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749111	5388	PASS	C	A	7650	0.960784	2147483647	0,0,7647,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749111	5986	PASS	C	T	14649	0.975561	2147483647	0,0,14639,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749111	6954	PASS	T	C	27995	0.790641	0	0,8,3,27782	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749111	8760	PASS	C	T	30171	0.892678	0	5,0,30085,8	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A69V	nsp4	0.003379	0.892678	1	1	C>T
ERR5749111	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	41239	0.001164	161	18971,22220,48,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749111	10323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	20487	0.003319	0	0,20353,0,73	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749111	10996	PASS	G	A	25660	0.963406	0	0,5,0,25627	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaG/aaA	K8	nsp6	0.963406	0.980023	1	1	G>A
ERR5749111	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	23065	0.001994	0	22978,2,63,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749111	11287	PASS	GTCTGGTTTT	G	23055	0.997354	0	0,61,0,22994	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749111	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	43372	9.22E-4	0	26671,16613,27,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749111	12269	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	29546	4.4E-4	0	29533,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aag/	K61	nsp8	0.000434	0.213333	2	1	GA>G
ERR5749111	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	21277	0.00141	0	21212,0,31,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749111	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	13945	9.32E-4	0	13932,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749111	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	42222	0.001563	0	21085,21003,38,38	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749111	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	18329	0.005729	2147483647	17803,151,9,356	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749111	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	35426	9.88E-4	0	17780,17629,18,17	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749111	14408	PASS	C	T	35426	0.826737	7	2,6,17702,17416	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749111	14676	PASS	C	T	16730	0.81584	0	8,0,16683,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749111	15279	PASS	C	T	28178	0.926822	0	5,0,28148,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749111	15933	PASS	C	T	13939	0.980056	0	1,0,13930,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y831	RdRp	0.980056	0.983528	1	1	C>T
ERR5749111	16176	PASS	T	C	26584	0.979725	2	2,1,12635,13934	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749111	16508	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	28017	0.001285	0	27951,11,53,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGt/gTt	G91V	helicase	0.000561	0.074909	2	2	G>T
ERR5749111	17154	PASS	T	C	19923	0.983185	0	3,0,19911,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taT/taC	Y306	helicase	0.983096	0.984896	1	1	T>C
ERR5749111	18504	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	33742	7.71E-4	0	1,33217,0,451	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K155N	ExoN	0.000518	0.094148	4	3	A>C
ERR5749111	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	27388	4.38E-4	0	27376,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749111	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	28155	3.91E-4	0	0,28144,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749111	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	33682	0.002583	0	33572,0,90,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749111	21764	PASS	ATACATG	A	14706	0.996192	0	55,0,14650,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749111	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	14705	6.12E-4	0	14696,0,9,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749111	21990	PASS	TTTA	T	14717	0.996671	0	0,49,13,14655	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749111	22293	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TACATA	T	38030	5.52E-4	4	11165,26834,4,17	HIGH	NONE	FRAME_SHIFT	S	ttacataga/	LHR244	S	0.000308	0.160511	4	1	TACATA>T
ERR5749111	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34659	8.94E-4	6	14801,19795,11,23	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749111	23063	PASS	A	T	14798	0.850453	0	0,5,0,14704	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749111	23271	PASS	C	A	26160	0.923509	0	1,0,26127,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749111	23403	PASS	A	G	26148	0.960647	0	0,6,0,26115	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749111	23604	PASS	C	A	17967	0.951856	0	13,0,17941,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749111	23709	PASS	C	T	17943	0.934961	0	0,7,6,17897	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749111	24506	PASS	T	G	22856	0.975236	0	8,0,22846,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749111	24914	PASS	G	C	42342	0.958812	0	0,1,21110,21203	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749111	25496	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	39671	7.31E-4	119	19621,19438,198,364	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aTa/aGa	I35R	orf3a	0.000369	0.96555	3	2	T>G
ERR5749111	25587	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19883	0.002565	0	1,19807,0,64	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	ctC/ctT	L65	orf3a	0.000598	0.813206	6	2	C>T
ERR5749111	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	29386	0.001225	451	29271,26,18,19	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749111	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	29341	4.77E-4	0	29327,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749111	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	29609	0.00152	1682	29099,193,149,119	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749111	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	57758	3.81E-4	0	1,57732,0,22	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749111	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	14571	0.001853	0	1,14537,0,27	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749111	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	14571	8.24E-4	0	0,14557,0,12	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749111	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	14573	0.003294	0	0,14521,0,48	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749111	27476	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	48728	9.44E-4	8	28212,20441,33,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	aCa/aTa	T28I	orf7a	0.000547	0.22827	4	2	C>T
ERR5749111	27494	PASS	C	T	48739	0.949835	3	22,12,28226,20446	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	cCt/cTt	P34L	orf7a	0.000672	0.961447	2	2	C>T
ERR5749111	27972	PASS	C	T	13317	0.89825	18	1,1,13168,83	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749111	28048	PASS	G	T	13233	0.919973	0	0,16,0,13204	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749111	28111	PASS	A	G	35170	0.976258	2	1,2,21921,13235	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749111	28270	PASS	TA	T	42309	0.994517	448	224,16,21639,20438	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749111	28280	PASS	G	C	42219	0.932069	14	10,2,21694,20409	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749111	28281	PASS	A	T	42219	0.913712	27	22,5,21687,20423	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749111	28282	PASS	T	A	42221	0.905663	1	20,16,21638,20432	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749111	28856	PASS	A	C	11440	0.983392	0	7,0,11420,4	LOW	SILENT	SYNONYMOUS_CODING	N	Aga/Cga	R195	N	0.979416	0.983392	1	1	A>C
ERR5749111	28881	PASS	G	A	22368	0.767525	14	10,2,11159,10925	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749111	28882	PASS	G	A	22366	0.823795	9	8,2,11253,10865	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749111	28883	PASS	G	C	22366	0.937494	0	1,1,11273,11064	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749111	28977	PASS	C	T	11449	0.907765	0	0,2,0,11410	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749111	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	56419	0.001152	0	28330,27980,39,36	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749112	241	PASS	C	T	156	0.891026	0	0,0,77,78	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749112	745	PASS	C	T	1915	0.915927	2147483647	0,0,1912,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N160	leader	0.001671	0.915927	1	1	C>T
ERR5749112	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1912	0.017782	0	0,1876,0,36	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749112	913	PASS	C	T	1912	0.925732	2147483647	0,0,0,1910	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749112	1191	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2498	0.008407	0	0,2472,0,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCa/cTa	P129L	nsp2	0.000749	0.916048	3	2	C>T
ERR5749112	1643	PASS	A	T	4668	0.97665	0	2,0,4666,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Aac/Tac	N280Y	nsp2	0.001863	0.97665	1	1	A>T
ERR5749112	2144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	1069	0.006548	0	0,1062,0,7	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtc/Ctc	V447L	nsp2	0.004278	0.752119	2	1	G>C
ERR5749112	3037	PASS	C	T	968	0.833678	0	0,1,482,483	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749112	3267	PASS	C	T	1082	0.966728	2147483647	0,0,1081,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749112	3320	PASS	G	T	1082	0.68854	0	20,0,1061,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Ttt	V201F	nsp3	0.001049	0.745293	2	2	G>T
ERR5749112	4338	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	1668	0.007794	30	716,939,0,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	att/	I541	nsp3	0.000366	0.051643	2	2	CTA>C
ERR5749112	5388	PASS	C	A	269	0.966543	2147483647	0,0,269,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749112	5986	PASS	C	T	996	0.968876	2147483647	0,0,996,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749112	6573	PASS	C	T	442	0.957014	2147483647	0,0,441,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S1285F	nsp3	0.001862	0.957014	1	1	C>T
ERR5749112	6954	PASS	T	C	913	0.824754	2147483647	0,0,0,906	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749112	8084	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	1086	0.027624	0	1055,0,30,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E1789K	nsp3	0.000543	0.923413	4	2	G>A
ERR5749112	10323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	3514	0.005692	0	0,3477,0,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749112	11287	PASS	GTCTGGTTTT	G	3272	0.96577	0	0,112,0,3160	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749112	12269	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	1416	0.012712	0	1398,0,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aag/	K61	nsp8	0.000434	0.213333	2	1	GA>G
ERR5749112	12534	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1337	0.010471	0	1322,0,14,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T148I	nsp8	0.004454	0.90073	1	1	C>T
ERR5749112	13059	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTG	C	5626	0.006399	9	5169,421,36,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gta/	V13	nsp10	0.000448	0.855104	3	2	CTG>C
ERR5749112	13458	PASS	C	T	819	0.058608	0	769,0,49,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCg/tTg	S6L	nsp11	0.001017	0.058608	4	2	C>T
ERR5749112	14408	PASS	C	T	56	0.910714	0	0,0,28,28	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749112	14676	PASS	C	T	396	0.893939	2147483647	0,0,395,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749112	15279	PASS	C	T	1011	0.878338	0	1,0,1008,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749112	15774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3288	0.006387	0	0,3267,0,21	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	agC/agT	S778	RdRp	0.006387	0.078608	2	2	C>T
ERR5749112	16176	PASS	T	C	913	0.990142	0	0,0,243,670	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749112	18232	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	816	0.012255	0	0,805,0,10	HIGH	NONSENSE	STOP_GAINED	ORF1ab	Caa/Taa	Q65*	ExoN	0.002195	0.056093	1	1	C>T
ERR5749112	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	9291	0.001184	0	9280,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749112	18877	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	9290	0.022928	0	0,9077,0,213	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L280	ExoN	0.000848	0.953596	2	2	CT>C
ERR5749112	19983	PASS	C	CT	223	0.085202	0	204,0,19,0	HIGH	NONE	FRAME_SHIFT+STOP_GAINED	ORF1ab	gat/Tgat	D124*?	endoR	0.000884	0.981982	5	2	C>CT
ERR5749112	21764	PASS	ATACATG	A	1749	0.997141	0	5,0,1744,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749112	21990	PASS	TTTA	T	1749	0.999428	0	0,1,0,1748	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749112	22293	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	4725	0.014392	165	2017,2640,0,68	HIGH	NONE	FRAME_SHIFT	S	cat/	H245	S	0.000308	0.160511	4	1	TAC>T
ERR5749112	22295	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4725	0.01545	5	1988,2591,29,49	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Cat/Tat	H245Y	S	0.000662	0.930915	2	2	C>T
ERR5749112	22323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4722	0.017366	197	2014,2623,0,82	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCt/tTt	S254F	S	0.000812	0.978946	3	2	C>T
ERR5749112	22450	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2027	0.003947	0	2000,13,9,0	LOW	SILENT	SYNONYMOUS_CODING	S	ctC/ctT	L296	S	0.00215	0.803846	1	1	C>T
ERR5749112	23063	PASS	A	T	1364	0.8761	2147483647	0,0,0,1360	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749112	23249	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1830	0.00929	0	1807,0,18,0	HIGH	NONSENSE	STOP_GAINED	S	Caa/Taa	Q563*	S	0.001376	0.082558	1	1	C>T
ERR5749112	23271	PASS	C	A	1830	0.926776	0	1,0,1827,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749112	23403	PASS	A	G	1829	0.97977	2147483647	0,0,0,1827	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749112	23604	PASS	C	A	1546	0.963131	0	1,0,1545,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749112	23709	PASS	C	T	1545	0.942395	2147483647	0,0,0,1544	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749112	24506	PASS	T	G	2909	0.975937	0	2,0,2906,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749112	24745	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6350	0.008976	1	3412,2878,29,28	LOW	SILENT	SYNONYMOUS_CODING	S	gtC/gtT	V1061	S	0.00048	0.961619	3	2	C>T
ERR5749112	24914	PASS	G	C	6835	0.960497	0	0,0,3402,3427	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749112	25702	PASS	C	T	303	0.557756	0	111,0,192,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Cct/Tct	P104S	orf3a	0.557756	0.647933	1	1	C>T
ERR5749112	26091	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6617	0.003627	0	6580,0,28,0	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	taC/taT	Y233	orf3a	0.000569	0.128212	4	2	C>T
ERR5749112	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	6607	0.009687	0	0,6543,0,64	HIGH	NONE	FRAME_SHIFT	ORF3a	gtt/Agtt	V256S?	orf3a	0.000249	0.122153	5	2	T>TA
ERR5749112	26730	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	5725	0.007336	4	2828,2833,25,33	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Gtt/Ttt	V70F	M	0.000371	0.919543	3	2	G>T
ERR5749112	27078	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9183	0.002287	0	0,9154,0,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Cgt/Tgt	R186C	M	0.000415	0.05783	2	2	C>T
ERR5749112	27297	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5732	0.010119	0	5662,0,60,0	LOW	SILENT	SYNONYMOUS_CODING	ORF6	atC/atT	I32	orf6	0.000978	0.91266	1	1	C>T
ERR5749112	27312	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	5729	0.006109	0	5694,0,35,0	HIGH	NONE	FRAME_SHIFT	ORF6	aat/aaAt	N39K?	orf6	0.000911	0.088458	4	2	T>TA
ERR5749112	27739	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5030	0.009344	0	0,4980,0,48	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Ctc/Ttc	L116F	orf7a	0.001001	0.957506	1	1	C>T
ERR5749112	27741	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5030	0.014712	0	0,4948,0,75	LOW	SILENT	SYNONYMOUS_CODING	ORF7a	ctC/ctT	L116	orf7a	0.000363	0.954278	3	2	C>T
ERR5749112	27752	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5031	0.004969	0	0,5004,0,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	aCa/aTa	T120I	orf7a	0.000582	0.943806	2	2	C>T
ERR5749112	27972	PASS	C	T	672	0.90625	0	0,0,667,3	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749112	28005	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1329	0.007524	0	657,658,5,5	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	Cct/Tct	P38S	orf8	0.007524	0.778911	1	1	C>T
ERR5749112	28048	PASS	G	T	669	0.90583	0	0,2,0,666	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749112	28093	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	669	0.010463	0	0,662,0,7	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tCt/tTt	S67F	orf8	0.001515	0.967675	1	1	C>T
ERR5749112	28095	PASS	A	T	669	0.967115	2147483647	0,0,0,669	HIGH	NONSENSE	STOP_GAINED	ORF8	Aaa/Taa	K68*	orf8	0.002672	0.967672	2	2	A>T
ERR5749112	28111	PASS	A	G	690	0.950725	0	0,0,20,670	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749112	28245	PASS	T	G	19	0.894737	2147483647	0,0,19,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	Tta/Gta	L118V	orf8	0.019165	0.950471	2	2	T>G
ERR5749112	28250	PASS	T	TCTG	19	0.947368	0	1,0,18,0	MODERATE	NONE	CODON_INSERTION	ORF8	ttc/CTGttc	F120LF	orf8	0.000494	0.993968	5	3	T>TCTG
ERR5749112	28253	PASS	CA	C	19	0.947368	0	1,0,18,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749112	28270	PASS	TA	T	33	0.969697	0	1,0,18,14	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749112	28280	PASS	G	C	33	0.969697	0	0,0,19,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749112	28281	PASS	A	T	33	0.909091	0	0,0,19,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749112	28282	PASS	T	A	34	0.852941	3	0,1,19,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749112	28512	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAGA	C	13682	6.58E-4	0	13673,0,9,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	N	ccagat/cct	PD80P	N	0.000621	0.172671	3	2	CAGA>C
ERR5749112	28603	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27268	8.43E-4	0	13600,13530,12,12	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F110	N	0.000427	0.883357	2	2	C>T
ERR5749112	28881	PASS	G	A	977	0.781986	0	0,0,484,488	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749112	28882	PASS	G	A	977	0.837257	0	0,0,487,483	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749112	28883	PASS	G	C	977	0.941658	0	0,0,485,490	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749112	28977	PASS	C	T	497	0.937626	0	0,1,0,496	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749112	29091	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	7299	0.006302	0	7253,0,46,0	HIGH	NONE	FRAME_SHIFT	N	ttc/	F274	N	0.000452	0.073908	3	1	CT>C
ERR5749112	29095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7299	0.002055	0	7278,0,15,0	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F274	N	0.000792	0.961279	2	2	C>T
ERR5749112	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	14494	0.001725	0	7275,7183,17,17	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749112	29555	PASS	C	T	6629	0.122643	11	3007,2764,473,381	.	.	.	.	.	.	.	0.000611	0.957048	3	1	C>T
ERR5749112	29642	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6631	0.002564	0	3460,3142,10,9	HIGH	NONSENSE	STOP_GAINED	ORF10	Caa/Taa	Q29*	orf10	0.001806	0.941176	2	2	C>T
ERR5749113	241	PASS	C	T	14327	0.860334	0	0,1,7116,7145	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749113	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	13024	0.002687	0	12984,9,35,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749113	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	13025	0.001152	0	12914,11,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749113	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	13025	0.001305	0	12914,11,17,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749113	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	13025	0.005144	0	12914,11,67,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749113	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	13014	0.001921	0	11982,12,856,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749113	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	13014	0.002228	0	12973,12,29,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749113	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	13012	9.99E-4	0	12974,11,13,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttatg/gtg	VM84V	leader	0.000554	0.991848	4	1	GTTA>G
ERR5749113	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	13012	8.45E-4	19	12974,11,10,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749113	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	13011	6.92E-4	0	12980,12,9,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749113	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	36717	6.26E-4	15	23657,13036,20,3	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749113	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	36716	4.09E-4	5	23594,13018,12,3	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749113	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	36716	0.002152	17	23594,13018,61,18	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749113	913	PASS	C	T	23673	0.925062	0	0,13,0,23629	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749113	3037	PASS	C	T	19657	0.808923	44	1,18,9816,9665	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749113	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	9932	0.001812	486	8,9896,18,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749113	3267	PASS	C	T	22294	0.972414	0	2,0,22275,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749113	3671	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAAAATTT	G	28438	4.22E-4	0	14231,14196,6,6	HIGH	NONE	FRAME_SHIFT	ORF1ab	gaaaatttt/	ENF318	nsp3	0.000351	0.0625	6	2	GAAAATTT>G
ERR5749113	5388	PASS	C	A	7199	0.957911	2147483647	0,0,7194,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749113	5986	PASS	C	T	13415	0.977264	2147483647	0,0,13407,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749113	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12615	0.001902	0	8,12465,0,31	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749113	6954	PASS	T	C	25629	0.823403	0	0,4,1,25513	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749113	8760	PASS	C	T	28139	0.836348	0	4,0,28029,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A69V	nsp4	0.003379	0.892678	1	1	C>T
ERR5749113	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	34092	5.87E-4	63	16480,17591,20,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749113	10681	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19157	0.001462	0	17,19101,0,28	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y209	3Cpro	0.000888	0.977192	2	2	C>T
ERR5749113	10996	PASS	G	A	12965	0.980023	0	0,2,0,12955	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaG/aaA	K8	nsp6	0.963406	0.980023	1	1	G>A
ERR5749113	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	20969	0.001765	0	20906,0,58,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749113	11287	PASS	GTCTGGTTTT	G	20966	0.997854	0	0,43,0,20921	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749113	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	43521	0.001195	0	21740,21676,28,29	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749113	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10259	0.003802	2351	10043,83,1,128	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749113	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	20005	7.0E-4	0	10026,9977,7,7	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749113	14408	PASS	C	T	20005	0.84074	6	1,4,9979,9888	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749113	14676	PASS	C	T	14471	0.791583	0	6,0,14411,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749113	15279	PASS	C	T	25258	0.885224	0	10,0,25206,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749113	15933	PASS	C	T	11915	0.981704	0	1,0,11912,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y831	RdRp	0.980056	0.983528	1	1	C>T
ERR5749113	16176	PASS	T	C	22919	0.981762	0	1,2,10996,11910	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749113	17154	PASS	T	C	17156	0.983096	0	4,0,17141,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taT/taC	Y306	helicase	0.983096	0.984896	1	1	T>C
ERR5749113	18504	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	30844	8.11E-4	0	5,30439,0,367	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K155N	ExoN	0.000518	0.094148	4	3	A>C
ERR5749113	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	24689	5.67E-4	0	24675,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749113	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	26251	6.86E-4	0	0,26233,0,18	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749113	19343	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTTTTGTTAAT	C	20384	6.38E-4	0	20366,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tttgttaattta/	FVNL436	ExoN	0.000519	0.192257	7	2	CTTTTGTTAAT>C
ERR5749113	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	31357	0.002009	0	31261,1,63,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749113	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	35443	8.46E-4	2	17657,17760,13,17	HIGH	NONE	FRAME_SHIFT	S	ctt/Tctt	L5S?	S	0.000394	0.091869	4	1	G>GT
ERR5749113	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	35398	0.001074	1	17313,17694,23,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749113	21764	PASS	ATACATG	A	13027	0.997467	0	33,0,12994,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749113	21990	PASS	TTTA	T	13035	0.997775	0	0,29,7,12999	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749113	22225	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	23165	0.001554	0	0,23124,0,37	LOW	SILENT	SYNONYMOUS_CODING	S	tcG/tcA	S221	S	0.001195	0.94526	3	1	G>A
ERR5749113	22323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTTCTTCAGG	C	32734	0.001283	224	9523,23169,42,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tcttcaggttgg/tgg	SSGW255W	S	0.000812	0.978946	3	2	CTTCTTCAGG>C
ERR5749113	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30257	9.25E-4	0	13485,16713,13,15	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749113	23063	PASS	A	T	13490	0.862639	2147483647	0,0,0,13426	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749113	23271	PASS	C	A	23822	0.926077	2147483647	0,0,23792,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749113	23403	PASS	A	G	23827	0.973308	0	0,1,0,23815	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749113	23604	PASS	C	A	16375	0.95542	0	9,0,16357,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749113	23709	PASS	C	T	16361	0.941813	0	0,1,9,16325	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749113	24506	PASS	T	G	20026	0.974733	0	4,0,20021,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749113	24914	PASS	G	C	37488	0.959961	3	1,0,18667,18787	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749113	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	26853	0.00175	79	17333,9455,55,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749113	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	25850	0.001393	396	25744,12,21,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749113	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	25821	5.81E-4	0	25805,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749113	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	25989	0.001077	934	25605,173,115,69	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749113	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	51256	3.51E-4	0	0,51234,0,18	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749113	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	12692	7.09E-4	0	0,12676,0,9	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749113	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	12692	0.001182	0	0,12677,0,15	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749113	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	12692	0.003073	0	0,12651,0,39	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749113	27494	PASS	C	T	42779	0.939667	1	7,4,24440,18296	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	cCt/cTt	P34L	orf7a	0.000672	0.961447	2	2	C>T
ERR5749113	27972	PASS	C	T	11747	0.905933	72	4,4,11636,60	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749113	28048	PASS	G	T	11697	0.928016	0	0,15,0,11677	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749113	28111	PASS	A	G	32782	0.97883	1	3,3,21069,11697	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749113	28270	PASS	TA	T	40917	0.994574	578	223,4,20756,19939	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749113	28280	PASS	G	C	40833	0.938138	25	19,4,20814,19922	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749113	28281	PASS	A	T	40833	0.90995	40	34,8,20801,19917	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749113	28282	PASS	T	A	40834	0.914875	30	27,7,20774,19936	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749113	28856	PASS	A	C	9862	0.979416	0	4,0,9840,17	LOW	SILENT	SYNONYMOUS_CODING	N	Aga/Cga	R195	N	0.979416	0.983392	1	1	A>C
ERR5749113	28881	PASS	G	A	19355	0.777629	16	9,1,9582,9562	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749113	28882	PASS	G	A	19354	0.842255	9	4,0,9690,9518	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749113	28883	PASS	G	C	19354	0.947814	2	1,2,9703,9628	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749113	28977	PASS	C	T	9867	0.932705	0	0,2,3,9839	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749113	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	36682	0.00109	187	26795,9811,4,41	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749113	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	53232	0.001071	0	26717,26410,37,37	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749114	241	PASS	C	T	8041	0.866808	3	0,1,3999,3994	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749114	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	11048	0.001086	0	11041,0,12,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749114	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	11045	0.002626	0	10143,6,877,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749114	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29848	0.001541	10	18729,11032,36,12	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L140	leader	0.000316	0.135802	3	2	C>T
ERR5749114	913	PASS	C	T	18773	0.915677	0	0,13,0,18735	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749114	2185	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	22570	4.43E-4	0	5,22555,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L462S?	nsp2	0.000441	0.963529	4	3	G>GT
ERR5749114	2453	PASS	C	T	14344	0.733756	0	0,13,0,14122	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L550F	nsp2	0.00429	0.842201	2	2	C>T
ERR5749114	3037	PASS	C	T	17568	0.815403	33	1,14,8777,8661	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749114	3267	PASS	C	T	18260	0.971084	0	5,0,18239,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749114	5388	PASS	C	A	5295	0.959396	0	1,0,5292,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749114	5986	PASS	C	T	12728	0.969202	2147483647	0,0,12716,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749114	6606	PASS	C	T	12372	0.942289	0	4,0,12357,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S1296F	nsp3	0.002262	0.945412	1	1	C>T
ERR5749114	6954	PASS	T	C	21586	0.810155	0	0,4,0,21450	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749114	7070	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	34699	0.002421	237	12960,21643,83,11	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggc/Tgc	G1451C	nsp3	0.000698	0.101434	3	1	G>T
ERR5749114	7945	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21181	0.001841	0	7,21124,0,42	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y1742	nsp3	0.001244	0.950558	2	2	C>T
ERR5749114	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	24418	6.96E-4	29	15837,8563,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749114	10323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	18676	0.001178	0	0,18606,0,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749114	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	21252	0.002212	0	20679,1,47,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749114	11082	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	21245	5.65E-4	0	21236,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000427	0.179468	2	1	TG>T
ERR5749114	11199	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	42293	7.09E-4	0	21010,21112,15,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCc/gTc	A76V	nsp6	0.000309	0.056758	3	2	C>T
ERR5749114	11287	PASS	GTCTGGTTTT	G	21234	0.998587	0	0,30,0,21204	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749114	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	34854	8.61E-4	0	21052,13757,19,11	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749114	11750	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	41189	0.001748	0	20958,20086,47,45	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L260F	nsp6	0.001019	0.70989	2	1	C>T
ERR5749114	12459	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	40885	0.001883	0	18912,21891,36,41	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T123I	nsp8	0.000658	0.986093	1	1	C>T
ERR5749114	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	33026	8.78E-4	0	16493,16458,16,16	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749114	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	4029	0.005212	1121	3929,31,4,65	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749114	14408	PASS	C	T	7813	0.84193	2	1,2,3911,3848	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749114	14676	PASS	C	T	12556	0.735983	0	6,0,12510,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749114	15279	PASS	C	T	20196	0.893593	2147483647	0,0,20172,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749114	16176	PASS	T	C	20443	0.979993	0	0,1,9017,11418	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749114	18131	PASS	C	T	11954	0.842563	0	0,0,11915,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T31I	ExoN	0.0025	0.853992	1	1	C>T
ERR5749114	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	26187	7.64E-4	0	26167,0,20,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749114	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	24449	4.09E-4	0	3,24436,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749114	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23218	0.002412	0	23148,0,58,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749114	21762	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTATACA	C	13474	0.002004	0	13447,0,27,0	MODERATE	NONE	CODON_DELETION	S	atacat/	IH68	S	0.001297	0.875707	2	2	CTATACA>C
ERR5749114	21764	PASS	ATACATG	A	13474	0.996215	0	51,0,13423,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749114	21990	PASS	TTTA	T	13480	0.998294	0	0,23,6,13451	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749114	23063	PASS	A	T	14246	0.863541	0	0,2,0,14173	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749114	23271	PASS	C	A	21555	0.919601	2147483647	0,0,21532,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749114	23403	PASS	A	G	21547	0.966677	0	0,5,0,21530	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749114	23604	PASS	C	A	16206	0.935826	0	17,0,16181,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749114	23709	PASS	C	T	16182	0.943332	0	0,2,0,16161	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749114	24237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13268	0.001357	0	13245,0,18,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gTt	A892V	S	0.001242	0.889739	1	1	C>T
ERR5749114	24244	PASS	A	G	13256	0.943874	0	5,0,13241,0	LOW	SILENT	SYNONYMOUS_CODING	S	ttA/ttG	L894	S	0.943874	0.943874	1	1	A>G
ERR5749114	24506	PASS	T	G	18408	0.97425	0	11,0,18394,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749114	24914	PASS	G	C	39075	0.959514	0	0,0,19454,19592	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749114	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	27056	8.87E-4	16	18979,8035,30,4	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749114	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	15092	0.001922	443	15021,18,11,19	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749114	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	13362	5.99E-4	0	0,13354,0,8	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749114	27972	PASS	C	T	9931	0.903434	0	0,0,9854,49	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749114	28048	PASS	G	T	9879	0.920539	0	0,12,0,9865	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749114	28087	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9898	0.001718	0	6,9873,0,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	gCt/gTt	A65V	orf8	0.001718	0.963754	2	1	C>T
ERR5749114	28093	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9898	0.001515	0	6,9868,0,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tCt/tTt	S67F	orf8	0.001515	0.967675	1	1	C>T
ERR5749114	28111	PASS	A	G	31327	0.979634	2	1,1,21426,9887	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749114	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21411	0.002615	0	21295,1,58,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749114	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	21404	5.14E-4	0	21399,1,11,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749114	28270	PASS	TA	T	41571	0.995574	451	191,7,21154,20233	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749114	28271	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AA	A	41567	6.25E-4	74	21304,20240,26,0	.	.	.	.	.	.	.	0.000482	0.924941	3	2	AA>A
ERR5749114	28280	PASS	G	C	41508	0.936012	29	14,1,21194,20204	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749114	28281	PASS	A	T	41508	0.909463	50	27,3,21185,20221	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749114	28282	PASS	T	A	41509	0.908213	11	28,15,21136,20224	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749114	28732	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26915	8.92E-4	3	7375,19503,8,16	LOW	SILENT	SYNONYMOUS_CODING	N	aaC/aaT	N153	N	0.000892	0.966905	2	2	C>T
ERR5749114	28881	PASS	G	A	14478	0.747824	9	4,0,7138,7110	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749114	28882	PASS	G	A	14478	0.820555	12	5,0,7242,7093	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749114	28883	PASS	G	C	14478	0.941428	0	3,2,7257,7209	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749114	28977	PASS	C	T	7384	0.928359	2147483647	0,0,0,7370	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749114	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	59603	0.001258	0	29960,29530,46,45	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749114	29386	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	9336	0.001285	0	9324,0,12,0	HIGH	NONE	FRAME_SHIFT	N	aag/aaAg	K373K?	N	0.000887	0.899197	4	2	C>CA
ERR5749115	71	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	990	0.014141	0	974,0,14,0	.	.	.	.	.	.	.	0.002088	0.926791	2	1	C>T
ERR5749115	241	PASS	C	T	1160	0.880172	0	0,0,578,578	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749115	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	2682	0.001864	0	2673,0,5,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749115	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	2679	0.002613	0	2672,0,7,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749115	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	14356	0.001463	16	11649,2686,21,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749115	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	14356	0.001115	12	11654,2686,16,0	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749115	913	PASS	C	T	11665	0.903215	0	0,4,0,11638	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749115	1544	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	11182	0.00161	0	0,11145,0,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gct/Act	A247T	nsp2	0.00161	0.936929	2	1	G>A
ERR5749115	2185	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	13102	0.001145	0	1,13086,0,15	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L462S?	nsp2	0.000441	0.963529	4	3	G>GT
ERR5749115	2293	PASS	G	T	8512	0.968398	0	4,0,8506,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caG/caT	Q496H	nsp2	0.001437	0.968398	1	1	G>T
ERR5749115	3037	PASS	C	T	9832	0.812856	21	0,7,4921,4827	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749115	3267	PASS	C	T	14659	0.969575	2147483647	0,0,14654,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749115	3671	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	13340	0.001949	0	6662,6653,13,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N319	nsp3	0.000351	0.0625	6	2	GA>G
ERR5749115	3802	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	11751	0.001447	40	5052,6682,0,17	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N363	nsp3	0.000554	0.064198	4	2	TA>T
ERR5749115	3832	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	5052	0.001386	0	5045,0,7,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTg	L373F?	nsp3	0.000689	0.327273	4	2	C>CT
ERR5749115	4317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	11737	0.001619	0	0,11704,0,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aGt/aCt	S533T	nsp3	0.001619	0.118421	2	1	G>C
ERR5749115	5388	PASS	C	A	2652	0.952866	2147483647	0,0,2652,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749115	5986	PASS	C	T	7994	0.977233	2147483647	0,0,7987,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749115	6335	PASS	T	A	15064	0.949947	0	3,0,15050,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tcg/Acg	S1206T	nsp3	0.000961	0.949947	2	1	T>A
ERR5749115	6359	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	30052	0.001065	59	15003,14970,54,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gac/Tac	D1214Y	nsp3	0.001065	0.085782	2	1	G>T
ERR5749115	6516	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	21909	0.001095	21	6820,15065,14,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	att/aAtt	I1268N?	nsp3	0.000479	0.186047	4	2	T>TA
ERR5749115	6539	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6834	0.002049	0	6808,0,14,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cac/Tac	H1274Y	nsp3	0.001998	0.979821	1	1	C>T
ERR5749115	6936	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24699	0.001619	1	12197,12132,21,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S1406F	nsp3	0.000553	0.91447	2	2	C>T
ERR5749115	6954	PASS	T	C	12400	0.815726	0	0,2,0,12315	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749115	8084	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAA	G	11139	8.98E-4	0	11122,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1790	nsp3	0.000543	0.923413	4	2	GAA>G
ERR5749115	8092	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	11139	0.001347	0	11124,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T1793	nsp3	0.000539	0.063953	3	2	CA>C
ERR5749115	8603	PASS	T	C	6510	0.964363	0	0,3,0,6504	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Ctc	F17L	nsp4	0.002607	0.974959	2	1	T>C
ERR5749115	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11471	0.002005	14	9822,1624,24,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ctC/ctT	L329	nsp4	0.000346	0.955771	2	2	C>T
ERR5749115	9559	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	9849	0.001523	0	9813,2,26,0	HIGH	NONSENSE	STOP_GAINED	ORF1ab	taC/taA	Y335*	nsp4	0.001348	0.062899	2	2	C>A
ERR5749115	10138	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	18682	9.63E-4	14	14790,3874,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggt/	G29	3Cpro	0.000458	0.983567	3	3	CG>C
ERR5749115	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	17737	0.001466	0	17694,0,41,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749115	11287	PASS	GTCTGGTTTT	G	17735	0.998872	0	0,20,0,17715	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749115	11750	PASS	C	T	29081	0.68543	43	0,13,14906,12802	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L260F	nsp6	0.001019	0.70989	2	1	C>T
ERR5749115	11750	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	G	29081	0.003301	0	0,13,36,1301	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Gtc	L260V	nsp6	0.001019	0.70989	2	1	C>G
ERR5749115	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	12450	0.002169	0	12417,0,28,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749115	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	12861	6.22E-4	0	12854,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749115	13468	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	10468	8.6E-4	0	10459,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggg/	G10	nsp11	0.000713	0.076498	2	2	CG>C
ERR5749115	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20904	0.001148	0	10441,10403,14,14	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749115	14408	PASS	C	T	3411	0.861624	3	0,1,1703,1680	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749115	14676	PASS	C	T	8946	0.720098	0	2,0,8898,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749115	14724	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8938	0.001566	0	8889,11,18,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F428	RdRp	0.000952	0.789267	3	2	C>T
ERR5749115	15279	PASS	C	T	9490	0.890727	2147483647	0,0,9482,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749115	16176	PASS	T	C	11510	0.976021	0	0,0,3096,8411	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749115	16524	PASS	A	G	16544	0.926983	0	5,0,16515,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acA/acG	T96	helicase	0.00047	0.926983	2	2	A>G
ERR5749115	16575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16541	0.001088	0	16501,0,22,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D113	helicase	0.001088	0.827968	1	1	C>T
ERR5749115	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	14687	0.001498	0	14665,0,22,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749115	17122	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCT	G	23112	4.76E-4	48	8414,14687,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctctac/	LY297	helicase	0.000476	0.056834	3	2	GCT>G
ERR5749115	17602	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	11591	0.001035	33	11191,11533,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/	Y457	helicase	0.001035	0.156682	1	1	GT>G
ERR5749115	17615	PASS	A	G	11545	0.890948	0	0,1,0,11498	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749115	17626	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CATAAA	C	11553	0.001039	0	0,11541,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	cataaa/	HK464	helicase	0.001039	0.946125	2	2	CATAAA>C
ERR5749115	18658	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	22822	0.001271	0	22776,9,30,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tgt/Cgt	C207R	ExoN	0.000507	0.115741	3	2	T>C
ERR5749115	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	22813	6.58E-4	0	22798,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749115	18803	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	45555	9.44E-4	31	22688,22637,81,130	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aGc/aTc	S255I	ExoN	0.000786	0.897116	2	1	G>T
ERR5749115	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9616	0.0026	0	9585,0,26,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749115	20592	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	19764	0.001063	0	19725,0,21,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taT/taC	Y324	endoR	0.001063	0.971458	1	1	T>C
ERR5749115	20719	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19721	0.001268	0	0,19465,0,25	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L21	MethTr	0.000341	0.209091	2	2	C>T
ERR5749115	20857	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	36776	5.44E-4	67	16987,19769,20,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/	V67	MethTr	0.000531	0.099366	2	2	GT>G
ERR5749115	20987	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTT	C	33896	0.001062	1	16941,16922,17,19	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L111	MethTr	0.000276	0.056129	4	2	CTT>C
ERR5749115	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	17005	0.001353	0	0,16982,0,23	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TA>T
ERR5749115	21077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17010	0.003116	0	5,16936,0,53	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T140I	MethTr	0.000492	0.955529	4	2	C>T
ERR5749115	21101	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	17011	0.001528	0	5,16962,0,44	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGt/gTt	G148V	MethTr	0.001498	0.083467	2	2	G>T
ERR5749115	21234	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	21056	7.12E-4	0	21041,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/Tgtt	V194C?	MethTr	0.000472	0.857572	5	2	C>CT
ERR5749115	21516	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	8552	0.001403	0	8540,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	agagtt/	RV287	MethTr	0.000412	0.905456	2	2	CAG>C
ERR5749115	21764	PASS	ATACATG	A	10446	0.996841	0	33,0,10413,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749115	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	10445	0.001723	0	10427,0,18,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749115	21990	PASS	TTTA	T	10449	0.997129	0	0,30,2,10417	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749115	22690	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	12881	0.001397	0	12706,0,19,0	LOW	SILENT	SYNONYMOUS_CODING	S	acT/acC	T376	S	0.000815	0.051311	2	1	T>C
ERR5749115	23063	PASS	A	T	11174	0.869161	0	0,2,0,11123	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749115	23271	PASS	C	A	17933	0.915352	0	2,0,17913,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749115	23403	PASS	A	G	17927	0.965583	0	0,9,0,17910	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749115	23604	PASS	C	A	10595	0.940916	0	13,0,10581,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749115	23709	PASS	C	T	10581	0.939514	0	0,3,0,10565	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749115	24506	PASS	T	G	11514	0.973511	0	6,0,11504,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749115	24914	PASS	G	C	40022	0.958123	0	1,2,19937,20059	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749115	25437	PASS	G	T	17630	0.968066	0	5,0,17610,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	ttG/ttT	L15F	orf3a	0.001128	0.971411	2	2	G>T
ERR5749115	25587	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	17639	0.001247	0	0,17615,0,22	HIGH	NONE	FRAME_SHIFT	ORF3a	aag/	K67	orf3a	0.000598	0.813206	6	2	CAA>C
ERR5749115	25626	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	22033	4.54E-4	6	4392,17631,0,10	HIGH	NONE	FRAME_SHIFT	ORF3a	ttt/	F79	orf3a	0.000403	0.915633	3	2	CT>C
ERR5749115	26895	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23814	0.002016	0	23753,1,49,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Cat/Tat	H125Y	M	0.000874	0.97046	1	1	C>T
ERR5749115	27065	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	23800	0.001008	0	0,23752,0,39	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	ttG/ttT	L181F	M	0.001008	0.897124	3	2	G>T
ERR5749115	27346	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	33523	8.95E-4	4	16690,16600,29,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF6	Tat/Aat	Y49N	orf6	0.000895	0.888737	2	1	T>A
ERR5749115	27972	PASS	C	T	6654	0.903667	35	2,2,6577,43	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749115	28048	PASS	G	T	6608	0.915254	0	0,6,0,6599	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749115	28111	PASS	A	G	23792	0.979321	0	2,1,17169,6612	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749115	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17169	0.001165	0	17109,10,21,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749115	28270	PASS	TA	T	33325	0.994929	312	157,12,16945,16211	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749115	28280	PASS	G	C	33263	0.934372	5	13,7,16976,16199	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749115	28281	PASS	A	T	33263	0.915432	19	18,5,16975,16202	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749115	28282	PASS	T	A	33264	0.907047	0	14,14,16936,16211	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749115	28394	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	G	17195	0.001221	461	0,17164,15,7	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Cgg/Ggg	R41G	N	0.001221	0.917026	3	2	C>G
ERR5749115	28881	PASS	G	A	10435	0.735026	24	8,0,5119,5134	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749115	28882	PASS	G	A	10435	0.828558	12	5,0,5208,5122	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749115	28883	PASS	G	C	10435	0.944035	6	0,2,5217,5203	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749115	28977	PASS	C	T	5304	0.93043	2147483647	0,0,0,5294	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749115	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	59166	0.001014	0	29724,29341,42,40	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749116	241	PASS	C	T	379	0.815303	0	0,0,189,190	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749116	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	981	0.008155	0	973,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749116	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	980	0.006122	0	974,0,6,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749116	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	980	0.004082	0	973,0,4,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749116	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	979	0.005107	0	972,0,5,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TA>T
ERR5749116	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	23176	0.004919	10	22079,983,113,1	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749116	695	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	23176	0.001683	465	22186,946,5,38	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gac/Tac	D144Y	leader	0.001683	0.073625	1	1	G>T
ERR5749116	843	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	44297	0.001219	2	22127,22085,36,41	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cAt	P13H	nsp2	0.000301	0.050923	4	2	C>A
ERR5749116	913	PASS	C	T	22186	0.921347	0	0,9,0,22156	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749116	1191	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9274	0.003235	0	0,9234,0,31	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCa/cTa	P129L	nsp2	0.000749	0.916048	3	2	C>T
ERR5749116	1813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	7763	0.003993	0	0,7723,0,36	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcA	A336	nsp2	0.001022	0.152738	4	2	T>A
ERR5749116	1820	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	7770	0.004376	0	0,7726,0,34	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggt/Agt	G339S	nsp2	0.001189	0.949024	2	2	G>A
ERR5749116	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	36996	0.001487	2590	18471,17382,34,1016	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749116	3037	PASS	C	T	3313	0.823725	9	0,3,1655,1633	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749116	3047	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	1685	0.005341	50	16,1655,4,9	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gat/Tat	D110Y	nsp3	0.004044	0.233775	2	1	G>T
ERR5749116	3267	PASS	C	T	15451	0.971264	0	2,0,15437,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749116	3638	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	5679	0.003698	0	5645,0,32,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggt/Tgt	G307C	nsp3	0.003698	0.896828	1	1	G>T
ERR5749116	4230	PASS	C	T	13529	0.819055	2	1,2,6753,6654	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T504I	nsp3	0.005128	0.819055	1	1	C>T
ERR5749116	4276	PASS	C	T	6800	0.112206	0	0,5867,0,925	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y519	nsp3	0.00102	0.812261	1	1	C>T
ERR5749116	4317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	6804	0.004262	0	0,6761,0,38	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aGt/aTt	S533I	nsp3	0.001619	0.118421	2	1	G>T
ERR5749116	5388	PASS	C	A	821	0.962241	2147483647	0,0,821,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749116	5986	PASS	C	T	4129	0.97457	0	1,0,4127,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749116	6272	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	11563	0.003632	0	11505,2,44,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y1185H	nsp3	0.001735	0.156069	2	1	T>C
ERR5749116	6310	PASS	C	T	11561	0.94715	2147483647	0,0,11553,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	agC/agT	S1197	nsp3	0.00099	0.94715	2	2	C>T
ERR5749116	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	3289	0.011554	0	0,3251,0,38	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L1328S?	nsp3	0.000731	0.14377	4	2	C>CT
ERR5749116	6954	PASS	T	C	10693	0.809876	2147483647	0,0,0,10620	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749116	7564	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	8471	9.44E-4	0	0,8463,0,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/	Y1617	nsp3	0.000586	0.056194	4	2	CT>C
ERR5749116	7764	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12564	0.005333	0	12486,0,69,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCc/tTc	S1682F	nsp3	0.001052	0.964731	1	1	C>T
ERR5749116	8906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	3634	0.005779	0	3,3601,0,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Gtt	F118V	nsp4	0.005779	0.091549	2	1	T>G
ERR5749116	10323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	9915	0.002118	0	0,9873,0,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749116	10702	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	14296	0.005666	0	108,14107,0,81	HIGH	NONE	FRAME_SHIFT	ORF1ab	agg/	R217	3Cpro	0.000396	0.098214	2	2	CAG>C
ERR5749116	11095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	20937	6.69E-4	0	20922,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L43	nsp6	0.000515	0.887707	7	2	CT>C
ERR5749116	11185	PASS	G	A	37811	0.883658	1	3,1,20826,16963	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttG/ttA	L71	nsp6	0.000356	0.883658	3	3	G>A
ERR5749116	11287	PASS	GTCTGGTTTT	G	20935	0.998615	0	0,29,0,20906	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749116	12439	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5685	0.002639	0	4,5650,0,28	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P116	nsp8	0.000666	0.637117	2	2	C>T
ERR5749116	13059	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	14566	0.001442	32	10810,3727,27,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aAt	T12N	nsp10	0.000448	0.855104	3	2	C>A
ERR5749116	13356	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21331	0.001453	103	10452,10834,38,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T111I	nsp10	0.000806	0.091518	1	1	C>T
ERR5749116	13459	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	10489	0.002002	0	10468,0,21,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L8	nsp11	0.000691	0.060726	5	2	GT>G
ERR5749116	13498	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	20953	0.007111	0	10399,10352,79,76	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Aca/Gca	T20A	RdRp	0.001341	0.952048	1	1	A>G
ERR5749116	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20964	0.001097	0	10471,10446,12,13	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749116	13712	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	1425	0.005614	0	1417,0,8,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K91R	RdRp	0.001252	0.300156	1	1	A>G
ERR5749116	14408	PASS	C	T	215	0.823256	0	0,0,106,107	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749116	14599	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTATTACTAGA	C	10963	6.39E-4	0	10956,0,7,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttactagataaa/	LLDK388	RdRp	0.000639	0.922766	3	2	CTATTACTAGA>C
ERR5749116	14676	PASS	C	T	10961	0.82529	0	5,0,10936,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749116	15279	PASS	C	T	8124	0.886509	2147483647	0,0,8114,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749116	16176	PASS	T	C	12162	0.982158	0	0,2,638,11522	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749116	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	6649	0.003008	0	6626,0,21,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E201K	helicase	0.000535	0.100775	3	2	G>A
ERR5749116	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	6649	0.001053	0	6642,0,7,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749116	16946	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6644	0.003763	0	6609,0,26,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCa/gTa	A237V	helicase	0.001418	0.951893	1	1	C>T
ERR5749116	17615	PASS	A	G	7329	0.905035	0	0,7,0,7300	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749116	18504	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	35127	0.005409	0	0,34504,0,210	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaA/aaG	K155	ExoN	0.000518	0.094148	4	3	A>G
ERR5749116	18647	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGAGCGCACCTGTTGTCTATG	C	59453	7.06E-4	164	24162,35249,42,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gagcgcacctgttgtctatgtgat/gat	ERTCCLCD204D	ExoN	0.000283	0.970507	4	2	CTGAGCGCACCTGTTGTCTATG>C
ERR5749116	18658	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	24209	0.002437	0	24145,5,59,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tgt/	C207	ExoN	0.000507	0.115741	3	2	TG>T
ERR5749116	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	24203	5.78E-4	0	24189,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749116	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	26675	0.003936	0	1,26569,0,105	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749116	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	4510	0.004656	0	4489,0,21,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F123	endoR	0.000884	0.981982	5	2	CT>C
ERR5749116	21764	PASS	ATACATG	A	6698	0.998059	0	13,0,6685,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749116	21786	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	6698	0.006569	0	6645,0,52,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gGt/gTt	G75V	S	0.001992	0.058409	1	1	G>T
ERR5749116	21990	PASS	TTTA	T	6699	0.997014	0	0,20,2,6677	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749116	22014	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	15388	0.004614	0	15273,2,104,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aGt/aTt	S151I	S	0.001357	0.20398	2	1	G>T
ERR5749116	22293	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	20570	0.002382	59	5180,15289,0,49	HIGH	NONE	FRAME_SHIFT	S	tta/	L244	S	0.000308	0.160511	4	1	TA>T
ERR5749116	22293	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TACATA	T	20570	0.002528	21	5180,15289,5,47	HIGH	NONE	FRAME_SHIFT	S	ttacataga/	LHR244	S	0.000308	0.160511	4	1	TACATA>T
ERR5749116	22295	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20570	0.00141	25	5178,15303,1,30	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Cat/Tat	H245Y	S	0.000662	0.930915	2	2	C>T
ERR5749116	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	14889	0.001209	0	0,14866,0,18	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749116	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20868	0.003163	60	5946,14825,3,64	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749116	23063	PASS	A	T	5967	0.864756	0	0,1,0,5935	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749116	23271	PASS	C	A	27184	0.923632	2147483647	0,0,27161,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749116	23403	PASS	A	G	27181	0.971524	0	0,4,0,27163	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749116	23604	PASS	C	A	6094	0.939449	0	4,0,6085,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749116	23709	PASS	C	T	6089	0.937264	0	0,1,0,6083	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749116	24319	PASS	C	T	5696	0.86394	0	0,3,39,5643	LOW	SILENT	SYNONYMOUS_CODING	S	aaC/aaT	N919	S	0.86394	0.86394	1	1	C>T
ERR5749116	24506	PASS	T	G	11188	0.972113	0	25,0,11160,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749116	24850	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	20193	0.002228	0	20133,0,46,0	LOW	SILENT	SYNONYMOUS_CODING	S	gtT/gtC	V1096	S	0.002228	0.980819	2	1	T>C
ERR5749116	24914	PASS	G	C	40177	0.960077	0	0,0,20013,20144	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749116	25138	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	6971	0.001865	0	6931,0,25,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aaT/aaA	N1192K	S	0.001865	0.901453	2	2	T>A
ERR5749116	25217	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	6957	0.002444	0	0,6925,0,32	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ggt/Tgt	G1219C	S	0.002444	0.80324	1	1	G>T
ERR5749116	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	23494	0.001617	64	16470,6970,43,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749116	25413	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16553	0.00145	0	16507,0,24,0	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	atC/atT	I7	orf3a	0.00145	0.968329	2	1	C>T
ERR5749116	25422	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGGAACTGTA	T	16553	0.003021	0	16503,0,50,0	MODERATE	NONE	CODON_DELETION	ORF3a	ggaactgta/	GTV11	orf3a	0.000545	0.213989	6	1	TGGAACTGTA>T
ERR5749116	25510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	16572	0.002957	0	37,16460,0,54	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Tca/Cca	S40P	orf3a	0.001771	0.96355	3	1	T>C
ERR5749116	25587	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	16555	0.001933	0	0,16523,0,32	HIGH	NONE	FRAME_SHIFT	ORF3a	aag/	K67	orf3a	0.000598	0.813206	6	2	CA>C
ERR5749116	25596	PASS	A	G	16555	0.988281	0	0,1,0,16551	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	agA/agG	R68	orf3a	0.001691	0.988281	1	1	A>G
ERR5749116	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	2094	0.006686	288	2067,11,0,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749116	25711	PASS	T	C	2069	0.954084	2147483647	0,0,2068,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Tat/Cat	Y107H	orf3a	0.954084	0.954084	1	1	T>C
ERR5749116	26062	PASS	G	T	11753	0.890241	0	15,0,11708,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Ggt/Tgt	G224C	orf3a	0.001077	0.906894	1	1	G>T
ERR5749116	26065	PASS	G	T	11753	0.906322	0	34,0,11714,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gtt/Ttt	V225F	orf3a	0.001242	0.906322	2	1	G>T
ERR5749116	26158	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTT	G	11738	8.52E-4	0	0,11728,0,10	HIGH	NONE	FRAME_SHIFT	ORF3a	gtt/	V256	orf3a	0.000297	0.905181	6	2	GTT>G
ERR5749116	26159	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	11739	0.001704	0	0,11670,0,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	gTt/gCt	V256A	orf3a	0.000311	0.053032	2	2	T>C
ERR5749116	26526	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	8970	0.002453	0	6,8935,0,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Gca/Tca	A2S	M	0.001224	0.951192	3	1	G>T
ERR5749116	26532	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TCCAACGGTACTA	T	8970	0.003567	0	6,8932,0,32	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tccaacggtactatt/ttt	SNGTI4F	M	0.001836	0.05891	2	2	TCCAACGGTACTA>T
ERR5749116	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	5879	0.002551	0	0,5864,0,15	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749116	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	5878	0.004934	0	0,5849,0,29	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749116	26936	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	25463	0.004399	0	25344,0,116,0	LOW	SILENT	SYNONYMOUS_CODING	M	ctC/ctA	L138	M	0.001308	0.968147	2	1	C>A
ERR5749116	27297	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14447	0.002146	0	14315,0,32,0	LOW	SILENT	SYNONYMOUS_CODING	ORF6	atC/atT	I32	orf6	0.000978	0.91266	1	1	C>T
ERR5749116	27312	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	14444	0.001385	0	14425,0,20,0	HIGH	NONE	FRAME_SHIFT	ORF6	aat/aaAt	N39K?	orf6	0.000911	0.088458	4	2	T>TA
ERR5749116	27476	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	30317	6.6E-4	64	15860,14437,0,20	HIGH	NONE	FRAME_SHIFT	ORF7a	acagta/	TV28	orf7a	0.000547	0.22827	4	2	CAG>C
ERR5749116	27494	PASS	C	T	30317	0.274137	162	11628,9978,4217,4478	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	cCt/cTt	P34L	orf7a	0.000672	0.961447	2	2	C>T
ERR5749116	27567	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTTTAGCACTCAATTTGCT	C	15859	0.001576	0	15834,0,25,0	MODERATE	NONE	CODON_DELETION	ORF7a	agcactcaatttgctttt/	STQFAF60	orf7a	0.000449	0.998291	4	1	CTTTAGCACTCAATTTGCT>C
ERR5749116	27670	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	15883	0.002392	0	81,15680,0,40	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Gtt/Att	V93I	orf7a	0.002392	0.990588	3	2	G>A
ERR5749116	27972	PASS	C	T	2891	0.899689	0	0,0,2866,14	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749116	28048	PASS	G	T	2875	0.92	0	0,5,0,2869	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749116	28111	PASS	A	G	28002	0.978787	0	6,0,25109,2879	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749116	28147	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	25125	4.38E-4	0	25114,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF8	ttt/	F86	orf8	0.000438	0.981624	4	2	CT>C
ERR5749116	28254	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	25098	0.002072	0	24950,0,103,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	Atc/Ttc	I121F	orf8	0.000541	0.914398	3	2	A>T
ERR5749116	28270	PASS	TA	T	48863	0.995027	624	248,6,24798,23822	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749116	28280	PASS	G	C	48791	0.934353	24	9,0,24878,23793	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749116	28281	PASS	A	T	48791	0.915374	47	39,9,24855,23804	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749116	28282	PASS	T	A	48792	0.904677	19	31,13,24819,23816	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749116	28292	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	50028	5.2E-4	0	24946,25056,13,13	HIGH	NONE	FRAME_SHIFT	N	aat/	N8	N	0.000304	0.055324	4	2	CA>C
ERR5749116	28881	PASS	G	A	4140	0.785266	3	1,0,2035,2041	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749116	28882	PASS	G	A	4140	0.828019	0	0,0,2046,2037	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749116	28883	PASS	G	C	4140	0.951449	0	0,0,2050,2079	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749116	28887	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTTCTCCTGCTA	C	4140	0.002174	24	2052,2079,0,9	HIGH	NONE	FRAME_SHIFT	N	acttctcctgctaga/	TSPAR205	N	0.002174	0.814997	2	2	CTTCTCCTGCTA>C
ERR5749116	28977	PASS	C	T	2088	0.917146	2147483647	0,0,0,2086	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749116	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	25695	0.008095	2362	23578,1867,3,218	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749116	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	46924	0.001172	0	23528,23302,36,36	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749116	29311	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23607	0.001906	0	0,23528,0,51	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F346	N	0.000335	0.790798	3	2	C>T
ERR5749117	241	PASS	C	T	4612	0.864918	0	0,0,2293,2301	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749117	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	7160	0.002095	0	7146,0,15,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749117	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	7159	9.78E-4	0	7147,0,7,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749117	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	7156	0.001956	0	6675,0,442,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749117	676	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21167	9.92E-4	37	13988,7155,6,17	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G137	leader	0.000799	0.919273	2	1	C>T
ERR5749117	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	21167	4.72E-4	17	13958,7172,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749117	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	21167	0.001087	28	13958,7172,22,1	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749117	913	PASS	C	T	13988	0.910495	0	0,8,0,13958	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749117	1813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	18428	0.001194	0	0,18386,0,27	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcA	A336	nsp2	0.001022	0.152738	4	2	T>A
ERR5749117	3037	PASS	C	T	13588	0.813218	30	0,10,6789,6690	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749117	3164	PASS	G	A	6851	0.962341	231	7,0,0,6843	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gct/Act	A149T	nsp3	0.962341	0.970235	1	1	G>A
ERR5749117	3177	PASS	C	T	14063	0.879755	0	1,0,7217,6833	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P153L	nsp3	0.000773	0.96008	3	2	C>T
ERR5749117	3267	PASS	C	T	7218	0.970629	2147483647	0,0,7213,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749117	4529	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTTTAC	T	11014	8.17E-4	0	4,11001,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	tacttt/	YF605	nsp3	0.000527	0.402778	3	1	TTTTAC>T
ERR5749117	5388	PASS	C	A	4831	0.958808	2147483647	0,0,4828,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749117	5986	PASS	C	T	1186	0.974705	2147483647	0,0,1185,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749117	6266	PASS	G	A	18404	0.950772	77	1,2,18390,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gcc/Acc	A1183T	nsp3	0.000676	0.950772	2	2	G>A
ERR5749117	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11037	0.001903	0	0,10900,0,32	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749117	6954	PASS	T	C	17001	0.806776	0	0,1,0,16895	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749117	7067	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	25326	0.015518	1829	7868,17050,398,7	HIGH	NONSENSE	STOP_GAINED	ORF1ab	Gaa/Taa	E1450*	nsp3	0.000274	0.059217	5	3	G>T
ERR5749117	7600	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12551	0.012987	0	0,12373,0,169	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C1627	nsp3	0.001321	0.973632	1	1	C>T
ERR5749117	8664	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11315	0.003182	0	11271,0,37,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T37I	nsp4	0.003182	0.985915	1	1	C>T
ERR5749117	9198	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	14495	6.9E-4	0	0,14485,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F216	nsp4	0.000543	0.93476	4	2	CT>C
ERR5749117	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	17532	7.42E-4	10	13786,3733,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749117	10323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	18714	0.001122	0	0,18642,0,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749117	11199	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	39357	8.13E-4	0	19557,19636,17,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCc/gTc	A76V	nsp6	0.000309	0.056758	3	2	C>T
ERR5749117	11287	PASS	GTCTGGTTTT	G	19772	0.997269	0	0,54,0,19718	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749117	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23973	0.001752	0	11968,11932,21,22	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749117	14408	PASS	C	T	3453	0.841877	0	0,0,1727,1700	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749117	14676	PASS	C	T	10003	0.745076	0	6,0,9963,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749117	15279	PASS	C	T	13799	0.923473	2147483647	0,0,13787,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749117	16176	PASS	T	C	15172	0.978513	0	0,0,6414,8753	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749117	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	26557	9.41E-4	0	26532,0,25,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749117	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17161	0.002156	0	17110,0,40,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749117	20091	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	17125	5.26E-4	0	0,17116,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	caa/Acaa	Q159T?	endoR	0.000368	0.051583	1	1	C>CA
ERR5749117	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	19317	8.8E-4	0	0,19300,0,17	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TA>T
ERR5749117	21762	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTATACA	C	12439	0.002331	0	12410,0,29,0	MODERATE	NONE	CODON_DELETION	S	atacat/	IH68	S	0.001297	0.875707	2	2	CTATACA>C
ERR5749117	21764	PASS	ATACATG	A	12439	0.996463	0	44,0,12395,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749117	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	12439	8.04E-4	0	12429,0,10,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749117	21990	PASS	TTTA	T	12441	0.99783	0	0,27,1,12413	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749117	22225	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	17907	0.001229	0	0,17872,0,33	LOW	SILENT	SYNONYMOUS_CODING	S	tcG/tcT	S221	S	0.001195	0.94526	3	1	G>T
ERR5749117	23063	PASS	A	T	13463	0.865335	0	0,3,0,13392	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749117	23271	PASS	C	A	16520	0.925908	0	1,0,16501,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749117	23403	PASS	A	G	16511	0.963721	0	0,3,0,16500	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749117	23604	PASS	C	A	14010	0.945753	0	5,0,13997,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749117	23709	PASS	C	T	13995	0.939121	0	0,1,0,13968	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749117	24320	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	8395	9.53E-4	0	0,8360,0,8	HIGH	NONE	FRAME_SHIFT	S	aaa/	K921	S	0.000763	0.138365	4	2	CAA>C
ERR5749117	24506	PASS	T	G	13836	0.972391	0	2,0,13834,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749117	24914	PASS	G	C	37953	0.95671	0	0,1,18905,19029	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749117	25391	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTA	T	19682	7.62E-4	0	19667,0,15,0	HIGH	NONE	FRAME_SHIFT+START_LOST	ORF3a	atg/	M1	orf3a	0.000585	0.191026	1	1	TTA>T
ERR5749117	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	7830	0.003193	395	7781,15,7,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749117	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	11676	6.85E-4	0	3,11665,0,8	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749117	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	11678	0.001113	0	3,11662,0,13	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749117	27145	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	25925	5.4E-4	0	7,25904,0,14	HIGH	NONE	FRAME_SHIFT	M	gac/	D209	M	0.000476	0.863895	2	2	CAG>C
ERR5749117	27972	PASS	C	T	7529	0.910479	37	1,2,7445,57	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749117	28048	PASS	G	T	7474	0.923602	0	0,8,0,7464	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749117	28111	PASS	A	G	28030	0.978987	3	7,4,20538,7472	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749117	28147	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	20560	6.32E-4	0	20540,7,13,0	HIGH	NONE	FRAME_SHIFT	ORF8	aca/Taca	T87Y?	orf8	0.000438	0.981624	4	2	C>CT
ERR5749117	28237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTGT	G	20543	6.33E-4	0	20529,1,13,0	MODERATE	NONE	CODON_DELETION	ORF8	gtt/	V117	orf8	0.000442	0.966707	4	2	GTGT>G
ERR5749117	28270	PASS	TA	T	39828	0.99543	422	181,7,20292,19354	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749117	28280	PASS	G	C	39749	0.939168	19	16,4,20313,19330	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749117	28281	PASS	A	T	39749	0.919923	18	21,7,20322,19339	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749117	28282	PASS	T	A	39751	0.912757	9	24,13,20266,19342	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749117	28881	PASS	G	A	8271	0.741869	18	7,0,4066,4066	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749117	28882	PASS	G	A	8271	0.836295	0	0,0,4139,4042	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749117	28883	PASS	G	C	8271	0.93846	0	0,0,4150,4111	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749117	28977	PASS	C	T	4203	0.928622	0	0,3,0,4190	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749117	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	31625	7.91E-4	186	27393,4167,3,25	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcA	A254	N	0.000601	0.054952	4	2	T>A
ERR5749117	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	54415	0.001433	1	27324,26966,49,45	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749118	241	PASS	C	T	324	0.861111	0	0,0,162,162	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749118	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	691	0.017366	0	679,0,12,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749118	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	691	0.005789	0	687,0,4,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749118	635	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	693	0.011544	0	0,684,0,9	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgt/Tgt	R124C	leader	0.00148	0.880435	1	1	C>T
ERR5749118	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4538	0.01212	1	3794,686,49,7	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L140	leader	0.000316	0.135802	3	2	C>T
ERR5749118	823	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3838	0.003127	0	3820,0,16,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V6	nsp2	0.001213	0.901722	1	1	C>T
ERR5749118	913	PASS	C	T	3844	0.906868	0	0,2,0,3840	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749118	967	PASS	T	C	8235	0.973649	3	0,1,4382,3843	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caT/caC	H54	nsp2	0.973649	0.978486	1	1	T>C
ERR5749118	1820	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	5522	0.002535	0	0,5502,0,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggt/Agt	G339S	nsp2	0.001189	0.949024	2	2	G>A
ERR5749118	2166	PASS	A	G	3551	0.932132	0	0,2,0,3543	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K454R	nsp2	0.932132	0.94762	1	1	A>G
ERR5749118	3037	PASS	C	T	2067	0.797775	9	1,5,1033,1012	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749118	3096	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1040	0.028846	0	0,1009,0,31	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCa/tTa	S126L	nsp3	0.001801	0.932094	1	1	C>T
ERR5749118	3267	PASS	C	T	4436	0.969567	2147483647	0,0,4434,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749118	3335	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	8799	0.006592	15	4388,4306,41,63	HIGH	NONSENSE	STOP_GAINED	ORF1ab	Gaa/Taa	E206*	nsp3	0.001289	0.891976	4	3	G>T
ERR5749118	3466	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	4438	0.004507	0	2,4406,0,22	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caT/caC	H249	nsp3	0.000976	0.051008	3	3	T>C
ERR5749118	3832	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	1826	0.003834	0	1819,0,7,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTg	L373F?	nsp3	0.000689	0.327273	4	2	C>CT
ERR5749118	3998	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	1818	0.009351	0	0,1798,0,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E427K	nsp3	0.009351	0.060629	2	1	G>A
ERR5749118	4255	PASS	G	A	6459	0.826599	9	4,0,3201,3198	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccG/ccA	P512	nsp3	0.001102	0.871853	2	1	G>A
ERR5749118	4423	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	3185	0.004082	0	3170,2,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K569	nsp3	0.00063	0.953796	2	2	CA>C
ERR5749118	4764	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	AT	3884	0.002317	0	3875,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	att/Tatt	I684Y?	nsp3	0.000673	0.93404	4	2	A>AT
ERR5749118	5388	PASS	C	A	667	0.955023	2147483647	0,0,667,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749118	5986	PASS	C	T	3096	0.980297	0	2,0,3093,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749118	6266	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	4216	0.004269	0	4192,2,19,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gcc/Acc	A1183T	nsp3	0.000676	0.950772	2	2	G>A
ERR5749118	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	2457	0.01628	0	0,2417,0,40	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L1328S?	nsp3	0.000731	0.14377	4	2	C>CT
ERR5749118	6954	PASS	T	C	6975	0.810036	2147483647	0,0,0,6934	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749118	7945	PASS	C	T	7572	0.914686	204	6,0,0,7555	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y1742	nsp3	0.001244	0.950558	2	2	C>T
ERR5749118	8084	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	4385	0.005701	0	4360,0,25,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1790	nsp3	0.000543	0.923413	4	2	GA>G
ERR5749118	8964	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4874	0.003693	0	4853,0,18,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCa/tTa	S137L	nsp4	0.000553	0.981649	4	2	C>T
ERR5749118	10097	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	1993	0.006523	0	4,1976,0,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggt/Agt	G15S	3Cpro	0.006523	0.955146	1	1	G>A
ERR5749118	10323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	7030	0.001991	0	0,6996,0,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749118	11152	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11854	0.004387	0	11774,0,53,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V60	nsp6	0.000678	0.974465	2	2	C>T
ERR5749118	11287	PASS	GTCTGGTTTT	G	11864	0.992245	0	0,92,0,11772	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749118	11507	PASS	G	A	2744	0.895773	0	1,0,1379,1358	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Att	V179I	nsp6	0.007744	0.914418	2	2	G>A
ERR5749118	11511	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2744	0.009111	0	1365,1343,13,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T180I	nsp6	0.001772	0.119454	1	1	C>T
ERR5749118	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	6381	0.001881	69	4989,1371,1,12	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749118	12020	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10984	0.002913	0	10917,0,36,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Ttt	L60F	nsp7	0.000994	0.968243	3	2	C>T
ERR5749118	12784	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	1376	0.005814	0	1365,2,9,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaC/aaA	N33K	nsp9	0.005814	0.966507	2	2	C>A
ERR5749118	13458	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3958	0.020465	0	3873,0,84,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCg/tTg	S6L	nsp11	0.001017	0.058608	4	2	C>T
ERR5749118	14408	PASS	C	T	195	0.866667	0	0,0,99,96	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749118	14676	PASS	C	T	2682	0.781133	0	3,0,2665,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749118	15099	PASS	A	G	2544	0.871069	2147483647	0,0,0,2537	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	agA/agG	R553	RdRp	0.871069	0.907239	1	1	A>G
ERR5749118	15107	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2549	0.003531	0	0,2539,0,9	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCc/aTc	T556I	RdRp	0.003531	0.078788	2	1	C>T
ERR5749118	15279	PASS	C	T	3636	0.890264	2147483647	0,0,3631,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749118	15839	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	6791	0.002209	0	0,6769,0,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tGg/tCg	W800S	RdRp	0.001405	0.074516	2	1	G>C
ERR5749118	15983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	2537	0.002365	0	2531,0,6,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T850	RdRp	0.000701	0.338235	2	1	TA>T
ERR5749118	16176	PASS	T	C	3175	0.979843	0	0,0,633,2542	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749118	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	5341	0.001498	0	5333,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749118	17167	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2953	0.003386	0	2942,0,11,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cat/Tat	H311Y	helicase	0.001728	0.238095	1	1	C>T
ERR5749118	17762	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTG	C	5587	0.004654	0	5561,0,26,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtc/	V510	helicase	0.000697	0.912542	2	2	CTG>C
ERR5749118	18232	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2290	0.00393	0	0,2280,0,10	HIGH	NONSENSE	STOP_GAINED	ORF1ab	Caa/Taa	Q65*	ExoN	0.002195	0.056093	1	1	C>T
ERR5749118	18647	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGAGCGCACCTGTTGTCTATG	C	25063	0.001795	77	16634,8384,45,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gagcgcacctgttgtctatgtgat/gat	ERTCCLCD204D	ExoN	0.000283	0.970507	4	2	CTGAGCGCACCTGTTGTCTATG>C
ERR5749118	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16679	0.001619	0	16639,0,28,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C216	ExoN	0.000374	0.981963	3	2	C>T
ERR5749118	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9472	0.002956	0	0,9437,0,32	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCc/gTc	A371V	ExoN	0.00034	0.247423	2	2	C>T
ERR5749118	19343	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4897	0.002655	0	4868,0,15,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A435V	ExoN	0.000519	0.192257	7	2	C>T
ERR5749118	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2365	0.009302	0	2342,0,23,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749118	20823	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	11344	0.006171	107	8180,3084,80,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaC/aaA	N55K	MethTr	0.001138	0.982544	2	2	C>A
ERR5749118	20951	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8258	0.003996	0	8215,0,37,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCa/tTa	S98L	MethTr	0.000431	0.138667	3	3	C>T
ERR5749118	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	8257	0.007267	0	0,8197,0,60	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TA>T
ERR5749118	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8172	0.005996	0	3990,4061,28,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749118	21764	PASS	ATACATG	A	4313	0.997913	0	9,0,4304,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749118	21990	PASS	TTTA	T	4314	0.999073	0	0,4,0,4310	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749118	22690	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	11830	0.00262	0	11683,0,38,0	LOW	SILENT	SYNONYMOUS_CODING	S	acT/acC	T376	S	0.000815	0.051311	2	1	T>C
ERR5749118	22759	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	11858	0.004301	0	2,11805,0,51	HIGH	NONE	FRAME_SHIFT	S	ttt/	F400	S	0.000578	0.12649	2	2	AT>A
ERR5749118	22787	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11868	0.003118	0	0,11820,0,38	HIGH	NONSENSE	STOP_GAINED	S	Caa/Taa	Q409*	S	0.000599	0.053914	2	2	C>T
ERR5749118	23063	PASS	A	T	3845	0.854096	2147483647	0,0,0,3824	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749118	23271	PASS	C	A	5988	0.923347	2147483647	0,0,5978,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749118	23403	PASS	A	G	5988	0.960087	0	0,1,0,5966	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749118	23604	PASS	C	A	4572	0.935477	0	2,0,4569,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749118	23690	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	4559	0.002413	0	0,4523,0,11	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aac/Gac	N710D	S	0.002413	0.929812	1	1	A>G
ERR5749118	23709	PASS	C	T	4565	0.93713	0	0,3,1,4552	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749118	23758	PASS	C	T	4574	0.959117	0	0,0,1,4571	LOW	SILENT	SYNONYMOUS_CODING	S	acC/acT	T732	S	0.001489	0.964055	1	1	C>T
ERR5749118	24506	PASS	T	G	5804	0.97295	0	4,0,5798,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749118	24835	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	8432	0.002491	0	8403,0,21,0	LOW	SILENT	SYNONYMOUS_CODING	S	cgT/cgC	R1091	S	0.002491	0.740648	1	1	T>C
ERR5749118	24914	PASS	G	C	16757	0.956555	0	0,1,8349,8389	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749118	25413	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12025	0.00499	0	11948,0,63,0	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	atC/atT	I7	orf3a	0.00145	0.968329	2	1	C>T
ERR5749118	25572	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	12022	0.002745	0	0,11989,0,33	HIGH	NONE	FRAME_SHIFT	ORF3a	atc/aAtc	I62N?	orf3a	0.000543	0.959687	4	2	C>CA
ERR5749118	26416	PASS	G	T	7992	0.90478	0	13,13,3943,4012	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	Gtt/Ttt	V58F	E	0.000457	0.913418	2	2	G>T
ERR5749118	26768	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3834	0.003912	0	1,3812,0,18	LOW	SILENT	SYNONYMOUS_CODING	M	atC/atT	I82	M	0.001479	0.055024	1	1	C>T
ERR5749118	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	3833	0.012001	0	0,3787,0,46	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749118	26985	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13952	0.002294	0	13906,0,37,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Cat/Tat	H155Y	M	0.001017	0.889358	1	1	C>T
ERR5749118	27145	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13955	0.004944	0	1,13871,0,82	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	aCa/aTa	T208I	M	0.000476	0.863895	2	2	C>T
ERR5749118	27297	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9195	0.001958	0	9169,0,18,0	LOW	SILENT	SYNONYMOUS_CODING	ORF6	atC/atT	I32	orf6	0.000978	0.91266	1	1	C>T
ERR5749118	27425	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9205	0.002499	0	0,9174,0,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	aCa/aTa	T11I	orf7a	0.001016	0.856486	2	1	C>T
ERR5749118	27532	PASS	C	T	10923	0.975739	163	3,5,10914,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Cat/Tat	H47Y	orf7a	0.001165	0.982473	2	1	C>T
ERR5749118	27577	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10916	0.002015	0	10884,0,28,0	HIGH	NONSENSE	STOP_GAINED	ORF7a	Caa/Taa	Q62*	orf7a	0.000614	0.952205	4	2	C>T
ERR5749118	27741	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	10915	0.004489	0	0,10866,0,49	HIGH	NONE	FRAME_SHIFT	ORF7a	aga/	R118	orf7a	0.000363	0.954278	3	2	CA>C
ERR5749118	27972	PASS	C	T	1599	0.896811	0	0,0,1582,13	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749118	28048	PASS	G	T	1587	0.901071	0	0,3,0,1584	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749118	28111	PASS	A	G	15407	0.980723	0	1,0,13809,1588	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749118	28192	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	13815	0.001954	0	13776,0,29,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	gTg/gCg	V100A	orf8	0.001134	0.980889	2	1	T>C
ERR5749118	28198	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	13815	0.00333	0	13759,0,47,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tGt/tCt	C102S	orf8	0.000718	0.94386	4	2	G>C
ERR5749118	28237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	13814	0.001375	0	13762,0,51,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	cGt/cTt	R115L	orf8	0.000442	0.966707	4	2	G>T
ERR5749118	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13804	0.035135	0	13227,3,531,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749118	28270	PASS	TA	T	26633	0.994556	377	148,3,13612,12876	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749118	28280	PASS	G	C	26587	0.930906	12	11,3,13611,12833	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749118	28281	PASS	A	T	26587	0.903863	65	36,4,13598,12840	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749118	28282	PASS	T	A	26589	0.917033	20	60,32,13581,12847	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749118	28282	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TTA	26589	0.001805	1	13649,12861,26,22	HIGH	NONE	FRAME_SHIFT+STOP_GAINED	N	aat/TAaat	N4*?	N	0.001009	0.957283	3	2	T>TTA
ERR5749118	28292	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	27485	5.82E-4	0	13698,13772,8,8	HIGH	NONE	FRAME_SHIFT	N	aat/	N8	N	0.000304	0.055324	4	2	CA>C
ERR5749118	28396	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GC	G	13824	0.001374	0	7,13798,0,19	HIGH	NONE	FRAME_SHIFT	N	caa/	Q43	N	0.000496	0.946059	5	2	GC>G
ERR5749118	28407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TACCCAATA	T	13824	0.001591	0	7,13795,0,22	HIGH	NONE	FRAME_SHIFT	N	cccaataat/	PNN46	N	0.000382	0.179673	1	1	TACCCAATA>T
ERR5749118	28516	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	11645	0.001975	0	11615,0,23,0	LOW	SILENT	SYNONYMOUS_CODING	N	gaT/gaC	D81	N	0.001273	0.990661	2	2	T>C
ERR5749118	28603	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23228	0.005597	0	11531,11425,73,73	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F110	N	0.000427	0.883357	2	2	C>T
ERR5749118	28732	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	12350	0.001296	0	704,11630,0,16	HIGH	NONE	FRAME_SHIFT	N	aat/	N154	N	0.000892	0.966905	2	2	CA>C
ERR5749118	28881	PASS	G	A	1389	0.717783	6	3,0,684,682	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749118	28882	PASS	G	A	1387	0.811103	0	0,0,694,670	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749118	28883	PASS	G	C	1387	0.94881	0	0,0,695,689	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749118	28977	PASS	C	T	704	0.93892	2147483647	0,0,0,702	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749118	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	23258	0.001161	0	11699,11522,16,16	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749118	29520	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6004	0.001999	50	2262,3725,12,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCa/tTa	S416L	N	0.001999	0.073434	1	1	C>T
ERR5749118	29555	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6008	0.002497	36	2259,3727,14,3	.	.	.	.	.	.	.	0.000611	0.957048	3	1	C>T
ERR5749119	71	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	766	0.015666	0	753,0,13,0	.	.	.	.	.	.	.	0.002088	0.926791	2	1	C>A
ERR5749119	241	PASS	C	T	676	0.87426	3	0,2,336,336	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749119	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	3320	0.002711	0	3312,0,9,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749119	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	3320	0.004819	0	3299,0,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749119	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	3317	0.001809	0	3311,0,6,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749119	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	3319	0.003013	0	3299,2,10,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttatg/gtg	VM84V	leader	0.000554	0.991848	4	1	GTTA>G
ERR5749119	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	3319	0.00241	0	3299,2,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749119	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	3319	0.013257	0	3273,2,44,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749119	520	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTT	G	3322	0.002709	0	3308,5,9,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttgag/gag	VE86E	leader	0.000583	0.051154	1	1	GGTT>G
ERR5749119	635	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3325	0.006015	0	0,3303,0,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgt/Tgt	R124C	leader	0.00148	0.880435	1	1	C>T
ERR5749119	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21768	0.004594	32	18365,3295,75,30	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L140	leader	0.000316	0.135802	3	2	C>T
ERR5749119	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	21768	0.001654	23	18406,3324,36,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749119	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	21768	0.001838	25	18402,3323,40,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749119	913	PASS	C	T	18434	0.903711	0	0,13,0,18378	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749119	1862	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	15487	0.001679	0	0,15445,0,26	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/	Y354	nsp2	0.000585	0.936867	4	2	CT>C
ERR5749119	1862	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTTTATGCA	C	15487	0.001033	0	0,15445,0,16	HIGH	NONE	FRAME_SHIFT	ORF1ab	tatgcattt/	YAF354	nsp2	0.000585	0.936867	4	2	CTTTATGCA>C
ERR5749119	2151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATTGGCTTGAAGAGAAG	A	19298	0.002176	0	0,19256,0,42	HIGH	NONE	FRAME_SHIFT	ORF1ab	tggcttgaagagaagttt/	WLEEKF450	nsp2	0.000402	0.971954	3	2	ATTGGCTTGAAGAGAAG>A
ERR5749119	2185	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	19303	9.32E-4	0	1,19284,0,18	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L462S?	nsp2	0.000441	0.963529	4	3	G>GT
ERR5749119	2403	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	10514	9.51E-4	0	32,10504,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	aag/	K534	nsp2	0.000951	0.061776	2	1	CA>C
ERR5749119	2947	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAT	C	5161	0.001938	0	5151,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	att/	I77	nsp3	0.001938	0.860703	2	2	CAT>C
ERR5749119	3037	PASS	C	T	10242	0.818688	24	0,8,5123,5036	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749119	3096	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5156	0.002715	0	0,5138,0,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCa/tTa	S126L	nsp3	0.001801	0.932094	1	1	C>T
ERR5749119	3177	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	22324	0.001165	27	17137,5161,26,0	HIGH	NONE	FRAME_SHIFT+STOP_GAINED	ORF1ab	gaa/Tgaa	E154*?	nsp3	0.000773	0.96008	3	2	C>CT
ERR5749119	3267	PASS	C	T	17163	0.972382	2147483647	0,0,17157,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749119	3320	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	17152	0.001049	0	17134,0,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/Tgtt	V202C?	nsp3	0.001049	0.745293	2	2	G>GT
ERR5749119	3671	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	20456	0.002151	0	10198,10088,23,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E318K	nsp3	0.000351	0.0625	6	2	G>A
ERR5749119	3671	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	20450	4.89E-4	0	10236,10210,5,5	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N319	nsp3	0.000351	0.0625	6	2	GA>G
ERR5749119	3802	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	15103	0.001324	98	4820,10263,20,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N363	nsp3	0.000554	0.064198	4	2	TA>T
ERR5749119	4456	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12020	0.002579	0	11970,0,33,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A579	nsp3	0.002579	0.964648	1	1	C>T
ERR5749119	5388	PASS	C	A	2503	0.964043	0	1,0,2501,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749119	5986	PASS	C	T	8881	0.977142	0	2,0,8874,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749119	6272	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	16718	0.001735	0	16661,4,30,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y1185H	nsp3	0.001735	0.156069	2	1	T>C
ERR5749119	6320	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	16710	0.001197	0	16674,0,26,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Ttt	V1201F	nsp3	0.001197	0.080147	2	2	G>T
ERR5749119	6336	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16704	0.001317	0	16660,0,24,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCg/tTg	S1206L	nsp3	0.001317	0.951419	1	1	C>T
ERR5749119	6516	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	25735	6.22E-4	58	9004,16715,15,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	att/aAtt	I1268N?	nsp3	0.000479	0.186047	4	2	T>TA
ERR5749119	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8990	0.00178	0	0,8878,0,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749119	6936	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26548	0.001582	0	13094,13055,22,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S1406F	nsp3	0.000553	0.91447	2	2	C>T
ERR5749119	6954	PASS	T	C	13318	0.816189	0	0,1,0,13239	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749119	7058	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	13361	0.001871	0	0,13320,0,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggt/Agt	G1447S	nsp3	0.000616	0.910617	2	2	G>A
ERR5749119	7811	PASS	C	T	22787	0.883442	0	3,0,22720,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cat/Tat	H1698Y	nsp3	0.000971	0.883442	2	2	C>T
ERR5749119	7834	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	45406	0.001079	0	22593,22623,31,31	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N1705	nsp3	0.000523	0.86555	3	2	C>T
ERR5749119	8208	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14880	0.001142	0	0,14847,0,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T1830I	nsp3	0.001142	0.84438	1	1	C>T
ERR5749119	8247	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14890	0.001545	0	0,14862,0,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S1843F	nsp3	0.001545	0.971733	1	1	C>T
ERR5749119	8602	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	7513	9.32E-4	0	2,7504,0,7	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttc/ttTc	F17F?	nsp4	0.000932	0.056	3	2	G>GT
ERR5749119	8964	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	19340	7.24E-4	0	19318,8,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K138	nsp4	0.000553	0.981649	4	2	CA>C
ERR5749119	9016	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	19332	0.001138	0	19290,0,35,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcG	A154	nsp4	0.001138	0.950039	2	1	T>G
ERR5749119	10507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15441	0.00123	0	15385,0,24,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N151	3Cpro	0.00123	0.842913	2	2	C>T
ERR5749119	10595	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	15441	0.001295	0	17,15390,0,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F181L	3Cpro	0.000964	0.076408	1	1	T>C
ERR5749119	11073	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	21587	9.26E-4	0	21552,0,25,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTc/tCc	F34S	nsp6	0.000385	0.092251	6	2	T>C
ERR5749119	11095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTT	C	21572	6.49E-4	0	21525,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L43	nsp6	0.000515	0.887707	7	2	CTT>C
ERR5749119	11095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTTTTTACCTT	C	21572	0.001391	0	21525,0,30,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tttttacctttt/	FLPF42	nsp6	0.000515	0.887707	7	2	CTTTTTACCTT>C
ERR5749119	11135	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTTGCAATGATG	T	21565	0.001762	0	21527,0,38,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gcaatgatgttt/	AMMF56	nsp6	0.001762	0.169157	2	2	TTTGCAATGATG>T
ERR5749119	11287	PASS	GTCTGGTTTT	G	21570	0.997589	0	0,52,0,21518	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749119	11339	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28487	0.002071	11	6890,21531,9,53	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L123	nsp6	0.002071	0.968425	1	1	C>T
ERR5749119	11344	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28487	0.001229	40	6899,21551,0,35	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I124	nsp6	0.001229	0.964849	1	1	C>T
ERR5749119	11507	PASS	G	A	13692	0.898262	0	16,16,6851,6764	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Att	V179I	nsp6	0.007744	0.914418	2	2	G>A
ERR5749119	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	25339	0.001223	30	18395,6894,31,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749119	12125	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	22681	0.001014	0	6,22547,0,30	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y12H	nsp8	0.000847	0.113436	1	1	T>C
ERR5749119	12162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	32425	8.94E-4	47	9725,22633,0,32	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cAg/cGg	Q24R	nsp8	0.000894	0.982497	1	1	A>G
ERR5749119	12459	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26418	9.08E-4	38	16662,9720,25,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T123I	nsp8	0.000658	0.986093	1	1	C>T
ERR5749119	13384	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	12358	0.002023	0	12333,0,25,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggt/	G121	nsp10	0.000578	0.056161	3	3	CG>C
ERR5749119	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24683	0.002147	0	12311,12282,28,30	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749119	14408	PASS	C	T	983	0.843337	0	0,0,490,488	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749119	14676	PASS	C	T	10788	0.83287	0	2,0,10749,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749119	15071	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTAAG	T	24593	8.13E-4	0	12285,12289,10,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtat/	KY545	RdRp	0.000813	0.0625	2	2	TTAAG>T
ERR5749119	15279	PASS	C	T	10939	0.890666	2147483647	0,0,10925,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749119	15797	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	20446	0.001418	0	13,20345,0,32	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cTt/cCt	L786P	RdRp	0.001418	0.07734	2	1	T>C
ERR5749119	16176	PASS	T	C	13028	0.978201	0	0,0,2836,10174	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749119	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAA	G	16244	7.39E-4	0	16204,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GAA>G
ERR5749119	17678	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13887	0.001224	0	0,13863,0,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aTg	T481M	helicase	0.001162	0.968704	2	1	C>T
ERR5749119	18357	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	29183	0.001782	0	29102,0,55,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccT/ccC	P106	ExoN	0.001226	0.057597	1	1	T>C
ERR5749119	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	32381	9.88E-4	0	32349,0,32,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749119	19034	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTGG	T	27123	0.001475	0	27084,0,40,0	MODERATE	NONE	CODON_DELETION	ORF1ab	ggt/	G333	ExoN	0.000384	0.060908	2	2	TTGG>T
ERR5749119	19521	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	15641	0.001343	0	0,15605,0,26	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taT/taC	Y494	ExoN	0.001343	0.957831	1	1	T>C
ERR5749119	21077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	21426	0.002007	0	9,21374,0,43	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K141	MethTr	0.000492	0.955529	4	2	CA>C
ERR5749119	21123	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	47084	9.13E-4	96	25623,21418,42,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F156	MethTr	0.000257	0.90982	5	2	GT>G
ERR5749119	21334	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	25652	8.97E-4	0	1,25592,0,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gca/Cca	A226P	MethTr	0.000897	0.077475	3	1	G>C
ERR5749119	21516	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	10668	0.002625	0	10640,0,28,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	agagtt/	RV287	MethTr	0.000412	0.905456	2	2	CAG>C
ERR5749119	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21195	0.004152	0	10337,10539,49,53	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749119	21762	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTATACA	C	12081	0.001821	0	12059,0,22,0	MODERATE	NONE	CODON_DELETION	S	atacat/	IH68	S	0.001297	0.875707	2	2	CTATACA>C
ERR5749119	21764	PASS	ATACATG	A	12081	0.997351	0	32,0,12049,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749119	21854	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	24095	0.001411	1	12030,11980,18,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tct/Cct	S98P	S	0.00132	0.05283	1	1	T>C
ERR5749119	21889	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	12055	0.001659	0	0,11925,0,36	LOW	SILENT	SYNONYMOUS_CODING	S	acT/acC	T109	S	0.00091	0.065772	2	2	T>C
ERR5749119	21990	PASS	TTTA	T	12095	0.997933	0	0,25,15,12055	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749119	22290	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	16617	0.001745	0	0,16588,0,29	HIGH	NONE	FRAME_SHIFT	S	tta/	L244	S	0.000389	0.578006	2	2	CT>C
ERR5749119	22293	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TACATA	T	25738	0.001476	38	9118,16582,3,35	HIGH	NONE	FRAME_SHIFT	S	ttacataga/	LHR244	S	0.000308	0.160511	4	1	TACATA>T
ERR5749119	22363	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	9122	0.004714	0	9076,0,45,0	LOW	SILENT	SYNONYMOUS_CODING	S	gtG/gtT	V267	S	0.004714	0.976137	1	1	G>T
ERR5749119	23063	PASS	A	T	11713	0.8634	0	0,1,0,11666	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749119	23271	PASS	C	A	22316	0.917996	0	3,0,22295,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749119	23403	PASS	A	G	22308	0.963869	0	0,3,0,22284	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749119	23426	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTGCTA	G	22322	6.27E-4	0	0,22308,0,14	MODERATE	NONE	CODON_DELETION	S	gctatt/	AI623	S	0.000428	0.916192	4	2	GTTGCTA>G
ERR5749119	23525	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAT	C	11805	0.001101	0	11792,0,13,0	HIGH	NONE	FRAME_SHIFT	S	cat/	H655	S	0.001101	0.97751	2	2	CAT>C
ERR5749119	23604	PASS	C	A	11802	0.942044	0	7,0,11789,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749119	23709	PASS	C	T	11786	0.943492	0	0,1,0,11775	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749119	23712	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	11787	6.79E-4	0	0,11779,0,8	HIGH	NONE	FRAME_SHIFT	S	ttt/	F718	S	0.000679	0.958955	3	2	AT>A
ERR5749119	23817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	17897	0.002179	22	6076,11766,6,37	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTt/cCt	L752P	S	0.000646	0.066832	1	1	T>C
ERR5749119	24320	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	10310	0.001455	0	0,10295,0,15	HIGH	NONE	FRAME_SHIFT	S	aaa/	K921	S	0.000763	0.138365	4	2	CA>C
ERR5749119	24506	PASS	T	G	12406	0.975899	0	2,0,12399,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749119	24616	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	12379	0.001373	0	2,12362,0,17	HIGH	NONE	FRAME_SHIFT	S	agagct/	RA1019	S	0.001268	0.127917	3	2	CAG>C
ERR5749119	24914	PASS	G	C	52332	0.960426	3	1,0,26064,26242	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749119	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	28449	0.002179	59	22955,5424,68,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749119	25413	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23131	0.00147	0	23072,0,34,0	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	atC/atT	I7	orf3a	0.00145	0.968329	2	1	C>T
ERR5749119	25496	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	46153	0.001018	11	22848,22753,24,38	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aTa/aCa	I35T	orf3a	0.000369	0.96555	3	2	T>C
ERR5749119	25603	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23137	0.007175	0	3,22949,0,180	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	Cta/Tta	L71	orf3a	0.001967	0.924436	1	1	C>T
ERR5749119	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	2942	0.008158	374	2888,23,3,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749119	26091	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAAT	C	24594	5.69E-4	0	24586,0,14,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF3a	aataaa/aaa	NK234K	orf3a	0.000569	0.128212	4	2	CAAT>C
ERR5749119	26156	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	24603	0.001097	0	0,24540,0,30	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	gTt/gCt	V255A	orf3a	0.001058	0.924104	2	2	T>C
ERR5749119	26208	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24639	0.001583	0	2,24571,0,43	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	agC/agT	S272	orf3a	0.000315	0.922222	2	2	C>T
ERR5749119	26526	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	9719	0.001543	0	0,9693,0,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Gca/Tca	A2S	M	0.001224	0.951192	3	1	G>T
ERR5749119	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTT	G	10699	9.35E-4	0	0,10672,0,10	HIGH	NONE	FRAME_SHIFT	M	gcttgt/	AC85	M	0.000483	0.943732	7	2	GGCTT>G
ERR5749119	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	10699	7.48E-4	0	0,10672,0,8	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749119	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTTT	G	10699	8.41E-4	0	0,10672,0,9	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgtttgcg/gcg	ACLVGLMWLSYFIASFRLFA85A	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTTT>G
ERR5749119	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	10701	8.41E-4	0	0,10692,0,9	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749119	26895	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25434	9.04E-4	0	25397,7,23,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Cat/Tat	H125Y	M	0.000874	0.97046	1	1	C>T
ERR5749119	26958	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25427	0.001023	0	25392,0,27,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Cgt/Tgt	R146C	M	0.00096	0.122326	1	1	C>T
ERR5749119	27312	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	21526	0.004227	0	21438,0,91,0	HIGH	NONE	FRAME_SHIFT	ORF6	aat/aaAt	N39K?	orf6	0.000911	0.088458	4	2	T>TA
ERR5749119	27972	PASS	C	T	5258	0.922784	0	0,0,5218,25	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749119	28048	PASS	G	T	5236	0.92055	0	0,4,0,5229	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749119	28111	PASS	A	G	28296	0.981093	3	2,1,23049,5237	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749119	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23032	0.017801	0	22547,2,444,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749119	28270	PASS	TA	T	44676	0.995523	451	199,9,22787,21689	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749119	28280	PASS	G	C	44585	0.936234	40	23,3,22786,21636	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749119	28281	PASS	A	T	44585	0.912145	12	27,13,22771,21645	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749119	28282	PASS	T	A	44588	0.912622	6	42,30,22722,21671	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749119	28282	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TTA	44588	0.001009	1	22844,21682,25,20	HIGH	NONE	FRAME_SHIFT+STOP_GAINED	N	aat/TAaat	N4*?	N	0.001009	0.957283	3	2	T>TTA
ERR5749119	28292	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	45871	9.59E-4	16	22840,22917,42,67	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Caa/Aaa	Q7K	N	0.000304	0.055324	4	2	C>A
ERR5749119	28651	PASS	C	T	21645	0.914576	0	0,10,0,21583	LOW	SILENT	SYNONYMOUS_CODING	N	aaC/aaT	N126	N	0.000502	0.918117	3	2	C>T
ERR5749119	28881	PASS	G	A	7046	0.757451	9	8,2,3466,3461	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749119	28882	PASS	G	A	7046	0.832955	0	0,0,3528,3446	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749119	28883	PASS	G	C	7046	0.944508	2	1,2,3532,3507	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749119	28977	PASS	C	T	3592	0.928174	0	0,2,0,3575	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749119	28978	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGGTAAAGGCCAACAACAACAAGGCCAAACTGTCACTA	T	3597	0.001946	0	4,3585,0,7	HIGH	NONE	FRAME_SHIFT	N	ggtaaaggccaacaacaacaaggccaaactgtcactaag/	GKGQQQQGQTVTK236	N	0.001946	0.976785	2	2	TGGTAAAGGCCAACAACAACAAGGCCAAACTGTCACTA>T
ERR5749119	29140	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	35607	9.55E-4	0	35558,0,42,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	caG/caT	Q289H	N	0.000955	0.888232	2	1	G>T
ERR5749119	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	70746	0.001399	0	35500,35100,64,63	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749119	29386	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	5490	0.001639	0	5481,0,9,0	HIGH	NONE	FRAME_SHIFT	N	aag/aaAg	K373K?	N	0.000887	0.899197	4	2	C>CA
ERR5749119	29675	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	10203	0.001176	0	5109,5083,6,6	.	.	.	.	.	.	.	0.000624	0.883495	2	1	CA>C
ERR5749119	29743	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5119	0.008009	0	0,5064,0,50	.	.	.	.	.	.	.	0.001027	0.859785	2	1	C>T
ERR5749120	241	PASS	C	T	686	0.857143	0	0,0,340,343	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749120	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	2630	0.005323	0	2616,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749120	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	2627	0.003045	0	2417,0,190,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749120	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	18256	0.001315	14	15600,2632,24,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749120	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	18256	0.00378	33	15556,2631,68,1	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749120	913	PASS	C	T	15620	0.916005	0	0,8,0,15575	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749120	1190	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12041	0.002242	0	0,12000,0,31	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cca/Tca	P129S	nsp2	0.002242	0.938547	1	1	C>T
ERR5749120	1973	PASS	C	T	17397	0.114158	0	15361,0,2031,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L390	nsp2	0.114158	0.114158	1	1	C>T
ERR5749120	2151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATTGGCTTGAAGAGAAG	A	17395	0.002414	0	0,17353,0,42	HIGH	NONE	FRAME_SHIFT	ORF1ab	tggcttgaagagaagttt/	WLEEKF450	nsp2	0.000402	0.971954	3	2	ATTGGCTTGAAGAGAAG>A
ERR5749120	2185	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	17401	0.001264	0	5,17374,0,22	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L462S?	nsp2	0.000441	0.963529	4	3	G>GT
ERR5749120	2293	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	8534	0.003633	0	8497,0,36,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caG/caT	Q496H	nsp2	0.001437	0.968398	1	1	G>T
ERR5749120	3037	PASS	C	T	7056	0.819161	11	1,6,3524,3485	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749120	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	3572	0.003919	352	4,3551,14,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749120	3267	PASS	C	T	15098	0.972513	2147483647	0,0,15095,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749120	3366	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	15154	0.001518	0	96,14991,0,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cTt/cAt	L216H	nsp3	0.001518	0.050542	2	1	T>A
ERR5749120	4276	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9470	0.001901	0	0,9444,0,23	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y519	nsp3	0.00102	0.812261	1	1	C>T
ERR5749120	4586	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	10994	0.002001	0	0,10972,0,22	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L623	nsp3	0.001842	0.935691	2	2	CTA>C
ERR5749120	5388	PASS	C	A	2038	0.96369	2147483647	0,0,2038,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749120	5849	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10675	0.016206	0	0,10447,0,208	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cct/Tct	P1044S	nsp3	0.00146	0.830206	2	1	C>T
ERR5749120	5986	PASS	C	T	7524	0.972621	2147483647	0,0,7519,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749120	6286	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13583	0.001767	0	13540,0,25,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acC/acT	T1189	nsp3	0.000549	0.949782	2	2	C>T
ERR5749120	6516	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	20460	8.31E-4	28	6875,13568,0,17	HIGH	NONE	FRAME_SHIFT	ORF1ab	att/aAtt	I1268N?	nsp3	0.000479	0.186047	4	2	T>TA
ERR5749120	6894	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	12021	0.003161	0	11943,0,46,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tGt/tAt	C1392Y	nsp3	0.00096	0.897867	3	2	G>A
ERR5749120	6954	PASS	T	C	12010	0.844629	2147483647	0,0,0,11958	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749120	8603	PASS	T	C	5508	0.972767	37	1,0,0,5506	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Ctc	F17L	nsp4	0.002607	0.974959	2	1	T>C
ERR5749120	8653	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	5554	0.002521	0	5535,1,15,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atT	M33I	nsp4	0.001328	0.132353	2	2	G>T
ERR5749120	8964	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	14115	0.001559	0	14090,3,22,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Actt	L139T?	nsp4	0.000553	0.981649	4	2	C>CA
ERR5749120	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	9623	0.002078	8	8508,1095,20,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749120	10228	PASS	C	T	14236	0.961998	2147483647	0,0,14214,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ctC/ctT	L58	3Cpro	0.000533	0.961998	2	2	C>T
ERR5749120	10595	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	12706	0.001259	0	0,12677,0,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F181L	3Cpro	0.000964	0.076408	1	1	T>C
ERR5749120	10642	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	12716	0.001494	0	0,12691,0,21	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acG/acT	T196	3Cpro	0.001264	0.951979	3	1	G>T
ERR5749120	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	18702	0.002727	0	18630,0,68,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749120	11185	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTACCTTCTC	G	36536	3.56E-4	35	18622,17901,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttaccttctctt/	LPSL72	nsp6	0.000356	0.883658	3	3	GTTACCTTCTC>G
ERR5749120	11287	PASS	GTCTGGTTTT	G	18701	0.996524	0	0,65,0,18636	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749120	11325	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	18712	0.001283	0	0,18680,0,27	HIGH	NONSENSE	STOP_GAINED	ORF1ab	tCa/tAa	S118*	nsp6	0.001283	0.892049	2	2	C>A
ERR5749120	11956	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18480	0.00119	0	18445,0,25,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D38	nsp7	0.00119	0.936616	1	1	C>T
ERR5749120	12388	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	8398	0.001786	0	0,8366,0,17	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaT/gaC	D99	nsp8	0.001786	0.961473	1	1	T>C
ERR5749120	12676	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	12090	0.00182	0	0,12068,0,22	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K196	nsp8	0.000716	0.87302	3	2	CA>C
ERR5749120	12784	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4591	0.014376	0	4520,2,68,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N33	nsp9	0.005814	0.966507	2	2	C>T
ERR5749120	13134	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	13192	6.82E-4	0	13183,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	atc/	I38	nsp10	0.000682	0.107576	2	2	CA>C
ERR5749120	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	13191	0.00144	0	13173,0,19,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749120	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18300	0.001202	0	9146,9118,11,11	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749120	14408	PASS	C	T	955	0.839791	0	0,0,476,474	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749120	14676	PASS	C	T	8849	0.793762	0	13,0,8809,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749120	15279	PASS	C	T	8821	0.890149	2147483647	0,0,8805,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749120	15411	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	8808	0.002725	0	0,8683,0,120	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaT/aaG	N657K	RdRp	0.00222	0.952192	2	2	T>G
ERR5749120	15983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	8677	0.002881	0	8652,0,25,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/aAca	T850N?	RdRp	0.000701	0.338235	2	1	T>TA
ERR5749120	16117	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	8689	0.001841	0	0,8667,0,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gat/Tat	D893Y	RdRp	0.001841	0.244898	3	1	G>T
ERR5749120	16176	PASS	T	C	10610	0.98115	0	0,0,1919,8687	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749120	17122	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCT	G	20095	7.96E-4	37	8547,11532,0,16	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctctac/	LY297	helicase	0.000476	0.056834	3	2	GCT>G
ERR5749120	17615	PASS	A	G	10685	0.910342	2147483647	0,0,0,10658	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749120	18658	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	27375	0.001717	0	27309,9,48,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tgt/Cgt	C207R	ExoN	0.000507	0.115741	3	2	T>C
ERR5749120	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	27366	8.4E-4	0	27343,0,23,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749120	18984	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	20930	0.004491	0	20817,0,112,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atT	M315I	ExoN	0.000419	0.950929	5	2	G>T
ERR5749120	19343	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	12178	0.00156	0	12160,0,19,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F436	ExoN	0.000519	0.192257	7	2	CT>C
ERR5749120	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8326	0.003003	0	8297,0,26,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749120	20481	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	23586	0.001272	0	7,23529,0,32	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcA/tcG	S287	endoR	0.001272	0.966106	1	1	A>G
ERR5749120	20719	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18799	0.001596	0	0,18541,0,32	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L21	MethTr	0.000341	0.209091	2	2	C>T
ERR5749120	20823	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	36922	0.001138	92	18079,18784,5,49	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaC/aaA	N55K	MethTr	0.001138	0.982544	2	2	C>A
ERR5749120	21123	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	39099	7.42E-4	97	21011,18059,0,29	HIGH	NONE	FRAME_SHIFT	ORF1ab	ata/Tata	I157Y?	MethTr	0.000257	0.90982	5	2	G>GT
ERR5749120	21622	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	8272	8.46E-4	0	0,8265,0,7	HIGH	NONE	FRAME_SHIFT	S	aga/	R21	S	0.000846	0.946634	3	2	CAG>C
ERR5749120	21764	PASS	ATACATG	A	9403	0.997554	0	23,0,9380,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749120	21990	PASS	TTTA	T	9407	0.998405	0	0,15,2,9390	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749120	22690	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	13767	0.001162	0	13569,0,17,0	LOW	SILENT	SYNONYMOUS_CODING	S	acT/acC	T376	S	0.000815	0.051311	2	1	T>C
ERR5749120	22759	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	13779	0.001524	0	0,13758,0,21	HIGH	NONE	FRAME_SHIFT	S	ttt/	F400	S	0.000578	0.12649	2	2	AT>A
ERR5749120	22981	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	8990	0.001557	0	8946,0,16,0	LOW	SILENT	SYNONYMOUS_CODING	S	taT/taC	Y473	S	0.001557	0.861194	3	2	T>C
ERR5749120	23063	PASS	A	T	8985	0.872788	0	0,3,0,8937	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749120	23191	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17967	0.001057	0	17938,1,20,0	LOW	SILENT	SYNONYMOUS_CODING	S	ttC/ttT	F543	S	0.000538	0.973337	2	2	C>T
ERR5749120	23271	PASS	C	A	17963	0.904359	2147483647	0,0,17946,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749120	23311	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	17942	0.001115	0	17896,1,45,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gaG/gaT	E583D	S	0.001115	0.705903	2	1	G>T
ERR5749120	23403	PASS	A	G	17959	0.974553	0	0,1,0,17944	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749120	23426	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	17965	0.001225	0	0,17909,0,33	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gtt/Ttt	V622F	S	0.000428	0.916192	4	2	G>T
ERR5749120	23604	PASS	C	A	9501	0.940848	0	7,0,9489,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749120	23709	PASS	C	T	9492	0.942899	0	0,3,0,9477	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749120	24331	PASS	T	A	8548	0.817033	0	0,1,0,8505	LOW	SILENT	SYNONYMOUS_CODING	S	atT/atA	I923	S	0.707916	0.817033	1	1	T>A
ERR5749120	24506	PASS	T	G	10270	0.974002	0	4,0,10266,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749120	24616	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	10255	0.001268	0	3,10241,0,13	HIGH	NONE	FRAME_SHIFT	S	agagct/	RA1019	S	0.001268	0.127917	3	2	CAG>C
ERR5749120	24914	PASS	G	C	39007	0.95829	0	0,0,19430,19559	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749120	25437	PASS	G	T	19073	0.965868	0	9,0,19049,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	ttG/ttT	L15F	orf3a	0.001128	0.971411	2	2	G>T
ERR5749120	25495	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	38070	7.35E-4	2	18976,18989,40,46	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Ata/Cta	I35L	orf3a	0.000735	0.911134	2	1	A>C
ERR5749120	25626	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	20905	0.001339	7	1819,19058,0,28	HIGH	NONE	FRAME_SHIFT	ORF3a	ttt/	F79	orf3a	0.000403	0.915633	3	2	CT>C
ERR5749120	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	1863	0.012882	423	1813,20,0,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749120	26510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	8231	0.002308	0	0,8204,0,20	.	.	.	.	.	.	.	0.001235	0.933642	2	1	T>C
ERR5749120	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	8367	9.56E-4	0	0,8359,0,8	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749120	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	8368	0.002151	0	0,8350,0,18	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749120	26907	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21392	0.002945	0	21315,3,69,0	LOW	SILENT	SYNONYMOUS_CODING	M	Ctg/Ttg	L129	M	0.000817	0.976032	1	1	C>T
ERR5749120	27145	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	21392	8.88E-4	0	1,21372,0,19	HIGH	NONE	FRAME_SHIFT	M	gac/	D209	M	0.000476	0.863895	2	2	CAG>C
ERR5749120	27312	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	16982	0.002002	0	16948,0,34,0	HIGH	NONE	FRAME_SHIFT	ORF6	aat/aaAt	N39K?	orf6	0.000911	0.088458	4	2	T>TA
ERR5749120	27476	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	32106	0.001246	84	15100,16952,2,39	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	aCa/aTa	T28I	orf7a	0.000547	0.22827	4	2	C>T
ERR5749120	27955	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	4156	0.001684	0	4147,2,7,0	HIGH	NONE	FRAME_SHIFT	ORF8	tta/ttTa	L22F?	orf8	0.001684	0.879424	3	2	G>GT
ERR5749120	27972	PASS	C	T	4170	0.904796	0	0,0,4138,17	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749120	28001	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	8300	0.001807	0	4137,4139,9,9	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ccG/ccA	P36	orf8	0.00085	0.830607	2	1	G>A
ERR5749120	28048	PASS	G	T	4156	0.926131	2147483647	0,0,0,4154	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749120	28111	PASS	A	G	24069	0.978977	2	3,1,19908,4151	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749120	28147	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19916	0.001004	0	19877,3,20,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	cCt/cTt	P85L	orf8	0.000438	0.981624	4	2	C>T
ERR5749120	28147	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	19916	7.53E-4	0	19898,3,15,0	HIGH	NONE	FRAME_SHIFT	ORF8	ttt/	F86	orf8	0.000438	0.981624	4	2	CT>C
ERR5749120	28270	PASS	TA	T	38649	0.995498	393	173,8,19662,18813	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749120	28280	PASS	G	C	38581	0.939374	16	13,3,19696,18800	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749120	28281	PASS	A	T	38581	0.916021	34	31,8,19680,18800	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749120	28282	PASS	T	A	38583	0.915818	1	11,13,19663,18808	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749120	28321	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	19898	6.53E-4	0	0,19885,0,13	HIGH	NONE	FRAME_SHIFT	N	ggt/Tggt	G18W?	N	0.00045	0.947809	3	2	G>GT
ERR5749120	28396	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GC	G	19926	8.53E-4	0	13,19896,0,17	HIGH	NONE	FRAME_SHIFT	N	caa/	Q43	N	0.000496	0.946059	5	2	GC>G
ERR5749120	28881	PASS	G	A	6562	0.728589	9	3,0,3199,3230	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749120	28882	PASS	G	A	6562	0.824749	9	4,0,3270,3219	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749120	28883	PASS	G	C	6562	0.941481	0	1,0,3280,3279	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749120	28977	PASS	C	T	3339	0.929919	0	0,3,0,3335	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749120	29077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	24494	4.08E-4	0	24484,0,10,0	HIGH	NONE	FRAME_SHIFT	N	aat/	N269	N	0.000408	0.88565	3	2	CA>C
ERR5749120	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	48656	0.001171	0	24422,24151,34,33	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749120	29386	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	6290	0.002544	0	6274,0,16,0	HIGH	NONE	FRAME_SHIFT	N	aag/aaAg	K373K?	N	0.000887	0.899197	4	2	C>CA
ERR5749121	179	PASS	T	G	6395	0.850195	0	12,0,6376,1	.	.	.	.	.	.	.	0.850195	0.857981	1	1	T>G
ERR5749121	239	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTC	T	12753	0.001333	0	6220,6516,8,9	.	.	.	.	.	.	.	0.000495	0.25	4	1	TTC>T
ERR5749121	241	PASS	C	T	12750	0.863529	0	0,1,6201,6489	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749121	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	15035	0.002195	0	15001,4,33,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749121	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	15036	9.31E-4	0	14919,5,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749121	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	15036	0.001463	0	14919,5,22,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749121	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	15036	0.004789	0	14919,5,72,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749121	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	15030	0.002329	39	14990,5,33,2	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749121	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	15033	0.001197	0	14996,13,18,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749121	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	36956	3.52E-4	1	21889,15054,7,6	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749121	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	36961	0.001677	9	21840,15046,43,19	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749121	913	PASS	C	T	21897	0.922683	0	0,10,2,21868	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749121	1684	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17468	0.001145	0	17433,0,21,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I293	nsp2	0.000638	0.973136	2	2	C>T
ERR5749121	2445	PASS	C	T	21322	0.752978	0	0,20,3,21094	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T547I	nsp2	0.001663	0.815808	1	1	C>T
ERR5749121	3037	PASS	C	T	23428	0.812575	64	1,25,11716,11529	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749121	3267	PASS	C	T	19367	0.970465	0	1,0,19349,4	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749121	4136	PASS	G	T	43559	0.967401	25	9,1,18498,25033	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Ttt	V473F	nsp3	0.00075	0.974623	4	2	G>T
ERR5749121	5388	PASS	C	A	8062	0.957083	2147483647	0,0,8060,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749121	5986	PASS	C	T	16688	0.977409	0	1,0,16667,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749121	6954	PASS	T	C	22603	0.823829	0	0,7,4,22477	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749121	7926	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26507	0.001471	0	0,26459,0,39	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCa/gTa	A1736V	nsp3	0.000531	0.97019	5	2	C>T
ERR5749121	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	34480	0.001421	136	17931,16500,49,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749121	10077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	5562	0.002517	263	6,5529,11,4	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTc/tCc	F8S	3Cpro	0.001833	0.454545	1	1	T>C
ERR5749121	11287	PASS	GTCTGGTTTT	G	14947	0.997056	25	1,43,0,14903	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749121	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28488	0.001123	0	14226,14196,17,18	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749121	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	17219	0.003194	2147483647	16820,161,8,224	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749121	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	33500	0.001403	1	16788,16697,25,22	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749121	14408	PASS	C	T	33500	0.843373	5	2,5,16706,16532	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749121	14676	PASS	C	T	12424	0.834997	0	9,0,12387,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749121	15279	PASS	C	T	20899	0.89832	0	3,0,20876,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749121	16176	PASS	T	C	21137	0.982826	0	0,0,11634,9495	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749121	17747	PASS	C	T	12271	0.968462	99	4,3,12253,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P504L	helicase	0.000839	0.968462	2	2	C>T
ERR5749121	17999	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25600	0.001094	2	13309,12252,18,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T588I	helicase	0.001094	0.974498	2	1	C>T
ERR5749121	18756	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	28332	0.0012	0	28264,6,53,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccG/ccT	P239	ExoN	0.000392	0.942688	3	2	G>T
ERR5749121	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	37787	0.002249	0	37666,1,93,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749121	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	32815	9.75E-4	0	32731,1,33,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749121	21034	PASS	C	T	20079	0.915185	0	0,4,0,20031	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L126F	MethTr	0.001871	0.915185	1	1	C>T
ERR5749121	21302	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	36874	0.001031	0	8,36806,0,44	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCa/cTa	P215L	MethTr	0.001031	0.843069	1	1	C>T
ERR5749121	21304	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	36879	7.86E-4	0	7,36798,0,51	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgc/Agc	R216S	MethTr	0.000411	0.605296	3	2	C>A
ERR5749121	21305	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	36879	9.76E-4	0	7,36764,0,52	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cGc/cAc	R216H	MethTr	0.000727	0.703943	1	1	G>A
ERR5749121	21764	PASS	ATACATG	A	16239	0.995074	0	80,0,16159,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749121	21990	PASS	TTTA	T	16252	0.998154	0	0,30,7,16215	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749121	22927	PASS	G	T	12494	0.909717	0	24,0,12456,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	ttG/ttT	L455F	S	0.000791	0.909717	4	3	G>T
ERR5749121	23063	PASS	A	T	12469	0.860374	0	0,3,0,12405	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749121	23271	PASS	C	A	20412	0.930972	0	1,0,20393,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749121	23403	PASS	A	G	20411	0.969771	0	0,5,3,20390	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749121	23604	PASS	C	A	18804	0.935812	0	15,0,18780,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749121	23709	PASS	C	T	18783	0.940851	0	0,3,3,18752	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749121	24506	PASS	T	G	16127	0.973275	0	6,0,16116,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749121	24914	PASS	G	C	36641	0.963647	0	1,2,18239,18366	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749121	25429	PASS	G	T	20482	0.904013	0	15,0,20436,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gta/Tta	V13L	orf3a	0.00064	0.906678	5	2	G>T
ERR5749121	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	27402	0.001204	305	27285,33,20,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749121	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	27351	4.39E-4	0	27339,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749121	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	27555	9.8E-4	993	27107,202,138,77	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749121	25954	PASS	G	T	92955	0.984476	0	12,5,65569,27344	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Ggt/Tgt	G188C	orf3a	0.983612	0.984476	1	1	G>T
ERR5749121	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	65455	3.67E-4	0	6,65420,0,24	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749121	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	11777	0.001104	0	2,11754,0,13	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749121	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	11777	0.001274	0	2,11760,0,15	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749121	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	11776	0.003397	0	1,11731,0,40	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749121	27972	PASS	C	T	11773	0.905207	39	1,2,11656,69	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749121	28048	PASS	G	T	11721	0.921423	0	0,22,2,11692	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749121	28111	PASS	A	G	26031	0.980984	1	3,1,14288,11728	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749121	28270	PASS	TA	T	27719	0.994589	347	145,5,14098,13471	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749121	28280	PASS	G	C	27648	0.935583	14	8,1,14119,13468	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749121	28281	PASS	A	T	27648	0.91815	46	23,2,14107,13462	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749121	28282	PASS	T	A	27649	0.909147	25	19,4,14092,13473	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749121	28292	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	28416	4.22E-4	0	14165,14237,6,6	HIGH	NONE	FRAME_SHIFT	N	aat/	N8	N	0.000304	0.055324	4	2	CA>C
ERR5749121	28881	PASS	G	A	12082	0.766016	2	7,4,5994,5922	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749121	28882	PASS	G	A	12082	0.834547	6	5,1,6054,5910	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749121	28883	PASS	G	C	12081	0.942803	0	0,0,6066,6003	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749121	28977	PASS	C	T	6166	0.931074	0	0,1,8,6145	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749121	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	47800	9.62E-4	1	25568,22135,34,26	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749121	29721	PASS	C	T	13334	0.783111	0	0,100,0,12952	.	.	.	.	.	.	.	0.001062	0.880471	2	1	C>T
ERR5749121	29749	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	13562	0.001475	0	0,13335,0,191	.	.	.	.	.	.	.	0.00126	0.997197	2	1	A>C
ERR5749122	241	PASS	C	T	627	0.864434	0	0,0,312,315	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749122	412	PASS	C	T	1720	0.97907	2147483647	0,0,1719,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G49	leader	0.968277	0.983986	1	1	C>T
ERR5749122	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	1719	0.007563	0	1705,0,13,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749122	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	1719	0.002909	0	1706,0,5,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749122	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	18149	0.002424	9	16380,1719,43,1	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749122	913	PASS	C	T	16414	0.921652	0	0,5,0,16386	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749122	1643	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	9124	0.001863	0	9103,0,18,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Aac/Tac	N280Y	nsp2	0.001863	0.97665	1	1	A>T
ERR5749122	1813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	9116	0.001645	0	0,9094,0,17	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcA	A336	nsp2	0.001022	0.152738	4	2	T>A
ERR5749122	2151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATTGGC	A	18511	0.001675	0	0,18454,0,31	HIGH	NONE	FRAME_SHIFT	ORF1ab	tggcttgaa/	WLE450	nsp2	0.000402	0.971954	3	2	ATTGGC>A
ERR5749122	2151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATTGGCTTGAAGAGAAG	A	18511	0.001405	0	0,18454,0,26	HIGH	NONE	FRAME_SHIFT	ORF1ab	tggcttgaagagaagttt/	WLEEKF450	nsp2	0.000402	0.971954	3	2	ATTGGCTTGAAGAGAAG>A
ERR5749122	2185	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	18521	0.003078	0	4,18460,0,57	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L462S?	nsp2	0.000441	0.963529	4	3	G>GT
ERR5749122	3037	PASS	C	T	4543	0.812239	9	0,3,2272,2238	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749122	3230	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	14626	0.001231	0	14607,0,18,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggt/Agt	G171S	nsp3	0.001231	0.979167	2	1	G>A
ERR5749122	3267	PASS	C	T	14624	0.969229	0	3,0,14612,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749122	3575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	5382	0.002973	0	5366,0,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/ttTa	L287F?	nsp3	0.000594	0.059126	3	1	G>GT
ERR5749122	4002	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3312	0.01087	0	0,3265,0,41	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T428I	nsp3	0.001296	0.806154	2	1	C>T
ERR5749122	4338	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	17509	0.001085	42	10281,7209,19,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	att/	I541	nsp3	0.000366	0.051643	2	2	CTA>C
ERR5749122	5170	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	7083	0.0048	0	0,7049,0,34	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T819	nsp3	0.000565	0.894036	2	2	CCA>C
ERR5749122	5388	PASS	C	A	1249	0.952762	2147483647	0,0,1248,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749122	5986	PASS	C	T	4880	0.979098	2147483647	0,0,4879,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749122	6185	PASS	C	T	4882	0.948587	0	0,1,0,4878	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cac/Tac	H1156Y	nsp3	0.910265	0.954999	1	1	C>T
ERR5749122	6954	PASS	T	C	10527	0.807353	0	0,1,30,10433	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749122	7067	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	10935	0.001097	0	400,10523,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	gaa/	E1450	nsp3	0.000274	0.059217	5	3	GA>G
ERR5749122	7564	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	8808	0.002044	0	0,8783,0,18	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/	Y1617	nsp3	0.000586	0.056194	4	2	CT>C
ERR5749122	7740	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	13062	0.002986	0	13017,0,44,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gAt/gTt	D1674V	nsp3	0.000834	0.078818	3	2	A>T
ERR5749122	9286	PASS	C	T	985	0.949239	2147483647	0,0,985,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N244	nsp4	0.949239	0.971567	1	1	C>T
ERR5749122	11071	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	17868	0.002239	0	17822,0,40,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttc/ttTc	F34F?	nsp6	0.001292	0.087481	5	3	G>GT
ERR5749122	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17868	0.003638	0	17758,0,88,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749122	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	17862	0.002071	0	17806,0,55,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749122	11095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	17861	0.00112	0	17841,0,20,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L43	nsp6	0.000515	0.887707	7	2	CT>C
ERR5749122	11173	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17796	0.041582	0	16521,0,1200,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ctC/ctT	L67	nsp6	0.00115	0.587518	1	1	C>T
ERR5749122	11287	PASS	GTCTGGTTTT	G	17863	0.998377	0	0,29,0,17834	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749122	11417	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	3363	0.003271	0	3352,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/tTat	Y150L?	nsp6	0.00274	0.951155	2	2	G>GT
ERR5749122	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	18461	0.002167	11	15059,3351,28,12	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749122	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	8696	0.003105	0	8663,0,27,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749122	14408	PASS	C	T	264	0.890152	0	0,0,133,130	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749122	14599	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8320	0.002885	0	8290,0,25,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L387	RdRp	0.000639	0.922766	3	2	C>T
ERR5749122	14676	PASS	C	T	8319	0.771727	0	5,0,8283,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749122	15026	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAT	C	5747	0.001218	0	5742,0,7,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tataca/	YT530	RdRp	0.000503	0.869455	2	2	CAT>C
ERR5749122	15279	PASS	C	T	8013	0.881193	2147483647	0,0,8001,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749122	15451	PASS	G	A	8011	0.069405	0	0,7435,0,569	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggt/Agt	G671S	RdRp	0.069405	0.980299	1	1	G>A
ERR5749122	15620	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	10804	0.001388	0	10773,0,17,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cTt/cCt	L727P	RdRp	0.001388	0.088584	1	1	T>C
ERR5749122	15905	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AG	A	8621	9.28E-4	0	8613,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggt/	G823	RdRp	0.000835	0.057692	2	1	AG>A
ERR5749122	15983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	8611	0.002439	0	8590,0,21,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/aAca	T850N?	RdRp	0.000701	0.338235	2	1	T>TA
ERR5749122	16176	PASS	T	C	9860	0.979919	0	0,0,1237,8619	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749122	16794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	23233	8.61E-4	30	7312,15902,0,20	HIGH	NONE	FRAME_SHIFT	ORF1ab	gta/	V187	helicase	0.000354	0.077626	2	2	TG>T
ERR5749122	17615	PASS	A	G	7425	0.912189	0	0,1,0,7406	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749122	17749	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	8089	0.001731	0	8073,0,14,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gct/Cct	A505P	helicase	0.001521	0.987943	4	2	G>C
ERR5749122	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	22335	8.06E-4	0	22317,0,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749122	18744	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22330	0.001926	0	22260,0,47,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y235	ExoN	0.000912	0.953624	2	2	C>T
ERR5749122	18897	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	22348	9.84E-4	0	3,22304,0,22	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttT/ttC	F286	ExoN	0.00046	0.060685	3	3	T>C
ERR5749122	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	20228	0.002324	0	0,20181,0,47	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749122	19269	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	27712	0.001696	40	7459,20197,3,51	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaC/aaA	N410K	ExoN	0.000773	0.954777	2	2	C>A
ERR5749122	19343	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTTTTGTTAAT	C	7462	0.002412	0	7444,0,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tttgttaattta/	FVNL436	ExoN	0.000519	0.192257	7	2	CTTTTGTTAAT>C
ERR5749122	20420	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	20261	0.001431	0	0,20232,0,29	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F268	endoR	0.000383	0.069626	2	1	AT>A
ERR5749122	21134	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	30155	0.001194	85	13013,17096,0,36	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cAa/cGa	Q159R	MethTr	0.001194	0.689661	1	1	A>G
ERR5749122	21764	PASS	ATACATG	A	6430	0.996734	0	21,0,6409,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749122	21990	PASS	TTTA	T	6432	0.999223	0	0,5,1,6426	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749122	22264	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAT	C	14149	0.001131	0	4,14129,0,16	HIGH	NONE	FRAME_SHIFT	S	atc/	I235	S	0.001131	0.963496	2	2	CAT>C
ERR5749122	22323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19036	0.001523	34	4889,14104,0,29	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCt/tTt	S254F	S	0.000812	0.978946	3	2	C>T
ERR5749122	22432	PASS	C	T	4888	0.743249	2147483647	0,0,4836,0	LOW	SILENT	SYNONYMOUS_CODING	S	gaC/gaT	D290	S	0.002959	0.755028	1	1	C>T
ERR5749122	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	12276	0.001466	0	0,12254,0,18	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749122	23063	PASS	A	T	6953	0.871422	2147483647	0,0,0,6929	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749122	23271	PASS	C	A	18294	0.916694	2147483647	0,0,18273,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749122	23403	PASS	A	G	18295	0.968297	0	0,3,0,18282	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749122	23575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	6426	0.002646	0	6409,0,17,0	HIGH	NONE	FRAME_SHIFT	S	gct/	A672	S	0.001569	0.894896	2	2	CG>C
ERR5749122	23604	PASS	C	A	6425	0.956731	0	3,0,6421,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749122	23606	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	6425	0.001401	0	6416,0,9,0	HIGH	NONE	FRAME_SHIFT	S	cgg/	R682	S	0.001401	0.064309	2	2	CG>C
ERR5749122	23709	PASS	C	T	6418	0.944064	0	0,3,0,6404	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749122	24506	PASS	T	G	10554	0.974891	0	8,0,10546,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749122	24914	PASS	G	C	30029	0.960771	0	0,0,14977,15041	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749122	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	19152	0.001201	22	14005,5117,25,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749122	25413	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14058	0.001707	0	14019,0,24,0	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	atC/atT	I7	orf3a	0.00145	0.968329	2	1	C>T
ERR5749122	25429	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTAACTT	G	14056	6.4E-4	0	14047,0,9,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF3a	gtaactttg/gtg	VTL13V	orf3a	0.00064	0.906678	5	2	GTAACTT>G
ERR5749122	25587	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	14058	0.00128	0	0,14040,0,18	HIGH	NONE	FRAME_SHIFT	ORF3a	aag/aaAg	K67K?	orf3a	0.000598	0.813206	6	2	C>CA
ERR5749122	26158	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	13952	0.001147	0	2,13934,0,16	HIGH	NONE	FRAME_SHIFT	ORF3a	gtt/	V256	orf3a	0.000297	0.905181	6	2	GT>G
ERR5749122	26159	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTAATCCAG	T	13953	0.001648	0	2,13928,0,23	HIGH	NONE	FRAME_SHIFT	ORF3a	ccagtaatg/	PVM258	orf3a	0.000311	0.053032	2	2	TTAATCCAG>T
ERR5749122	26257	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	21782	0.001056	41	7799,13960,0,23	HIGH	NONE	FRAME_SHIFT	E	tcg/tTcg	S6F?	E	0.000247	0.948926	4	2	G>GT
ERR5749122	26270	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	G	21782	0.002433	0	7778,13940,19,37	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	aCa/aGa	T9R	E	0.000586	0.930791	3	2	C>G
ERR5749122	27065	PASS	G	A	22090	0.773019	0	0,4,0,21843	LOW	SILENT	SYNONYMOUS_CODING	M	ttG/ttA	L181	M	0.001008	0.897124	3	2	G>A
ERR5749122	27209	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATC	A	12496	8.8E-4	0	12485,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF6	ctc/	L4	orf6	0.00088	0.957103	3	2	ATC>A
ERR5749122	27312	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	12489	0.001441	0	12472,0,18,0	HIGH	NONE	FRAME_SHIFT	ORF6	aat/aaAt	N39K?	orf6	0.000911	0.088458	4	2	T>TA
ERR5749122	27506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	26617	9.02E-4	51	14094,12472,3,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	gGa/gTa	G38V	orf7a	0.000715	0.985435	4	2	G>T
ERR5749122	27741	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	14116	0.001629	0	0,14093,0,23	HIGH	NONE	FRAME_SHIFT	ORF7a	aga/	R118	orf7a	0.000363	0.954278	3	2	CA>C
ERR5749122	27972	PASS	C	T	2977	0.921061	0	0,0,2956,14	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749122	28048	PASS	G	T	2964	0.92274	0	0,5,0,2958	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749122	28111	PASS	A	G	22941	0.979251	2	7,0,19954,2967	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749122	28198	PASS	G	T	19968	0.94386	0	6,0,19910,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tGt/tTt	C102F	orf8	0.000718	0.94386	4	2	G>T
ERR5749122	28239	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTGTTTTAGAT	G	19963	0.002455	0	19915,0,49,0	HIGH	NONE	FRAME_SHIFT	ORF8	gttttagatttc/	VLDF117	orf8	0.000417	0.984998	9	2	GTTGTTTTAGAT>G
ERR5749122	28250	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	19953	0.001253	0	19858,0,27,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	gaT/gaC	D119	orf8	0.000494	0.993968	5	3	T>C
ERR5749122	28270	PASS	TA	T	38783	0.994224	580	228,5,19654,18905	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749122	28271	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AA	A	38777	0.001573	177	19812,18910,61,0	.	.	.	.	.	.	.	0.000482	0.924941	3	2	AA>A
ERR5749122	28280	PASS	G	C	38694	0.934564	9	8,2,19721,18881	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749122	28281	PASS	A	T	38694	0.91226	41	28,5,19705,18888	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749122	28282	PASS	T	A	38694	0.915465	11	25,13,19680,18891	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749122	28321	PASS	G	T	19946	0.947809	0	0,10,0,19916	LOW	SILENT	SYNONYMOUS_CODING	N	acG/acT	T16	N	0.00045	0.947809	3	2	G>T
ERR5749122	28657	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12968	0.001311	0	0,12942,0,21	LOW	SILENT	SYNONYMOUS_CODING	N	gaC/gaT	D128	N	0.00124	0.862766	1	1	C>T
ERR5749122	28881	PASS	G	A	5808	0.722624	3	1,0,2839,2871	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749122	28882	PASS	G	A	5808	0.818871	9	4,0,2890,2864	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749122	28883	PASS	G	C	5808	0.936123	3	1,0,2896,2907	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749122	28977	PASS	C	T	2960	0.9375	2147483647	0,0,0,2954	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749122	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	36124	0.001246	0	18133,17931,27,26	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749122	29642	PASS	C	T	8716	0.827673	7	2,0,3463,5219	HIGH	NONSENSE	STOP_GAINED	ORF10	Caa/Taa	Q29*	orf10	0.001806	0.941176	2	2	C>T
ERR5749122	29679	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	6962	0.001149	0	3480,3475,4,4	.	.	.	.	.	.	.	0.000443	0.838763	2	1	CT>C
ERR5749122	29774	PASS	C	T	3494	0.973955	2147483647	0,0,0,3493	.	.	.	.	.	.	.	0.002525	0.973955	1	1	C>T
ERR5749123	241	PASS	C	T	20724	0.87155	0	0,0,10289,10359	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749123	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	16797	0.003036	0	16748,0,51,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749123	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	16797	7.74E-4	0	16680,1,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749123	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	16797	0.00125	0	16680,1,21,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749123	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	16797	0.004763	0	16680,1,80,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749123	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	16785	0.001787	0	15323,3,1240,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749123	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	16785	0.001787	0	16752,3,30,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749123	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	16785	7.75E-4	0	16758,3,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749123	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	16784	9.53E-4	0	16749,6,16,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749123	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	38936	3.6E-4	9	22094,16826,11,3	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749123	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	38939	4.88E-4	14	22039,16792,6,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749123	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	38939	0.002234	9	22039,16792,57,30	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749123	913	PASS	C	T	22085	0.916504	0	0,5,0,22056	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749123	2508	PASS	C	A	23200	0.96125	48	2,8,11,23165	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCc/cAc	P568H	nsp2	0.008471	0.96125	2	1	C>A
ERR5749123	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	42521	0.001458	2806	21183,20037,44,1133	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749123	3037	PASS	C	T	28345	0.861986	42	0,14,14169,14051	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749123	3267	PASS	C	T	20099	0.970844	0	3,0,20087,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749123	5388	PASS	C	A	8630	0.961066	2147483647	0,0,8624,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749123	5986	PASS	C	T	17705	0.973793	0	2,0,17686,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749123	6894	PASS	G	T	22833	0.897867	0	67,0,22749,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tGt/tTt	C1392F	nsp3	0.00096	0.897867	3	2	G>T
ERR5749123	6954	PASS	T	C	22835	0.822684	0	0,4,2,22708	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749123	8581	PASS	G	T	17369	0.96131	0	0,2,0,17337	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caG/caT	Q9H	nsp4	0.005201	0.96131	2	2	G>T
ERR5749123	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	37067	0.001214	122	19670,17352,45,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749123	11287	PASS	GTCTGGTTTT	G	16190	0.997159	0	0,46,0,16144	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749123	11507	PASS	G	A	35876	0.908825	14	8,1,17923,17823	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Att	V179I	nsp6	0.007744	0.914418	2	2	G>A
ERR5749123	12493	PASS	C	T	20277	0.855797	0	1,0,20230,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D134	nsp8	0.000671	0.855797	2	2	C>T
ERR5749123	12865	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	15186	0.001515	0	15150,1,23,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaT/gaC	D60	nsp9	0.001515	0.98494	1	1	T>C
ERR5749123	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30357	0.001416	0	15158,15121,22,22	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749123	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	17109	0.002572	3077	16784,143,6,169	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749123	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	33402	9.28E-4	0	16757,16635,16,15	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749123	14408	PASS	C	T	33402	0.850997	14	2,9,16667,16460	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749123	14676	PASS	C	T	13307	0.726835	0	10,0,13237,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749123	15279	PASS	C	T	22244	0.879338	2147483647	0,0,22211,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749123	16176	PASS	T	C	22988	0.983687	7	0,2,13103,9872	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749123	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	31109	8.36E-4	0	31083,0,26,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749123	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	39880	0.002106	0	39755,0,90,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749123	21762	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTATACA	C	17760	0.001464	0	17734,0,26,0	MODERATE	NONE	CODON_DELETION	S	atacat/	IH68	S	0.001297	0.875707	2	2	CTATACA>C
ERR5749123	21764	PASS	ATACATG	A	17760	0.99634	0	65,0,17695,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749123	21990	PASS	TTTA	T	17773	0.998312	0	0,30,6,17737	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749123	23063	PASS	A	T	14272	0.87528	2147483647	0,0,0,14211	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749123	23271	PASS	C	A	20962	0.919378	0	4,0,20941,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749123	23403	PASS	A	G	20961	0.982253	0	0,2,0,20953	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749123	23604	PASS	C	A	19944	0.936974	0	17,0,19916,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749123	23709	PASS	C	T	19936	0.942014	0	0,7,5,19902	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749123	24506	PASS	T	G	17128	0.973669	0	6,0,17121,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749123	24914	PASS	G	C	35248	0.964395	0	1,1,17572,17659	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749123	25290	PASS	G	T	6767	0.869662	186	7,11,0,6748	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tGt/tTt	C1243F	S	0.001422	0.869662	1	1	G>T
ERR5749123	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	24838	0.002496	85	18004,6758,73,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749123	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	27975	0.001001	928	27573,164,137,69	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749123	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	72122	2.77E-4	0	0,72100,0,20	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749123	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	14342	7.67E-4	0	2,14326,0,11	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749123	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	14343	0.002161	0	2,14304,0,31	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749123	27972	PASS	C	T	14251	0.900288	34	3,2,14122,84	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749123	28048	PASS	G	T	14170	0.928511	0	0,12,0,14149	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749123	28111	PASS	A	G	32853	0.978997	11	5,0,18663,14174	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749123	28250	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TCTG	18652	6.43E-4	0	18641,0,12,0	MODERATE	NONE	CODON_INSERTION	ORF8	ttc/CTGttc	F120LF	orf8	0.000494	0.993968	5	3	T>TCTG
ERR5749123	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	18649	6.43E-4	0	18637,2,12,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749123	28270	PASS	TA	T	36343	0.995212	421	175,6,18426,17743	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749123	28280	PASS	G	C	36275	0.941254	27	13,1,18455,17730	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749123	28281	PASS	A	T	36275	0.920606	41	28,5,18457,17725	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749123	28282	PASS	T	A	36277	0.915291	19	23,8,18417,17739	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749123	28516	PASS	T	C	16597	0.990661	0	4,0,16589,0	LOW	SILENT	SYNONYMOUS_CODING	N	gaT/gaC	D81	N	0.001273	0.990661	2	2	T>C
ERR5749123	28881	PASS	G	A	15014	0.755295	6	2,0,7395,7398	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749123	28882	PASS	G	A	15013	0.841204	0	1,0,7495,7393	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749123	28883	PASS	G	C	15013	0.947845	3	0,1,7516,7480	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749123	28977	PASS	C	T	7637	0.931256	0	0,2,1,7627	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749123	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	56984	0.001193	0	28586,28276,41,40	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749123	29781	PASS	G	C	12139	0.972321	0	0,3,0,12125	.	.	.	.	.	.	.	0.00173	0.972321	2	1	G>C
ERR5749124	241	PASS	C	T	1767	0.862479	0	0,0,880,883	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749124	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	5319	0.002068	0	5311,0,11,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749124	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	5319	0.001316	0	5303,0,7,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749124	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	5317	0.002821	0	4882,1,404,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749124	913	PASS	C	T	3902	0.937212	0	0,2,0,3894	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749124	1005	PASS	A	T	8470	0.956316	0	0,0,8462,6	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aTg	K67M	nsp2	0.956316	0.956316	1	1	A>T
ERR5749124	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	25289	0.001265	1992	12633,11816,23,766	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749124	3037	PASS	C	T	6696	0.82273	9	0,3,3346,3303	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749124	3267	PASS	C	T	7368	0.971634	0	2,0,7359,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749124	3671	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	10948	0.001461	0	5455,5416,8,9	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E318K	nsp3	0.000351	0.0625	6	2	G>A
ERR5749124	4255	PASS	G	A	18413	0.815945	33	12,0,9158,9100	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccG/ccA	P512	nsp3	0.001102	0.871853	2	1	G>A
ERR5749124	4980	PASS	C	T	13139	0.982571	2	0,2,4594,8541	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T754I	nsp3	0.005479	0.982571	1	1	C>T
ERR5749124	5388	PASS	C	A	2546	0.957188	2147483647	0,0,2544,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749124	5986	PASS	C	T	6142	0.971019	0	1,0,6136,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749124	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5353	0.002242	0	0,5278,0,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749124	6954	PASS	T	C	7568	0.81871	2147483647	0,0,0,7523	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749124	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	10043	8.96E-4	6	7887,2146,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749124	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	9723	0.003394	0	9685,0,37,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749124	11287	PASS	GTCTGGTTTT	G	9724	0.998972	0	0,10,0,9714	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749124	11355	PASS	C	T	15725	0.978315	0	0,1,5993,9730	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCa/gTa	A128V	nsp6	0.000455	0.982262	3	2	C>T
ERR5749124	11507	PASS	G	A	11916	0.908946	0	1,0,5964,5919	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Att	V179I	nsp6	0.007744	0.914418	2	2	G>A
ERR5749124	12269	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	7550	0.00106	0	7543,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aag/	K61	nsp8	0.000434	0.213333	2	1	GA>G
ERR5749124	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12186	0.001723	0	6085,6062,12,12	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749124	13898	PASS	A	G	5284	0.963096	2147483647	0,0,0,5278	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gAt/gGt	D153G	RdRp	0.963096	0.963096	1	1	A>G
ERR5749124	14408	PASS	C	T	1853	0.862925	0	0,0,932,909	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749124	14676	PASS	C	T	4940	0.773077	0	4,0,4924,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749124	15141	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8106	0.002591	0	0,8078,0,22	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acC/acT	T567	RdRp	0.002591	0.952167	1	1	C>T
ERR5749124	15279	PASS	C	T	7488	0.882479	2147483647	0,0,7467,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749124	15371	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	14936	0.001071	0	7471,7449,8,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	acg/	T644	RdRp	0.00056	0.786959	4	2	CG>C
ERR5749124	16176	PASS	T	C	8247	0.981812	0	0,0,3434,4811	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749124	16293	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3432	0.003205	0	3417,0,11,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C19	helicase	0.001538	0.968351	1	1	C>T
ERR5749124	17122	PASS	G	T	17560	0.056834	0	6519,9988,413,636	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gct/Tct	A296S	helicase	0.000476	0.056834	3	2	G>T
ERR5749124	18252	PASS	C	T	5869	0.924007	2147483647	0,0,0,5858	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N71	ExoN	0.000968	0.924007	2	2	C>T
ERR5749124	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	16289	9.21E-4	0	16274,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749124	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	10007	8.99E-4	0	0,9998,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749124	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8921	0.001794	0	8899,0,16,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749124	21764	PASS	ATACATG	A	6929	0.997258	0	19,0,6910,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749124	21990	PASS	TTTA	T	6931	0.998269	0	0,12,2,6917	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749124	22127	PASS	C	T	8044	0.908628	2147483647	0,0,8005,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L189F	S	0.908628	0.908628	1	1	C>T
ERR5749124	23063	PASS	A	T	7454	0.863563	0	0,1,0,7418	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749124	23271	PASS	C	A	8993	0.923051	2147483647	0,0,8982,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749124	23403	PASS	A	G	8990	0.973971	2147483647	0,0,0,8987	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749124	23604	PASS	C	A	7897	0.935545	0	2,0,7888,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749124	23709	PASS	C	T	7886	0.934187	0	0,1,0,7870	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749124	24506	PASS	T	G	7067	0.974388	0	3,0,7062,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749124	24914	PASS	G	C	23165	0.960371	3	1,0,11540,11608	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749124	25587	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	11284	8.86E-4	0	0,11274,0,10	HIGH	NONE	FRAME_SHIFT	ORF3a	aag/	K67	orf3a	0.000598	0.813206	6	2	CA>C
ERR5749124	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	3291	0.00395	131	3260,11,6,7	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749124	26333	PASS	C	T	4315	0.943221	0	6,0,4308,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	aCa/aTa	T30I	E	0.00158	0.943221	1	1	C>T
ERR5749124	27312	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	10974	9.11E-4	0	10965,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF6	aat/aaAt	N39K?	orf6	0.000911	0.088458	4	2	T>TA
ERR5749124	27668	PASS	A	G	7949	0.931312	0	0,0,71,7860	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	gAa/gGa	E92G	orf7a	0.931312	0.931312	1	1	A>G
ERR5749124	27972	PASS	C	T	4236	0.903683	41	0,2,4180,36	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749124	28048	PASS	G	T	4199	0.909264	0	0,6,0,4190	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749124	28111	PASS	A	G	13553	0.97661	2	1,1,9350,4198	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749124	28195	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	9351	0.001497	0	9325,0,19,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	cGt/cTt	R101L	orf8	0.000851	0.926081	3	2	G>T
ERR5749124	28270	PASS	TA	T	17977	0.995216	185	87,5,9241,8650	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749124	28280	PASS	G	C	17942	0.936072	23	9,0,9250,8645	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749124	28281	PASS	A	T	17942	0.918125	12	16,6,9254,8643	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749124	28282	PASS	T	A	17946	0.906887	5	13,7,9231,8650	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749124	28881	PASS	G	A	4934	0.766315	6	3,0,2448,2410	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749124	28882	PASS	G	A	4932	0.821979	3	2,0,2468,2401	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749124	28883	PASS	G	C	4932	0.937956	0	0,0,2473,2449	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749124	28977	PASS	C	T	2505	0.930938	2147483647	0,0,0,2496	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749124	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	34184	0.001375	0	17164,16950,28,28	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749124	29386	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	3400	0.002059	0	3393,0,7,0	HIGH	NONE	FRAME_SHIFT	N	aag/aaAg	K373K?	N	0.000887	0.899197	4	2	C>CA
ERR5749124	29746	PASS	AGTACGATCGAGT	A	4630	0.242549	0	0,3507,0,1123	.	.	.	.	.	.	.	0.004773	0.242549	2	1	AGTACGATCGAGT>A
ERR5749125	241	PASS	C	T	10420	0.865547	0	0,1,5163,5204	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749125	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	14958	0.001471	0	14937,0,22,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749125	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	14958	0.002273	0	14913,0,34,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749125	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	14951	0.001873	0	13837,0,1021,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749125	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	14951	9.36E-4	0	14937,0,14,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749125	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	14950	9.36E-4	0	14930,0,14,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749125	656	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	14981	0.001202	0	2,14955,0,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gct/Cct	A131P	leader	0.001202	0.131429	1	1	G>C
ERR5749125	657	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14981	0.001202	0	2,14955,0,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A131V	leader	0.001202	0.365979	3	1	C>T
ERR5749125	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	37901	5.01E-4	0	22909,14971,11,8	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749125	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22909	0.001004	0	0,22855,0,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749125	913	PASS	C	T	22910	0.920995	0	0,14,0,22860	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749125	932	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAC	G	22922	4.8E-4	0	0,22911,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T44	nsp2	0.00048	0.184416	2	2	GAC>G
ERR5749125	1510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	22588	0.003675	0	0,22259,0,93	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G235	nsp2	0.002159	0.937304	1	1	T>C
ERR5749125	1912	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	48455	6.81E-4	16	27389,21021,26,8	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S369	nsp2	0.000681	0.08802	2	1	C>T
ERR5749125	2445	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16832	0.001663	0	1,16794,0,31	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T547I	nsp2	0.001663	0.815808	1	1	C>T
ERR5749125	2453	PASS	C	T	16833	0.720133	0	0,11,1,16542	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L550F	nsp2	0.00429	0.842201	2	2	C>T
ERR5749125	2494	PASS	G	T	16851	0.951457	0	0,3,0,16837	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gaG/gaT	E563D	nsp2	0.002624	0.951457	2	2	G>T
ERR5749125	3037	PASS	C	T	19995	0.818205	50	1,20,9992,9826	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749125	3096	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10062	0.002186	0	0,10030,0,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCa/tTa	S126L	nsp3	0.001801	0.932094	1	1	C>T
ERR5749125	3267	PASS	C	T	21327	0.970038	0	2,0,21308,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749125	4331	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34869	0.001061	16	14986,19802,10,30	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L538	nsp3	0.000987	0.928955	1	1	C>T
ERR5749125	5178	PASS	C	T	12649	0.870662	0	0,11,0,12561	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T820I	nsp3	0.00175	0.88249	2	1	C>T
ERR5749125	5388	PASS	C	A	6634	0.956889	2147483647	0,0,6632,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749125	5986	PASS	C	T	14797	0.975738	2147483647	0,0,14788,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749125	6525	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	37348	0.002865	7	14060,23165,48,60	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T1269I	nsp3	0.000813	0.968636	1	1	C>T
ERR5749125	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14073	0.00135	0	2,13896,0,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749125	6954	PASS	T	C	22427	0.815847	0	0,10,0,22287	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749125	7067	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	45286	3.53E-4	45	22775,22495,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gaa/	E1450	nsp3	0.000274	0.059217	5	3	GA>G
ERR5749125	7945	PASS	C	T	24061	0.924608	407	13,11,0,24004	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y1742	nsp3	0.001244	0.950558	2	2	C>T
ERR5749125	8141	PASS	T	A	79	0.164557	33	13,32,0,32	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tta/Ata	L1808I	nsp3	0.164557	0.238095	1	1	T>A
ERR5749125	8512	PASS	A	G	13530	0.818995	0	0,2,4,13437	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caA/caG	Q1931	nsp3	0.8	0.822278	1	1	A>G
ERR5749125	8692	PASS	C	T	25472	0.97884	2147483647	0,0,25452,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y46	nsp4	0.967679	0.97884	1	1	C>T
ERR5749125	9430	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16079	0.003918	0	6,15973,0,65	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I292	nsp4	0.001411	0.960894	1	1	C>T
ERR5749125	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	34664	3.46E-4	31	18559,16093,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749125	10323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	20002	0.00175	0	1,19929,0,35	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749125	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21384	0.001964	0	21313,2,49,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749125	11082	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	21371	4.68E-4	0	21372,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000427	0.179468	2	1	TG>T
ERR5749125	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	21371	0.001872	0	21300,0,57,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749125	11287	PASS	GTCTGGTTTT	G	21360	0.997285	0	0,56,0,21302	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749125	11455	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17690	0.00147	0	17652,0,27,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A161	nsp6	0.00147	0.968698	1	1	C>T
ERR5749125	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	40621	9.85E-4	3	22887,17668,26,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749125	12459	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	46171	0.001841	5	21782,24292,46,40	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T123I	nsp8	0.000658	0.986093	1	1	C>T
ERR5749125	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	14327	6.98E-4	0	14317,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749125	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	35262	0.00173	0	17603,17545,33,35	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749125	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10623	0.004142	2407	10371,108,3,138	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749125	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	20660	7.74E-4	0	10356,10301,8,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749125	14408	PASS	C	T	20660	0.848112	9	0,3,10323,10202	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749125	14676	PASS	C	T	13589	0.833247	0	3,0,13566,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749125	15279	PASS	C	T	22944	0.896836	0	5,0,22915,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749125	16176	PASS	T	C	23512	0.982775	6	1,4,12069,11428	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749125	16508	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	21616	0.001665	0	21559,10,46,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGt/gTt	G91V	helicase	0.000561	0.074909	2	2	G>T
ERR5749125	16794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	43724	0.001144	1	22088,21566,25,28	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	cgT/cgC	R186	helicase	0.000354	0.077626	2	2	T>C
ERR5749125	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	22124	0.001627	0	22071,0,36,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749125	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAA	G	22124	7.68E-4	0	22071,0,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GAA>G
ERR5749125	18171	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28704	8.71E-4	0	14320,14287,13,13	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G44	ExoN	0.000859	0.892019	1	1	C>T
ERR5749125	18501	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	29952	6.01E-4	0	3,29931,0,18	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K155	ExoN	0.000336	0.857143	4	2	CA>C
ERR5749125	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	27184	7.73E-4	0	27163,0,21,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749125	18747	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	27185	5.15E-4	0	27169,3,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tataat/	YN237	ExoN	0.000375	0.982946	4	2	CTA>C
ERR5749125	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	25898	7.72E-4	0	3,25877,0,20	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749125	19164	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	25900	4.63E-4	0	0,25887,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K376	ExoN	0.000358	0.075732	4	2	CA>C
ERR5749125	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	32726	0.001497	0	32652,1,50,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749125	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	35290	8.78E-4	0	35218,0,33,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749125	20719	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	35226	3.41E-4	0	0,35214,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctatta/	LL21	MethTr	0.000341	0.209091	2	2	CTA>C
ERR5749125	21305	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	36773	8.16E-4	0	4,36679,0,41	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cGc/cAc	R216H	MethTr	0.000727	0.703943	1	1	G>A
ERR5749125	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	31704	0.001451	2	15532,15807,23,28	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749125	21764	PASS	ATACATG	A	14593	0.997533	0	35,0,14557,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749125	21990	PASS	TTTA	T	14599	0.995616	0	0,64,5,14530	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749125	22290	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	21896	5.94E-4	0	7,21876,0,13	HIGH	NONE	FRAME_SHIFT	S	tta/	L244	S	0.000389	0.578006	2	2	CT>C
ERR5749125	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	31254	0.001024	5	15580,15626,19,13	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749125	23063	PASS	A	T	15599	0.867363	0	0,0,2,15535	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749125	23271	PASS	C	A	23299	0.931585	0	4,0,23269,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749125	23403	PASS	A	G	23297	0.968751	0	0,8,0,23268	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749125	23604	PASS	C	A	18315	0.943107	0	16,0,18292,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749125	23709	PASS	C	T	18305	0.945643	0	0,5,3,18269	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749125	23817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	36884	7.86E-4	5	18536,18279,12,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTt/cCt	L752P	S	0.000646	0.066832	1	1	T>C
ERR5749125	23855	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18568	0.001239	0	18535,0,24,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Cgt/Tgt	R765C	S	0.000815	0.181818	2	2	C>T
ERR5749125	24506	PASS	T	G	19164	0.976623	0	8,0,19153,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749125	24914	PASS	G	C	43209	0.957231	0	0,0,21509,21657	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749125	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	28741	0.002818	112	20174,8458,93,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749125	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	24140	0.001491	410	24036,25,19,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749125	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	24305	0.001193	1108	23929,177,91,78	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749125	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	56993	3.51E-4	0	9,56963,0,20	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749125	26270	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	68430	6.43E-4	2	11343,57019,9,37	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	aCa/aTa	T9I	E	0.000586	0.930791	3	2	C>T
ERR5749125	26526	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	11353	0.001409	0	3,11315,0,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Gca/Tca	A2S	M	0.001224	0.951192	3	1	G>T
ERR5749125	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	14546	0.002062	0	4,14507,0,30	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749125	26895	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	33384	9.29E-4	0	33326,12,32,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Cat/Tat	H125Y	M	0.000874	0.97046	1	1	C>T
ERR5749125	27371	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21187	0.001888	0	37,21084,0,45	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF6	cCa/cTa	P57L	orf6	0.00148	0.066731	2	2	C>T
ERR5749125	27557	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24227	9.49E-4	0	24184,1,24,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	gCa/gTa	A55V	orf7a	0.000949	0.267468	2	2	C>T
ERR5749125	27739	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24225	0.001156	0	3,24166,0,30	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Ctc/Ttc	L116F	orf7a	0.001001	0.957506	1	1	C>T
ERR5749125	27816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	37850	4.23E-4	5	13610,24224,8,8	HIGH	NONE	FRAME_SHIFT	ORF7b	tta/	L22	orf7b	0.000423	0.053007	1	1	GT>G
ERR5749125	27972	PASS	C	T	13695	0.898722	50	4,3,13572,87	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749125	28048	PASS	G	T	13608	0.918283	0	0,15,0,13585	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749125	28111	PASS	A	G	31190	0.977845	0	2,2,17564,13608	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749125	28270	PASS	TA	T	33943	0.994874	355	157,7,17343,16426	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749125	28270	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAA	T	33943	4.42E-4	47	157,7,8,7	.	.	.	.	.	.	.	0.000322	1	2	1	TAA>T
ERR5749125	28280	PASS	G	C	33884	0.93646	10	13,5,17395,16408	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749125	28281	PASS	A	T	33884	0.919874	19	20,6,17393,16409	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749125	28282	PASS	T	A	33885	0.911141	9	21,11,17368,16427	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749125	28881	PASS	G	A	18590	0.786606	2	3,1,9238,9148	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749125	28882	PASS	G	A	18590	0.833835	0	2,1,9306,9109	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749125	28883	PASS	G	C	18592	0.945138	3	0,1,9317,9251	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749125	28977	PASS	C	T	9427	0.931367	0	0,3,0,9406	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749125	29091	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	28734	4.52E-4	0	28720,0,13,0	HIGH	NONE	FRAME_SHIFT	N	ttc/	F274	N	0.000452	0.073908	3	1	CT>C
ERR5749125	29095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28734	0.001566	0	28676,0,47,0	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F274	N	0.000792	0.961279	2	2	C>T
ERR5749125	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	57131	0.001453	0	28647,28367,48,48	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749125	29675	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	22441	6.24E-4	0	11234,11198,7,7	.	.	.	.	.	.	.	0.000624	0.883495	2	1	CA>C
ERR5749125	29686	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22455	0.003117	0	11166,11170,42,40	.	.	.	.	.	.	.	0.001045	0.802514	2	1	C>T
ERR5749126	241	PASS	C	T	4333	0.860605	0	0,1,2154,2160	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749126	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	3129	0.003516	0	3120,0,11,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749126	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	3129	0.003196	0	3109,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749126	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	14171	7.76E-4	8	10977,3136,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749126	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	14171	8.47E-4	10	10977,3136,12,0	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749126	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTTGACTT	A	14171	0.00247	35	10977,3136,35,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcatttgactta/	KSFDL141	leader	0.000303	0.999303	4	1	AAAGTCATTTGACTT>A
ERR5749126	913	PASS	C	T	11030	0.908341	0	0,3,0,11005	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749126	1461	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	24798	9.27E-4	20	12219,12174,31,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K219R	nsp2	0.000518	0.90899	2	2	A>G
ERR5749126	1820	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	13125	0.001295	0	0,13095,0,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggt/Agt	G339S	nsp2	0.001189	0.949024	2	2	G>A
ERR5749126	3037	PASS	C	T	7012	0.813748	3	0,1,3505,3456	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749126	3267	PASS	C	T	11270	0.96992	0	1,0,11261,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749126	3466	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	11272	9.76E-4	0	1,11260,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	gga/	G250	nsp3	0.000976	0.051008	3	3	TG>T
ERR5749126	4237	PASS	T	C	15741	0.911569	1	3,4,7903,7794	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaT/aaC	N506	nsp3	0.000302	0.918634	2	2	T>C
ERR5749126	4255	PASS	G	A	15779	0.828063	27	13,1,7849,7820	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccG/ccA	P512	nsp3	0.001102	0.871853	2	1	G>A
ERR5749126	4529	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTTTAC	T	9035	9.96E-4	0	0,9026,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	tacttt/	YF605	nsp3	0.000527	0.402778	3	1	TTTTAC>T
ERR5749126	5170	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9563	0.001569	0	0,9538,0,17	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y817	nsp3	0.000565	0.894036	2	2	C>T
ERR5749126	5388	PASS	C	A	2685	0.962384	2147483647	0,0,2684,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749126	5575	PASS	C	T	2685	0.950466	2147483647	0,0,0,2682	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y952	nsp3	0.01018	0.961493	1	1	C>T
ERR5749126	5986	PASS	C	T	6623	0.971463	0	1,0,6618,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749126	6310	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14580	0.001509	0	14528,0,22,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	agC/agT	S1197	nsp3	0.00099	0.94715	2	2	C>T
ERR5749126	6414	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAGT	A	14576	5.49E-4	0	1,14567,0,8	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gtagtg/gtg	VV1233V	nsp3	0.000549	0.930413	2	2	AAGT>A
ERR5749126	6954	PASS	T	C	16176	0.82406	0	0,1,0,16110	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749126	7058	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTT	G	16222	6.16E-4	0	0,16212,0,10	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggttac/gac	GY1447D	nsp3	0.000616	0.910617	2	2	GGTT>G
ERR5749126	8964	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10012	0.001798	0	9991,0,18,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCa/tTa	S137L	nsp4	0.000553	0.981649	4	2	C>T
ERR5749126	8964	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	10012	7.99E-4	0	10004,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K138	nsp4	0.000553	0.981649	4	2	CA>C
ERR5749126	9928	PASS	G	T	5598	0.950518	0	9,0,5582,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atT	M458I	nsp4	0.006785	0.950518	1	1	G>T
ERR5749126	10502	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTTAACATAGATTATGACTGTGTCTCTTTTTGTTA	T	14118	9.92E-4	0	14104,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tttaacatagattatgactgtgtctctttttgttac/	FNIDYDCVSFCY150	3Cpro	0.000992	0.998494	3	2	TTTAACATAGATTATGACTGTGTCTCTTTTTGTTA>T
ERR5749126	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21973	0.002002	0	21908,0,46,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749126	11199	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	43731	9.6E-4	0	21718,21840,23,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCc/gTc	A76V	nsp6	0.000309	0.056758	3	2	C>T
ERR5749126	11287	PASS	GTCTGGTTTT	G	21966	0.996859	0	0,68,0,21897	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749126	11507	PASS	G	A	11647	0.907873	0	1,1,5836,5774	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Att	V179I	nsp6	0.007744	0.914418	2	2	G>A
ERR5749126	12067	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	31424	0.001146	0	15662,15667,19,19	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atA	M75I	nsp7	0.001146	0.086511	2	1	G>A
ERR5749126	13384	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	13835	5.78E-4	0	13827,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggt/	G121	nsp10	0.000578	0.056161	3	3	CG>C
ERR5749126	13458	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13834	0.002747	0	13785,0,39,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCg/tTg	S6L	nsp11	0.001017	0.058608	4	2	C>T
ERR5749126	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27625	0.001484	0	13786,13754,23,24	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749126	14097	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	13047	6.13E-4	0	13014,25,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggt/	G220	RdRp	0.000613	0.981481	2	2	CG>C
ERR5749126	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	1971	0.00761	0	982,974,7,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749126	14408	PASS	C	T	1971	0.838153	0	0,0,976,965	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749126	14676	PASS	C	T	8564	0.760042	0	1,0,8530,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749126	14805	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	8565	0.001051	0	0,8556,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/	Y456	RdRp	0.001051	0.904964	2	2	CT>C
ERR5749126	15237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12691	0.00134	0	12670,4,17,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H599	RdRp	0.001014	0.955128	2	2	C>T
ERR5749126	15279	PASS	C	T	12686	0.896658	0	1,0,12672,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749126	15396	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	12670	0.001421	0	12,12640,0,18	HIGH	NONE	FRAME_SHIFT	ORF1ab	tataga/	YR653	RdRp	0.000524	0.116667	1	1	CTA>C
ERR5749126	15420	PASS	T	G	12676	0.908883	0	0,31,9,12630	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcG	A660	RdRp	0.908883	0.934773	1	1	T>G
ERR5749126	16176	PASS	T	C	11612	0.982174	0	0,0,3584,8026	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749126	16792	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CGT	C	31232	4.16E-4	28	12667,18552,0,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	gta/	V187	helicase	0.000335	0.072562	5	2	CGT>C
ERR5749126	17502	PASS	C	T	8815	0.9865	2147483647	0,0,8810,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F422	helicase	0.000611	0.9865	2	2	C>T
ERR5749126	17747	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTG	C	11602	0.001379	0	11586,0,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctgct/	PA504	helicase	0.000839	0.968462	2	2	CTG>C
ERR5749126	18501	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	17466	0.001031	0	36,17412,0,18	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K155	ExoN	0.000336	0.857143	4	2	CAA>C
ERR5749126	18504	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AGGACTTCCTT	A	17451	8.6E-4	0	15,17421,0,15	HIGH	NONE	FRAME_SHIFT	ORF1ab	cttccttggaat/	LPWN157	ExoN	0.000518	0.094148	4	3	AGGACTTCCTT>A
ERR5749126	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	20302	0.001034	0	20281,0,21,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749126	19011	PASS	C	T	18749	0.965972	0	21,0,18721,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D324	ExoN	0.000408	0.975746	4	2	C>T
ERR5749126	19079	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	18732	0.001121	0	18695,0,28,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gAa/gTa	E347V	ExoN	0.001121	0.967175	2	1	A>T
ERR5749126	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	18728	5.34E-4	0	0,18718,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749126	20262	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AG	A	26913	4.83E-4	0	26900,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gaa/	E215	endoR	0.000483	0.963481	2	2	AG>A
ERR5749126	20857	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	26056	6.91E-4	17	18034,8004,17,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/	V67	MethTr	0.000531	0.099366	2	2	GT>G
ERR5749126	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	18048	0.001773	0	0,18016,0,32	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TA>T
ERR5749126	21077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	18056	0.001218	0	8,18026,0,22	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K141	MethTr	0.000492	0.955529	4	2	CA>C
ERR5749126	21234	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	19062	4.72E-4	0	19059,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/Tgtt	V194C?	MethTr	0.000472	0.857572	5	2	C>CT
ERR5749126	21304	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	19050	0.001102	0	0,19005,0,31	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgc/Agc	R216S	MethTr	0.000411	0.605296	3	2	C>A
ERR5749126	21305	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	19050	0.001837	0	0,18997,0,38	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cGc/cAc	R216H	MethTr	0.000727	0.703943	1	1	G>A
ERR5749126	21361	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	19080	0.001101	0	7,19007,0,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Aat/Gat	N235D	MethTr	0.001101	0.958339	1	1	A>G
ERR5749126	21764	PASS	ATACATG	A	8837	0.997397	0	23,0,8814,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749126	21889	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTTA	T	8828	0.001586	0	0,8814,0,14	MODERATE	NONE	CODON_DELETION	S	tta/	L110	S	0.00091	0.065772	2	2	TTTA>T
ERR5749126	21990	PASS	TTTA	T	8846	0.998757	0	0,11,7,8828	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749126	22484	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	7072	0.007212	0	77,6901,0,89	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gta/Tta	V308L	S	0.003485	0.765485	2	1	G>T
ERR5749126	23063	PASS	A	T	7623	0.859898	0	0,3,0,7587	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749126	23170	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	20233	7.91E-4	67	12591,7626,0,16	HIGH	NONE	FRAME_SHIFT	S	aaa/	K537	S	0.000408	0.975449	3	2	CAA>C
ERR5749126	23271	PASS	C	A	12587	0.921904	0	3,0,12569,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749126	23403	PASS	A	G	12582	0.971229	0	0,2,0,12571	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749126	23604	PASS	C	A	8630	0.946582	0	7,0,8620,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749126	23709	PASS	C	T	8624	0.946545	0	0,2,0,8612	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749126	24127	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TTTTTG	15395	6.5E-4	26	7443,7952,0,10	HIGH	NONE	FRAME_SHIFT+STOP_GAINED	S	aac/TTTTGaac	N856F*?	S	0.000324	0.111888	4	1	T>TTTTTG
ERR5749126	24506	PASS	T	G	14032	0.975698	0	3,0,14026,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749126	24914	PASS	G	C	22982	0.96023	0	0,0,11449,11527	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749126	25469	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14822	0.001214	0	14791,0,18,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	tCa/tTa	S26L	orf3a	0.001214	0.959377	2	2	C>T
ERR5749126	25531	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATT	A	14820	8.77E-4	0	0,14807,0,13	HIGH	NONE	FRAME_SHIFT	ORF3a	att/	I47	orf3a	0.000473	0.975891	5	2	ATT>A
ERR5749126	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	5739	0.001568	0	5730,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749126	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	21352	5.62E-4	0	0,21340,0,12	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749126	26730	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	13730	0.001384	0	6841,6881,10,9	HIGH	NONE	FRAME_SHIFT	M	tac/	Y71	M	0.000371	0.919543	3	2	GT>G
ERR5749126	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	6914	0.001591	0	0,6903,0,11	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749126	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	6914	0.00188	0	0,6901,0,13	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749126	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	6914	0.003327	0	0,6888,0,23	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749126	27312	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	13394	0.001792	0	13370,0,24,0	HIGH	NONE	FRAME_SHIFT	ORF6	aat/aaAt	N39K?	orf6	0.000911	0.088458	4	2	T>TA
ERR5749126	27577	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAATTTGCTTTTGCTTGTCCTGACGGCGTAAAACACGTCTATCAGTT	C	17916	6.14E-4	0	17898,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF7a	caatttgcttttgcttgtcctgacggcgtaaaacacgtctatcagtta/	QFAFACPDGVKHVYQL62	orf7a	0.000614	0.952205	4	2	CAATTTGCTTTTGCTTGTCCTGACGGCGTAAAACACGTCTATCAGTT>C
ERR5749126	27765	PASS	C	T	17930	0.9657	0	0,1,0,17912	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7b	Ctt/Ttt	L4F	orf7b	0.00109	0.970449	1	1	C>T
ERR5749126	27972	PASS	C	T	3099	0.893191	0	0,0,3072,23	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749126	28048	PASS	G	T	3115	0.904013	0	0,3,0,3109	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749126	28111	PASS	A	G	23245	0.980254	2	5,1,20119,3116	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749126	28144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	23257	9.89E-4	11	20109,3118,24,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tTa/tCa	L84S	orf8	0.000989	0.980793	1	1	T>C
ERR5749126	28239	PASS	GTTGTT	G	20101	0.981195	0	376,0,19723,0	HIGH	NONE	FRAME_SHIFT	ORF8	gtttta/	VL117	orf8	0.000417	0.984998	9	2	GTTGTT>G
ERR5749126	28249	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	ATC	19812	0.00106	0	19788,0,21,0	HIGH	NONE	FRAME_SHIFT	ORF8	ttc/CTttc	F120L?	orf8	0.000443	0.063605	3	2	A>ATC
ERR5749126	28250	PASS	T	TCTG	19812	0.993085	0	117,0,19675,0	MODERATE	NONE	CODON_INSERTION	ORF8	ttc/CTGttc	F120LF	orf8	0.000494	0.993968	5	3	T>TCTG
ERR5749126	28253	PASS	CA	C	19812	0.994498	0	109,0,19703,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749126	28254	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	ATC	19812	8.08E-4	0	19794,0,16,0	HIGH	NONE	FRAME_SHIFT+STOP_LOST+SPLICE_SITE_REGION	ORF8	taa/tCTaa	*122S?	orf8	0.000541	0.914398	3	2	A>ATC
ERR5749126	28270	PASS	TA	T	37795	0.990528	704	339,19,19473,17964	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749126	28271	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AA	A	37795	0.001111	100	19766,17982,41,1	.	.	.	.	.	.	.	0.000482	0.924941	3	2	AA>A
ERR5749126	28280	PASS	G	C	37794	0.93581	538	210,3,19533,17960	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749126	28281	PASS	A	T	37794	0.929671	32	31,8,19737,17963	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749126	28282	PASS	T	A	37795	0.891308	545	231,7,19484,17968	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749126	28881	PASS	G	A	4400	0.784091	3	2,0,2185,2175	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749126	28882	PASS	G	A	4400	0.83	0	1,1,2198,2171	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749126	28883	PASS	G	C	4400	0.9375	0	0,0,2202,2193	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749126	28977	PASS	C	T	2236	0.941413	0	0,2,0,2231	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749126	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	29045	9.64E-4	1	14592,14400,19,16	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749127	241	PASS	C	T	6496	0.86407	3	0,2,3233,3240	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749127	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	10016	0.001597	0	10004,0,16,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749127	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	10017	0.001497	0	9995,1,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749127	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10012	0.001898	0	9247,1,712,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749127	556	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10023	0.001497	0	17,9988,0,15	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y97	leader	0.001497	0.173414	1	1	C>T
ERR5749127	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	26058	7.29E-4	0	16012,10027,12,7	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749127	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16016	0.001311	0	0,15977,0,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749127	913	PASS	C	T	16016	0.915335	0	0,9,0,15984	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749127	3037	PASS	C	T	14292	0.815421	39	0,13,7139,7027	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749127	3177	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	22108	0.001131	47	14869,7199,35,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cAt	P153H	nsp3	0.000773	0.96008	3	2	C>A
ERR5749127	3267	PASS	C	T	14905	0.970345	0	3,0,14898,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749127	5388	PASS	C	A	4705	0.962593	2147483647	0,0,4703,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749127	5986	PASS	C	T	9694	0.977718	0	1,0,9688,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749127	6762	PASS	C	T	26084	0.966761	0	2,1,17204,8861	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T1348I	nsp3	0.001474	0.966761	2	1	C>T
ERR5749127	6954	PASS	T	C	17142	0.822133	0	0,2,2,17070	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749127	8664	PASS	C	T	16332	0.956405	2147483647	0,0,16315,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T37I	nsp4	0.003182	0.985915	1	1	C>T
ERR5749127	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	20794	7.21E-4	31	12638,8141,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749127	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	17638	0.001701	0	17592,0,44,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749127	11287	PASS	GTCTGGTTTT	G	17635	0.998979	0	0,18,0,17617	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749127	11417	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	10947	0.00274	0	10910,0,33,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Ttt	V149F	nsp6	0.00274	0.951155	2	2	G>T
ERR5749127	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	27581	9.43E-4	0	16605,10934,16,10	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749127	12162	PASS	A	G	30259	0.972438	11	5,0,16343,13897	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cAg/cGg	Q24R	nsp8	0.000894	0.982497	1	1	A>G
ERR5749127	12269	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	16351	6.12E-4	0	16342,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aag/	K61	nsp8	0.000434	0.213333	2	1	GA>G
ERR5749127	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28137	0.001137	0	14051,14020,18,19	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749127	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	4773	0.003562	1464	4649,36,3,84	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749127	14408	PASS	C	T	9272	0.838654	4	1,3,4628,4575	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749127	14676	PASS	C	T	11114	0.826525	0	4,0,11092,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749127	15279	PASS	C	T	17817	0.895212	0	1,0,17788,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749127	16176	PASS	T	C	16966	0.982789	0	2,2,7559,9400	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749127	16939	PASS	T	C	15565	0.950337	0	1,0,15544,4	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Tta/Cta	L235	helicase	0.000959	0.959205	2	2	T>C
ERR5749127	17615	PASS	A	G	11760	0.912755	0	0,1,0,11728	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749127	18246	PASS	C	T	9744	0.961823	0	0,3,0,9737	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y69	ExoN	0.960724	0.984848	1	1	C>T
ERR5749127	18504	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	22101	9.05E-4	0	1,21796,0,276	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K155N	ExoN	0.000518	0.094148	4	3	A>C
ERR5749127	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	20529	7.79E-4	0	20513,0,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749127	19164	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20225	0.002571	0	0,20156,0,59	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D375	ExoN	0.000358	0.075732	4	2	C>T
ERR5749127	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19394	0.001805	0	19344,0,39,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749127	21764	PASS	ATACATG	A	10171	0.998525	0	15,0,10156,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749127	21990	PASS	TTTA	T	10179	0.998428	0	0,16,6,10157	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749127	23063	PASS	A	T	11332	0.8521	0	0,3,0,11263	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749127	23271	PASS	C	A	18036	0.925981	2147483647	0,0,18018,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749127	23403	PASS	A	G	18033	0.973881	0	0,6,0,18013	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749127	23604	PASS	C	A	12725	0.944047	0	9,0,12710,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749127	23709	PASS	C	T	12716	0.943693	0	0,3,0,12696	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749127	24506	PASS	T	G	16164	0.977481	0	3,0,16158,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749127	24914	PASS	G	C	31185	0.959532	0	0,1,15543,15611	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749127	25571	PASS	C	T	14219	0.922217	0	0,7,0,14196	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	tCc/tTc	S60F	orf3a	0.001558	0.922217	1	1	C>T
ERR5749127	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	15076	0.001857	437	14991,20,11,19	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749127	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	15082	7.29E-4	0	15071,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749127	25855	PASS	G	T	15105	0.902483	0	0,36,48,15009	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gac/Tac	D155Y	orf3a	0.001326	0.969697	1	1	G>T
ERR5749127	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	10100	9.9E-4	0	3,10085,0,10	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749127	27972	PASS	C	T	8341	0.900492	21	1,1,8283,26	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749127	28048	PASS	G	T	8310	0.912876	0	0,16,0,8292	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749127	28111	PASS	A	G	24298	0.979587	1	4,3,15964,8317	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749127	28270	PASS	TA	T	30766	0.995645	276	135,9,15790,14842	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749127	28280	PASS	G	C	30718	0.937398	9	8,2,15822,14827	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749127	28281	PASS	A	T	30718	0.914675	8	15,7,15820,14825	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749127	28282	PASS	T	A	30718	0.903151	0	14,12,15780,14833	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749127	28881	PASS	G	A	12461	0.772891	9	6,1,6180,6126	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749127	28882	PASS	G	A	12460	0.837881	18	7,0,6234,6101	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749127	28883	PASS	G	C	12459	0.944859	0	0,0,6240,6208	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749127	28977	PASS	C	T	6334	0.935428	0	0,1,2,6323	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749127	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	29085	8.94E-4	126	22744,6288,4,25	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749127	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	45176	0.001483	1	22689,22393,42,38	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749127	29386	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	7626	0.001574	0	7614,0,12,0	HIGH	NONE	FRAME_SHIFT	N	aag/aaAg	K373K?	N	0.000887	0.899197	4	2	C>CA
ERR5749128	241	PASS	C	T	2356	0.866299	0	0,0,1173,1174	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749128	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	5727	0.002968	0	5704,1,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749128	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	5730	0.002792	0	5275,9,413,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749128	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	5730	0.002094	0	5709,9,12,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749128	673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27183	9.93E-4	66	21427,5714,11,20	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y136	leader	0.000454	0.602236	3	2	C>T
ERR5749128	676	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27183	0.004083	569	21419,5611,17,112	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G137	leader	0.000799	0.919273	2	1	C>T
ERR5749128	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	27186	0.001104	0	21407,5737,23,7	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749128	823	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21436	0.001213	0	21386,8,29,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V6	nsp2	0.001213	0.901722	1	1	C>T
ERR5749128	913	PASS	C	T	21428	0.902231	0	0,13,0,21392	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749128	1510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	18097	0.003205	0	0,17848,0,66	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G235	nsp2	0.002159	0.937304	1	1	T>C
ERR5749128	1760	PASS	T	C	16172	0.969639	0	1,0,16153,5	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Ctc	F319L	nsp2	0.969639	0.969639	1	1	T>C
ERR5749128	1813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	16180	0.001236	0	0,16144,0,26	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcA	A336	nsp2	0.001022	0.152738	4	2	T>A
ERR5749128	2151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATTGGC	A	24850	6.04E-4	0	0,24825,0,15	HIGH	NONE	FRAME_SHIFT	ORF1ab	tggcttgaa/	WLE450	nsp2	0.000402	0.971954	3	2	ATTGGC>A
ERR5749128	2151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATTGGCTTGAAGAGAAG	A	24850	4.02E-4	0	0,24825,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	tggcttgaagagaagttt/	WLEEKF450	nsp2	0.000402	0.971954	3	2	ATTGGCTTGAAGAGAAG>A
ERR5749128	3037	PASS	C	T	11464	0.825454	18	0,6,5731,5643	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749128	3177	PASS	C	T	27030	0.908287	6	8,0,21208,5768	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P153L	nsp3	0.000773	0.96008	3	2	C>T
ERR5749128	3267	PASS	C	T	21247	0.97049	2147483647	0,0,21229,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749128	3802	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	21581	6.95E-4	3	11787,9779,10,5	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N363	nsp3	0.000554	0.064198	4	2	TA>T
ERR5749128	5388	PASS	C	A	3593	0.962149	2147483647	0,0,3591,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749128	5986	PASS	C	T	10181	0.975346	0	1,0,10170,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749128	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8594	0.002094	0	0,8463,0,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749128	6954	PASS	T	C	18341	0.813533	0	0,1,0,18246	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749128	6990	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	18400	5.98E-4	0	0,18389,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L1425	nsp3	0.000504	0.101156	4	2	CT>C
ERR5749128	8964	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	14521	6.89E-4	0	14510,1,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K138	nsp4	0.000553	0.981649	4	2	CA>C
ERR5749128	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	16233	0.00117	33	10622,5591,19,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749128	10138	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21337	0.001359	0	15474,5825,22,8	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N28	3Cpro	0.000458	0.983567	3	3	C>T
ERR5749128	11008	PASS	C	T	1419	0.955603	137	6,0,4,1408	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H12	nsp6	0.955603	0.955603	1	1	C>T
ERR5749128	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	11531	0.002688	0	11255,0,31,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749128	11287	PASS	GTCTGGTTTT	G	11525	0.996356	0	0,42,0,11483	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749128	12125	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	16109	0.001117	0	4,16030,0,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y12H	nsp8	0.000847	0.113436	1	1	T>C
ERR5749128	12459	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34027	0.001469	1	15208,18763,21,30	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T123I	nsp8	0.000658	0.986093	1	1	C>T
ERR5749128	12781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11774	0.001869	0	11744,0,23,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y32	nsp9	0.001869	0.974683	2	2	C>T
ERR5749128	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	33857	0.001388	1	16904,16857,25,28	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749128	14408	PASS	C	T	2964	0.849528	0	1,1,1479,1466	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749128	14676	PASS	C	T	12190	0.741591	0	5,0,12137,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749128	15279	PASS	C	T	16782	0.892325	0	2,0,16753,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749128	16176	PASS	T	C	14569	0.978928	0	0,0,4105,10453	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749128	16647	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	20641	9.2E-4	0	0,20482,0,20	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acG/acA	T137	helicase	0.000746	0.885245	2	1	G>A
ERR5749128	18032	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	19876	6.04E-4	51	7379,12485,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L600	helicase	0.000604	0.973948	2	2	CT>C
ERR5749128	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	20310	9.35E-4	0	20291,0,19,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749128	18747	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20308	0.002167	0	20236,0,51,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V236	ExoN	0.000375	0.982946	4	2	C>T
ERR5749128	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	25011	6.4E-4	0	9,24986,0,16	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749128	19343	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	15634	5.76E-4	0	15625,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F436	ExoN	0.000519	0.192257	7	2	CT>C
ERR5749128	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15820	0.004298	0	15744,0,70,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749128	21094	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGAGGGTTT	A	22586	5.76E-4	0	4,22569,0,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaagagggtttt/	KEGF146	MethTr	0.000554	0.211111	5	2	AAAGAGGGTTT>A
ERR5749128	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	27028	0.001147	0	13478,13522,15,16	HIGH	NONE	FRAME_SHIFT	S	ctt/Tctt	L5S?	S	0.000394	0.091869	4	1	G>GT
ERR5749128	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27010	0.001037	0	13226,13467,16,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749128	21764	PASS	ATACATG	A	11278	0.997429	0	29,0,11249,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749128	21990	PASS	TTTA	T	11284	0.997962	0	0,23,6,11255	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749128	22293	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	28342	6.35E-4	0	8547,19743,5,13	HIGH	NONE	FRAME_SHIFT	S	cat/	H245	S	0.000308	0.160511	4	1	TAC>T
ERR5749128	22293	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TACA	T	28342	8.47E-4	4	8547,19743,5,19	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	ttacat/ttt	LH244F	S	0.000308	0.160511	4	1	TACA>T
ERR5749128	22295	PASS	C	T	28342	0.930915	2	2,9,8541,19705	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Cat/Tat	H245Y	S	0.000662	0.930915	2	2	C>T
ERR5749128	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	15646	0.00147	0	0,15609,0,27	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749128	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27014	0.001036	3	11354,15613,10,19	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749128	23063	PASS	A	T	11353	0.868405	0	0,1,0,11303	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749128	23086	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11365	0.00176	0	0,11327,0,30	LOW	SILENT	SYNONYMOUS_CODING	S	taC/taT	Y508	S	0.00176	0.131707	2	2	C>T
ERR5749128	23271	PASS	C	A	23073	0.926017	2147483647	0,0,23043,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749128	23403	PASS	A	G	23057	0.968426	0	0,4,0,23036	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749128	23426	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTT	G	23076	6.07E-4	0	0,23062,0,14	HIGH	NONE	FRAME_SHIFT	S	gtt/	V622	S	0.000428	0.916192	4	2	GTT>G
ERR5749128	23604	PASS	C	A	12206	0.942323	0	9,0,12190,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749128	23709	PASS	C	T	12187	0.934685	0	0,4,0,12164	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749128	24506	PASS	T	G	15132	0.97383	0	5,0,15127,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749128	24914	PASS	G	C	32435	0.960105	0	0,1,16167,16246	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749128	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	23609	0.001948	78	16774,6771,56,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749128	25587	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	16959	8.26E-4	0	0,16943,0,14	HIGH	NONE	FRAME_SHIFT	ORF3a	aag/	K67	orf3a	0.000598	0.813206	6	2	CA>C
ERR5749128	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	8418	0.002495	433	8374,13,3,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749128	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	33038	3.63E-4	0	0,33020,0,12	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749128	26159	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTAATCCAG	T	33044	0.001483	0	0,32995,0,49	HIGH	NONE	FRAME_SHIFT	ORF3a	ccagtaatg/	PVM258	orf3a	0.000311	0.053032	2	2	TTAATCCAG>T
ERR5749128	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	10891	0.001194	0	0,10874,0,13	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749128	27684	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19176	0.001043	0	6,19119,0,22	LOW	SILENT	SYNONYMOUS_CODING	ORF7a	taC/taT	Y97	orf7a	0.000478	0.90411	2	2	C>T
ERR5749128	27972	PASS	C	T	7937	0.900592	0	1,0,7858,55	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749128	28048	PASS	G	T	7883	0.917417	0	0,9,0,7871	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749128	28111	PASS	A	G	27356	0.979456	3	4,3,19455,7886	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749128	28270	PASS	TA	T	37531	0.995257	354	175,12,19199,18154	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749128	28280	PASS	G	C	37459	0.934568	9	8,2,19229,18140	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749128	28281	PASS	A	T	37459	0.918044	36	30,7,19222,18149	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749128	28282	PASS	T	A	37460	0.910171	11	21,10,19187,18156	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749128	28370	PASS	A	T	19459	0.935248	0	0,3,0,19429	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Agt/Tgt	S33C	N	0.935248	0.946374	1	1	A>T
ERR5749128	28881	PASS	G	A	17340	0.766494	12	5,0,8628,8474	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749128	28882	PASS	G	A	17340	0.829066	2	3,1,8709,8470	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749128	28883	PASS	G	C	17340	0.945386	0	0,0,8719,8605	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749128	28977	PASS	C	T	8825	0.924193	0	0,1,0,8800	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749128	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	59116	0.001303	0	29709,29294,46,46	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749128	29386	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	10900	0.001193	0	10887,0,13,0	HIGH	NONE	FRAME_SHIFT	N	aag/aaAg	K373K?	N	0.000887	0.899197	4	2	C>CA
ERR5749129	219	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GATC	G	8707	0.001608	0	4335,4361,7,7	.	.	.	.	.	.	.	0.001608	0.789851	2	1	GATC>G
ERR5749129	222	PASS	C	T	8702	0.864859	0	1,1,4303,4336	.	.	.	.	.	.	.	0.002134	0.864859	1	1	C>T
ERR5749129	241	PASS	C	T	8694	0.862204	0	1,1,4306,4345	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749129	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	10490	0.003718	0	10452,2,39,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749129	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	10493	0.001144	0	10404,5,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749129	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	10493	0.00162	0	10404,5,17,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749129	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	10493	0.005146	0	10404,5,54,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749129	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10492	0.001811	0	9551,11,778,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749129	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	10492	0.001334	0	10467,11,14,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749129	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	10492	0.001048	0	10460,12,11,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749129	657	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10520	0.001711	0	6,10493,0,19	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A131V	leader	0.001202	0.365979	3	1	C>T
ERR5749129	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	26350	4.55E-4	8	15786,10495,10,2	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749129	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	26350	0.001708	1	15786,10495,26,19	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749129	913	PASS	C	T	15825	0.91406	0	0,11,0,15793	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749129	3037	PASS	C	T	18023	0.804084	47	1,19,8997,8855	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749129	3267	PASS	C	T	15268	0.969348	0	1,0,15261,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749129	5388	PASS	C	A	6510	0.958525	2147483647	0,0,6508,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749129	5730	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15617	0.001601	0	15578,0,26,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T1004I	nsp3	0.001601	0.721782	1	1	C>T
ERR5749129	5986	PASS	C	T	11316	0.975168	2147483647	0,0,11308,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749129	6954	PASS	T	C	16151	0.820259	0	0,3,0,16073	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749129	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	26220	0.001411	97	14224,11959,37,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749129	10681	PASS	C	T	13767	0.977192	702	23,2,0,13740	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y209	3Cpro	0.000888	0.977192	2	2	C>T
ERR5749129	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	15199	0.002369	0	14767,3,36,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749129	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15199	0.001974	0	15139,3,31,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749129	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	15189	0.001712	0	15140,0,38,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749129	11287	PASS	GTCTGGTTTT	G	15196	0.997039	0	0,43,0,15151	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749129	12880	PASS	C	T	13092	0.894516	0	3,0,13039,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I65	nsp9	0.004753	0.894516	2	2	C>T
ERR5749129	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24937	0.001764	0	12443,12412,26,27	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749129	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	14090	0.003265	2147483647	13794,105,7,180	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749129	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	27452	0.001275	0	13772,13662,18,17	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749129	14408	PASS	C	T	27452	0.849082	18	0,6,13720,13516	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749129	14676	PASS	C	T	9647	0.694413	0	6,0,9579,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749129	15279	PASS	C	T	17227	0.907064	0	2,0,17208,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749129	16176	PASS	T	C	17285	0.981255	6	0,2,9302,7969	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749129	16647	PASS	G	T	16618	0.885245	0	0,10,0,16555	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acG/acT	T137	helicase	0.000746	0.885245	2	1	G>T
ERR5749129	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	21313	7.51E-4	0	21297,0,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749129	19687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14462	0.001245	0	14431,0,20,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cca/Tca	P23S	endoR	0.001245	0.889118	2	1	C>T
ERR5749129	19961	PASS	C	T	111	0.927928	0	0,0,110,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aTg	T114M	endoR	0.008648	0.927928	1	1	C>T
ERR5749129	19983	PASS	C	T	111	0.981982	0	0,0,110,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749129	20233	PASS	C	T	20758	0.980008	0	3,0,20743,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ccc/Tcc	P205S	endoR	0.000964	0.980008	2	1	C>T
ERR5749129	21635	PASS	C	T	11590	0.832355	0	0,1041,2,10533	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ccc/Tcc	P25S	S	0.832355	0.832355	1	1	C>T
ERR5749129	21764	PASS	ATACATG	A	11189	0.995621	0	49,0,11140,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749129	21990	PASS	TTTA	T	11193	0.997409	0	0,29,0,11164	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749129	23063	PASS	A	T	11887	0.863296	0	0,2,0,11823	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749129	23271	PASS	C	A	16860	0.921767	0	6,0,16838,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749129	23403	PASS	A	G	16851	0.96831	0	0,2,0,16834	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749129	23604	PASS	C	A	13941	0.947278	0	3,0,13930,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749129	23709	PASS	C	T	13924	0.939816	0	0,7,2,13896	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749129	24506	PASS	T	G	14240	0.973947	0	7,0,14232,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749129	24914	PASS	G	C	31465	0.956841	0	1,1,15673,15763	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749129	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	17627	0.001418	283	17561,12,16,12	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749129	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	43216	4.17E-4	0	6,43190,0,18	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749129	26209	PASS	G	T	43289	0.234679	7	6,30608,0,12651	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gtg/Ttg	V273L	orf3a	0.000792	0.234679	3	1	G>T
ERR5749129	26526	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	7992	0.001752	0	4,7955,0,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Gca/Tca	A2S	M	0.001224	0.951192	3	1	G>T
ERR5749129	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	11239	9.79E-4	0	3,11217,0,11	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749129	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	11236	0.004094	0	0,11188,0,46	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749129	27972	PASS	C	T	10494	0.909186	0	1,0,10390,78	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749129	28048	PASS	G	T	10426	0.921446	0	0,18,0,10401	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749129	28111	PASS	A	G	23074	0.975254	2	1,2,12633,10429	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749129	28250	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TCTG	12637	0.001583	0	12614,4,20,0	MODERATE	NONE	CODON_INSERTION	ORF8	ttc/CTGttc	F120LF	orf8	0.000494	0.993968	5	3	T>TCTG
ERR5749129	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	12630	0.001742	0	12606,5,22,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749129	28270	PASS	TA	T	24423	0.994882	271	118,5,12464,11834	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749129	28280	PASS	G	C	24380	0.934947	9	8,2,12485,11812	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749129	28281	PASS	A	T	24380	0.910131	9	17,8,12479,11824	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749129	28282	PASS	T	A	24382	0.909072	4	17,11,12460,11825	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749129	28881	PASS	G	A	13345	0.779918	6	3,0,6628,6572	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749129	28882	PASS	G	A	13345	0.843087	9	6,1,6675,6544	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749129	28883	PASS	G	C	13345	0.939528	3	2,0,6690,6643	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749129	28977	PASS	C	T	6792	0.930801	0	0,4,1,6778	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749129	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	42194	9.48E-4	1	21195,20928,27,23	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749129	29679	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16766	0.001372	0	8357,8293,13,13	.	.	.	.	.	.	.	0.000443	0.838763	2	1	C>T
ERR5749130	241	PASS	C	T	6861	0.856143	2	1,2,3418,3400	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749130	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	6236	0.002886	0	6207,0,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749130	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	6241	0.001442	0	6221,11,9,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749130	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	20667	0.001935	37	14376,6246,38,2	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749130	913	PASS	C	T	14410	0.899514	0	0,9,0,14382	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749130	1573	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	15987	0.001376	423	0,15941,14,8	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acA/acG	T256	nsp2	0.001231	0.75	1	1	A>G
ERR5749130	3037	PASS	C	T	14518	0.804794	61	0,20,7267,7102	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749130	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	7347	0.002314	461	4,7321,17,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749130	3177	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	23311	9.87E-4	25	15958,7317,32,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cAt	P153H	nsp3	0.000773	0.96008	3	2	C>A
ERR5749130	3267	PASS	C	T	15991	0.970483	2147483647	0,0,15984,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749130	4237	PASS	T	C	28363	0.909495	0	1,1,14215,14094	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaT/aaC	N506	nsp3	0.000302	0.918634	2	2	T>C
ERR5749130	4255	PASS	G	A	28419	0.8267	30	21,4,14136,14095	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccG/ccA	P512	nsp3	0.001102	0.871853	2	1	G>A
ERR5749130	5388	PASS	C	A	4386	0.961468	2147483647	0,0,4384,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749130	5575	PASS	C	T	4389	0.952837	95	3,0,1,4385	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y952	nsp3	0.01018	0.961493	1	1	C>T
ERR5749130	5986	PASS	C	T	10599	0.97613	2147483647	0,0,10594,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749130	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10382	0.001445	0	5,10244,0,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749130	6954	PASS	T	C	18861	0.813584	0	0,6,5,18735	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749130	7070	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	27961	0.001252	89	9001,18914,34,10	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggc/Tgc	G1451C	nsp3	0.000698	0.101434	3	1	G>T
ERR5749130	11287	PASS	GTCTGGTTTT	G	18434	0.997776	0	0,41,0,18393	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749130	11507	PASS	G	A	20327	0.901068	4	4,1,10178,10077	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Att	V179I	nsp6	0.007744	0.914418	2	2	G>A
ERR5749130	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	5105	0.004897	1500	4971,43,2,86	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749130	14408	PASS	C	T	9896	0.836399	6	0,2,4948,4857	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749130	14676	PASS	C	T	9897	0.725573	0	8,0,9838,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749130	15246	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	14720	0.001495	486	14675,9,4,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttA/ttT	L602F	RdRp	0.001432	0.633333	1	1	A>T
ERR5749130	15279	PASS	C	T	14691	0.894017	0	1,0,14672,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749130	15420	PASS	T	G	14673	0.914946	0	0,34,0,14631	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcG	A660	RdRp	0.908883	0.934773	1	1	T>G
ERR5749130	16176	PASS	T	C	13839	0.977744	7	2,0,5644,8188	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749130	17502	PASS	C	T	12906	0.979777	2147483647	0,0,12896,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F422	helicase	0.000611	0.9865	2	2	C>T
ERR5749130	19011	PASS	C	T	21400	0.972383	0	2,0,21382,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D324	ExoN	0.000408	0.975746	4	2	C>T
ERR5749130	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	21374	7.95E-4	0	0,21357,0,17	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749130	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20018	0.001149	0	19975,0,24,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749130	21764	PASS	ATACATG	A	10801	0.997593	0	26,0,10775,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749130	21990	PASS	TTTA	T	10802	0.998519	0	0,16,1,10785	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749130	23063	PASS	A	T	11654	0.851725	0	0,1,0,11589	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749130	23271	PASS	C	A	16225	0.919877	0	1,0,16208,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749130	23403	PASS	A	G	16216	0.962815	0	0,4,0,16200	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749130	23604	PASS	C	A	12604	0.945097	0	8,0,12585,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749130	23709	PASS	C	T	12574	0.92564	0	0,3,0,12545	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749130	24506	PASS	T	G	14379	0.973503	0	5,0,14373,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749130	24914	PASS	G	C	28924	0.954467	0	0,1,14413,14483	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749130	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	20996	0.001476	40	15790,5169,35,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749130	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	11360	0.004313	0	11311,0,49,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749130	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	10352	9.66E-4	0	5,10337,0,10	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749130	27765	PASS	C	T	17568	0.961293	0	0,3,1,17548	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7b	Ctt/Ttt	L4F	orf7b	0.00109	0.970449	1	1	C>T
ERR5749130	27972	PASS	C	T	7906	0.907792	0	0,0,7841,46	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749130	28048	PASS	G	T	7863	0.916317	0	0,9,0,7844	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749130	28111	PASS	A	G	26517	0.978844	0	2,0,18642,7862	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749130	28239	PASS	GTTGTT	G	18600	0.983763	0	301,0,18298,0	HIGH	NONE	FRAME_SHIFT	ORF8	gtttta/	VL117	orf8	0.000417	0.984998	9	2	GTTGTT>G
ERR5749130	28249	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	ATC	18386	0.001033	0	18361,0,19,0	HIGH	NONE	FRAME_SHIFT	ORF8	ttc/CTttc	F120L?	orf8	0.000443	0.063605	3	2	A>ATC
ERR5749130	28250	PASS	T	TCTG	18386	0.991026	0	140,0,18221,0	MODERATE	NONE	CODON_INSERTION	ORF8	ttc/CTGttc	F120LF	orf8	0.000494	0.993968	5	3	T>TCTG
ERR5749130	28253	PASS	CA	C	18386	0.992766	0	133,0,18253,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749130	28270	PASS	TA	T	35350	0.9957	206	134,18,18252,16946	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749130	28271	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AA	A	35350	0.001471	145	18331,16964,52,0	.	.	.	.	.	.	.	0.000482	0.924941	3	2	AA>A
ERR5749130	28280	PASS	G	C	35355	0.940291	28	16,2,18331,16941	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749130	28281	PASS	A	T	35355	0.932768	35	40,12,18313,16939	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749130	28282	PASS	T	A	35359	0.906078	11	28,14,18303,16948	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749130	28881	PASS	G	A	9773	0.736724	0	1,0,4818,4784	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749130	28882	PASS	G	A	9773	0.827791	12	5,0,4895,4770	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749130	28883	PASS	G	C	9773	0.941778	6	0,2,4907,4856	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749130	28977	PASS	C	T	4980	0.921084	0	0,3,0,4965	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749130	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	49713	8.85E-4	1	24967,24673,29,26	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749130	29386	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	7883	0.001269	0	7873,0,10,0	HIGH	NONE	FRAME_SHIFT	N	aag/aaAg	K373K?	N	0.000887	0.899197	4	2	C>CA
ERR5749131	241	PASS	C	T	20961	0.863699	0	1,2,10432,10440	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749131	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	8106	0.00111	0	8099,0,9,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749131	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	8105	0.003208	0	8063,0,26,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749131	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	8104	0.001974	0	7472,4,568,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749131	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	8104	0.001604	0	8087,4,13,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749131	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	25502	7.06E-4	28	17359,8125,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749131	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	25502	0.001608	13	17341,8118,34,7	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749131	913	PASS	C	T	17371	0.917564	0	0,5,0,17335	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749131	3037	PASS	C	T	15664	0.83427	12	3,10,7815,7731	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749131	3267	PASS	C	T	16690	0.97166	0	3,0,16675,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749131	4586	PASS	C	T	11989	0.935691	0	0,4,0,11950	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L623	nsp3	0.001842	0.935691	2	2	C>T
ERR5749131	5388	PASS	C	A	4991	0.962733	0	1,0,4989,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749131	5986	PASS	C	T	10235	0.976258	0	2,0,10225,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749131	6659	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	9647	0.001866	0	9612,0,22,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Agt/Ggt	S1314G	nsp3	0.001866	0.056322	1	1	A>G
ERR5749131	6706	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9644	0.002592	0	7,9593,0,27	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N1329	nsp3	0.000687	0.883999	2	2	C>T
ERR5749131	6954	PASS	T	C	18599	0.833432	0	0,2,0,18501	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749131	8603	PASS	T	C	9602	0.970527	223	8,11,0,9572	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Ctc	F17L	nsp4	0.002607	0.974959	2	1	T>C
ERR5749131	10116	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18162	0.001266	14	13366,4763,23,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T21I	3Cpro	0.001266	0.952096	1	1	C>T
ERR5749131	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	13668	0.001536	0	13629,0,32,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749131	11287	PASS	GTCTGGTTTT	G	13667	0.998098	0	0,26,0,13641	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749131	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	7440	9.41E-4	0	7433,0,7,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749131	13208	PASS	A	C	14836	0.953357	25	4,18,7415,7393	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Aat/Cat	N62H	nsp10	0.000407	0.953357	4	2	A>C
ERR5749131	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23879	0.001089	0	11926,11892,14,14	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749131	13712	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	15177	0.001252	0	15148,0,22,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K91R	RdRp	0.001252	0.300156	1	1	A>G
ERR5749131	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	8530	0.003986	1797	8349,71,6,102	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749131	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	16630	8.42E-4	0	8340,8293,7,7	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749131	14408	PASS	C	T	16630	0.844077	4	1,3,8289,8202	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749131	14676	PASS	C	T	10774	0.78346	0	1,0,10748,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749131	15279	PASS	C	T	18711	0.887339	0	3,0,18679,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749131	16176	PASS	T	C	15354	0.980917	3	1,0,6926,8425	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749131	17615	PASS	A	G	11618	0.907041	0	0,0,2,11581	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749131	17894	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21373	0.00131	0	10620,10706,17,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A553V	helicase	0.00131	0.598574	1	1	C>T
ERR5749131	17906	PASS	A	G	10738	0.956975	0	0,1,1,10719	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAt/aGt	N557S	helicase	0.956975	0.956975	1	1	A>G
ERR5749131	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	17098	8.19E-4	0	17084,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749131	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24588	0.001952	0	24526,0,48,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749131	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22560	9.31E-4	0	22498,0,22,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749131	21255	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	45944	6.75E-4	0	23684,22211,18,16	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcG/gcA	A199	MethTr	0.000341	0.917425	4	2	G>A
ERR5749131	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27232	8.08E-4	0	13335,13591,13,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749131	21764	PASS	ATACATG	A	10198	0.996862	0	32,0,10166,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749131	21990	PASS	TTTA	T	10202	0.997255	0	0,28,3,10171	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749131	23063	PASS	A	T	8986	0.872023	0	0,3,0,8945	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749131	23271	PASS	C	A	18025	0.926879	0	1,0,18009,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749131	23403	PASS	A	G	18021	0.97292	0	0,4,0,17998	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749131	23533	PASS	C	T	12085	0.969797	0	4,0,12068,0	LOW	SILENT	SYNONYMOUS_CODING	S	aaC/aaT	N657	S	0.969797	0.969797	1	1	C>T
ERR5749131	23604	PASS	C	A	12084	0.951175	0	6,0,12072,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749131	23709	PASS	C	T	12067	0.931963	0	0,1,3,12040	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749131	23817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	27848	0.001005	5	15730,12069,21,10	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTt/cCt	L752P	S	0.000646	0.066832	1	1	T>C
ERR5749131	24506	PASS	T	G	14167	0.974236	0	10,0,14153,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749131	24914	PASS	G	C	24500	0.957265	0	0,1,12204,12282	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749131	25437	PASS	G	T	13696	0.966268	0	3,0,13665,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	ttG/ttT	L15F	orf3a	0.001128	0.971411	2	2	G>T
ERR5749131	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	22300	0.001345	247	22213,19,19,11	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749131	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	22266	6.74E-4	0	22251,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749131	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	42192	4.5E-4	0	0,42172,0,19	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749131	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	8928	0.00112	0	0,8918,0,10	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749131	27972	PASS	C	T	8986	0.907078	0	0,0,8918,42	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749131	28001	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	17870	0.001119	0	8910,8915,13,12	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ccG/ccA	P36	orf8	0.00085	0.830607	2	1	G>A
ERR5749131	28048	PASS	G	T	8947	0.930815	0	0,8,0,8935	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749131	28111	PASS	A	G	26857	0.975984	1	7,2,17888,8952	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749131	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	17883	5.59E-4	0	17876,1,10,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749131	28270	PASS	TA	T	34738	0.993955	602	220,2,17607,16921	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749131	28280	PASS	G	C	34654	0.936948	37	22,3,17665,16907	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749131	28281	PASS	A	T	34654	0.878715	30	25,6,17641,16905	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749131	28282	PASS	T	A	34660	0.929025	5	20,13,17656,16911	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749131	28310	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17900	0.001341	0	9,17853,0,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Ccc/Tcc	P13S	N	0.00095	0.92832	2	1	C>T
ERR5749131	28881	PASS	G	A	12791	0.756235	9	4,0,6301,6292	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749131	28882	PASS	G	A	12791	0.830115	9	4,0,6388,6300	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749131	28883	PASS	G	C	12791	0.941287	0	0,0,6407,6372	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749131	28977	PASS	C	T	6510	0.922427	0	0,2,0,6497	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749131	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	39027	0.001102	0	19605,19366,26,25	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749132	232	PASS	T	C	87	0.183908	0	35,34,8,9	.	.	.	.	.	.	.	0.183908	0.183908	1	1	T>C
ERR5749132	241	PASS	C	T	87	0.850575	0	0,0,44,42	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749132	913	PASS	C	T	683	0.896047	2147483647	0,0,0,681	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749132	1492	PASS	T	G	451	0.321508	0	0,298,0,153	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tgT/tgG	C229W	nsp2	0.000868	0.321508	3	3	T>G
ERR5749132	2453	PASS	C	T	98	0.734694	2147483647	0,0,0,97	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L550F	nsp2	0.00429	0.842201	2	2	C>T
ERR5749132	3037	PASS	C	T	95	0.768421	0	0,0,45,46	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749132	3267	PASS	C	T	485	0.958763	0	1,0,484,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749132	5388	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	8	1.0	2147483647	0,0,8,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749132	5986	PASS	C	T	129	0.976744	2147483647	0,0,128,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749132	6091	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	127	0.031496	0	0,122,0,5	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaC/aaA	N1124K	nsp3	0.002493	0.918485	2	2	C>A
ERR5749132	6568	PASS	C	T	276	0.974638	2147483647	0,0,276,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D1283	nsp3	0.000975	0.974638	3	3	C>T
ERR5749132	6954	PASS	T	C	282	0.812057	2147483647	0,0,0,281	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749132	7771	PASS	T	C	26	1.0	2147483647	0,0,26,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caT/caC	H1684	nsp3	0.001343	1	2	2	T>C
ERR5749132	11020	PASS	C	T	33	1.0	2147483647	0,0,0,33	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ctC/ctT	L16	nsp6	0.00116	1	1	1	C>T
ERR5749132	12125	PASS	T	C	2724	0.113436	0	0,2396,0,323	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y12H	nsp8	0.000847	0.113436	1	1	T>C
ERR5749132	12893	PASS	G	C	310	0.177419	0	255,0,55,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Caa	E70Q	nsp9	0.177419	0.177419	1	1	G>C
ERR5749132	13384	PASS	CG	C	1193	0.056161	0	1126,0,67,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggt/	G121	nsp10	0.000578	0.056161	3	3	CG>C
ERR5749132	14408	PASS	C	T	1066	0.839587	0	0,0,534,522	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749132	14676	PASS	C	T	592	0.809122	2147483647	0,0,590,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749132	15107	PASS	C	A	165	0.078788	0	0,148,0,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCc/aAc	T556N	RdRp	0.003531	0.078788	2	1	C>A
ERR5749132	15279	PASS	C	T	396	0.906566	2147483647	0,0,395,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749132	15620	PASS	T	C	1095	0.088584	0	988,0,100,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cTt/cCt	L727P	RdRp	0.001388	0.088584	1	1	T>C
ERR5749132	15802	PASS	T	C	1096	0.092153	0	0,990,0,106	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y788H	RdRp	0.092153	0.092153	1	1	T>C
ERR5749132	15951	PASS	C	T	410	0.334146	0	266,0,144,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I837	RdRp	0.027848	0.334146	1	1	C>T
ERR5749132	16176	PASS	T	C	538	0.973978	0	0,0,128,410	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749132	16974	PASS	T	G	757	0.055482	0	0,707,0,50	HIGH	NONSENSE	STOP_GAINED	ORF1ab	taT/taG	Y246*	helicase	0.000586	0.055482	2	2	T>G
ERR5749132	17356	PASS	GATGAAATT	G	263	0.057034	0	0,248,0,15	HIGH	NONE	FRAME_SHIFT	ORF1ab	gatgaaatt/	DEI374	helicase	0.00087	0.057034	1	1	GATGAAATT>G
ERR5749132	18803	PASS	G	T	10021	0.897116	5	6,2,4997,4995	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aGc/aTc	S255I	ExoN	0.000786	0.897116	2	1	G>T
ERR5749132	21604	PASS	G	T	404	0.878713	0	0,1,0,403	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	caG/caT	Q14H	S	0.00775	0.878713	1	1	G>T
ERR5749132	21764	PASS	ATACATG	A	412	1.0	2147483647	0,0,412,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749132	21783	PASS	A	T	412	0.145631	0	345,0,67,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aAt/aTt	N74I	S	0.145631	0.145631	1	1	A>T
ERR5749132	21990	PASS	TTTA	T	412	0.997573	0	0,1,0,411	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749132	22187	PASS	C	T	1333	0.054014	0	0,1254,0,79	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Cct/Tct	P209S	S	0.054014	0.054014	1	1	C>T
ERR5749132	22776	PASS	A	G	1317	0.1959	0	0,1050,0,265	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D405G	S	0.000652	0.1959	2	2	A>G
ERR5749132	23063	PASS	A	T	92	0.836957	2147483647	0,0,0,92	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749132	23271	PASS	C	A	2266	0.914828	2147483647	0,0,2265,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749132	23403	PASS	A	G	2265	0.965121	2147483647	0,0,0,2264	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749132	23604	PASS	C	A	61	0.967213	2147483647	0,0,61,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749132	23709	PASS	C	T	61	1.0	2147483647	0,0,0,61	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749132	24506	PASS	T	G	617	0.972447	2147483647	0,0,617,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749132	24914	PASS	G	C	7104	0.958474	0	0,0,3549,3551	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749132	27881	PASS	C	A	48	0.979167	2147483647	0,0,48,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7b	caC/caA	H42Q	orf7b	0.001798	0.979167	2	2	C>A
ERR5749132	27972	PASS	C	T	48	0.958333	2147483647	0,0,48,0	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749132	28048	PASS	G	T	48	0.979167	2147483647	0,0,0,48	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749132	28111	PASS	A	G	54	0.981481	0	0,0,6,48	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749132	28270	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	9	1.0	0	0,0,6,3	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749132	28280	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	9	0.666667	0	0,0,6,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749132	28281	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	9	0.888889	0	0,0,6,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749132	28282	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	10	0.8	3	0,1,6,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749132	28881	PASS	G	A	347	0.78098	0	0,0,174,170	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749132	28882	PASS	G	A	347	0.804035	0	0,0,176,165	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749132	28883	PASS	G	C	347	0.936599	0	0,0,176,171	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749132	28977	PASS	C	T	178	0.91573	0	0,1,0,177	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749132	29091	PASS	C	CT	893	0.073908	0	827,0,66,0	HIGH	NONE	FRAME_SHIFT	N	ttc/ttTc	F274F?	N	0.000452	0.073908	3	1	C>CT
ERR5749133	241	PASS	C	T	5841	0.872967	3	0,2,2901,2918	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749133	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	8002	0.005749	0	7955,0,46,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749133	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	8002	0.003124	0	7915,0,25,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749133	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	8002	0.006998	0	7915,0,56,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749133	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	7999	0.00175	0	7270,7,558,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749133	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	7999	0.002125	0	7975,7,17,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749133	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	8000	0.001125	0	7976,8,9,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749133	656	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	8018	0.00237	0	0,7995,0,19	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gct/Cct	A131P	leader	0.001202	0.131429	1	1	G>C
ERR5749133	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25853	8.9E-4	11	17810,8000,20,3	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L140	leader	0.000316	0.135802	3	2	C>T
ERR5749133	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	25853	5.03E-4	1	17752,7992,10,3	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749133	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	25853	0.003443	6	17752,7992,67,22	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749133	913	PASS	C	T	17840	0.91435	0	0,16,0,17789	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749133	2453	PASS	C	T	10651	0.729697	0	0,9,3,10479	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L550F	nsp2	0.00429	0.842201	2	2	C>T
ERR5749133	2509	PASS	C	T	10676	0.94305	337	10,0,0,10653	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P568	nsp2	0.001408	0.949382	1	1	C>T
ERR5749133	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	16411	0.002255	0	10,15379,0,996	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749133	3037	PASS	C	T	11713	0.815589	15	0,5,5850,5762	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749133	3267	PASS	C	T	17961	0.970937	2147483647	0,0,17951,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749133	4529	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTTTAC	T	12338	6.48E-4	0	7,12319,0,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	tacttt/	YF605	nsp3	0.000527	0.402778	3	1	TTTTAC>T
ERR5749133	5388	PASS	C	A	3924	0.965596	0	2,0,3920,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749133	5986	PASS	C	T	9440	0.97447	0	1,0,9431,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749133	6516	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	29224	6.16E-4	27	9107,20099,0,18	HIGH	NONE	FRAME_SHIFT	ORF1ab	att/aAtt	I1268N?	nsp3	0.000479	0.186047	4	2	T>TA
ERR5749133	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	9078	0.003635	0	1,9043,0,33	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L1328S?	nsp3	0.000731	0.14377	4	2	C>CT
ERR5749133	6954	PASS	T	C	18576	0.817722	0	0,7,0,18461	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749133	7070	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	27803	0.002698	371	9089,18622,77,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggc/Agc	G1451S	nsp3	0.000698	0.101434	3	1	G>A
ERR5749133	7600	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13623	0.001321	0	0,13591,0,19	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C1627	nsp3	0.001321	0.973632	1	1	C>T
ERR5749133	8964	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	12789	7.82E-4	0	12776,3,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K138	nsp4	0.000553	0.981649	4	2	CA>C
ERR5749133	9198	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	12788	9.38E-4	0	0,12776,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F216	nsp4	0.000543	0.93476	4	2	CT>C
ERR5749133	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	18534	0.001133	39	11594,6919,21,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749133	10060	PASS	T	C	6089	0.932994	2147483647	0,0,0,6082	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G2	3Cpro	0.932994	0.932994	1	1	T>C
ERR5749133	10156	PASS	C	T	14734	0.940953	65	6,2,14721,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D34	3Cpro	0.001207	0.949463	1	1	C>T
ERR5749133	10969	PASS	C	T	9461	0.921996	0	0,1,0,9451	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F305	3Cpro	0.004039	0.921996	1	1	C>T
ERR5749133	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	19905	0.001909	0	19844,0,57,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749133	11104	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	19896	0.001659	0	19779,0,33,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccT/ccC	P44	nsp6	0.000866	0.675414	2	1	T>C
ERR5749133	11287	PASS	GTCTGGTTTT	G	19903	0.996533	0	0,67,0,19834	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749133	11830	PASS	A	G	20556	0.969936	0	0,2,0,20531	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtA/gtG	V286	nsp6	0.001792	0.969936	1	1	A>G
ERR5749133	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	11248	9.78E-4	0	11237,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749133	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	31135	0.00106	0	15555,15506,18,17	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749133	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	11441	0.002972	2406	11188,105,7,138	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749133	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	22270	0.001796	0	11167,11079,20,20	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749133	14408	PASS	C	T	22270	0.843916	1	4,5,11106,10956	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749133	14676	PASS	C	T	11685	0.746256	0	4,0,11633,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749133	15279	PASS	C	T	16851	0.900243	0	3,0,16826,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749133	15720	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14398	0.00132	0	4,14358,0,22	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D760	RdRp	0.001002	0.917823	1	1	C>T
ERR5749133	16176	PASS	T	C	15888	0.980866	0	0,0,5915,9967	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749133	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	16213	0.001295	0	16184,0,21,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749133	18131	PASS	C	T	8479	0.853992	0	2,0,8447,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T31I	ExoN	0.0025	0.853992	1	1	C>T
ERR5749133	18501	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	24647	4.46E-4	0	0,24636,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K155	ExoN	0.000336	0.857143	4	2	CA>C
ERR5749133	18877	PASS	C	T	21593	0.953596	0	0,4,0,21573	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L280	ExoN	0.000848	0.953596	2	2	C>T
ERR5749133	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	19840	0.001008	0	0,19814,0,20	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TA>T
ERR5749133	21077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19847	0.004081	0	3,19739,0,85	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T140I	MethTr	0.000492	0.955529	4	2	C>T
ERR5749133	21123	PASS	G	T	40297	0.90982	5	15,9,20420,19816	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggG/ggT	G155	MethTr	0.000257	0.90982	5	2	G>T
ERR5749133	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	27744	6.49E-4	0	13847,13881,8,10	HIGH	NONE	FRAME_SHIFT	S	ctt/Tctt	L5S?	S	0.000394	0.091869	4	1	G>GT
ERR5749133	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27713	0.002093	1	13563,13779,33,37	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749133	21764	PASS	ATACATG	A	9865	0.954486	0	424,0,9416,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749133	21764	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATACAT	A	9865	0.002027	0	424,0,20,0	HIGH	NONE	FRAME_SHIFT	S	atacat/	IH68	S	0.001908	1	3	1	ATACAT>A
ERR5749133	21772	PASS	C	T	9865	0.869843	0	1,0,9433,0	LOW	SILENT	SYNONYMOUS_CODING	S	gtC/gtT	V70	S	0.011355	0.869843	1	1	C>T
ERR5749133	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	9865	8.11E-4	0	9857,0,8,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749133	21990	PASS	TTTA	T	9869	0.995947	0	0,40,2,9827	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749133	23063	PASS	A	T	11557	0.86917	0	0,3,2,11500	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749133	23191	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	20432	5.38E-4	0	20419,2,11,0	HIGH	NONE	FRAME_SHIFT	S	aat/	N544	S	0.000538	0.973337	2	2	CA>C
ERR5749133	23271	PASS	C	A	20432	0.925411	0	3,0,20399,5	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749133	23403	PASS	A	G	20412	0.968744	0	0,4,0,20388	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749133	23604	PASS	C	A	11975	0.949228	0	15,0,11953,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749133	23709	PASS	C	T	11959	0.942721	0	0,3,3,11942	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749133	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	24319	8.22E-4	0	12333,11966,10,10	HIGH	NONE	FRAME_SHIFT	S	ttg/	L753	S	0.000334	0.080808	2	2	CT>C
ERR5749133	24127	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TTTTTG	22355	4.92E-4	27	10023,12332,0,11	HIGH	NONE	FRAME_SHIFT+STOP_GAINED	S	aac/TTTTGaac	N856F*?	S	0.000324	0.111888	4	1	T>TTTTTG
ERR5749133	24506	PASS	T	G	15667	0.973001	0	5,0,15660,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749133	24914	PASS	G	C	32308	0.958246	0	1,1,16091,16182	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749133	26065	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	29968	0.002269	0	29883,0,77,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gtt/Att	V225I	orf3a	0.001242	0.906322	2	1	G>A
ERR5749133	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	29912	7.35E-4	0	0,29887,0,22	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749133	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	10041	0.001593	0	0,10017,0,16	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749133	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	10041	0.001195	0	0,10029,0,12	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749133	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	10041	0.004482	0	0,9994,0,45	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749133	27972	PASS	C	T	7800	0.901795	56	1,3,7706,62	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749133	28048	PASS	G	T	7745	0.910136	0	0,13,0,7727	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749133	28111	PASS	A	G	25642	0.97976	0	4,2,17880,7747	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749133	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17890	0.001956	0	17796,11,39,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749133	28270	PASS	TA	T	34501	0.994348	504	198,4,17616,16690	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749133	28280	PASS	G	C	34410	0.937315	7	10,4,17656,16658	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749133	28281	PASS	A	T	34410	0.913601	25	21,5,17653,16666	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749133	28282	PASS	T	A	34413	0.906547	6	22,14,17598,16680	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749133	28292	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	35556	5.06E-4	0	17703,17830,9,9	HIGH	NONE	FRAME_SHIFT	N	aat/	N8	N	0.000304	0.055324	4	2	CA>C
ERR5749133	28881	PASS	G	A	5927	0.769698	3	1,0,2919,2945	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749133	28882	PASS	G	A	5927	0.833305	0	0,0,2947,2925	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749133	28883	PASS	G	C	5927	0.94078	0	0,0,2950,2973	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749133	28977	PASS	C	T	2978	0.93452	2147483647	0,0,0,2975	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749133	29095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25453	0.001179	0	25407,0,31,0	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F274	N	0.000792	0.961279	2	2	C>T
ERR5749133	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	50588	0.001483	0	25383,25106,44,43	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749134	241	PASS	C	T	15302	0.870148	11	1,7,7607,7624	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749134	478	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	8765	7.99E-4	0	8759,0,7,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K72	leader	0.000799	0.109934	2	2	CA>C
ERR5749134	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	8747	0.001143	0	8742,0,10,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749134	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	8748	0.003086	0	8713,1,27,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749134	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	8746	0.001143	0	8730,4,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749134	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	32445	4.62E-4	17	23661,8766,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749134	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	32444	8.01E-4	15	23646,8765,24,2	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749134	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23662	0.001268	0	0,23610,0,34	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749134	913	PASS	C	T	23662	0.913448	0	0,12,0,23609	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749134	1510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	22403	0.002767	0	2,22126,0,70	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G235	nsp2	0.002159	0.937304	1	1	T>C
ERR5749134	1813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	19418	0.001184	0	0,19361,0,31	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcA	A336	nsp2	0.001022	0.152738	4	2	T>A
ERR5749134	1955	PASS	A	G	25219	0.980531	178	4,5,25201,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Aag/Gag	K384E	nsp2	0.980531	0.980531	1	1	A>G
ERR5749134	3037	PASS	C	T	19255	0.814022	45	0,15,9627,9464	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749134	3267	PASS	C	T	23394	0.97183	0	1,0,23387,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749134	4754	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15665	0.001787	0	15630,0,29,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cct/Tct	P679S	nsp3	0.001054	0.947507	1	1	C>T
ERR5749134	5144	PASS	C	T	23576	0.822022	41	1,17,11764,11601	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L809	nsp3	0.000909	0.822022	1	1	C>T
ERR5749134	5388	PASS	C	A	6116	0.961086	2147483647	0,0,6112,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749134	5986	PASS	C	T	13634	0.977409	0	2,0,13626,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749134	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12840	0.001324	0	4,12677,0,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749134	6954	PASS	T	C	24331	0.792692	0	0,3,1,24186	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749134	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	31365	7.33E-4	70	15461,15881,23,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749134	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	21720	0.001289	0	21666,0,39,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749134	11287	PASS	GTCTGGTTTT	G	21717	0.997698	0	0,50,0,21667	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749134	12357	PASS	C	T	27503	0.94706	0	0,7,0,27474	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T89I	nsp8	0.000909	0.956941	3	2	C>T
ERR5749134	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	18706	0.001283	0	18662,0,24,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749134	12865	PASS	T	C	15339	0.98494	0	6,0,15327,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaT/gaC	D60	nsp9	0.001515	0.98494	1	1	T>C
ERR5749134	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34831	0.002239	0	17377,17327,42,44	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749134	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	9115	0.004937	2641	8854,89,7,158	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749134	14408	PASS	C	T	17640	0.844955	4	1,3,8813,8696	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749134	14676	PASS	C	T	13934	0.822449	0	7,0,13897,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749134	15096	PASS	T	C	19523	0.965989	0	0,6,12,19497	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaT/aaC	N552	RdRp	0.941667	0.970182	1	1	T>C
ERR5749134	15279	PASS	C	T	22355	0.93062	0	2,0,22334,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749134	16176	PASS	T	C	19146	0.980309	0	7,8,8158,10964	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749134	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	27517	6.54E-4	0	1,27498,0,18	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749134	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	31841	0.002136	0	31752,0,69,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749134	21304	PASS	C	A	32389	0.108864	8	0,27692,1,4682	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgc/Agc	R216S	MethTr	0.000411	0.605296	3	2	C>A
ERR5749134	21305	PASS	G	A	32389	0.128037	8	0,27620,1,4718	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cGc/cAc	R216H	MethTr	0.000727	0.703943	1	1	G>A
ERR5749134	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	38769	0.002425	0	18939,19324,51,53	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749134	21764	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATACATG	A	7	1.0	2147483647	0,0,7,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749134	21990	PASS	TTTA	T	12770	0.99906	0	0,12,6,12752	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749134	22014	PASS	G	T	23128	0.161449	0	19023,3,4102,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aGt/aTt	S151I	S	0.001357	0.20398	2	1	G>T
ERR5749134	23063	PASS	A	T	14095	0.869528	0	0,6,0,14024	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749134	23271	PASS	C	A	24019	0.919272	0	1,0,23988,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749134	23403	PASS	A	G	24016	0.966148	0	0,7,0,23989	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749134	23604	PASS	C	A	15954	0.949668	0	8,0,15938,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749134	23709	PASS	C	T	15936	0.941579	0	0,4,4,15904	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749134	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	34958	3.72E-4	5	18995,15950,5,8	HIGH	NONE	FRAME_SHIFT	S	ttg/	L753	S	0.000334	0.080808	2	2	CT>C
ERR5749134	24506	PASS	T	G	18521	0.975541	0	5,0,18513,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749134	24914	PASS	G	C	33233	0.954954	0	1,1,16551,16653	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749134	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	25961	0.001194	52	18866,7048,39,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749134	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	23933	0.001462	243	23828,33,24,12	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749134	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	23886	5.02E-4	0	23874,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749134	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	24035	0.001331	1348	23659,120,139,93	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749134	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	12638	0.001108	0	3,12620,0,14	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749134	27972	PASS	C	T	11774	0.909292	18	2,1,11669,57	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749134	28048	PASS	G	T	11709	0.920489	0	0,13,0,11691	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749134	28095	PASS	A	T	11724	0.96247	201	6,2,0,11708	HIGH	NONSENSE	STOP_GAINED	ORF8	Aaa/Taa	K68*	orf8	0.002672	0.967672	2	2	A>T
ERR5749134	28111	PASS	A	G	31692	0.978543	1	3,3,19961,11714	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749134	28270	PASS	TA	T	38700	0.995607	391	161,5,19742,18788	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749134	28280	PASS	G	C	38642	0.935795	21	13,2,19773,18779	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749134	28281	PASS	A	T	38642	0.914368	30	25,6,19765,18769	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749134	28282	PASS	T	A	38643	0.90878	16	30,13,19716,18783	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749134	28871	PASS	G	T	20555	0.78881	32	82,127,10406,9883	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Ggc/Tgc	G200C	N	0.78881	0.78881	1	1	G>T
ERR5749134	28881	PASS	G	A	20437	0.767089	14	10,2,10226,9960	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749134	28882	PASS	G	A	20437	0.835005	9	4,0,10355,9895	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749134	28883	PASS	G	C	20437	0.94373	3	0,1,10372,10047	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749134	28977	PASS	C	T	10555	0.928944	0	0,2,0,10538	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749134	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	41878	0.001504	257	31290,10489,9,59	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749134	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	62196	0.001254	0	31237,30844,47,47	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749134	29348	PASS	G	T	42612	0.968413	13	4,2,11285,31314	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gca/Tca	A359S	N	0.000865	0.968413	2	1	G>T
ERR5749135	241	PASS	C	T	7734	0.854409	1	2,4,3847,3851	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749135	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	10989	8.19E-4	0	10975,7,9,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749135	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	10989	9.1E-4	0	10929,7,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749135	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	10989	7.28E-4	0	10929,7,8,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749135	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	10989	0.002821	0	10929,7,31,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749135	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10987	0.002002	0	10167,11,731,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749135	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	10987	0.001638	0	10958,11,18,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749135	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	10985	0.002094	166	10954,4,16,7	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749135	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	26080	9.2E-4	56	15048,11007,24,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749135	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	26080	0.001074	7	15051,10998,20,8	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749135	913	PASS	C	T	15067	0.908874	0	0,10,0,15027	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749135	1813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	16209	0.001234	0	0,16169,0,27	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcA	A336	nsp2	0.001022	0.152738	4	2	T>A
ERR5749135	3037	PASS	C	T	14571	0.807357	28	3,17,7275,7152	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749135	3177	PASS	C	T	22296	0.89146	1	6,4,14931,7317	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P153L	nsp3	0.000773	0.96008	3	2	C>T
ERR5749135	3267	PASS	C	T	14960	0.968449	2147483647	0,0,14953,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749135	4668	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14146	0.002686	0	14100,2,40,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S650F	nsp3	0.002266	0.970109	2	1	C>T
ERR5749135	5388	PASS	C	A	4106	0.953726	2147483647	0,0,4104,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749135	5986	PASS	C	T	10482	0.971666	2147483647	0,0,10477,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749135	6954	PASS	T	C	19848	0.820486	0	0,6,0,19756	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749135	7067	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	34853	0.008694	956	14569,19905,307,12	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E1450K	nsp3	0.000274	0.059217	5	3	G>A
ERR5749135	7067	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	34853	0.001033	132	14892,19924,36,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gaa/	E1450	nsp3	0.000274	0.059217	5	3	GA>G
ERR5749135	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	20530	7.79E-4	29	13288,7226,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749135	10077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	6390	0.002191	269	1,6346,10,5	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTc/tCc	F8S	3Cpro	0.001833	0.454545	1	1	T>C
ERR5749135	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	19129	0.002666	0	18587,1,51,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749135	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19129	0.001307	0	19076,1,29,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749135	11082	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	19116	5.23E-4	0	19117,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000427	0.179468	2	1	TG>T
ERR5749135	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	19116	0.001674	0	19048,0,49,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749135	11287	PASS	GTCTGGTTTT	G	19117	0.997751	0	0,42,0,19074	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749135	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27771	8.64E-4	0	13878,13830,14,15	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749135	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	6077	0.00543	1698	5914,57,4,100	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749135	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	11777	7.64E-4	0	5909,5870,5,4	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749135	14408	PASS	C	T	11777	0.840282	6	0,2,5880,5799	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749135	14676	PASS	C	T	10267	0.82546	0	2,0,10243,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749135	15279	PASS	C	T	17175	0.87377	0	1,0,17145,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749135	16176	PASS	T	C	17513	0.981271	3	1,0,7991,9511	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749135	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	21984	6.82E-4	0	21969,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749135	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21723	0.001887	0	21665,0,46,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749135	20091	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	21673	5.54E-4	0	0,21661,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	caa/Acaa	Q159T?	endoR	0.000368	0.051583	1	1	C>CA
ERR5749135	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26506	9.43E-4	0	13018,13223,15,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749135	21764	PASS	ATACATG	A	10519	0.997053	0	31,0,10488,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749135	21990	PASS	TTTA	T	10524	0.996769	0	0,34,5,10485	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749135	23063	PASS	A	T	12094	0.846535	0	0,3,1,12002	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749135	23271	PASS	C	A	17185	0.911667	0	3,0,17170,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749135	23403	PASS	A	G	17179	0.967169	0	0,4,0,17159	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749135	23604	PASS	C	A	13532	0.940807	0	14,0,13508,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749135	23709	PASS	C	T	13506	0.930772	0	0,5,4,13476	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749135	24506	PASS	T	G	16194	0.974682	0	6,0,16185,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749135	24745	PASS	C	A	33715	0.961619	15	0,5,17519,16178	LOW	SILENT	SYNONYMOUS_CODING	S	gtC/gtA	V1061	S	0.00048	0.961619	3	2	C>A
ERR5749135	24914	PASS	G	C	34860	0.957258	6	0,3,17372,17465	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749135	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	14586	7.54E-4	0	14575,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749135	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	G	11180	7.16E-4	0	1,11167,0,8	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/	ACLVGLMWLSYFIASF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT>G
ERR5749135	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	11183	0.001431	0	0,11165,0,16	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749135	27209	PASS	A	T	16901	0.957103	0	4,0,16869,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF6	cAt/cTt	H3L	orf6	0.00088	0.957103	3	2	A>T
ERR5749135	27494	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	36653	0.001391	4	19715,16870,26,29	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	cCt/cTt	P34L	orf7a	0.000672	0.961447	2	2	C>T
ERR5749135	27972	PASS	C	T	8576	0.89937	22	0,1,8493,48	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749135	28048	PASS	G	T	8533	0.916442	0	0,4,0,8521	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749135	28111	PASS	A	G	26576	0.978627	2	1,1,18029,8536	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749135	28270	PASS	TA	T	34656	0.994777	390	182,10,17786,16689	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749135	28280	PASS	G	C	34587	0.932373	11	9,2,17828,16670	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749135	28281	PASS	A	T	34587	0.908318	5	19,11,17824,16665	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749135	28282	PASS	T	A	34588	0.902278	6	28,18,17769,16677	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749135	28813	PASS	T	C	5873	0.979908	0	2,0,5868,0	LOW	SILENT	SYNONYMOUS_CODING	N	agT/agC	S180	N	0.005063	0.979908	1	1	T>C
ERR5749135	28881	PASS	G	A	11555	0.772479	9	4,0,5717,5672	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749135	28882	PASS	G	A	11555	0.826655	0	2,1,5788,5675	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749135	28883	PASS	G	C	11555	0.943574	3	0,1,5794,5753	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749135	28977	PASS	C	T	5872	0.9203	2147483647	0,0,0,5858	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749135	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	31219	8.33E-4	96	25310,5845,6,20	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749135	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	50305	0.00157	0	25263,24928,46,45	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749136	241	PASS	C	T	3260	0.868405	3	0,1,1626,1624	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749136	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	8811	0.001248	0	8784,20,11,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749136	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	8811	0.004086	0	8748,20,36,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749136	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	8812	0.002043	5	8135,27,587,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749136	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	8812	0.001816	0	8769,27,16,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749136	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	8811	0.004994	423	8759,7,24,20	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749136	673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26139	0.001224	147	17324,8746,1,34	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y136	leader	0.000454	0.602236	3	2	C>T
ERR5749136	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	26139	6.12E-4	17	17312,8811,15,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749136	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	26139	7.27E-4	0	17314,8805,12,7	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749136	913	PASS	C	T	17316	0.907427	0	0,10,0,17286	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749136	1420	PASS	C	T	15775	0.870681	0	3,0,15724,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A205	nsp2	0.006673	0.870681	1	1	C>T
ERR5749136	3037	PASS	C	T	15601	0.824242	33	0,11,7799,7695	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749136	3267	PASS	C	T	17599	0.970169	0	3,0,17576,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749136	3802	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	24781	6.05E-4	7	14352,10412,6,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N363	nsp3	0.000554	0.064198	4	2	TA>T
ERR5749136	4651	PASS	T	C	11392	0.973578	182	5,0,0,11384	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcC	A644	nsp3	0.973578	0.973578	1	1	T>C
ERR5749136	5170	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	10189	9.81E-4	0	4,10175,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T819	nsp3	0.000565	0.894036	2	2	CCA>C
ERR5749136	5388	PASS	C	A	4975	0.96402	2147483647	0,0,4974,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749136	5986	PASS	C	T	11950	0.974728	2147483647	0,0,11943,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749136	6706	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	11643	6.87E-4	0	10,11625,0,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1330	nsp3	0.000687	0.883999	2	2	CA>C
ERR5749136	6954	PASS	T	C	18561	0.812241	0	0,5,0,18440	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749136	8247	PASS	C	T	20625	0.971733	0	0,3,0,20614	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S1843F	nsp3	0.001545	0.971733	1	1	C>T
ERR5749136	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	18330	5.46E-4	11	13648,4672,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749136	10507	PASS	C	T	15785	0.736015	0	1,0,15684,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N151	3Cpro	0.00123	0.842913	2	2	C>T
ERR5749136	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21090	0.001944	0	20996,1,44,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749136	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	21075	0.001756	0	20993,0,55,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749136	11287	PASS	GTCTGGTTTT	G	21068	0.998291	0	0,36,0,21032	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749136	11747	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19886	0.001307	0	19827,3,33,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L259	nsp6	0.001145	0.737282	1	1	C>T
ERR5749136	11824	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19889	0.00362	0	0,19794,0,78	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I284	nsp6	0.000465	0.922016	2	2	C>T
ERR5749136	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	18004	0.001389	0	17960,0,25,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749136	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	14282	6.3E-4	0	14271,2,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749136	13459	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	13771	7.99E-4	0	13760,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/ttTa	L8F?	nsp11	0.000691	0.060726	5	2	G>GT
ERR5749136	14408	PASS	C	T	4615	0.84572	3	0,1,2309,2285	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749136	14676	PASS	C	T	10886	0.803601	2147483647	0,0,10854,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749136	15279	PASS	C	T	16217	0.894678	0	2,0,16182,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749136	16176	PASS	T	C	17417	0.97956	7	2,0,7543,9864	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749136	16524	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATG	A	21268	4.7E-4	0	21258,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/	V98	helicase	0.00047	0.926983	2	2	ATG>A
ERR5749136	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAA	G	19297	5.7E-4	0	19260,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GAA>G
ERR5749136	17615	PASS	A	G	14928	0.918341	0	0,0,7,14885	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749136	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	26043	8.45E-4	0	26022,0,22,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749136	18744	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26039	0.001536	0	25950,0,42,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y235	ExoN	0.000912	0.953624	2	2	C>T
ERR5749136	18981	PASS	C	T	23194	0.929465	0	11,0,23160,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H314	ExoN	0.001184	0.929465	1	1	C>T
ERR5749136	19079	PASS	A	G	23154	0.962123	0	5,0,23131,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gAa/gGa	E347G	ExoN	0.001121	0.967175	2	1	A>G
ERR5749136	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	23172	6.9E-4	0	0,23156,0,16	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749136	19854	PASS	C	T	16346	0.960602	154	4,0,0,16328	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D78	endoR	0.950322	0.965654	1	1	C>T
ERR5749136	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11773	0.003058	0	11729,0,37,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749136	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	24811	5.24E-4	2	12375,12424,5,8	HIGH	NONE	FRAME_SHIFT	S	ctt/Tctt	L5S?	S	0.000394	0.091869	4	1	G>GT
ERR5749136	21764	PASS	ATACATG	A	13086	0.996179	0	49,0,13029,7	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749136	21990	PASS	TTTA	T	13100	0.998473	0	0,20,15,13065	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749136	23063	PASS	A	T	14558	0.875258	0	0,6,0,14494	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749136	23271	PASS	C	A	20591	0.913409	2147483647	0,0,20562,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749136	23323	PASS	T	C	40772	0.947881	2	6,8,20489,20220	LOW	SILENT	SYNONYMOUS_CODING	S	atT/atC	I587	S	0.000758	0.951252	2	2	T>C
ERR5749136	23403	PASS	A	G	20585	0.970172	0	0,2,0,20570	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749136	23604	PASS	C	A	15581	0.939413	0	15,0,15550,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749136	23625	PASS	C	T	15564	0.901054	0	0,0,15515,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gTt	A688V	S	0.002362	0.901054	2	2	C>T
ERR5749136	23709	PASS	C	T	15561	0.940749	0	0,4,0,15538	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749136	24506	PASS	T	G	16745	0.97659	0	10,0,16731,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749136	24914	PASS	G	C	40053	0.959104	0	0,0,19962,20066	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749136	25587	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	15694	6.37E-4	0	2,15664,0,10	HIGH	NONE	FRAME_SHIFT	ORF3a	aag/	K67	orf3a	0.000598	0.813206	6	2	CAA>C
ERR5749136	25624	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28097	8.9E-4	3	12394,15675,9,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Cac/Tac	H78Y	orf3a	0.00089	0.983312	1	1	C>T
ERR5749136	25660	PASS	G	T	12432	0.907899	789	10,29,12380,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gtt/Ttt	V90F	orf3a	0.000716	0.91928	2	2	G>T
ERR5749136	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	12432	0.00177	240	12375,18,11,11	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749136	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	12400	8.87E-4	0	12389,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749136	26509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTT	C	10002	9.0E-4	0	0,9993,0,9	.	.	.	.	.	.	.	0.000852	0.946613	3	1	CTT>C
ERR5749136	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	13316	9.01E-4	0	2,13302,0,12	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749136	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	13316	0.001202	0	2,13298,0,16	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749136	27604	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	21785	0.001515	0	21716,0,34,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Gta/Ata	V71I	orf7a	0.001008	0.967671	3	2	G>A
ERR5749136	27972	PASS	C	T	11626	0.905384	19	1,1,11533,59	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749136	28048	PASS	G	T	11566	0.917171	0	0,14,0,11549	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749136	28111	PASS	A	G	29556	0.975809	0	3,1,17963,11578	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749136	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17957	0.001058	0	17882,2,21,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749136	28270	PASS	TA	T	34810	0.99503	497	184,2,17709,16928	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749136	28280	PASS	G	C	34728	0.936708	23	14,2,17747,16894	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749136	28281	PASS	A	T	34728	0.918394	32	20,3,17736,16909	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749136	28282	PASS	T	A	34733	0.911324	11	21,10,17704,16919	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749136	28881	PASS	G	A	15797	0.78401	12	5,0,7843,7776	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749136	28882	PASS	G	A	15796	0.830084	3	2,0,7906,7715	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749136	28883	PASS	G	C	15796	0.942517	2	1,2,7914,7866	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749136	28977	PASS	C	T	8051	0.926593	0	0,3,0,8033	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749136	29140	PASS	G	T	30966	0.888232	0	90,0,30862,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	caG/caT	Q289H	N	0.000955	0.888232	2	1	G>T
ERR5749136	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	61543	8.77E-4	0	30906,30560,33,32	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749137	241	PASS	C	T	16517	0.849186	0	0,1,8206,8218	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749137	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	12300	0.004878	0	12233,7,60,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749137	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	12302	0.001138	0	12189,8,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749137	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	12302	9.75E-4	0	12189,8,12,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749137	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	12302	0.005528	13	12189,8,67,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749137	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTTGA	G	12302	7.32E-4	0	12189,8,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTTGA>G
ERR5749137	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	12301	0.001382	0	12272,12,17,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749137	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	12300	6.5E-4	0	12279,11,8,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttatg/gtg	VM84V	leader	0.000554	0.991848	4	1	GTTA>G
ERR5749137	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	12295	0.001139	0	12254,13,14,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749137	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATGGTTG	T	12295	7.32E-4	0	12254,13,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	atggttgag/	MVE85	leader	0.000587	0.476744	4	1	TATGGTTG>T
ERR5749137	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	33518	0.001134	2	21179,12291,26,12	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749137	714	PASS	G	T	21215	0.979496	136	6,4,21197,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGc/gTc	G150V	leader	0.001941	0.984148	2	1	G>T
ERR5749137	913	PASS	C	T	21203	0.916238	0	0,13,1,21167	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749137	3037	PASS	C	T	23217	0.80721	67	1,26,11609,11394	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749137	3267	PASS	C	T	20913	0.96978	0	4,0,20897,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749137	3310	PASS	A	G	20900	0.952297	0	5,0,20888,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaA/gaG	E197	nsp3	0.938803	0.952297	1	1	A>G
ERR5749137	5388	PASS	C	A	6581	0.961556	2147483647	0,0,6578,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749137	5986	PASS	C	T	11305	0.976382	0	1,0,11297,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749137	6414	PASS	A	G	24633	0.926237	0	0,3,0,24597	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gAa/gGa	E1232G	nsp3	0.000549	0.930413	2	2	A>G
ERR5749137	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9004	0.00211	0	7,8870,0,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749137	6954	PASS	T	C	9666	0.820401	0	0,2,0,9610	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749137	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	30745	0.004749	345	17674,12924,146,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749137	10193	PASS	G	A	20960	0.862261	0	0,0,20932,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E47K	3Cpro	0.000774	0.869819	2	2	G>A
ERR5749137	10195	PASS	A	T	20960	0.962548	0	11,0,20935,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gaA/gaT	E47D	3Cpro	0.951998	0.969772	1	1	A>T
ERR5749137	11095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18261	0.001314	0	18199,0,27,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A41	nsp6	0.000515	0.887707	7	2	C>T
ERR5749137	11287	PASS	GTCTGGTTTT	G	18256	0.99644	0	0,65,0,18191	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749137	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	31570	0.001077	2	19412,12102,24,12	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749137	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26910	0.001412	0	13443,13395,21,22	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749137	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	16754	0.004417	2147483647	16331,163,7,249	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749137	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	32507	0.001477	0	16291,16184,25,23	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749137	14408	PASS	C	T	32507	0.834559	7	2,6,16214,16009	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749137	14676	PASS	C	T	10388	0.770023	0	2,0,10356,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749137	15279	PASS	C	T	18517	0.88011	0	6,0,18486,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749137	16176	PASS	T	C	19436	0.979677	0	1,1,9944,9477	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749137	16794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	42327	3.54E-4	50	22746,19566,0,15	HIGH	NONE	FRAME_SHIFT	ORF1ab	gta/	V187	helicase	0.000354	0.077626	2	2	TG>T
ERR5749137	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19498	0.002616	0	19433,0,51,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749137	20148	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	19492	5.13E-4	0	0,19482,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N177	endoR	0.000513	0.969223	2	2	CA>C
ERR5749137	21764	PASS	ATACATG	A	14348	0.993309	0	96,0,14252,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749137	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	14348	0.001324	0	14329,0,19,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749137	21990	PASS	TTTA	T	14353	0.998746	0	0,18,4,14331	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749137	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	13659	0.001318	0	1,13630,0,19	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749137	23063	PASS	A	T	14005	0.86105	0	0,1,0,13951	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749137	23271	PASS	C	A	21984	0.918486	2147483647	0,0,21962,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749137	23403	PASS	A	G	21979	0.968151	0	0,7,0,21955	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749137	23604	PASS	C	A	17680	0.945362	0	11,0,17655,4	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749137	23709	PASS	C	T	17652	0.933832	0	0,6,6,17607	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749137	24506	PASS	T	G	16627	0.974199	0	6,0,16615,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749137	24914	PASS	G	C	44079	0.959459	0	0,0,21964,22070	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749137	25391	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTA	T	21944	7.75E-4	0	21926,1,17,0	HIGH	NONE	FRAME_SHIFT+START_LOST	ORF3a	atg/	M1	orf3a	0.000585	0.191026	1	1	TTA>T
ERR5749137	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	22519	0.001687	503	22419,22,21,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749137	25782	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22460	0.001113	0	22364,2,26,0	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	tgC/tgT	C130	orf3a	0.000916	0.955348	1	1	C>T
ERR5749137	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	22678	0.001764	1695	22283,138,117,115	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749137	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	15858	6.31E-4	0	2,15835,0,10	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749137	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	15858	8.2E-4	0	1,15844,0,13	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749137	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	15860	0.002522	0	1,15816,0,40	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749137	27506	PASS	G	A	39820	0.98227	6	4,11,17406,22384	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	gGa/gAa	G38E	orf7a	0.000715	0.985435	4	2	G>A
ERR5749137	27972	PASS	C	T	12087	0.906097	21	0,1,11965,78	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749137	28048	PASS	G	T	12013	0.916257	0	0,16,0,11990	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749137	28111	PASS	A	G	31093	0.978677	1	5,4,19062,12017	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749137	28270	PASS	TA	T	36825	0.995031	405	186,10,18804,17838	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749137	28280	PASS	G	C	36745	0.934413	5	9,4,18847,17816	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749137	28281	PASS	A	T	36745	0.915363	29	23,5,18836,17824	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749137	28282	PASS	T	A	36748	0.907424	9	27,15,18796,17833	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749137	28881	PASS	G	A	21851	0.772367	11	7,1,10844,10746	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749137	28882	PASS	G	A	21850	0.825263	0	4,4,10926,10729	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749137	28883	PASS	G	C	21851	0.943069	1	3,4,10940,10878	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749137	28977	PASS	C	T	11099	0.93594	2147483647	0,0,0,11083	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749137	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	47668	9.02E-4	164	36526,11054,9,39	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749137	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	72621	0.001322	0	36453,36020,60,60	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749137	29284	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	36554	9.03E-4	0	0,36441,0,35	LOW	SILENT	SYNONYMOUS_CODING	N	atC/atT	I337	N	0.000393	0.931014	3	2	C>T
ERR5749137	29779	PASS	G	T	12436	0.954567	0	0,3,0,12427	.	.	.	.	.	.	.	0.001489	0.975228	1	1	G>T
ERR5749138	241	PASS	C	T	165	0.884848	0	0,0,82,83	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749138	442	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	494	0.022267	0	483,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/	V60	leader	0.001641	0.297974	2	2	CG>C
ERR5749138	913	PASS	C	T	1207	0.913836	2147483647	0,0,0,1206	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749138	1594	PASS	C	T	1478	0.961434	0	0,2,0,1475	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S263	nsp2	0.0019	0.963177	1	1	C>T
ERR5749138	3037	PASS	C	T	1008	0.804563	6	0,2,504,497	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749138	3267	PASS	C	T	1111	0.966697	2147483647	0,0,1111,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749138	4057	PASS	T	C	441	0.977324	2147483647	0,0,0,440	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caT/caC	H446	nsp3	0.977324	0.977324	1	1	T>C
ERR5749138	5388	PASS	C	A	224	0.964286	2147483647	0,0,224,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749138	5986	PASS	C	T	350	0.985714	2147483647	0,0,350,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749138	6954	PASS	T	C	965	0.810363	2147483647	0,0,0,954	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749138	11074	PASS	CT	C	4117	0.058538	0	3876,0,241,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000965	0.945355	5	2	CT>C
ERR5749138	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	4117	0.026233	0	4007,0,108,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CT
ERR5749138	11095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	4116	0.015549	0	4052,0,64,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/ttTa	L43F?	nsp6	0.000515	0.887707	7	2	C>CT
ERR5749138	11152	PASS	C	T	4112	0.974465	2147483647	0,0,4111,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V60	nsp6	0.000678	0.974465	2	2	C>T
ERR5749138	11287	PASS	GTCTGGTTTT	G	4114	0.999028	0	0,4,0,4110	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749138	13176	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	3003	0.022311	0	2929,0,74,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aAt	T51N	nsp10	0.002004	0.919962	2	1	C>A
ERR5749138	14408	PASS	C	T	2823	0.856181	0	0,0,1409,1386	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749138	14676	PASS	C	T	901	0.768036	2147483647	0,0,899,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749138	15279	PASS	C	T	1293	0.87007	0	17,0,1272,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749138	16176	PASS	T	C	1160	0.987069	0	0,0,354,805	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749138	17799	PASS	A	G	963	0.98027	2147483647	0,0,963,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtA/gtG	V521	helicase	0.001548	0.98027	1	1	A>G
ERR5749138	18457	PASS	C	T	797	0.944793	0	1,0,795,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cca/Tca	P140S	ExoN	0.001253	0.951352	2	1	C>T
ERR5749138	21101	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	2084	0.020633	0	0,2041,0,43	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttc/ttTc	F150F?	MethTr	0.001498	0.083467	2	2	G>GT
ERR5749138	21764	PASS	ATACATG	A	1335	0.997753	0	3,0,1332,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749138	21990	PASS	TTTA	T	1336	0.991018	0	0,12,1,1323	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749138	21991	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTAT	T	1336	0.008982	0	1,1323,0,12	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.00078	0.991378	2	1	TTAT>T
ERR5749138	23063	PASS	A	T	1742	0.862227	2147483647	0,0,0,1736	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749138	23271	PASS	C	A	2539	0.924774	2147483647	0,0,2537,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749138	23403	PASS	A	G	2538	0.966903	2147483647	0,0,0,2538	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749138	23541	PASS	A	T	1416	0.934322	0	1,0,1415,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tAt/tTt	Y660F	S	0.000911	0.950734	4	2	A>T
ERR5749138	23604	PASS	C	A	1416	0.947034	0	1,0,1414,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749138	23709	PASS	C	T	1414	0.937058	2147483647	0,0,0,1410	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749138	24506	PASS	T	G	1395	0.977061	2147483647	0,0,1395,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749138	24914	PASS	G	C	15693	0.959345	0	0,0,7827,7858	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749138	25572	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	6941	8.64E-4	0	0,6935,0,6	HIGH	NONE	FRAME_SHIFT	ORF3a	atc/	I62	orf3a	0.000543	0.959687	4	2	CA>C
ERR5749138	26571	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1213	0.018961	0	1187,0,26,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Ctt/Ttt	L17F	M	0.000508	0.905823	3	2	C>T
ERR5749138	27972	PASS	C	T	383	0.890339	0	0,0,379,1	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749138	28048	PASS	G	T	382	0.926702	2147483647	0,0,0,382	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749138	28111	PASS	A	G	8074	0.980803	0	0,0,7690,382	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749138	28270	PASS	TA	T	14912	0.99544	109	62,7,7602,7242	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749138	28280	PASS	G	C	14888	0.935048	9	4,0,7617,7237	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749138	28281	PASS	A	T	14888	0.917114	14	8,1,7611,7246	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749138	28282	PASS	T	A	14888	0.914428	2	8,5,7602,7246	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749138	28881	PASS	G	A	418	0.770335	0	0,0,206,205	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749138	28882	PASS	G	A	418	0.820574	0	0,0,210,208	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749138	28883	PASS	G	C	418	0.937799	0	0,0,210,208	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749138	28977	PASS	C	T	213	0.934272	2147483647	0,0,0,212	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749139	241	PASS	C	T	1694	0.867178	0	0,0,845,841	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749139	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	2919	0.001713	0	2914,1,5,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749139	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	2919	0.002055	0	2910,1,6,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749139	657	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2924	0.004104	0	1,2904,0,19	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A131V	leader	0.001202	0.365979	3	1	C>T
ERR5749139	806	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	11536	0.001474	0	11513,0,18,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gca/Aca	A1T	nsp2	0.001474	0.948499	1	1	G>A
ERR5749139	913	PASS	C	T	11537	0.910982	0	0,1,0,11518	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749139	1594	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11123	0.007192	0	1,11031,0,82	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S263	nsp2	0.0019	0.963177	1	1	C>T
ERR5749139	2189	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	10022	6.98E-4	0	3,10012,0,7	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/	L462	nsp2	0.000491	0.960061	3	2	CT>C
ERR5749139	2403	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	6986	0.002147	0	26,6971,0,15	HIGH	NONE	FRAME_SHIFT	ORF1ab	aag/	K534	nsp2	0.000951	0.061776	2	1	CA>C
ERR5749139	3037	PASS	C	T	6482	0.816106	24	0,8,3242,3179	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749139	3177	PASS	C	T	15736	0.913129	13	0,2,12461,3249	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P153L	nsp3	0.000773	0.96008	3	2	C>T
ERR5749139	3267	PASS	C	T	12477	0.968903	0	1,0,12471,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749139	4764	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	8085	9.89E-4	0	8073,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F683	nsp3	0.000673	0.93404	4	2	AT>A
ERR5749139	5113	PASS	A	C	6996	0.766581	0	1321,0,5674,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K798N	nsp3	0.760467	0.766581	1	1	A>C
ERR5749139	5388	PASS	C	A	2319	0.963777	2147483647	0,0,2317,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749139	5986	PASS	C	T	7468	0.976701	2147483647	0,0,7465,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749139	6337	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	13823	5.79E-4	0	13813,3,8,0	HIGH	NONE	FRAME_SHIFT+STOP_GAINED	ORF1ab	gat/Tgat	D1208*?	nsp3	0.000579	0.91624	3	2	G>GT
ERR5749139	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6240	0.002885	0	4,6153,0,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749139	6954	PASS	T	C	12068	0.804607	2147483647	0,0,0,12012	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749139	7528	PASS	C	T	8050	0.89354	0	0,7,3,8021	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V1603	nsp3	0.002527	0.916131	1	1	C>T
ERR5749139	8151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	21805	8.71E-4	528	10678,10905,196,4	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gTc/gGc	V1811G	nsp3	0.00055	0.34	2	1	T>G
ERR5749139	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	9204	0.001086	6	7527,1667,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749139	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	15553	0.001222	0	15508,0,32,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749139	11095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTT	C	15551	8.36E-4	0	15534,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L43	nsp6	0.000515	0.887707	7	2	CTT>C
ERR5749139	11287	PASS	GTCTGGTTTT	G	15557	0.998779	0	0,19,0,15538	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749139	11747	PASS	C	T	14468	0.737282	0	1661,0,12742,3	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L259	nsp6	0.001145	0.737282	1	1	C>T
ERR5749139	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17242	0.001682	0	8602,8588,16,16	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749139	14408	PASS	C	T	1574	0.84371	2	1,2,786,776	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749139	14676	PASS	C	T	5721	0.809299	0	1,0,5704,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749139	15279	PASS	C	T	8854	0.918229	0	4,0,8837,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749139	16176	PASS	T	C	7950	0.979119	0	0,0,2194,5746	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749139	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	11938	0.001927	0	11915,0,23,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749139	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	16515	0.001211	0	16495,0,20,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749139	18813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	32958	9.1E-4	0	16338,16461,16,17	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaT/gaC	D258	ExoN	0.000618	0.934482	1	1	T>C
ERR5749139	19328	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	11686	6.85E-4	0	11678,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F431	ExoN	0.000459	0.937906	4	2	CT>C
ERR5749139	20445	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	21139	8.52E-4	0	0,21121,0,18	HIGH	NONE	FRAME_SHIFT	ORF1ab	aac/	N277	endoR	0.000518	0.059736	4	2	TA>T
ERR5749139	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7155	0.002096	0	7131,0,15,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749139	20786	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	7167	0.001953	316	0,7142,11,4	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAt/aTt	N43I	MethTr	0.001392	1	1	1	A>T
ERR5749139	20930	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14766	0.001219	0	14739,0,19,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aTg	T91M	MethTr	0.000902	0.95585	2	2	C>T
ERR5749139	21101	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	14775	0.001624	0	8,14729,0,38	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGt/gTt	G148V	MethTr	0.001498	0.083467	2	2	G>T
ERR5749139	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	15694	0.001848	0	7823,7842,15,14	HIGH	NONE	FRAME_SHIFT	S	ctt/Tctt	L5S?	S	0.000394	0.091869	4	1	G>GT
ERR5749139	21622	PASS	C	T	7866	0.930079	0	0,3,0,7854	LOW	SILENT	SYNONYMOUS_CODING	S	acC/acT	T20	S	0.000846	0.946634	3	2	C>T
ERR5749139	21764	PASS	ATACATG	A	8609	0.996631	0	29,0,8580,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749139	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	8609	0.00151	0	8596,0,13,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749139	21990	PASS	TTTA	T	8610	0.997329	0	0,23,1,8586	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749139	22450	PASS	C	T	7499	0.801707	0	1,0,7348,56	LOW	SILENT	SYNONYMOUS_CODING	S	ctC/ctT	L296	S	0.00215	0.803846	1	1	C>T
ERR5749139	23063	PASS	A	T	8012	0.85684	0	0,4,0,7968	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749139	23271	PASS	C	A	13705	0.920978	0	1,0,13691,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749139	23403	PASS	A	G	13702	0.97015	0	0,1,0,13693	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749139	23604	PASS	C	A	9232	0.9349	0	11,0,9213,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749139	23709	PASS	C	T	9231	0.933702	0	0,1,0,9215	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749139	24010	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	6586	0.002429	136	40,6519,9,14	LOW	SILENT	SYNONYMOUS_CODING	S	tcA/tcT	S816	S	0.000455	0.926398	4	2	A>T
ERR5749139	24506	PASS	T	G	11500	0.976348	0	1,0,11494,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749139	24914	PASS	G	C	21296	0.963561	3	1,0,10613,10672	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749139	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	18837	0.001486	26	15384,3419,33,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749139	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	8622	8.12E-4	0	0,8613,0,7	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749139	27389	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15288	0.003925	0	24,15188,0,66	.	.	.	.	.	.	.	0.001157	0.899553	2	1	C>T
ERR5749139	27972	PASS	C	T	5200	0.901538	23	0,1,5159,22	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749139	28048	PASS	G	T	5180	0.924324	0	0,7,0,5169	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749139	28111	PASS	A	G	21642	0.979115	12	0,2,16450,5186	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749139	28195	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	16451	8.51E-4	0	16437,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF8	tgt/	C102	orf8	0.000851	0.926081	3	2	GT>G
ERR5749139	28270	PASS	TA	T	31886	0.994857	419	171,5,16229,15493	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749139	28280	PASS	G	C	31812	0.934773	5	6,2,16268,15468	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749139	28281	PASS	A	T	31812	0.917515	16	20,7,16262,15474	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749139	28282	PASS	T	A	31815	0.911897	12	16,6,16232,15484	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749139	28292	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	32716	7.95E-4	0	16299,16391,13,13	HIGH	NONE	FRAME_SHIFT	N	aat/	N8	N	0.000304	0.055324	4	2	CA>C
ERR5749139	28310	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	16458	0.002856	0	12,16372,0,64	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Ccc/Acc	P13T	N	0.00095	0.92832	2	1	C>A
ERR5749139	28881	PASS	G	A	8405	0.755503	3	5,2,4149,4129	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749139	28882	PASS	G	A	8405	0.826532	1	4,2,4201,4121	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749139	28883	PASS	G	C	8405	0.942058	0	1,0,4213,4184	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749139	28977	PASS	C	T	4267	0.93274	0	0,2,0,4262	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749139	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	26346	9.87E-4	130	22082,4213,6,23	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749139	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	43889	0.001322	0	22036,21771,36,36	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749140	186	PASS	C	T	5288	0.136157	0	4518,0,765,0	.	.	.	.	.	.	.	0.002255	0.966959	1	1	C>T
ERR5749140	241	PASS	C	T	10525	0.859477	0	1,1,5240,5235	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749140	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	10956	0.001552	0	10933,0,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749140	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10945	0.001827	0	10157,0,750,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749140	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	29026	4.82E-4	0	18028,10971,9,5	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749140	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18042	0.001053	0	0,18004,0,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749140	913	PASS	C	T	18043	0.921133	0	0,7,0,18015	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749140	1510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	18588	0.00468	0	0,18328,0,93	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G235	nsp2	0.002159	0.937304	1	1	T>C
ERR5749140	3037	PASS	C	T	17012	0.820715	30	0,10,8503,8402	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749140	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	8585	0.002097	498	1,8557,18,4	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749140	3267	PASS	C	T	18011	0.972017	0	3,0,18000,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749140	5388	PASS	C	A	5791	0.963391	2147483647	0,0,5789,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749140	5986	PASS	C	T	11674	0.9773	2147483647	0,0,11671,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749140	6954	PASS	T	C	19586	0.797355	0	0,7,3,19451	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749140	7070	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	32885	0.001642	182	13191,19627,53,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggc/Agc	G1451S	nsp3	0.000698	0.101434	3	1	G>A
ERR5749140	7423	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14156	0.001907	0	14119,0,29,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1568	nsp3	0.000941	0.970543	2	2	C>T
ERR5749140	8760	PASS	C	T	18617	0.846216	0	3,0,18553,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A69V	nsp4	0.003379	0.892678	1	1	C>T
ERR5749140	10077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	7195	0.002641	442	10,7152,18,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTc/tCc	F8S	3Cpro	0.001833	0.454545	1	1	T>C
ERR5749140	10996	PASS	G	A	4063	0.971204	0	0,2,0,4058	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaG/aaA	K8	nsp6	0.963406	0.980023	1	1	G>A
ERR5749140	11287	PASS	GTCTGGTTTT	G	18560	0.997953	0	0,38,0,18522	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749140	13176	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12710	0.007474	0	12599,1,105,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T51I	nsp10	0.002004	0.919962	2	1	C>T
ERR5749140	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	3980	0.004271	1027	3884,35,1,58	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749140	14408	PASS	C	T	7742	0.844097	0	2,2,3868,3827	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749140	14676	PASS	C	T	11782	0.822356	0	9,0,11757,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749140	15279	PASS	C	T	18248	0.89018	0	7,0,18217,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749140	15933	PASS	C	T	10199	0.983528	0	2,0,10194,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y831	RdRp	0.980056	0.983528	1	1	C>T
ERR5749140	16176	PASS	T	C	18602	0.980163	0	1,1,8399,10195	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749140	17154	PASS	T	C	14648	0.983274	0	2,0,14638,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taT/taC	Y306	helicase	0.983096	0.984896	1	1	T>C
ERR5749140	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	23117	4.76E-4	0	23106,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749140	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22337	0.002149	0	22274,0,51,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749140	21255	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	58442	0.004124	794	29978,28167,278,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcG/gcT	A199	MethTr	0.000341	0.917425	4	2	G>T
ERR5749140	21764	PASS	ATACATG	A	12089	0.997932	0	25,0,12064,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749140	21990	PASS	TTTA	T	12090	0.996278	0	0,45,2,12043	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749140	23063	PASS	A	T	12919	0.875919	0	0,1,0,12857	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749140	23271	PASS	C	A	19304	0.922866	0	4,0,19276,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749140	23403	PASS	A	G	19308	0.967682	0	0,1,3,19296	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749140	23604	PASS	C	A	14394	0.943935	0	11,0,14377,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749140	23709	PASS	C	T	14384	0.947094	0	0,5,0,14361	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749140	24382	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11801	0.002118	0	0,11773,0,26	LOW	SILENT	SYNONYMOUS_CODING	S	tcC/tcT	S940	S	0.002118	0.920404	2	1	C>T
ERR5749140	24506	PASS	T	G	16255	0.974654	0	3,0,16248,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749140	24914	PASS	G	C	35311	0.959276	0	0,0,17589,17691	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749140	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	24734	0.002305	94	16734,7926,66,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749140	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	12715	7.86E-4	0	12705,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749140	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	12433	9.65E-4	0	0,12417,0,12	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749140	27494	PASS	C	T	37412	0.955442	10	2,7,19529,17851	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	cCt/cTt	P34L	orf7a	0.000672	0.961447	2	2	C>T
ERR5749140	27972	PASS	C	T	9025	0.903269	19	1,1,8939,50	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749140	28048	PASS	G	T	8975	0.925571	0	0,6,0,8964	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749140	28111	PASS	A	G	28221	0.979306	0	2,1,19231,8978	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749140	28270	PASS	TA	T	37294	0.995629	400	164,5,19002,18129	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749140	28280	PASS	G	C	37226	0.936254	8	12,5,19029,18102	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749140	28281	PASS	A	T	37226	0.920674	11	18,8,19019,18104	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749140	28282	PASS	T	A	37228	0.913721	16	23,9,18980,18126	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749140	28456	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	17592	0.001535	0	17550,12,28,0	LOW	SILENT	SYNONYMOUS_CODING	N	aaG/aaA	K61	N	0.001535	0.070307	3	2	G>A
ERR5749140	28856	PASS	A	C	7949	0.98201	0	2,0,7936,6	LOW	SILENT	SYNONYMOUS_CODING	N	Aga/Cga	R195	N	0.979416	0.983392	1	1	A>C
ERR5749140	28881	PASS	G	A	15652	0.759967	4	4,1,7695,7697	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749140	28882	PASS	G	A	15652	0.839637	2	6,3,7819,7702	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749140	28883	PASS	G	C	15652	0.943458	0	0,0,7840,7799	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749140	28977	PASS	C	T	7949	0.930306	0	0,1,0,7939	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749140	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	36823	0.001113	252	28845,7900,2,42	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749140	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	57358	0.001063	0	28803,28469,34,34	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749141	241	PASS	C	T	8326	0.846505	0	0,1,4087,4190	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749141	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	11268	0.001686	0	11248,3,19,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749141	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	11266	0.001953	0	11233,3,22,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749141	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	11259	0.002398	0	10248,6,941,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749141	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	11259	0.001066	0	11241,6,12,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749141	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	28893	0.001834	0	17569,11266,33,20	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749141	913	PASS	C	T	17596	0.91822	0	0,9,0,17567	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749141	1323	PASS	G	A	18762	0.966688	201	0,6,18748,5	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGt/gAt	G173D	nsp2	0.966688	0.969402	1	1	G>A
ERR5749141	2947	PASS	C	T	8891	0.836914	2147483647	0,0,8862,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G76	nsp3	0.001938	0.860703	2	2	C>T
ERR5749141	3037	PASS	C	T	17654	0.810864	57	0,19,8819,8686	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749141	3267	PASS	C	T	16574	0.970134	0	2,0,16566,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749141	5388	PASS	C	A	5134	0.956954	2147483647	0,0,5130,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749141	5986	PASS	C	T	11050	0.977919	2147483647	0,0,11045,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749141	6272	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	17814	0.005277	0	17685,2,118,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Aat	Y1185N	nsp3	0.001735	0.156069	2	1	T>A
ERR5749141	6274	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	17812	0.00539	0	17710,0,98,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taT/taC	Y1185	nsp3	0.000755	0.990148	2	2	T>C
ERR5749141	6579	PASS	T	C	10659	0.968477	2147483647	0,0,10647,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cTt/cCt	L1287P	nsp3	0.003451	0.968477	2	1	T>C
ERR5749141	6706	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	10635	8.46E-4	0	0,10625,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1330	nsp3	0.000687	0.883999	2	2	CA>C
ERR5749141	6954	PASS	T	C	18965	0.820933	0	0,3,1,18880	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749141	8368	PASS	G	T	10566	0.947284	0	5,0,10558,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcG/gcT	A1883	nsp3	0.947284	0.950161	1	1	G>T
ERR5749141	8950	PASS	C	T	34274	0.974879	5	0,3,12963,21302	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I132	nsp4	0.002808	0.982604	1	1	C>T
ERR5749141	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	27673	0.001156	101	13337,14304,32,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749141	10077	PASS	T	C	22	0.454545	33	3,9,10,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTc/tCc	F8S	3Cpro	0.001833	0.454545	1	1	T>C
ERR5749141	10156	PASS	C	T	14702	0.949463	278	7,9,14685,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D34	3Cpro	0.001207	0.949463	1	1	C>T
ERR5749141	10244	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14681	0.003065	0	14614,0,50,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cat/Tat	H64Y	3Cpro	0.001845	0.074194	2	2	C>T
ERR5749141	10369	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14697	0.001225	0	3,14667,0,18	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	cgC/cgT	R105	3Cpro	0.001225	0.120075	1	1	C>T
ERR5749141	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	14875	0.004034	0	14796,0,73,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749141	11287	PASS	GTCTGGTTTT	G	14872	0.998319	0	0,25,0,14847	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749141	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27341	9.14E-4	0	13667,13623,13,13	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749141	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10586	0.00444	2778	10352,71,6,154	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749141	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	20619	9.7E-4	0	10335,10272,10,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749141	14408	PASS	C	T	20619	0.841845	4	1,3,10292,10174	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749141	14676	PASS	C	T	11305	0.837329	0	5,0,11277,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749141	14805	PASS	C	T	11301	0.904964	0	0,6,0,11267	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y455	RdRp	0.001051	0.904964	2	2	C>T
ERR5749141	14913	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16934	0.011397	0	16723,4,199,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N491	RdRp	0.011397	0.981624	1	1	C>T
ERR5749141	15025	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	16920	0.001418	0	16849,0,49,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gca/Tca	A529S	RdRp	0.000933	0.946354	3	2	G>T
ERR5749141	15279	PASS	C	T	18828	0.896643	0	3,0,18795,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749141	16176	PASS	T	C	16587	0.981009	0	0,0,7936,8643	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749141	16506	PASS	T	C	9812	0.966062	171	10,6,9783,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttT/ttC	F90	helicase	0.966062	0.970785	1	1	T>C
ERR5749141	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	19947	5.51E-4	0	19936,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749141	19160	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19755	0.001215	0	0,19718,0,28	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S374F	ExoN	0.001215	0.871076	1	1	C>T
ERR5749141	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26019	0.005458	0	25844,0,152,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749141	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	26647	6.38E-4	0	13283,13348,8,9	HIGH	NONE	FRAME_SHIFT	S	ctt/Tctt	L5S?	S	0.000394	0.091869	4	1	G>GT
ERR5749141	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26615	0.001202	0	12994,13280,20,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749141	21764	PASS	ATACATG	A	10936	0.995611	23	48,1,10888,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749141	21990	PASS	TTTA	T	10937	0.998537	0	0,16,1,10920	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749141	22801	PASS	G	T	12360	0.885032	0	0,3,0,12349	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggT	G413	S	0.001101	0.887758	3	2	G>T
ERR5749141	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12360	0.001456	0	0,12339,0,18	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749141	23063	PASS	A	T	8120	0.853202	0	0,2,0,8085	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749141	23271	PASS	C	A	17693	0.921777	0	2,0,17676,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749141	23403	PASS	A	G	17684	0.972518	0	0,6,0,17667	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749141	23604	PASS	C	A	13856	0.942696	0	12,0,13838,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749141	23709	PASS	C	T	13844	0.937374	0	0,3,0,13821	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749141	24506	PASS	T	G	15240	0.975394	0	6,0,15230,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749141	24914	PASS	G	C	29156	0.960043	3	1,0,14526,14608	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749141	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	21658	0.001431	312	21564,13,18,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749141	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	9550	0.001675	0	0,9531,0,16	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749141	27972	PASS	C	T	9339	0.914231	85	6,5,9250,51	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749141	28048	PASS	G	T	9285	0.931179	0	0,7,1,9274	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749141	28111	PASS	A	G	22428	0.978955	7	0,2,13130,9288	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749141	28195	PASS	G	T	13136	0.926081	0	12,0,13121,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	cGt/cTt	R101L	orf8	0.000851	0.926081	3	2	G>T
ERR5749141	28270	PASS	TA	T	25539	0.994675	306	130,5,12952,12451	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749141	28271	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AA	A	25535	0.001057	77	13051,12460,27,0	.	.	.	.	.	.	.	0.000482	0.924941	3	2	AA>A
ERR5749141	28280	PASS	G	C	25496	0.939716	9	4,0,12999,12449	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749141	28281	PASS	A	T	25496	0.914026	9	17,8,12991,12445	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749141	28282	PASS	T	A	25497	0.921206	10	13,5,12981,12458	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749141	28881	PASS	G	A	12236	0.759807	5	6,2,6041,6017	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749141	28882	PASS	G	A	12235	0.833102	9	6,1,6114,6008	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749141	28883	PASS	G	C	12237	0.940263	0	2,2,6125,6102	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749141	28977	PASS	C	T	6263	0.92304	0	0,2,1,6247	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749141	29348	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	24428	0.002866	4	7251,17081,30,57	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gca/Tca	A359S	N	0.000865	0.968413	2	1	G>T
ERR5749142	241	PASS	C	T	832	0.84976	0	0,0,410,418	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749142	379	PASS	C	A	5758	0.847169	0	9,0,5326,420	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtA	V38	leader	0.847169	0.944238	2	1	C>A
ERR5749142	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	5335	0.002999	0	5319,0,16,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749142	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	5335	0.003187	0	5311,0,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749142	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	5329	0.001689	0	4900,0,383,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749142	657	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	5339	0.002248	0	0,5306,0,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A131D	leader	0.001202	0.365979	3	1	C>A
ERR5749142	657	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5339	0.002435	0	0,5306,0,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A131V	leader	0.001202	0.365979	3	1	C>T
ERR5749142	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	19900	7.54E-4	4	14548,5337,13,2	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749142	913	PASS	C	T	14549	0.91862	0	0,7,0,14514	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749142	1813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	12868	0.001321	0	0,12832,0,20	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcA	A336	nsp2	0.001022	0.152738	4	2	T>A
ERR5749142	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	35068	0.001055	1711	17468,16749,30,705	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749142	3037	PASS	C	T	8645	0.824292	27	0,9,4312,4259	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749142	3267	PASS	C	T	12167	0.969508	0	2,0,12156,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749142	3811	PASS	C	T	13642	0.946635	13	7,3,4888,8741	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ctC/ctT	L364	nsp3	0.002015	0.946635	1	1	C>T
ERR5749142	5388	PASS	C	A	2244	0.956328	0	1,0,2239,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749142	5501	PASS	A	G	2242	0.924621	0	0,1,0,2239	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Aga/Gga	R928G	nsp3	0.924621	0.941176	1	1	A>G
ERR5749142	5986	PASS	C	T	7771	0.975293	2147483647	0,0,7763,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749142	6582	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	6889	0.001597	0	6878,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	att/	I1289	nsp3	0.001257	0.973714	2	2	CTA>C
ERR5749142	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6873	0.002328	0	5,6781,0,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749142	6954	PASS	T	C	10228	0.828217	0	0,2,1,10171	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749142	7735	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	15817	7.59E-4	0	15805,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/	V1673	nsp3	0.000658	0.954659	3	2	CG>C
ERR5749142	9006	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	13870	0.001514	0	13816,1,25,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gTt/gGt	V151G	nsp4	0.001514	0.052053	1	1	T>G
ERR5749142	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	10803	9.26E-4	6	8854,1939,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749142	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13218	0.002043	0	13166,2,29,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749142	11082	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	13209	9.08E-4	0	13204,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000427	0.179468	2	1	TG>T
ERR5749142	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	13209	0.009615	0	13042,0,148,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749142	11287	PASS	GTCTGGTTTT	G	13207	0.99788	0	0,28,0,13179	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749142	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	18750	0.001173	0	12386,6332,15,7	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749142	11674	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTTTAGACTGACTCTTGGTGTTTATGATTACTTAGTTTCTACACAGGAG	C	12412	0.001128	0	12396,2,14,0	MODERATE	NONE	CODON_DELETION	ORF1ab	ctgactcttggtgtttatgattacttagtttctacacaggagtttaga/	LTLGVYDYLVSTQEFR237	nsp6	0.00054	0.985782	3	2	CTTTAGACTGACTCTTGGTGTTTATGATTACTTAGTTTCTACACAGGAG>C
ERR5749142	12125	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	14540	0.001651	0	0,14471,0,28	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y12H	nsp8	0.000847	0.113436	1	1	T>C
ERR5749142	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	13813	0.001737	0	13773,0,24,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749142	12756	PASS	C	T	18644	0.827398	8	5,5,4825,13796	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T24I	nsp9	0.000889	0.877514	1	1	C>T
ERR5749142	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	11083	9.93E-4	0	11072,1,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749142	13498	PASS	A	G	17038	0.952048	0	9,9,8532,8475	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Aca/Gca	T20A	RdRp	0.001341	0.952048	1	1	A>G
ERR5749142	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17071	0.001347	0	8527,8495,12,12	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749142	14216	PASS	C	T	7882	0.9627	0	0,5,0,7873	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T259I	RdRp	0.006249	0.962929	1	1	C>T
ERR5749142	14408	PASS	C	T	234	0.824786	0	0,0,118,112	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749142	14676	PASS	C	T	7648	0.789226	0	11,0,7616,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749142	15096	PASS	T	C	10866	0.970182	0	0,5,3,10856	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaT/aaC	N552	RdRp	0.941667	0.970182	1	1	T>C
ERR5749142	15279	PASS	C	T	8637	0.897997	0	4,0,8621,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749142	16176	PASS	T	C	9745	0.984813	0	0,0,2761,6982	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749142	16508	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	12236	0.001308	0	12204,2,30,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGt/gTt	G91V	helicase	0.000561	0.074909	2	2	G>T
ERR5749142	17615	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	10725	0.001492	0	0,10699,0,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749142	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	20855	5.27E-4	0	20844,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749142	18756	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	20847	5.76E-4	0	20836,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F240	ExoN	0.000392	0.942688	3	2	GT>G
ERR5749142	18788	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	41651	7.92E-4	0	20753,20792,18,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T250I	ExoN	0.000792	0.51652	2	1	C>T
ERR5749142	19328	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	11854	7.59E-4	0	11845,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F431	ExoN	0.000459	0.937906	4	2	CT>C
ERR5749142	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10557	0.003315	0	10509,0,38,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749142	20445	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAA	T	15323	9.14E-4	0	0,15300,0,14	HIGH	NONE	FRAME_SHIFT	ORF1ab	aac/	N277	endoR	0.000518	0.059736	4	2	TAA>T
ERR5749142	21234	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	21037	5.23E-4	0	21029,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/Tgtt	V194C?	MethTr	0.000472	0.857572	5	2	C>CT
ERR5749142	21255	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCA	G	41003	3.41E-4	0	21024,19965,7,7	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	tcatct/tct	SS201S	MethTr	0.000341	0.917425	4	2	GTCA>G
ERR5749142	21516	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	6525	0.002912	0	6499,7,19,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	agagtt/	RV287	MethTr	0.000412	0.905456	2	2	CAG>C
ERR5749142	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	12959	0.001698	2	6452,6487,9,13	HIGH	NONE	FRAME_SHIFT	S	ctt/Tctt	L5S?	S	0.000394	0.091869	4	1	G>GT
ERR5749142	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12935	0.00201	0	6301,6467,16,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749142	21764	PASS	ATACATG	A	9341	0.997324	0	25,0,9316,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749142	21976	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TCCA	T	9345	8.56E-4	0	2,9334,0,8	MODERATE	NONE	CODON_DELETION	S	cca/	P139	S	0.000856	0.977603	2	2	TCCA>T
ERR5749142	21990	PASS	TTTA	T	9345	0.99893	0	0,10,2,9333	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749142	23063	PASS	A	T	9798	0.875995	0	0,2,0,9750	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749142	23271	PASS	C	A	15098	0.920387	0	3,0,15076,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749142	23403	PASS	A	G	15094	0.974493	0	0,1,0,15080	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749142	23604	PASS	C	A	10326	0.936277	0	8,0,10312,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749142	23709	PASS	C	T	10317	0.940971	0	0,3,0,10301	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749142	24237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8767	0.001711	0	8745,0,18,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gTt	A892V	S	0.001242	0.889739	1	1	C>T
ERR5749142	24320	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	8760	0.005137	0	0,8706,0,45	HIGH	NONE	FRAME_SHIFT	S	aaa/	K921	S	0.000763	0.138365	4	2	CA>C
ERR5749142	24320	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	8760	0.001027	0	0,8706,0,9	HIGH	NONE	FRAME_SHIFT	S	aaa/	K921	S	0.000763	0.138365	4	2	CAA>C
ERR5749142	24506	PASS	T	G	9143	0.973094	0	1,0,9141,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749142	24914	PASS	G	C	34095	0.961783	0	0,0,16989,17077	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749142	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	20405	0.00245	54	15492,4849,57,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749142	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	3880	0.005928	352	3832,15,5,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749142	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	3847	0.002339	0	3838,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749142	26062	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	24150	0.001077	0	24102,10,33,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Ggt/Tgt	G224C	orf3a	0.001077	0.906894	1	1	G>T
ERR5749142	26065	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	24149	0.001242	0	24098,10,38,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gtt/Ttt	V225F	orf3a	0.001242	0.906322	2	1	G>T
ERR5749142	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	24107	4.15E-4	0	10,24087,0,10	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749142	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	9504	0.001052	0	0,9490,0,10	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749142	27972	PASS	C	T	6782	0.905043	125	7,7,6724,30	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749142	28001	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	13482	0.001335	0	6714,6730,11,11	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ccG/ccA	P36	orf8	0.00085	0.830607	2	1	G>A
ERR5749142	28048	PASS	G	T	6755	0.927609	0	0,6,0,6743	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749142	28095	PASS	A	T	6764	0.963779	101	3,1,0,6754	HIGH	NONSENSE	STOP_GAINED	ORF8	Aaa/Taa	K68*	orf8	0.002672	0.967672	2	2	A>T
ERR5749142	28111	PASS	A	G	17899	0.974691	12	0,3,11131,6758	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749142	28270	PASS	TA	T	21597	0.995138	260	105,3,10999,10493	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749142	28280	PASS	G	C	21551	0.943297	14	8,1,11012,10484	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749142	28281	PASS	A	T	21551	0.923623	32	15,1,11018,10486	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749142	28282	PASS	T	A	21551	0.911466	26	15,2,10975,10492	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749142	28498	PASS	C	T	16799	0.953211	0	13,0,16763,0	LOW	SILENT	SYNONYMOUS_CODING	N	aaC/aaT	N75	N	0.953211	0.95832	1	1	C>T
ERR5749142	28881	PASS	G	A	10323	0.783493	2	3,1,5125,5094	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749142	28882	PASS	G	A	10323	0.833963	0	2,2,5169,5062	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749142	28883	PASS	G	C	10323	0.949627	0	1,0,5171,5144	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749142	28977	PASS	C	T	5251	0.93068	0	0,0,2,5237	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749142	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	31607	0.002974	646	26315,5153,7,95	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749142	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	52337	0.00107	0	26273,25966,33,33	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749142	29542	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	12448	0.001366	15	6565,5854,6,15	.	.	.	.	.	.	.	0.00099	0.957487	2	1	A>T
ERR5749143	241	PASS	C	T	6722	0.859119	0	1,1,3346,3350	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749143	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	8361	9.57E-4	0	8354,2,8,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749143	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	8361	0.002033	0	8334,2,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749143	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	8346	0.002396	0	7576,2,720,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749143	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	8343	0.001199	0	8326,2,10,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749143	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	23835	0.001301	7	15428,8368,24,7	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749143	913	PASS	C	T	15450	0.915469	0	0,11,0,15407	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749143	2270	PASS	A	G	10790	0.965616	0	1,0,10781,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Aag/Gag	K489E	nsp2	0.965616	0.965616	1	1	A>G
ERR5749143	3037	PASS	C	T	13179	0.810608	47	1,19,6582,6492	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749143	3267	PASS	C	T	15141	0.96777	0	2,0,15133,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749143	3817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26535	0.001394	0	17434,9051,25,13	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D366	nsp3	0.000777	0.972816	2	2	C>T
ERR5749143	5388	PASS	C	A	4077	0.953397	2147483647	0,0,4076,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749143	5986	PASS	C	T	9204	0.973273	2147483647	0,0,9199,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749143	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	8744	0.008806	0	0,8666,0,77	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L1328S?	nsp3	0.000731	0.14377	4	2	C>CT
ERR5749143	6954	PASS	T	C	17370	0.815774	0	0,3,0,17285	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749143	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	19462	0.001079	43	11945,7496,21,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749143	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	17624	0.002213	0	17171,3,39,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749143	11287	PASS	GTCTGGTTTT	G	17613	0.998013	0	0,35,0,17578	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749143	12439	PASS	C	T	18714	0.637117	0	0,5,0,18599	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P116	nsp8	0.000666	0.637117	2	2	C>T
ERR5749143	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	6036	0.005964	2075	5863,46,4,121	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749143	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	11678	0.001113	0	5858,5817,7,6	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749143	14408	PASS	C	T	11678	0.849118	0	0,0,5831,5757	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749143	14676	PASS	C	T	10785	0.79898	0	4,0,10752,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749143	15279	PASS	C	T	17718	0.883903	2147483647	0,0,17678,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749143	16176	PASS	T	C	15518	0.980861	0	0,0,6937,8574	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749143	18813	PASS	T	C	38844	0.934482	0	0,0,19274,19542	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaT/gaC	D258	ExoN	0.000618	0.934482	1	1	T>C
ERR5749143	19188	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	20496	4.88E-4	0	0,20486,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	tgg/	W385	ExoN	0.000427	0.06319	2	1	AT>A
ERR5749143	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20867	0.002396	0	20799,2,53,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749143	20178	PASS	C	T	20864	0.839293	0	0,6,0,20846	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V186	endoR	0.000533	0.867727	2	2	C>T
ERR5749143	21764	PASS	ATACATG	A	9079	0.998017	0	18,0,9061,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749143	21990	PASS	TTTA	T	9086	0.998239	0	0,16,5,9065	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749143	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	12642	0.001345	0	0,12622,0,17	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749143	23063	PASS	A	T	10301	0.863703	2147483647	0,0,0,10250	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749143	23271	PASS	C	A	16742	0.925875	2147483647	0,0,16727,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749143	23403	PASS	A	G	16738	0.976282	0	0,2,0,16723	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749143	23604	PASS	C	A	11577	0.936858	0	10,0,11564,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749143	23709	PASS	C	T	11562	0.940149	0	0,1,5,11541	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749143	24506	PASS	T	G	15819	0.973576	0	7,0,15808,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749143	24914	PASS	G	C	27739	0.959696	0	0,0,13819,13896	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749143	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	15469	0.001939	551	15401,6,10,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749143	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	15442	5.83E-4	0	15433,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749143	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	9361	0.001389	0	0,9347,0,13	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749143	27972	PASS	C	T	7602	0.900421	0	0,0,7552,30	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749143	28048	PASS	G	T	7581	0.914919	0	0,11,0,7569	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749143	28111	PASS	A	G	24386	0.979332	4	4,0,16794,7583	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749143	28270	PASS	TA	T	32518	0.995695	330	143,6,16586,15792	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749143	28280	PASS	G	C	32464	0.946957	14	8,1,16623,15784	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749143	28281	PASS	A	T	32464	0.916862	14	23,10,16601,15770	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749143	28282	PASS	T	A	32467	0.902424	6	21,13,16567,15772	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749143	28407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TACCCAATA	T	16811	5.35E-4	0	9,16793,0,9	HIGH	NONE	FRAME_SHIFT	N	cccaataat/	PNN46	N	0.000382	0.179673	1	1	TACCCAATA>T
ERR5749143	28881	PASS	G	A	11169	0.760229	9	4,0,5504,5492	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749143	28882	PASS	G	A	11169	0.82729	12	5,0,5581,5491	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749143	28883	PASS	G	C	11169	0.941982	0	1,0,5588,5567	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749143	28977	PASS	C	T	5682	0.93453	2147483647	0,0,0,5673	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749143	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	43613	0.001261	0	21914,21621,35,32	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749144	241	PASS	C	T	8289	0.857884	0	0,0,4122,4134	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749144	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	9337	0.002249	0	9319,0,21,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749144	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	9338	0.002035	0	9264,1,19,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749144	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	9338	0.005462	0	9264,1,51,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749144	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	9333	0.002036	0	9313,1,19,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749144	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	9331	9.65E-4	0	9315,1,9,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttatg/gtg	VM84V	leader	0.000554	0.991848	4	1	GTTA>G
ERR5749144	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	9332	0.001072	0	9320,2,10,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749144	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	23456	0.001961	4	14072,9330,31,15	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749144	913	PASS	C	T	14103	0.909877	0	0,7,0,14065	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749144	1573	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	14659	0.001569	574	0,14614,19,5	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acA/acG	T256	nsp2	0.001231	0.75	1	1	A>G
ERR5749144	3037	PASS	C	T	16501	0.813466	26	2,14,8248,8123	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749144	3267	PASS	C	T	13652	0.971653	2147483647	0,0,13643,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749144	3671	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	21524	9.29E-4	0	10738,10641,10,10	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E318K	nsp3	0.000351	0.0625	6	2	G>A
ERR5749144	5388	PASS	C	A	5880	0.962245	2147483647	0,0,5876,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749144	5986	PASS	C	T	10471	0.974501	0	1,0,10456,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749144	6954	PASS	T	C	15738	0.813763	0	0,1,2,15631	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749144	7070	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	32219	8.69E-4	80	16378,15800,28,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggc/Agc	G1451S	nsp3	0.000698	0.101434	3	1	G>A
ERR5749144	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	22757	0.001186	63	13211,9518,27,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749144	10193	PASS	G	A	14523	0.838463	0	0,0,14504,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E47K	3Cpro	0.000774	0.869819	2	2	G>A
ERR5749144	10195	PASS	A	T	14523	0.969772	0	7,0,14507,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gaA/gaT	E47D	3Cpro	0.951998	0.969772	1	1	A>T
ERR5749144	10323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	14515	0.00186	0	1,14460,0,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749144	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	13338	0.001799	0	13294,0,35,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749144	11235	PASS	C	T	13341	0.942208	0	0,7,7,13311	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A88V	nsp6	0.000512	0.942208	2	2	C>T
ERR5749144	11287	PASS	GTCTGGTTTT	G	13341	0.997826	0	0,29,0,13312	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749144	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19726	0.001065	0	9850,9825,11,12	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749144	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	9828	0.004579	2608	9582,94,1,148	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749144	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	19066	0.001101	1	9567,9494,12,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749144	14408	PASS	C	T	19066	0.847372	15	0,5,9516,9402	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749144	14676	PASS	C	T	8713	0.8244	0	4,0,8692,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749144	15279	PASS	C	T	14676	0.937108	0	4,0,14657,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749144	16176	PASS	T	C	15238	0.981231	0	0,0,8534,6697	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749144	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	19723	8.62E-4	0	19706,0,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749144	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24041	0.002121	0	23979,0,55,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749144	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	21899	0.027581	1865	10943,10258,0,604	HIGH	NONE	FRAME_SHIFT	S	ctt/Tctt	L5S?	S	0.000394	0.091869	4	1	G>GT
ERR5749144	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GTT	21899	0.003379	232	10943,10258,0,74	HIGH	NONE	FRAME_SHIFT	S	ctt/TTctt	L5F?	S	0.000394	0.091869	4	1	G>GTT
ERR5749144	21575	PASS	C	T	21075	0.871696	0	7,7,9933,10849	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749144	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	21062	0.003276	195	10092,10895,0,69	HIGH	NONE	FRAME_SHIFT	S	gtt/Tgtt	V6C?	S	0.000619	0.877942	3	2	C>CT
ERR5749144	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	21062	8.07E-4	47	10092,10895,0,17	HIGH	NONE	FRAME_SHIFT	S	gtt/TTgtt	V6L?	S	0.000619	0.877942	3	2	C>CTT
ERR5749144	21764	PASS	ATACATG	A	10161	0.998032	0	20,0,10141,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749144	21990	PASS	TTTA	T	10167	0.996557	0	0,35,4,10128	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749144	23063	PASS	A	T	11452	0.862207	0	0,1,0,11400	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749144	23271	PASS	C	A	14288	0.913704	0	2,0,14272,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749144	23403	PASS	A	G	14280	0.966667	0	0,2,0,14259	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749144	23604	PASS	C	A	13088	0.957213	0	9,0,13075,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749144	23709	PASS	C	T	13077	0.943259	0	0,7,3,13052	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749144	24506	PASS	T	G	12425	0.97674	0	4,0,12417,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749144	24914	PASS	G	C	29626	0.956018	0	0,0,14766,14840	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749144	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	19199	0.001719	53	14247,4904,44,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749144	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	15029	7.32E-4	0	15018,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749144	26228	PASS	C	T	47338	0.94873	1	1,12,7263,40020	.	.	.	.	.	.	.	0.000649	0.94873	2	1	C>T
ERR5749144	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	10307	0.002911	0	0,10273,0,30	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749144	27476	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30701	8.79E-4	12	15512,15149,20,9	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	aCa/aTa	T28I	orf7a	0.000547	0.22827	4	2	C>T
ERR5749144	27972	PASS	C	T	9739	0.90574	36	2,2,9646,57	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749144	28048	PASS	G	T	9691	0.917552	0	0,10,0,9673	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749144	28111	PASS	A	G	21871	0.978785	7	0,2,12160,9691	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749144	28270	PASS	TA	T	23588	0.995082	282	113,3,12016,11456	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749144	28280	PASS	G	C	23536	0.936905	0	4,3,12039,11442	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749144	28281	PASS	A	T	23536	0.9095	21	13,2,12031,11447	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749144	28282	PASS	T	A	23539	0.897064	4	11,6,11995,11453	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749144	28881	PASS	G	A	11945	0.731436	16	8,1,5870,5882	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749144	28882	PASS	G	A	11942	0.817451	12	5,0,5967,5850	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749144	28883	PASS	G	C	11942	0.940881	0	1,0,5980,5948	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749144	28977	PASS	C	T	6081	0.936359	0	0,1,0,6075	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749144	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	42460	0.001319	2	21333,21031,37,32	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749145	241	PASS	C	T	10279	0.849888	0	0,1,5094,5139	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749145	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	8217	0.003286	0	8191,3,27,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749145	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	8218	0.001095	0	8145,3,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749145	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	8218	0.001825	0	8145,3,15,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749145	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	8218	0.004867	17	8145,3,39,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749145	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	8210	0.002436	0	7463,10,622,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749145	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	8210	0.001827	0	8184,11,15,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749145	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	21814	5.04E-4	6	13572,8230,9,2	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749145	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	21814	0.002063	32	13538,8222,39,6	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749145	913	PASS	C	T	13574	0.903713	0	0,10,0,13541	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749145	1267	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23308	0.016003	0	13590,9329,224,155	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G154	nsp2	0.001789	0.9811	2	1	C>T
ERR5749145	1510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	13790	0.003988	0	0,13621,0,64	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G235	nsp2	0.002159	0.937304	1	1	T>C
ERR5749145	3037	PASS	C	T	14914	0.799182	58	1,23,7450,7341	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749145	3267	PASS	C	T	13055	0.971812	2147483647	0,0,13050,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749145	3671	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GA	19436	6.69E-4	1	9722,9709,6,7	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/aaAt	N319K?	nsp3	0.000351	0.0625	6	2	G>GA
ERR5749145	5388	PASS	C	A	4824	0.963308	2147483647	0,0,4821,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749145	5512	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4821	0.003111	0	0,4804,0,16	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N931	nsp3	0.002299	0.987013	1	1	C>T
ERR5749145	5986	PASS	C	T	9922	0.971578	0	2,0,9913,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749145	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	9174	0.009265	0	5,9082,0,85	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L1328S?	nsp3	0.000731	0.14377	4	2	C>CT
ERR5749145	6954	PASS	T	C	14910	0.817975	0	0,4,0,14827	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749145	8950	PASS	C	T	27919	0.976503	0	2,2,11328,16578	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I132	nsp4	0.002808	0.982604	1	1	C>T
ERR5749145	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	11448	0.004368	0	11380,1,60,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749145	11287	PASS	GTCTGGTTTT	G	11442	0.996941	25	1,35,0,11407	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749145	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23791	9.67E-4	0	11879,11854,12,12	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749145	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	8688	0.005064	2234	8449,97,5,134	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749145	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	16843	0.001069	0	8439,8394,9,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749145	14408	PASS	C	T	16843	0.86202	3	6,9,8390,8326	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749145	14676	PASS	C	T	8204	0.755241	0	1,0,8178,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749145	15279	PASS	C	T	13564	0.889045	0	4,0,13542,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749145	16176	PASS	T	C	13347	0.983142	0	0,0,6937,6402	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749145	17181	PASS	T	C	8579	0.986595	0	4,0,8573,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaT/gaC	D315	helicase	0.986595	0.991193	1	1	T>C
ERR5749145	18576	PASS	C	T	18539	0.865904	0	0,2,0,18477	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D179	ExoN	0.005404	0.876866	2	2	C>T
ERR5749145	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	17557	6.83E-4	0	17545,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749145	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	15382	6.5E-4	0	0,15372,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749145	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23299	0.001888	0	23243,0,45,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749145	21234	PASS	C	T	23018	0.678469	0	18,0,22730,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A192	MethTr	0.000472	0.857572	5	2	C>T
ERR5749145	21658	PASS	C	T	10525	0.933302	0	0,1,1,10505	LOW	SILENT	SYNONYMOUS_CODING	S	ttC/ttT	F32	S	0.001649	0.937508	2	2	C>T
ERR5749145	21764	PASS	ATACATG	A	9277	0.997305	0	25,0,9252,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749145	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	9275	9.7E-4	0	9266,0,9,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749145	21990	PASS	TTTA	T	9282	0.998276	0	0,16,2,9264	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749145	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18908	0.001481	0	9407,9455,13,15	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749145	23063	PASS	A	T	9423	0.878807	0	0,2,2,9378	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749145	23271	PASS	C	A	13471	0.920867	2147483647	0,0,13448,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749145	23403	PASS	A	G	13467	0.9651	0	0,4,0,13455	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749145	23604	PASS	C	A	11700	0.944188	0	7,0,11689,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749145	23709	PASS	C	T	11678	0.929611	0	0,4,4,11644	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749145	24506	PASS	T	G	11305	0.976913	0	4,0,11301,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749145	24914	PASS	G	C	24798	0.957134	0	0,0,12350,12429	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749145	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	16848	0.002493	61	12521,4271,50,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749145	25844	PASS	C	T	16090	0.924798	0	0,7,9,16055	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aCt/aTt	T151I	orf3a	0.001226	0.938776	1	1	C>T
ERR5749145	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	8561	0.001168	0	2,8549,0,10	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749145	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	8560	0.005607	0	0,8510,0,48	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749145	27577	PASS	C	T	24747	0.851618	4	4,6,13450,11145	HIGH	NONSENSE	STOP_GAINED	ORF7a	Caa/Taa	Q62*	orf7a	0.000614	0.952205	4	2	C>T
ERR5749145	27672	PASS	TCAAGAACTTTACTCTCCAATTTTTCTTATTGTTGCGGCAATAGTGTTTATAACACTTTGCTTCACACTCAAAAGAAAG	T	13258	0.999321	476	28,254,0,13249	MODERATE	NONE	CODON_DELETION	ORF7a	caagaactttactctccaatttttcttattgttgcggcaatagtgtttataacactttgcttcacactcaaaagaaag/	QELYSPIFLIVAAIVFITLCFTLKRK94	orf7a	0.00102	0.999439	2	1	TCAAGAACTTTACTCTCCAATTTTTCTTATTGTTGCGGCAATAGTGTTTATAACACTTTGCTTCACACTCAAAAGAAAG>T
ERR5749145	27972	PASS	C	T	8237	0.902513	41	1,2,8166,38	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749145	28048	PASS	G	T	8202	0.931602	0	0,4,0,8196	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749145	28111	PASS	A	G	19909	0.976242	8	9,2,11686,8206	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749145	28270	PASS	TA	T	22731	0.994193	272	125,7,11542,11057	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749145	28280	PASS	G	C	22680	0.940079	4	4,1,11566,11055	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749145	28281	PASS	A	T	22680	0.920855	19	18,5,11567,11052	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749145	28282	PASS	T	A	22680	0.913007	23	16,3,11551,11062	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749145	28407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TACCCAATA	T	11718	7.68E-4	0	16,11693,0,9	HIGH	NONE	FRAME_SHIFT	N	cccaataat/	PNN46	N	0.000382	0.179673	1	1	TACCCAATA>T
ERR5749145	28881	PASS	G	A	10902	0.758852	9	4,0,5375,5363	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749145	28882	PASS	G	A	10899	0.829434	12	5,0,5449,5341	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749145	28883	PASS	G	C	10900	0.943211	9	0,3,5464,5419	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749145	28977	PASS	C	T	5554	0.926359	0	0,0,1,5542	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749145	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	36463	7.4E-4	0	18313,18101,16,16	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749146	241	PASS	C	T	75	0.906667	0	0,0,37,38	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749146	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	113	0.026549	0	110,0,3,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749146	2706	PASS	C	T	12931	0.821437	5	2,5,6524,6291	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T634I	nsp2	0.000591	0.821437	1	1	C>T
ERR5749146	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	13023	0.001229	873	6522,6138,11,339	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749146	3037	PASS	C	T	766	0.809399	0	0,0,385,376	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749146	3045	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	390	0.010256	9	384,382,0,4	HIGH	NONE	FRAME_SHIFT	ORF1ab	gat/	D110	nsp3	0.001332	0.07971	2	2	CAG>C
ERR5749146	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	396	0.020202	151	1,387,8,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749146	3671	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	3823	0.008632	0	1892,1876,18,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E318K	nsp3	0.000351	0.0625	6	2	G>A
ERR5749146	3802	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	2262	0.024757	37	337,1869,0,56	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/aaAt	N363K?	nsp3	0.000554	0.064198	4	2	T>TA
ERR5749146	3852	PASS	A	T	337	0.973294	2147483647	0,0,337,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gAa/gTa	E378V	nsp3	0.008354	0.97973	2	1	A>T
ERR5749146	3961	PASS	C	T	334	0.847305	2147483647	0,0,332,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I414	nsp3	0.000417	0.869983	2	2	C>T
ERR5749146	4504	PASS	G	T	6661	0.829905	21	14,32,3319,3293	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gaG/gaT	E595D	nsp3	0.001014	0.846766	1	1	G>T
ERR5749146	7735	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5011	0.008781	0	4956,0,51,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I1672	nsp3	0.000658	0.954659	3	2	C>T
ERR5749146	7798	PASS	G	T	5005	0.922677	0	2,0,5002,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaG/aaT	K1693N	nsp3	0.001127	0.936026	1	1	G>T
ERR5749146	9072	PASS	C	T	7355	0.92998	0	0,0,3838,3505	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCc/aTc	T173I	nsp4	0.001037	0.930675	2	1	C>T
ERR5749146	9891	PASS	C	T	1062	0.947269	0	1,0,1060,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A446V	nsp4	0.002963	0.958011	1	1	C>T
ERR5749146	10116	PASS	C	T	5511	0.952096	0	0,0,4449,1062	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T21I	3Cpro	0.001266	0.952096	1	1	C>T
ERR5749146	10156	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4452	0.008535	0	4408,3,40,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D34	3Cpro	0.001207	0.949463	1	1	C>T
ERR5749146	11074	PASS	C	CT	7694	0.050689	0	7262,0,390,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CT
ERR5749146	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	7694	0.004939	0	7262,0,38,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749146	11082	PASS	TG	T	7670	0.059192	0	7240,0,454,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000427	0.179468	2	1	TG>T
ERR5749146	11083	PASS	G	T	7670	0.901695	0	2,0,7208,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749146	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	7670	0.02412	0	7471,0,185,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/tTat	Y38L?	nsp6	0.000477	0.901695	5	2	G>GT
ERR5749146	11287	PASS	GTCTGGTTTT	G	7696	0.99948	0	0,4,0,7692	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749146	11782	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	5017	0.002193	0	0,4968,0,13	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaA/aaG	K270	nsp6	0.001073	0.917917	2	2	A>G
ERR5749146	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	4398	0.003865	0	4382,0,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749146	14408	PASS	C	T	63	0.873016	0	0,0,32,31	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749146	15277	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1527	0.012443	0	1506,0,20,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cac/Tac	H613Y	RdRp	0.006345	0.326816	1	1	C>T
ERR5749146	15872	PASS	A	G	3162	0.05155	0	2995,1,165,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gAa/gGa	E811G	RdRp	0.001683	0.05155	1	1	A>G
ERR5749146	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	1913	0.016205	0	1882,0,31,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749146	19329	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	2189	0.010964	0	2164,0,24,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcC	A430	ExoN	0.001217	0.228916	1	1	T>C
ERR5749146	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	1089	0.014692	0	1073,0,16,0	HIGH	NONE	FRAME_SHIFT+STOP_GAINED	ORF1ab	gat/Tgat	D124*?	endoR	0.000884	0.981982	5	2	C>CT
ERR5749146	20578	PASS	G	A	3667	0.958277	2147483647	0,0,3666,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtg/Atg	V320M	endoR	0.00085	0.958277	3	1	G>A
ERR5749146	20844	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10819	0.011646	225	7004,3661,135,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P62	MethTr	0.000293	0.905571	5	2	C>T
ERR5749146	21004	PASS	G	T	14164	0.856891	19	13,3,7028,7105	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gca/Tca	A116S	MethTr	0.000749	0.857814	3	1	G>T
ERR5749146	21846	PASS	C	T	4478	0.778919	3	0,1,2224,2211	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCt/aTt	T95I	S	0.001104	0.788523	1	1	C>T
ERR5749146	21990	PASS	TTTA	T	2254	0.999556	0	0,1,0,2253	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749146	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2243	0.015604	38	1687,521,35,0	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749146	22898	PASS	G	A	1722	0.981998	2147483647	0,0,1722,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ggt/Agt	G446S	S	0.062244	0.981998	1	1	G>A
ERR5749146	22981	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	1721	0.004648	0	1708,0,10,0	HIGH	NONSENSE	STOP_GAINED	S	taT/taA	Y473*	S	0.001557	0.861194	3	2	T>A
ERR5749146	23012	PASS	G	A	3292	0.897631	0	0,0,1706,1580	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gaa/Aaa	E484K	S	0.001756	0.909912	2	1	G>A
ERR5749146	23287	PASS	T	C	6154	0.943126	0	1,0,6145,0	LOW	SILENT	SYNONYMOUS_CODING	S	gcT/gcC	A575	S	0.001462	0.947477	1	1	T>C
ERR5749146	23403	PASS	A	G	6153	0.962457	0	0,2,0,6147	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749146	23604	PASS	C	A	1857	0.95692	2147483647	0,0,1857,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749146	23948	PASS	G	C	632	0.879747	2147483647	0,0,630,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gat/Cat	D796H	S	0.879747	0.913697	1	1	G>C
ERR5749146	24382	PASS	C	T	1583	0.920404	2147483647	0,0,0,1580	LOW	SILENT	SYNONYMOUS_CODING	S	tcC/tcT	S940	S	0.002118	0.920404	2	1	C>T
ERR5749146	24616	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2324	0.008606	0	1,2297,0,24	LOW	SILENT	SYNONYMOUS_CODING	S	atC/atT	I1018	S	0.001268	0.127917	3	2	C>T
ERR5749146	25276	PASS	C	A	1273	0.9348	0	0,1,0,1271	LOW	SILENT	SYNONYMOUS_CODING	S	acC/acA	T1238	S	0.005906	0.9348	2	2	C>A
ERR5749146	25429	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	8642	0.027656	0	8391,0,246,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gta/Cta	V13L	orf3a	0.00064	0.906678	5	2	G>C
ERR5749146	25555	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	8635	0.008454	0	0,8562,0,73	HIGH	NONE	FRAME_SHIFT	ORF3a	ttt/	F56	orf3a	0.000552	0.900573	5	2	GT>G
ERR5749146	25587	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	8640	0.015046	0	0,8510,0,130	HIGH	NONE	FRAME_SHIFT	ORF3a	aag/aaAg	K67K?	orf3a	0.000598	0.813206	6	2	C>CA
ERR5749146	26044	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3009	0.00565	0	2989,0,18,0	HIGH	NONSENSE	STOP_GAINED	ORF3a	Caa/Taa	Q218*	orf3a	0.000469	0.102679	3	3	C>T
ERR5749146	26319	PASS	A	G	2271	0.965214	2147483647	0,0,2268,0	LOW	SILENT	SYNONYMOUS_CODING	E	gtA/gtG	V25	E	0.001432	0.971582	2	1	A>G
ERR5749146	26767	PASS	T	C	1452	0.960055	2147483647	0,0,0,1450	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	aTc/aCc	I82T	M	0.954318	0.968313	2	1	T>C
ERR5749146	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTT	G	1452	0.032369	0	0,1405,0,47	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/tgc	CLVGLMWLSYFIASF86C	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTT>G
ERR5749146	27886	PASS	AAACGAACATGAAATT	A	412	0.997573	0	1,0,411,0	HIGH	NONE	GENE_FUSION	ORF7b+ORF8	.	.	.	0.997573	0.998916	1	1	AAACGAACATGAAATT>A
ERR5749146	28209	PASS	G	T	10398	0.963166	0	2,0,10388,0	HIGH	NONSENSE	STOP_GAINED	ORF8	Gaa/Taa	E106*	orf8	0.001409	0.963166	2	2	G>T
ERR5749146	28271	PASS	A	G	20694	0.919784	2	3,1,10365,10299	.	.	.	.	.	.	.	0.000482	0.924941	3	2	A>G
ERR5749146	28512	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4265	0.008206	0	4227,0,38,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	cCa/cTa	P80L	N	0.000621	0.172671	3	2	C>T
ERR5749146	28881	PASS	G	A	244	0.70082	0	0,0,46,192	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749146	28882	PASS	G	A	244	0.782787	7	1,0,46,196	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749146	28883	PASS	G	C	244	0.836066	0	0,0,47,196	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749146	28895	PASS	GCTA	G	248	0.814516	504	46,0,0,202	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	N	gctaga/gga	AR208G	N	0.814516	0.850664	1	1	GCTA>G
ERR5749146	29140	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	4279	0.012853	0	4213,0,66,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	caG/caT	Q289H	N	0.000955	0.888232	2	1	G>T
ERR5749146	29769	PASS	C	T	511	0.945205	2147483647	0,0,0,511	.	.	.	.	.	.	.	0.001999	0.945205	1	1	C>T
ERR5749147	241	PASS	C	T	16732	0.860148	0	1,1,8301,8366	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749147	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10182	0.002259	0	9366,0,790,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749147	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	10178	7.86E-4	0	10172,0,8,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749147	913	PASS	C	T	19591	0.918636	0	0,14,0,19549	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749147	3037	PASS	C	T	15881	0.830363	35	1,15,7922,7836	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749147	3267	PASS	C	T	18741	0.971933	0	4,0,18734,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749147	5388	PASS	C	A	4913	0.959088	2147483647	0,0,4911,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749147	5986	PASS	C	T	10442	0.974909	0	2,0,10431,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749147	6954	PASS	T	C	21815	0.831355	0	0,3,2,21713	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749147	8950	PASS	C	T	36511	0.977021	10	4,2,11769,24716	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I132	nsp4	0.002808	0.982604	1	1	C>T
ERR5749147	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	27455	4.01E-4	39	12080,15364,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749147	11287	PASS	GTCTGGTTTT	G	15938	0.998557	0	0,23,0,15915	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749147	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30940	0.001357	0	15456,15409,22,23	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749147	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	9550	0.005759	3100	9295,66,6,177	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749147	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	18515	7.02E-4	0	9292,9226,7,6	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749147	14408	PASS	C	T	18515	0.844342	0	1,1,9252,9151	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749147	14676	PASS	C	T	11872	0.746378	0	4,0,11819,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749147	15279	PASS	C	T	20544	0.890674	0	1,0,20507,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749147	16176	PASS	T	C	16844	0.979577	3	1,0,7648,9184	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749147	17181	PASS	T	C	13041	0.989495	0	2,0,13035,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaT/gaC	D315	helicase	0.986595	0.991193	1	1	T>C
ERR5749147	18576	PASS	C	T	26422	0.867156	0	0,2,0,26339	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D179	ExoN	0.005404	0.876866	2	2	C>T
ERR5749147	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	19875	6.54E-4	0	19862,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749147	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24660	0.002352	0	24580,2,63,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749147	20148	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24651	0.002475	0	0,24536,0,64	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F176	endoR	0.000513	0.969223	2	2	C>T
ERR5749147	21234	PASS	C	T	23039	0.638092	0	17,0,22714,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A192	MethTr	0.000472	0.857572	5	2	C>T
ERR5749147	21658	PASS	C	T	14978	0.937508	0	0,2,5,14943	LOW	SILENT	SYNONYMOUS_CODING	S	ttC/ttT	F32	S	0.001649	0.937508	2	2	C>T
ERR5749147	21764	PASS	ATACATG	A	10243	0.996388	0	37,0,10206,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749147	21990	PASS	TTTA	T	10248	0.997561	0	0,25,5,10218	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749147	23063	PASS	A	T	9154	0.869893	0	0,1,0,9102	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749147	23271	PASS	C	A	19628	0.921337	0	4,0,19600,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749147	23403	PASS	A	G	19627	0.969277	0	0,1,0,19617	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749147	23604	PASS	C	A	12341	0.939956	0	8,0,12324,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749147	23709	PASS	C	T	12321	0.938479	0	0,7,0,12296	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749147	24506	PASS	T	G	15861	0.974277	0	6,0,15852,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749147	24914	PASS	G	C	27803	0.956623	0	0,0,13838,13953	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749147	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	20096	0.002239	92	13480,6560,55,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749147	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	24438	0.001309	340	24347,13,20,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749147	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	24411	5.74E-4	0	24397,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749147	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	24540	0.001019	953	24198,116,138,68	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749147	25844	PASS	C	T	24365	0.921075	0	0,11,2,24321	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aCt/aTt	T151I	orf3a	0.001226	0.938776	1	1	C>T
ERR5749147	27577	PASS	C	T	36631	0.860173	1	4,5,19879,16639	HIGH	NONSENSE	STOP_GAINED	ORF7a	Caa/Taa	Q62*	orf7a	0.000614	0.952205	4	2	C>T
ERR5749147	27672	PASS	TCAAGAACTTTACTCTCCAATTTTTCTTATTGTTGCGGCAATAGTGTTTATAACACTTTGCTTCACACTCAAAAGAAAG	T	19653	0.999084	88	5,338,0,19635	MODERATE	NONE	CODON_DELETION	ORF7a	caagaactttactctccaatttttcttattgttgcggcaatagtgtttataacactttgcttcacactcaaaagaaag/	QELYSPIFLIVAAIVFITLCFTLKRK94	orf7a	0.00102	0.999439	2	1	TCAAGAACTTTACTCTCCAATTTTTCTTATTGTTGCGGCAATAGTGTTTATAACACTTTGCTTCACACTCAAAAGAAAG>T
ERR5749147	27913	PASS	T	C	8072	0.249628	0	5977,0,2075,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tTa/tCa	L7S	orf8	0.00234	0.249628	2	2	T>C
ERR5749147	27972	PASS	C	T	8089	0.896897	22	1,1,8037,21	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749147	28048	PASS	G	T	8066	0.916687	0	0,9,1,8052	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749147	28111	PASS	A	G	25295	0.978652	0	6,3,17209,8068	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749147	28270	PASS	TA	T	33410	0.99557	315	148,9,17018,16244	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749147	28280	PASS	G	C	33349	0.939339	26	10,0,17044,16236	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749147	28281	PASS	A	T	33349	0.91409	52	28,3,17036,16229	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749147	28282	PASS	T	A	33353	0.910413	13	24,11,16999,16243	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749147	28292	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	34275	7.29E-4	0	17083,17165,12,13	HIGH	NONE	FRAME_SHIFT	N	aat/	N8	N	0.000304	0.055324	4	2	CA>C
ERR5749147	28881	PASS	G	A	14875	0.793681	6	3,0,7403,7299	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749147	28882	PASS	G	A	14874	0.836829	18	7,0,7450,7290	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749147	28883	PASS	G	C	14874	0.943055	3	0,1,7467,7390	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749147	28977	PASS	C	T	7569	0.926542	0	0,0,1,7550	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749147	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	26227	8.77E-4	77	18647,7543,4,21	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749147	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	37052	0.00108	0	18596,18397,24,23	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749148	241	PASS	C	T	1278	0.85446	0	0,0,638,636	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749148	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	1784	0.006726	0	1771,0,12,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749148	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTTGA	G	1784	0.002803	0	1779,0,5,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTTGA>G
ERR5749148	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	1783	0.003365	0	1777,0,6,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749148	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	1785	0.003922	0	1774,2,7,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749148	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	12002	0.007665	60	10125,1785,92,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749148	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	12002	0.001583	0	10200,1781,17,2	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749148	1027	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	8631	0.002549	33	8589,10,21,2	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccT/ccC	P74	nsp2	0.001454	0.276316	1	1	T>C
ERR5749148	1684	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7635	0.001965	0	7618,0,15,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I293	nsp2	0.000638	0.973136	2	2	C>T
ERR5749148	1685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	7635	0.001965	0	7615,0,19,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gcc/Tcc	A294S	nsp2	0.001379	0.231183	3	2	G>T
ERR5749148	2151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATTGGCTTGAAGAGAAG	A	12652	0.002134	0	0,12625,0,27	HIGH	NONE	FRAME_SHIFT	ORF1ab	tggcttgaagagaagttt/	WLEEKF450	nsp2	0.000402	0.971954	3	2	ATTGGCTTGAAGAGAAG>A
ERR5749148	2185	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	12658	0.004819	0	2,12586,0,69	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gaG/gaT	E460D	nsp2	0.000441	0.963529	4	3	G>T
ERR5749148	2232	PASS	C	T	17417	0.381237	6	2730,7384,2033,5261	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A476V	nsp2	0.000499	0.381237	2	2	C>T
ERR5749148	2706	PASS	C	T	172	0.767442	0	0,0,86,85	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T634I	nsp2	0.000591	0.821437	1	1	C>T
ERR5749148	3037	PASS	C	T	4170	0.805036	12	0,4,2075,2035	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749148	3852	PASS	A	T	2960	0.97973	2147483647	0,0,2960,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gAa/gTa	E378V	nsp3	0.008354	0.97973	2	1	A>T
ERR5749148	3961	PASS	C	T	2949	0.852831	0	1,0,2921,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I414	nsp3	0.000417	0.869983	2	2	C>T
ERR5749148	4504	PASS	G	T	16676	0.829276	19	43,71,8288,8267	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gaG/gaT	E595D	nsp3	0.001014	0.846766	1	1	G>T
ERR5749148	4832	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13701	0.005547	0	6793,6772,51,52	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L705	nsp3	0.000542	0.727166	3	2	C>T
ERR5749148	5230	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	5964	0.002515	0	0,5936,0,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaG/aaT	K837N	nsp3	0.002515	0.902519	1	1	G>T
ERR5749148	5672	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10174	0.004226	0	10126,0,44,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cct/Tct	P985S	nsp3	0.004226	0.977953	2	1	C>T
ERR5749148	6954	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	8552	0.002105	0	0,8520,0,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749148	7798	PASS	G	T	12255	0.936026	0	3,0,12243,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaG/aaT	K1693N	nsp3	0.001127	0.936026	1	1	G>T
ERR5749148	7926	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	12271	0.002282	0	0,12243,0,28	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1737	nsp3	0.000531	0.97019	5	2	CAA>C
ERR5749148	9072	PASS	C	T	19816	0.925717	4	1,3,10385,9400	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCc/aTc	T173I	nsp4	0.001037	0.930675	2	1	C>T
ERR5749148	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	7617	0.001313	4	6420,1187,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749148	9561	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CATTCTTACCTGGTGTTTATTCTGTT	C	6432	0.00171	0	6419,2,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttcttacctggtgtttattctgttatt/	FLPGVYSVI337	nsp4	0.00171	0.161742	2	2	CATTCTTACCTGGTGTTTATTCTGTT>C
ERR5749148	9891	PASS	C	T	2714	0.957996	2147483647	0,0,2711,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A446V	nsp4	0.002963	0.958011	1	1	C>T
ERR5749148	10045	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	2710	0.003321	0	0,2699,0,11	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcG	A497	nsp4	0.003321	0.052632	2	2	T>G
ERR5749148	10116	PASS	C	T	12586	0.940013	0	0,0,9871,2714	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T21I	3Cpro	0.001266	0.952096	1	1	C>T
ERR5749148	10702	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11023	0.003992	0	3,10971,0,45	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D216	3Cpro	0.000396	0.098214	2	2	C>T
ERR5749148	11074	PASS	C	CT	15173	0.067422	0	13871,0,1023,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CT
ERR5749148	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	15173	0.014499	0	13871,0,220,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749148	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTTT	15173	0.003229	0	13871,0,49,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_INSERTION	ORF1ab	ttg/ttTTTg	L37FL	nsp6	0.000965	0.945355	5	2	C>CTTT
ERR5749148	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15173	0.008107	0	14996,0,144,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749148	11075	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TTC	15173	9.23E-4	0	15156,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/ttCTt	F35F?	nsp6	0.000555	0.885796	4	2	T>TTC
ERR5749148	11082	PASS	TG	T	15121	0.111765	0	13483,0,1690,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000427	0.179468	2	1	TG>T
ERR5749148	11083	PASS	G	T	15121	0.841479	0	5,0,13338,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749148	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	15121	0.029628	0	14582,0,448,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/tTat	Y38L?	nsp6	0.000477	0.901695	5	2	G>GT
ERR5749148	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GTT	15121	0.005357	0	14582,0,81,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/tTTat	Y38F?	nsp6	0.000477	0.901695	5	2	G>GTT
ERR5749148	11199	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30068	0.003193	0	14792,15044,51,52	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCc/gTc	A76V	nsp6	0.000309	0.056758	3	2	C>T
ERR5749148	11287	PASS	GTCTGGTTTT	G	15170	0.998286	0	0,26,0,15144	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749148	11824	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	13006	0.001384	0	0,12988,0,18	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K285	nsp6	0.000465	0.922016	2	2	CA>C
ERR5749148	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	8728	0.002062	0	8704,0,18,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749148	13356	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18976	0.001476	52	9265,9676,26,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T111I	nsp10	0.000806	0.091518	1	1	C>T
ERR5749148	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18566	0.0014	0	9270,9240,14,15	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749148	14408	PASS	C	T	1623	0.845964	0	0,0,811,801	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749148	15240	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	G	7129	0.001824	0	7106,8,14,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaC/aaG	N600K	RdRp	0.000934	0.931284	2	2	C>G
ERR5749148	15720	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10686	0.001684	0	0,10661,0,19	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D760	RdRp	0.001002	0.917823	1	1	C>T
ERR5749148	15797	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	10705	0.003456	0	0,10617,0,86	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cTt/cAt	L786H	RdRp	0.001418	0.07734	2	1	T>A
ERR5749148	15905	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AG	A	7896	0.001773	0	7882,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggt/	G823	RdRp	0.000835	0.057692	2	1	AG>A
ERR5749148	15983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	7889	0.002155	0	7872,0,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T850	RdRp	0.000701	0.338235	2	1	TA>T
ERR5749148	16508	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	13637	0.001393	0	13617,1,19,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L92	helicase	0.000561	0.074909	2	2	GT>G
ERR5749148	17418	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	14493	0.001518	52	7662,6800,4,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaG/aaT	K394N	helicase	0.001518	0.108696	2	1	G>T
ERR5749148	18232	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4246	0.003768	0	0,4226,0,17	HIGH	NONSENSE	STOP_GAINED	ORF1ab	Caa/Taa	Q65*	ExoN	0.002195	0.056093	1	1	C>T
ERR5749148	18498	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	17876	0.003077	0	55,17691,0,72	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atC	M153I	ExoN	0.001072	0.080328	3	1	G>C
ERR5749148	18501	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	17827	0.003141	0	55,17771,0,56	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K155	ExoN	0.000336	0.857143	4	2	CA>C
ERR5749148	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	20319	6.4E-4	0	20306,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749148	18744	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20316	0.004775	0	20201,0,100,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y235	ExoN	0.000912	0.953624	2	2	C>T
ERR5749148	19011	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17432	0.001893	0	17389,0,35,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D324	ExoN	0.000408	0.975746	4	2	C>T
ERR5749148	19113	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	34690	4.61E-4	45	17349,17342,0,16	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K359	ExoN	0.000461	0.125	4	3	CA>C
ERR5749148	19329	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	8596	0.00221	0	8569,0,23,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcC	A430	ExoN	0.001217	0.228916	1	1	T>C
ERR5749148	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5992	0.004172	0	5960,0,29,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749148	20578	PASS	G	A	12827	0.956576	0	1,0,12824,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtg/Atg	V320M	endoR	0.00085	0.958277	3	1	G>A
ERR5749148	20719	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	12800	0.002813	0	0,12764,0,36	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctatta/	LL21	MethTr	0.000341	0.209091	2	2	CTA>C
ERR5749148	20823	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27045	0.001257	116	14209,12788,0,36	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N55	MethTr	0.001138	0.982544	2	2	C>T
ERR5749148	21004	PASS	G	T	28215	0.84168	26	14,2,14027,14120	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gca/Tca	A116S	MethTr	0.000749	0.857814	3	1	G>T
ERR5749148	21123	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	26192	8.02E-4	71	11953,14218,21,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ata/Tata	I157Y?	MethTr	0.000257	0.90982	5	2	G>GT
ERR5749148	21304	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	11950	0.002427	0	0,11906,0,38	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgc/Agc	R216S	MethTr	0.000411	0.605296	3	2	C>A
ERR5749148	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14301	0.002517	25	6988,7113,11,31	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749148	21622	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	7201	0.001666	0	0,7189,0,12	HIGH	NONE	FRAME_SHIFT	S	aga/	R21	S	0.000846	0.946634	3	2	CAG>C
ERR5749148	21657	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	7203	0.00361	0	0,7168,0,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tTc/tCc	F32S	S	0.000702	0.06812	2	2	T>C
ERR5749148	21811	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6323	0.00253	0	6302,0,16,0	LOW	SILENT	SYNONYMOUS_CODING	S	gtC/gtT	V83	S	0.001327	0.179245	1	1	C>T
ERR5749148	21846	PASS	C	T	12550	0.785578	30	0,10,6272,6162	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCt/aTt	T95I	S	0.001104	0.788523	1	1	C>T
ERR5749148	21990	PASS	TTTA	T	6330	0.990363	0	0,61,3,6266	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749148	22293	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	17498	0.001314	31	4818,12657,0,23	HIGH	NONE	FRAME_SHIFT	S	tta/	L244	S	0.000308	0.160511	4	1	TA>T
ERR5749148	22388	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4823	0.003317	0	4799,0,18,0	LOW	SILENT	SYNONYMOUS_CODING	S	Cta/Tta	L276	S	0.003317	0.950604	1	1	C>T
ERR5749148	22898	PASS	G	A	6100	0.975902	2147483647	0,0,6100,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ggt/Agt	G446S	S	0.062244	0.981998	1	1	G>A
ERR5749148	23012	PASS	G	A	11585	0.895209	14	6,0,6019,5538	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gaa/Aaa	E484K	S	0.001756	0.909912	2	1	G>A
ERR5749148	23183	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTCAACTTCAATGGTTTA	T	20156	0.00258	78	13996,6100,52,0	HIGH	NONE	FRAME_SHIFT	S	ttcaacttcaatggttta/	FNFNGL541	S	0.000388	0.135922	2	2	TTCAACTTCAATGGTTTA>T
ERR5749148	23287	PASS	T	C	14051	0.947477	0	2,0,14040,0	LOW	SILENT	SYNONYMOUS_CODING	S	gcT/gcC	A575	S	0.001462	0.947477	1	1	T>C
ERR5749148	23309	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAGATTCTT	G	14031	0.003492	0	13982,0,49,0	HIGH	NONE	FRAME_SHIFT	S	gagattctt/	EIL583	S	0.003492	0.954191	2	2	GAGATTCTT>G
ERR5749148	23403	PASS	A	G	14045	0.970879	0	0,1,0,14037	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749148	23604	PASS	C	A	6293	0.946925	0	2,0,6286,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749148	23635	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6289	0.002385	0	6266,0,17,0	LOW	SILENT	SYNONYMOUS_CODING	S	tcC/tcT	S691	S	0.002385	0.958978	1	1	C>T
ERR5749148	23948	PASS	G	C	3059	0.913697	2147483647	0,0,3052,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gat/Cat	D796H	S	0.879747	0.913697	1	1	G>C
ERR5749148	24127	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	8793	0.00182	26	5714,3063,16,0	HIGH	NONE	FRAME_SHIFT	S	aac/	N856	S	0.000324	0.111888	4	1	TA>T
ERR5749148	24237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5727	0.00227	0	5704,0,14,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gTt	A892V	S	0.001242	0.889739	1	1	C>T
ERR5749148	24320	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	5723	0.005591	0	0,5691,0,32	HIGH	NONE	FRAME_SHIFT	S	aaa/	K921	S	0.000763	0.138365	4	2	CA>C
ERR5749148	24382	PASS	C	T	5729	0.915343	0	0,2,0,5716	LOW	SILENT	SYNONYMOUS_CODING	S	tcC/tcT	S940	S	0.002118	0.920404	2	1	C>T
ERR5749148	24998	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	14328	0.001186	0	1,14298,0,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Tac	D1146Y	S	0.001186	0.846993	3	1	G>T
ERR5749148	25276	PASS	C	A	4627	0.925438	0	0,1,0,4623	LOW	SILENT	SYNONYMOUS_CODING	S	acC/acA	T1238	S	0.005906	0.9348	2	2	C>A
ERR5749148	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	18721	0.001068	32	14064,4627,28,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749148	25413	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14124	0.001912	0	14074,0,28,0	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	atC/atT	I7	orf3a	0.00145	0.968329	2	1	C>T
ERR5749148	25469	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14170	0.001553	0	14080,54,22,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	tCa/tTa	S26L	orf3a	0.001214	0.959377	2	2	C>T
ERR5749148	25553	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14114	0.014666	0	0,13809,0,244	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	gCt/gTt	A54V	orf3a	0.001165	0.868131	3	2	C>T
ERR5749148	25571	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14122	0.001558	0	0,14093,0,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	tCc/tTc	S60F	orf3a	0.001558	0.922217	1	1	C>T
ERR5749148	25587	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	14124	0.00177	0	0,14058,0,25	HIGH	NONE	FRAME_SHIFT	ORF3a	aag/	K67	orf3a	0.000598	0.813206	6	2	CA>C
ERR5749148	25587	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	14124	0.002903	0	0,14058,0,41	HIGH	NONE	FRAME_SHIFT	ORF3a	aag/	K67	orf3a	0.000598	0.813206	6	2	CAA>C
ERR5749148	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	1520	0.009868	271	1485,12,1,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749148	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	11972	0.001086	0	0,11959,0,13	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749148	26256	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18400	0.002283	28	6384,11946,26,18	LOW	SILENT	SYNONYMOUS_CODING	E	ttC/ttT	F4	E	0.000748	0.969561	2	2	C>T
ERR5749148	26319	PASS	A	G	6411	0.969584	0	1,0,6409,0	LOW	SILENT	SYNONYMOUS_CODING	E	gtA/gtG	V25	E	0.001432	0.971582	2	1	A>G
ERR5749148	26416	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	12595	0.00127	48	6359,6337,0,16	HIGH	NONE	FRAME_SHIFT	E	tac/	Y59	E	0.000457	0.913418	2	2	GT>G
ERR5749148	26571	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTTGAACAATGGAACCTAGTAATAGGTTTCCTA	C	4606	0.003257	0	4591,0,15,0	HIGH	NONE	FRAME_SHIFT	M	gaacaatggaacctagtaataggtttcctattc/	EQWNLVIGFLF18	M	0.000508	0.905823	3	2	CTTGAACAATGGAACCTAGTAATAGGTTTCCTA>C
ERR5749148	26767	PASS	T	C	4629	0.956794	0	0,0,33,4595	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	aTc/aCc	I82T	M	0.954318	0.968313	2	1	T>C
ERR5749148	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	4601	0.00652	0	0,4571,0,30	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgct/	ACLVGLMWLSYFIA85	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749148	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	4601	0.009998	0	0,4555,0,46	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749148	26918	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	18203	0.001483	0	18160,0,37,0	LOW	SILENT	SYNONYMOUS_CODING	M	ccG/ccT	P132	M	0.000999	0.977086	2	1	G>T
ERR5749148	27209	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATC	A	11242	0.001868	0	11221,0,21,0	HIGH	NONE	FRAME_SHIFT	ORF6	ctc/	L4	orf6	0.00088	0.957103	3	2	ATC>A
ERR5749148	27476	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22084	0.001041	71	10840,11215,0,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	aCa/aTa	T28I	orf7a	0.000547	0.22827	4	2	C>T
ERR5749148	27513	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10847	0.003042	0	10800,5,34,0	LOW	SILENT	SYNONYMOUS_CODING	ORF7a	taC/taT	Y40	orf7a	0.001863	0.982462	2	2	C>T
ERR5749148	27684	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10799	0.003241	0	0,10744,0,40	LOW	SILENT	SYNONYMOUS_CODING	ORF7a	taC/taT	Y97	orf7a	0.000478	0.90411	2	2	C>T
ERR5749148	27765	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10839	0.003875	0	0,10784,0,42	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7b	Ctt/Ttt	L4F	orf7b	0.00109	0.970449	1	1	C>T
ERR5749148	27886	PASS	AAACGAACATGAAATT	A	2137	0.99766	0	2,0,2132,0	HIGH	NONE	GENE_FUSION	ORF7b+ORF8	.	.	.	0.997573	0.998916	1	1	AAACGAACATGAAATT>A
ERR5749148	27913	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAG	T	2137	0.00234	0	2132,0,5,0	HIGH	NONE	FRAME_SHIFT	ORF8	ttagga/	LG7	orf8	0.00234	0.249628	2	2	TAG>T
ERR5749148	28147	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	16503	0.001818	0	16473,0,30,0	HIGH	NONE	FRAME_SHIFT	ORF8	ttt/	F86	orf8	0.000438	0.981624	4	2	CT>C
ERR5749148	28209	PASS	G	T	16502	0.924433	0	11,0,16474,0	HIGH	NONSENSE	STOP_GAINED	ORF8	Gaa/Taa	E106*	orf8	0.001409	0.963166	2	2	G>T
ERR5749148	28271	PASS	A	G	32841	0.924941	0	2,2,16451,16333	.	.	.	.	.	.	.	0.000482	0.924941	3	2	A>G
ERR5749148	28292	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	32929	5.77E-4	0	16449,16465,10,9	HIGH	NONE	FRAME_SHIFT	N	aat/	N8	N	0.000304	0.055324	4	2	CA>C
ERR5749148	28657	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11478	0.003659	0	0,11422,0,48	LOW	SILENT	SYNONYMOUS_CODING	N	gaC/gaT	D128	N	0.00124	0.862766	1	1	C>T
ERR5749148	28881	PASS	G	A	2031	0.744461	7	1,0,316,1673	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749148	28882	PASS	G	A	2030	0.783251	7	1,0,325,1677	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749148	28883	PASS	G	C	2030	0.910837	0	0,1,326,1693	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749148	28895	PASS	GCTA	G	2042	0.837904	2147483647	326,5,0,1711	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	N	gctaga/gga	AR208G	N	0.814516	0.850664	1	1	GCTA>G
ERR5749148	29179	PASS	G	T	23158	0.251188	2147483647	8430,8307,6327,51	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccT	P302	N	0.000713	0.913732	2	1	G>T
ERR5749148	29253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CGG	C	14785	0.001691	0	0,14760,0,25	HIGH	NONE	FRAME_SHIFT	N	gga/	G328	N	0.000361	0.053998	4	2	CGG>C
ERR5749148	29284	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	14788	0.004666	0	0,14719,0,69	HIGH	NONE	FRAME_SHIFT	N	aaa/	K338	N	0.000393	0.931014	3	2	CAA>C
ERR5749148	29769	PASS	C	T	2005	0.94015	2147483647	0,0,0,2000	.	.	.	.	.	.	.	0.001999	0.945205	1	1	C>T
ERR5749149	71	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	420	0.045238	0	396,0,22,0	.	.	.	.	.	.	.	0.002088	0.926791	2	1	C>T
ERR5749149	189	PASS	G	A	353	0.926346	0	1,0,351,0	.	.	.	.	.	.	.	0.926346	0.937678	1	1	G>A
ERR5749149	241	PASS	C	T	703	0.869132	0	0,0,350,352	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749149	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	5153	0.001552	5	3381,1764,7,1	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749149	913	PASS	C	T	3388	0.912928	0	0,2,0,3385	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749149	1813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	6002	0.002999	0	0,5975,0,21	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcA	A336	nsp2	0.001022	0.152738	4	2	T>A
ERR5749149	1874	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	6015	0.002328	0	0,5997,0,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gca/Cca	A357P	nsp2	0.001611	0.344371	2	1	G>C
ERR5749149	2453	PASS	C	T	2753	0.709408	0	0,1,0,2710	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L550F	nsp2	0.00429	0.842201	2	2	C>T
ERR5749149	2862	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6369	0.002826	19	1533,4818,0,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T48I	nsp3	0.000547	0.850688	4	2	C>T
ERR5749149	3037	PASS	C	T	3047	0.806367	3	0,1,1523,1493	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749149	3267	PASS	C	T	3135	0.97193	2147483647	0,0,3134,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749149	3671	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	2656	0.003765	0	1326,1321,5,5	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N319	nsp3	0.000351	0.0625	6	2	GA>G
ERR5749149	4122	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAG	T	5297	0.002265	19	3504,1781,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	atagtg/	IV468	nsp3	0.002265	0.8595	2	2	TAG>T
ERR5749149	4285	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGA	G	3512	0.004271	0	0,3497,0,15	HIGH	NONE	FRAME_SHIFT	ORF1ab	gag/	E523	nsp3	0.000939	0.899038	2	2	GGA>G
ERR5749149	4423	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	2821	0.002836	0	2809,4,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K569	nsp3	0.00063	0.953796	2	2	CA>C
ERR5749149	5388	PASS	C	A	904	0.963496	2147483647	0,0,904,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749149	5986	PASS	C	T	2568	0.97352	2147483647	0,0,2567,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749149	6516	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	6784	0.003538	10	2893,3867,6,18	HIGH	NONE	FRAME_SHIFT	ORF1ab	att/aAtt	I1268N?	nsp3	0.000479	0.186047	4	2	T>TA
ERR5749149	6606	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2899	0.003105	0	2887,0,9,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S1296F	nsp3	0.002262	0.945412	1	1	C>T
ERR5749149	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	2889	0.012807	0	0,2851,0,37	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L1328S?	nsp3	0.000731	0.14377	4	2	C>CT
ERR5749149	6954	PASS	T	C	4847	0.837219	2147483647	0,0,0,4828	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749149	6990	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4862	0.002262	0	0,4769,0,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S1424F	nsp3	0.000504	0.101156	4	2	C>T
ERR5749149	7674	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CGA	C	3826	0.004966	0	3805,2,19,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gac/	D1654	nsp3	0.000682	0.109264	3	2	CGA>C
ERR5749149	8084	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAA	G	3272	0.002445	0	3264,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1790	nsp3	0.000543	0.923413	4	2	GAA>G
ERR5749149	8092	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3272	0.005807	0	3245,0,21,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ctC/ctT	L1791	nsp3	0.000539	0.063953	3	2	C>T
ERR5749149	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	4928	0.001218	0	4541,381,6,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749149	9694	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTA	T	9036	8.85E-4	24	4531,4499,0,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	atc/	I382	nsp4	0.000506	0.057471	1	1	TTA>T
ERR5749149	9712	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	4543	0.002641	0	6,4519,0,17	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcA	S386	nsp4	0.002641	0.893027	2	1	C>A
ERR5749149	10138	PASS	C	T	8763	0.983567	0	1,0,7116,1642	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N28	3Cpro	0.000458	0.983567	3	3	C>T
ERR5749149	10386	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	11315	0.001326	30	4182,7118,12,3	HIGH	NONE	FRAME_SHIFT	ORF1ab	tca/	S113	3Cpro	0.000642	0.160456	4	2	CT>C
ERR5749149	10595	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	4185	0.008363	0	0,4135,0,39	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F181L	3Cpro	0.000964	0.076408	1	1	T>C
ERR5749149	11104	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	9459	0.003806	0	9342,0,41,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccT/ccC	P44	nsp6	0.000866	0.675414	2	1	T>C
ERR5749149	11287	PASS	GTCTGGTTTT	G	9457	0.995347	0	0,44,0,9413	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749149	11300	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9462	0.004333	0	0,9412,0,48	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L110	nsp6	0.001087	0.873873	1	1	C>T
ERR5749149	11747	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5642	0.002659	0	5614,4,18,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L259	nsp6	0.001145	0.737282	1	1	C>T
ERR5749149	11767	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11259	0.002931	0	5600,5598,18,18	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	agC/agT	S265	nsp6	0.000949	0.854102	1	1	C>T
ERR5749149	12493	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	4723	0.001482	0	4716,0,7,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tataac/	YN135	nsp8	0.000671	0.855797	2	2	CTA>C
ERR5749149	12880	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	1683	0.004753	0	1675,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tataca/	YT66	nsp9	0.004753	0.894516	2	2	CTA>C
ERR5749149	13059	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8553	0.002338	11	6843,1682,22,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T12I	nsp10	0.000448	0.855104	3	2	C>T
ERR5749149	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	6863	0.001749	0	6852,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749149	13208	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	13713	0.001823	2	6792,6829,17,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Aat/Gat	N62D	nsp10	0.000407	0.953357	4	2	A>G
ERR5749149	13208	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAT	A	13712	0.001021	0	6851,6848,7,7	HIGH	NONE	FRAME_SHIFT	ORF1ab	atg/	M63	nsp10	0.000407	0.953357	4	2	AAT>A
ERR5749149	13994	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5227	0.003826	0	5204,0,21,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A185V	RdRp	0.000427	0.114441	3	2	C>T
ERR5749149	14097	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5235	0.002674	0	5210,9,15,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F219	RdRp	0.000613	0.981481	2	2	C>T
ERR5749149	14408	PASS	C	T	1509	0.861498	0	0,0,756,745	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749149	14599	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	2184	0.005495	0	2172,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctatta/	LL387	RdRp	0.000639	0.922766	3	2	CTA>C
ERR5749149	14676	PASS	C	T	2184	0.792582	2147483647	0,0,2181,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749149	15279	PASS	C	T	3631	0.897549	2147483647	0,0,3625,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749149	15652	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAC	G	5750	0.00313	0	5733,0,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T739	RdRp	0.000691	0.935936	2	2	GAC>G
ERR5749149	15981	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	2268	0.003527	0	2260,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gta/	V848	RdRp	0.001324	0.965686	2	2	CG>C
ERR5749149	16176	PASS	T	C	3393	0.981432	0	0,0,1124,2266	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749149	16792	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	G	14837	0.00155	58	6668,8138,0,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgt/Ggt	R186G	helicase	0.000335	0.072562	5	2	C>G
ERR5749149	16794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	14837	0.001348	50	6671,8146,0,20	HIGH	NONE	FRAME_SHIFT	ORF1ab	gta/	V187	helicase	0.000354	0.077626	2	2	TG>T
ERR5749149	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAA	G	6670	0.003748	0	6640,0,25,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GAA>G
ERR5749149	17762	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTG	C	4506	0.002663	0	4494,1,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtc/	V510	helicase	0.000697	0.912542	2	2	CTG>C
ERR5749149	18501	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	5635	0.003017	0	0,5618,0,17	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K155	ExoN	0.000336	0.857143	4	2	CA>C
ERR5749149	18674	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	12896	0.002094	0	12836,0,39,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aGa/aTa	R212I	ExoN	0.000413	0.056921	3	2	G>T
ERR5749149	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	12896	0.002094	0	12869,0,27,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749149	18897	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	12900	0.001783	0	3,12874,0,23	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/	V287	ExoN	0.00046	0.060685	3	3	TG>T
ERR5749149	19227	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAT	C	3480	0.002586	0	0,3471,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	att/	I397	ExoN	0.002586	0.982286	2	2	CAT>C
ERR5749149	19343	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4392	0.003415	0	4370,0,16,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A435V	ExoN	0.000519	0.192257	7	2	C>T
ERR5749149	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1877	0.004262	0	1869,0,8,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749149	20445	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	11844	0.002364	0	0,11816,0,28	HIGH	NONE	FRAME_SHIFT	ORF1ab	aac/aaAc	N277K?	endoR	0.000518	0.059736	4	2	T>TA
ERR5749149	21304	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	8730	0.00126	0	0,8719,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	cgc/	R216	MethTr	0.000411	0.605296	3	2	CG>C
ERR5749149	21727	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4200	0.005952	0	4157,7,29,0	LOW	SILENT	SYNONYMOUS_CODING	S	ttC/ttT	F55	S	0.000896	0.878141	2	2	C>T
ERR5749149	21732	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	4200	0.005714	0	4169,7,24,0	HIGH	NONE	FRAME_SHIFT	S	ttc/	F58	S	0.000576	0.076745	4	2	CT>C
ERR5749149	21764	PASS	ATACATG	A	4193	0.994753	0	14,0,4171,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749149	21764	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATACATGTC	A	4193	0.001908	0	14,0,8,0	HIGH	NONE	FRAME_SHIFT	S	atacatgtctct/	IHVS68	S	0.001908	1	3	1	ATACATGTC>A
ERR5749149	21990	PASS	TTTA	T	4194	0.997616	0	0,10,1,4183	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749149	22227	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	6880	0.002762	0	0,6861,0,19	HIGH	NONE	FRAME_SHIFT	S	tta/	L223	S	0.000419	0.824305	2	2	CT>C
ERR5749149	22264	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6883	0.003196	0	1,6855,0,25	LOW	SILENT	SYNONYMOUS_CODING	S	aaC/aaT	N234	S	0.001131	0.963496	2	2	C>T
ERR5749149	22776	PASS	A	G	8532	0.066338	0	0,7955,0,573	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D405G	S	0.000652	0.1959	2	2	A>G
ERR5749149	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	12965	0.001234	72	4411,8499,18,1	HIGH	NONSENSE	STOP_GAINED	S	tgC/tgA	C432*	S	0.000792	0.973187	2	2	C>A
ERR5749149	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12965	0.001697	26	4411,8499,1,21	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749149	23063	PASS	A	T	4426	0.861952	0	0,1,0,4393	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749149	23122	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	4431	0.002483	24	0,4409,1,13	LOW	SILENT	SYNONYMOUS_CODING	S	gcA/gcT	A520	S	0.002483	0.155172	2	1	A>T
ERR5749149	23271	PASS	C	A	4251	0.927076	2147483647	0,0,4246,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749149	23403	PASS	A	G	4248	0.976224	2147483647	0,0,0,4245	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749149	23604	PASS	C	A	4085	0.945165	0	1,0,4083,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749149	23709	PASS	C	T	4079	0.936749	0	0,2,0,4073	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749149	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	5806	0.001895	7	1719,4076,1,10	HIGH	NONE	FRAME_SHIFT	S	ttg/	L753	S	0.000334	0.080808	2	2	CT>C
ERR5749149	24257	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GC	G	3368	0.005048	0	3351,0,17,0	HIGH	NONE	FRAME_SHIFT	S	gct/	A899	S	0.005048	0.956056	2	2	GC>G
ERR5749149	24320	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	3365	0.003269	0	0,3354,0,11	HIGH	NONE	FRAME_SHIFT	S	aaa/	K921	S	0.000763	0.138365	4	2	CA>C
ERR5749149	24506	PASS	T	G	4704	0.980442	0	2,0,4702,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749149	24616	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	4697	0.002129	0	0,4687,0,10	HIGH	NONE	FRAME_SHIFT	S	agagct/	RA1019	S	0.001268	0.127917	3	2	CAG>C
ERR5749149	24899	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	15609	0.002178	0	7796,7779,18,16	HIGH	NONE	FRAME_SHIFT	S	atc/	I1114	S	0.000315	0.09021	5	3	CA>C
ERR5749149	24914	PASS	G	C	15526	0.95646	0	0,0,7716,7778	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749149	25302	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	11328	0.001324	7	9920,1387,16,5	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tGt/tTt	C1247F	S	0.001121	0.05002	1	1	G>T
ERR5749149	25422	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGGAACTGTAACTTTGAAGCAA	T	9965	7.02E-4	0	9958,0,7,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF3a	ggaactgtaactttgaagcaaggt/ggt	GTVTLKQG11G	orf3a	0.000545	0.213989	6	1	TGGAACTGTAACTTTGAAGCAA>T
ERR5749149	25572	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9965	0.003713	0	0,9918,0,41	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	tcC/tcT	S60	orf3a	0.000543	0.959687	4	2	C>T
ERR5749149	25572	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	9965	0.001104	0	0,9954,0,11	HIGH	NONE	FRAME_SHIFT	ORF3a	atc/	I62	orf3a	0.000543	0.959687	4	2	CA>C
ERR5749149	25660	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	1125	0.004444	0	1093,27,5,0	HIGH	NONE	FRAME_SHIFT	ORF3a	tac/	Y91	orf3a	0.000716	0.91928	2	2	GT>G
ERR5749149	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	1125	0.010667	152	1096,17,2,10	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749149	26257	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	12634	0.001029	15	3321,9300,0,13	HIGH	NONE	FRAME_SHIFT	E	tcg/tTcg	S6F?	E	0.000247	0.948926	4	2	G>GT
ERR5749149	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	3236	0.001854	0	0,3230,0,6	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749149	26936	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12483	0.002804	0	12447,0,36,0	LOW	SILENT	SYNONYMOUS_CODING	M	ctC/ctT	L138	M	0.001308	0.968147	2	1	C>T
ERR5749149	27078	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12474	0.002405	0	0,12431,0,36	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Cgt/Tgt	R186C	M	0.000415	0.05783	2	2	C>T
ERR5749149	27312	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	7791	0.001669	0	7779,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF6	aat/aaAt	N39K?	orf6	0.000911	0.088458	4	2	T>TA
ERR5749149	27384	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	7782	0.002699	0	0,7733,0,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF6	gaT/gaG	D61E	orf6	0.00154	0.931035	3	3	T>G
ERR5749149	27389	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	7782	0.003084	0	0,7758,0,24	.	.	.	.	.	.	.	0.001157	0.899553	2	1	CG>C
ERR5749149	27552	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	AT	7733	0.00194	0	7718,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF7a	gca/Tgca	A55C?	orf7a	0.000563	0.985801	6	1	A>AT
ERR5749149	27577	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7733	0.002716	0	7709,0,24,0	HIGH	NONSENSE	STOP_GAINED	ORF7a	Caa/Taa	Q62*	orf7a	0.000614	0.952205	4	2	C>T
ERR5749149	27741	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	7732	0.001164	0	1,7722,0,9	HIGH	NONE	FRAME_SHIFT	ORF7a	aga/	R118	orf7a	0.000363	0.954278	3	2	CA>C
ERR5749149	27972	PASS	C	T	1393	0.913855	0	0,0,1379,8	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749149	28048	PASS	G	T	1383	0.918294	0	0,2,0,1379	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749149	28111	PASS	A	G	12652	0.981821	9	0,1,11265,1382	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749149	28249	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	11262	0.00151	0	11246,0,17,0	HIGH	NONE	FRAME_SHIFT	ORF8	ttc/	F120	orf8	0.000443	0.063605	3	2	AT>A
ERR5749149	28270	PASS	TA	T	21890	0.995889	202	88,4,11150,10650	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749149	28280	PASS	G	C	21851	0.933504	6	8,3,11164,10635	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749149	28281	PASS	A	T	21851	0.918585	26	15,2,11156,10636	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749149	28282	PASS	T	A	21851	0.907693	0	9,8,11140,10644	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749149	28302	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	11419	0.002277	75	11178,11226,0,26	HIGH	NONE	FRAME_SHIFT	N	aat/	N11	N	0.001527	0.953728	4	2	GA>G
ERR5749149	28394	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	G	11272	0.001774	83	0,11244,3,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Cgg/Ggg	R41G	N	0.001221	0.917026	3	2	C>G
ERR5749149	28406	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTACCCAATA	T	11272	0.002928	0	3,11236,0,33	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	N	ttacccaataat/tat	LPNN45Y	N	0.00043	0.921074	3	2	TTACCCAATA>T
ERR5749149	28877	PASS	A	T	1422	0.877637	0	1,1,722,666	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Agt/Tgt	S202C	N	0.000959	0.88894	1	1	A>T
ERR5749149	28878	PASS	G	C	1422	0.909986	0	0,0,724,666	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGt/aCt	S202T	N	0.001	0.909986	3	2	G>C
ERR5749149	28881	PASS	G	A	1422	0.770042	0	1,0,722,649	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749149	28882	PASS	G	A	1422	0.772855	0	0,0,724,647	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749149	28883	PASS	G	C	1422	0.931786	0	0,0,724,668	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749149	28977	PASS	C	T	795	0.922013	2147483647	0,0,0,793	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749149	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	10678	0.001779	0	5359,5295,12,11	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749149	29445	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTG	C	2890	0.00173	0	2885,0,5,0	HIGH	NONE	FRAME_SHIFT	N	gtg/	V392	N	0.000907	0.853797	2	2	CTG>C
ERR5749150	222	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2939	0.003403	0	1460,1461,5,5	.	.	.	.	.	.	.	0.002134	0.864859	1	1	C>T
ERR5749150	241	PASS	C	T	2938	0.866236	0	0,0,1464,1468	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749150	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	3483	0.002297	0	3473,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749150	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	3479	0.002012	0	3472,0,7,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749150	635	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3486	0.009466	0	0,3449,0,35	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgt/Tgt	R124C	leader	0.00148	0.880435	1	1	C>T
ERR5749150	645	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	3490	0.004011	0	4,3469,0,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGt/gAt	G127D	leader	0.004011	0.185185	1	1	G>A
ERR5749150	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15911	0.002263	17	12400,3468,23,15	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L140	leader	0.000316	0.135802	3	2	C>T
ERR5749150	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	15911	6.28E-4	8	12414,3487,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749150	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	15911	0.00132	5	12400,3485,19,2	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749150	806	PASS	G	A	12427	0.948499	0	4,0,12404,11	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gca/Aca	A1T	nsp2	0.001474	0.948499	1	1	G>A
ERR5749150	892	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	12413	9.67E-4	0	0,12401,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K30	nsp2	0.000495	0.082222	2	2	TA>T
ERR5749150	913	PASS	C	T	12416	0.909552	0	0,3,0,12397	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749150	1191	PASS	C	T	7814	0.916048	0	0,7,0,7796	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCa/cTa	P129L	nsp2	0.000749	0.916048	3	2	C>T
ERR5749150	1813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	10631	0.001693	0	0,10599,0,23	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcA	A336	nsp2	0.001022	0.152738	4	2	T>A
ERR5749150	2306	PASS	C	T	6932	0.915753	2147483647	0,0,6922,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Ttt	L501F	nsp2	0.01927	0.915753	1	1	C>T
ERR5749150	2752	PASS	T	C	62	0.951613	2147483647	0,0,0,62	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T11	nsp3	0.951613	0.951613	1	1	T>C
ERR5749150	3037	PASS	C	T	6976	0.802322	30	0,10,3489,3407	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749150	3267	PASS	C	T	13424	0.968117	2147483647	0,0,13419,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749150	4255	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	17248	0.001102	0	8605,8606,12,12	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccG/ccA	P512	nsp3	0.001102	0.871853	2	1	G>A
ERR5749150	4529	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTTTACTTTTACACCAGTAAAACAAC	T	10758	0.001487	0	0,10742,0,16	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttttacttttacaccagtaaaacaact/	FYFYTSKTT604	nsp3	0.000527	0.402778	3	1	TTTTACTTTTACACCAGTAAAACAAC>T
ERR5749150	5388	PASS	C	A	2120	0.96934	2147483647	0,0,2119,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749150	5986	PASS	C	T	6156	0.98002	2147483647	0,0,6155,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749150	6336	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15731	0.001526	0	15696,0,24,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCg/tTg	S1206L	nsp3	0.001317	0.951419	1	1	C>T
ERR5749150	6954	PASS	T	C	16655	0.811108	2147483647	0,0,0,16564	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749150	7564	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	12078	7.45E-4	0	0,12069,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/	Y1617	nsp3	0.000586	0.056194	4	2	CT>C
ERR5749150	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	10914	0.002474	32	8085,2802,27,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749150	11287	PASS	GTCTGGTTTT	G	19827	0.997428	0	0,51,0,19776	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749150	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	22834	0.001752	5	16913,5862,36,8	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749150	12269	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	14798	6.08E-4	0	14789,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aag/	K61	nsp8	0.000434	0.213333	2	1	GA>G
ERR5749150	13459	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTT	G	11678	7.71E-4	0	11646,0,9,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ttttta/tta	FL7L	nsp11	0.000691	0.060726	5	2	GTTT>G
ERR5749150	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23320	0.001973	0	11638,11601,25,26	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749150	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	2887	0.00381	0	1446,1432,6,5	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749150	14408	PASS	C	T	2887	0.833045	0	0,0,1442,1412	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749150	14676	PASS	C	T	9145	0.800219	0	3,0,9117,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749150	15279	PASS	C	T	13048	0.898222	2147483647	0,0,13037,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749150	16176	PASS	T	C	12382	0.978598	0	0,0,3514,8862	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749150	16575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19189	0.001094	0	19144,0,24,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D113	helicase	0.001088	0.827968	1	1	C>T
ERR5749150	17167	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10033	0.003987	0	9987,0,41,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cat/Tat	H311Y	helicase	0.001728	0.238095	1	1	C>T
ERR5749150	18252	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAT	C	6196	9.68E-4	0	0,6190,0,6	HIGH	NONE	FRAME_SHIFT	ORF1ab	atg/	M72	ExoN	0.000968	0.924007	2	2	CAT>C
ERR5749150	19343	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTTTTGTTAATTTAAAACAA	C	9364	9.61E-4	0	9355,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tttgttaatttaaaacaatta/	FVNLKQL436	ExoN	0.000519	0.192257	7	2	CTTTTGTTAATTTAAAACAA>C
ERR5749150	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	18473	9.74E-4	0	8,18455,0,18	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TA>T
ERR5749150	21658	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12132	0.001649	0	0,12104,0,23	LOW	SILENT	SYNONYMOUS_CODING	S	ttC/ttT	F32	S	0.001649	0.937508	2	2	C>T
ERR5749150	21764	PASS	ATACATG	A	7234	0.997788	0	16,0,7218,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749150	21990	PASS	TTTA	T	7234	0.998341	0	0,12,0,7222	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749150	23063	PASS	A	T	7970	0.857842	0	0,4,0,7935	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749150	23271	PASS	C	A	15251	0.9303	0	2,0,15241,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749150	23403	PASS	A	G	15248	0.963536	0	0,2,0,15226	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749150	23604	PASS	C	A	8412	0.946029	0	6,0,8401,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749150	23709	PASS	C	T	8404	0.931104	0	0,2,3,8389	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749150	24320	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	7176	0.00432	0	0,7145,0,31	HIGH	NONE	FRAME_SHIFT	S	aaa/	K921	S	0.000763	0.138365	4	2	CA>C
ERR5749150	24506	PASS	T	G	13596	0.974698	0	7,0,13576,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749150	24704	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13605	0.00125	0	9,13570,0,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Cat/Tat	H1048Y	S	0.00125	0.173585	1	1	C>T
ERR5749150	24914	PASS	G	C	24638	0.958601	0	0,1,12280,12348	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749150	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	18173	0.009134	0	0,18007,0,166	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749150	26493	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	9891	0.001415	0	0,9877,0,14	.	.	.	.	.	.	.	0.001082	0.069277	3	1	G>GT
ERR5749150	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	6532	0.002756	0	0,6514,0,18	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749150	26936	PASS	C	T	26735	0.962184	2147483647	0,0,26707,0	LOW	SILENT	SYNONYMOUS_CODING	M	ctC/ctT	L138	M	0.001308	0.968147	2	1	C>T
ERR5749150	26958	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26734	0.001272	0	26692,0,37,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Cgt/Tgt	R146C	M	0.00096	0.122326	1	1	C>T
ERR5749150	27509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28456	8.43E-4	2	16626,11800,16,8	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	aCa/aTa	T39I	orf7a	0.000843	0.067888	1	1	C>T
ERR5749150	27567	PASS	CTTTAGCACTCAATTTGCTT	C	16644	0.973384	0	443,0,16201,0	HIGH	NONE	FRAME_SHIFT	ORF7a	tttagcactcaatttgctttt/	FSTQFAF59	orf7a	0.000449	0.998291	4	1	CTTTAGCACTCAATTTGCTT>C
ERR5749150	27972	PASS	C	T	3558	0.879708	23	0,1,3529,14	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749150	28048	PASS	G	T	3546	0.910886	0	0,5,0,3538	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749150	28111	PASS	A	G	25800	0.980814	8	3,2,22239,3548	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749150	28147	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTTTTACAA	C	22250	7.64E-4	0	22227,1,17,0	HIGH	NONE	FRAME_SHIFT	ORF8	tttacaatt/	FTI86	orf8	0.000438	0.981624	4	2	CTTTTACAA>C
ERR5749150	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22232	0.004048	0	22087,10,103,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749150	28270	PASS	TA	T	43112	0.995755	372	180,12,21987,20942	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749150	28280	PASS	G	C	43040	0.932063	31	17,2,22016,20927	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749150	28281	PASS	A	T	43040	0.912152	29	23,5,22018,20926	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749150	28282	PASS	T	A	43041	0.905439	7	21,12,21962,20941	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749150	28292	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	44260	9.72E-4	1	22063,22154,20,23	HIGH	NONE	FRAME_SHIFT	N	aat/	N8	N	0.000304	0.055324	4	2	CA>C
ERR5749150	28321	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	22232	4.5E-4	0	0,22222,0,10	HIGH	NONE	FRAME_SHIFT	N	ggt/Tggt	G18W?	N	0.00045	0.947809	3	2	G>GT
ERR5749150	28603	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25509	0.001019	0	12724,12608,15,16	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F110	N	0.000427	0.883357	2	2	C>T
ERR5749150	28651	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	12784	6.26E-4	0	6,12770,0,8	HIGH	NONE	FRAME_SHIFT	N	aaa/	K127	N	0.000502	0.918117	3	2	CA>C
ERR5749150	28881	PASS	G	A	7272	0.761551	9	4,0,3609,3564	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749150	28882	PASS	G	A	7270	0.822834	0	2,1,3638,3538	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749150	28883	PASS	G	C	7270	0.942503	0	1,0,3647,3616	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749150	28977	PASS	C	T	3688	0.924078	0	0,1,0,3664	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749150	28977	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	G	3688	0.004881	0	0,1,0,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tGt	S235C	N	0.001219	1	3	2	C>G
ERR5749150	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	19402	0.002886	449	15701,3606,0,62	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749150	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	31220	0.001185	0	15659,15504,22,22	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749150	29386	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	6029	0.001327	0	6021,0,8,0	HIGH	NONE	FRAME_SHIFT	N	aag/aaAg	K373K?	N	0.000887	0.899197	4	2	C>CA
ERR5749151	71	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3028	0.008917	0	2996,0,27,0	.	.	.	.	.	.	.	0.002088	0.926791	2	1	C>T
ERR5749151	189	PASS	G	A	2677	0.93164	0	1,0,2674,0	.	.	.	.	.	.	.	0.926346	0.937678	1	1	G>A
ERR5749151	241	PASS	C	T	5332	0.861403	0	0,0,2648,2662	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749151	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	9252	0.002702	0	9215,15,25,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749151	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTAT	G	9252	0.002918	324	9185,2,14,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatg/	GHVM82	leader	0.00045	0.081241	6	1	GGTCATGTTAT>G
ERR5749151	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	9252	0.003351	0	9185,2,31,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749151	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	9250	0.002703	0	8499,13,625,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749151	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	9250	8.65E-4	0	9216,26,8,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749151	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	9248	9.73E-4	0	9208,26,9,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749151	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	22895	5.24E-4	26	13646,9232,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749151	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	22895	0.001092	3	13641,9223,17,8	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749151	875	PASS	C	T	13633	0.878897	0	0,6,5,13587	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Ttt	L24F	nsp2	0.878897	0.878897	1	1	C>T
ERR5749151	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13657	0.002416	0	1,13612,0,36	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749151	913	PASS	C	T	13658	0.90943	0	0,11,1,13625	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749151	2453	PASS	C	T	14375	0.770852	0	0,13,2,14188	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L550F	nsp2	0.00429	0.842201	2	2	C>T
ERR5749151	3037	PASS	C	T	16491	0.809108	53	1,21,8240,8099	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749151	3267	PASS	C	T	14377	0.972804	0	1,0,14370,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749151	5388	PASS	C	A	4211	0.957492	2147483647	0,0,4210,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749151	5628	PASS	C	T	12369	0.973644	0	1,0,12361,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aTg	T970M	nsp3	0.000561	0.973644	3	2	C>T
ERR5749151	5986	PASS	C	T	12214	0.975111	2147483647	0,0,12204,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749151	6954	PASS	T	C	16295	0.81479	0	0,6,1,16203	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749151	11287	PASS	GTCTGGTTTT	G	15998	0.996875	0	0,50,0,15948	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749151	12676	PASS	C	T	17105	0.87302	0	0,4,0,17092	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V195	nsp8	0.000716	0.87302	3	2	C>T
ERR5749151	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21372	0.001123	0	10673,10648,13,14	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749151	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	9487	8.43E-4	0	4754,4730,4,4	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749151	14408	PASS	C	T	9487	0.843154	0	0,0,4736,4675	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749151	14676	PASS	C	T	9044	0.808824	0	4,0,9012,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749151	15279	PASS	C	T	12910	0.88172	2147483647	0,0,12888,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749151	16176	PASS	T	C	15278	0.980757	0	1,0,8002,7270	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749151	17678	PASS	C	T	2438	0.954471	59	2,1,0,2434	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aTg	T481M	helicase	0.001162	0.968704	2	1	C>T
ERR5749151	17749	PASS	G	T	8485	0.915027	0	4,0,8481,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gct/Tct	A505S	helicase	0.001521	0.987943	4	2	G>T
ERR5749151	17865	PASS	T	C	16548	0.850012	1	2,3,8405,8050	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taT/taC	Y543	helicase	0.850012	0.861515	1	1	T>C
ERR5749151	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	25046	7.19E-4	0	25028,0,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749151	19328	PASS	C	T	18311	0.937906	2147483647	0,0,18287,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A430V	ExoN	0.000459	0.937906	4	2	C>T
ERR5749151	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22798	0.00114	0	22757,0,26,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749151	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	16420	7.31E-4	0	0,16408,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TA>T
ERR5749151	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24781	0.001372	2	12109,12360,20,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749151	21764	PASS	ATACATG	A	12060	0.997015	0	36,0,12024,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749151	21811	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12057	0.001327	0	12031,0,16,0	LOW	SILENT	SYNONYMOUS_CODING	S	gtC/gtT	V83	S	0.001327	0.179245	1	1	C>T
ERR5749151	21990	PASS	TTTA	T	12064	0.997596	0	0,29,2,12033	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749151	23063	PASS	A	T	13714	0.862039	0	0,6,0,13637	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749151	23271	PASS	C	A	15354	0.896965	2147483647	0,0,15331,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749151	23401	PASS	G	T	15350	0.839283	0	0,82,0,15264	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	caG/caT	Q613H	S	0.000491	0.839283	2	2	G>T
ERR5749151	23403	PASS	A	G	15350	0.978371	2147483647	0,0,0,15340	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749151	23604	PASS	C	A	14852	0.938796	0	18,0,14825,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749151	23664	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29449	9.17E-4	0	14630,14749,15,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCa/gTa	A701V	S	0.000837	0.918	2	2	C>T
ERR5749151	23709	PASS	C	T	14834	0.932452	0	0,2,3,14797	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749151	24506	PASS	T	G	12682	0.975004	0	9,0,12671,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749151	24914	PASS	G	C	36225	0.960414	0	0,1,18042,18161	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749151	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	22492	0.001601	27	17937,4513,41,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749151	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	11416	0.001927	314	11355,19,8,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749151	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	11382	8.79E-4	0	11372,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749151	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	11337	9.7E-4	0	0,11324,0,11	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749151	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	11337	7.06E-4	0	0,11329,0,8	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749151	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	11338	0.002029	0	0,11310,0,23	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749151	27741	PASS	C	T	16119	0.954278	0	0,5,2,16087	LOW	SILENT	SYNONYMOUS_CODING	ORF7a	ctC/ctT	L116	orf7a	0.000363	0.954278	3	2	C>T
ERR5749151	27972	PASS	C	T	9589	0.898112	35	3,2,9498,52	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749151	28048	PASS	G	T	9550	0.92555	0	0,9,0,9538	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749151	28111	PASS	A	G	25208	0.978697	5	4,0,15641,9548	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749151	28270	PASS	TA	T	30388	0.995557	327	134,4,15472,14781	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749151	28280	PASS	G	C	30342	0.936095	21	11,1,15499,14766	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749151	28281	PASS	A	T	30342	0.914772	19	23,8,15496,14768	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749151	28282	PASS	T	A	30343	0.909666	19	26,10,15460,14774	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749151	28881	PASS	G	A	11268	0.759141	9	6,1,5552,5540	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749151	28882	PASS	G	A	11267	0.821337	12	5,0,5627,5514	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749151	28883	PASS	G	C	11266	0.940174	0	1,1,5635,5618	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749151	28977	PASS	C	T	5725	0.926463	2147483647	0,0,0,5712	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749151	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	57421	0.001149	0	28824,28500,38,38	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749152	241	PASS	C	T	6154	0.863991	6	1,4,3065,3059	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749152	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	8128	0.001107	0	8123,0,9,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749152	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	8149	0.001227	0	8115,21,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749152	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	8141	0.002702	0	7485,20,600,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749152	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	8141	0.001597	0	8107,21,13,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749152	597	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	8139	9.83E-4	0	0,8131,0,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggc/	G112	leader	0.000983	0.333333	2	2	TG>T
ERR5749152	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	28515	5.96E-4	3	20345,8141,14,3	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749152	1059	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13896	0.006477	0	13795,0,97,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCc/aTc	T85I	nsp2	0.001728	0.920973	1	1	C>T
ERR5749152	1230	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	13891	0.004607	0	0,13754,0,67	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K142R	nsp2	0.00129	0.969658	2	2	A>G
ERR5749152	1813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	17308	0.001271	0	0,17266,0,28	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcA	A336	nsp2	0.001022	0.152738	4	2	T>A
ERR5749152	2062	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25819	0.002827	0	25624,11,98,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A419	nsp2	0.001265	0.822961	2	1	C>T
ERR5749152	3037	PASS	C	T	14274	0.813507	70	0,23,7137,7009	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749152	3177	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	26475	9.82E-4	30	19248,7188,37,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cAt	P153H	nsp3	0.000773	0.96008	3	2	C>A
ERR5749152	3671	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GA	22058	4.99E-4	0	11040,11018,6,5	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/aaAt	N319K?	nsp3	0.000351	0.0625	6	2	G>GA
ERR5749152	3852	PASS	A	T	12972	0.979109	0	3,0,12961,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gAa/gTa	E378V	nsp3	0.008354	0.97973	2	1	A>T
ERR5749152	3961	PASS	C	T	12906	0.869983	0	2,0,12866,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I414	nsp3	0.000417	0.869983	2	2	C>T
ERR5749152	4504	PASS	G	T	29132	0.846766	57	55,117,14511,14424	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gaG/gaT	E595D	nsp3	0.001014	0.846766	1	1	G>T
ERR5749152	6573	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10740	0.001862	0	10711,0,20,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S1285F	nsp3	0.001862	0.957014	1	1	C>T
ERR5749152	7564	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTT	C	14916	0.001006	0	0,14897,0,15	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttttat/	FY1616	nsp3	0.000586	0.056194	4	2	CTT>C
ERR5749152	7798	PASS	G	T	20119	0.934142	0	13,0,20092,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaG/aaT	K1693N	nsp3	0.001127	0.936026	1	1	G>T
ERR5749152	8796	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	34206	4.09E-4	0	17125,17067,7,7	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/	Y82	nsp4	0.000257	0.25	2	2	GT>G
ERR5749152	9072	PASS	C	T	29167	0.930675	7	2,6,15187,13925	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCc/aTc	T173I	nsp4	0.001037	0.930675	2	1	C>T
ERR5749152	9198	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	15244	5.9E-4	0	0,15235,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F216	nsp4	0.000543	0.93476	4	2	CT>C
ERR5749152	9891	PASS	C	T	6970	0.954663	2147483647	0,0,6959,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A446V	nsp4	0.002963	0.958011	1	1	C>T
ERR5749152	10116	PASS	C	T	23859	0.944885	11	1,3,16869,6966	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T21I	3Cpro	0.001266	0.952096	1	1	C>T
ERR5749152	10323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	16869	0.001304	0	0,16808,0,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749152	10595	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	18061	0.001329	0	10,17990,0,29	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F181L	3Cpro	0.000964	0.076408	1	1	T>C
ERR5749152	10702	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	18094	5.53E-4	0	6,18078,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	agg/	R217	3Cpro	0.000396	0.098214	2	2	CAG>C
ERR5749152	11074	PASS	C	CT	21637	0.069279	0	19783,1,1499,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CT
ERR5749152	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	21637	0.011785	0	19783,1,255,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749152	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTTT	21637	0.002773	0	19783,1,60,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_INSERTION	ORF1ab	ttg/ttTTTg	L37FL	nsp6	0.000965	0.945355	5	2	C>CTTT
ERR5749152	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21637	0.003513	0	21495,1,97,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749152	11075	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TC	21636	5.55E-4	0	21618,1,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/tCtt	F35S?	nsp6	0.000555	0.885796	4	2	T>TC
ERR5749152	11082	PASS	TG	T	21545	0.090972	0	19676,0,1960,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000427	0.179468	2	1	TG>T
ERR5749152	11083	PASS	G	T	21545	0.863681	0	6,0,19476,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749152	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	21545	0.032583	0	20759,0,702,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/tTat	Y38L?	nsp6	0.000477	0.901695	5	2	G>GT
ERR5749152	11287	PASS	GTCTGGTTTT	G	21631	0.997966	0	0,44,0,21587	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749152	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	32024	9.68E-4	5	21390,10579,24,7	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749152	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	17453	0.00149	0	17400,0,29,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749152	13498	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	37278	0.001341	3	18608,18515,33,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Aca/Gca	T20A	RdRp	0.001341	0.952048	1	1	A>G
ERR5749152	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	37297	0.001019	1	18629,18572,22,24	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749152	13952	PASS	T	C	25850	0.799342	8	2630,2131,11890,9192	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I171T	RdRp	0.799342	0.799342	1	1	T>C
ERR5749152	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	3652	0.006572	907	3537,49,6,59	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749152	14408	PASS	C	T	7049	0.847496	0	0,0,3522,3479	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749152	15396	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	19070	5.24E-4	0	14,19048,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	tataga/	YR653	RdRp	0.000524	0.116667	1	1	CTA>C
ERR5749152	15960	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11796	0.001865	0	11758,0,28,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A840	RdRp	0.001581	0.81574	1	1	C>T
ERR5749152	16092	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11789	0.008313	0	0,11668,0,107	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y884	RdRp	0.002941	0.906832	1	1	C>T
ERR5749152	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	24862	9.25E-4	0	24839,0,23,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749152	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19635	0.002241	0	19577,0,46,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749152	20578	PASS	G	A	25982	0.950119	0	1,0,25964,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtg/Atg	V320M	endoR	0.00085	0.958277	3	1	G>A
ERR5749152	21004	PASS	G	T	44934	0.857814	19	28,12,22334,22477	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gca/Tca	A116S	MethTr	0.000749	0.857814	3	1	G>T
ERR5749152	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29048	0.001515	0	14206,14454,27,29	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749152	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	11788	0.001272	0	11773,0,15,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749152	21846	PASS	C	T	23421	0.788523	30	1,13,11677,11525	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCt/aTt	T95I	S	0.001104	0.788523	1	1	C>T
ERR5749152	21990	PASS	TTTA	T	11792	0.997541	0	0,29,1,11762	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749152	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17432	0.001262	4	12889,4515,15,8	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749152	22898	PASS	G	A	12910	0.980248	0	1,0,12909,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ggt/Agt	G446S	S	0.062244	0.981998	1	1	G>A
ERR5749152	23012	PASS	G	A	24551	0.904403	19	10,1,12754,11757	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gaa/Aaa	E484K	S	0.001756	0.909912	2	1	G>A
ERR5749152	23183	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTCAACTTCAATGGTTTA	T	36071	3.88E-4	24	23147,12910,14,0	HIGH	NONE	FRAME_SHIFT	S	ttcaacttcaatggttta/	FNFNGL541	S	0.000388	0.135922	2	2	TTCAACTTCAATGGTTTA>T
ERR5749152	23287	PASS	T	C	23156	0.943125	0	2,0,23126,2	LOW	SILENT	SYNONYMOUS_CODING	S	gcT/gcC	A575	S	0.001462	0.947477	1	1	T>C
ERR5749152	23403	PASS	A	G	23139	0.964994	0	0,12,0,23104	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749152	23604	PASS	C	A	13697	0.945316	0	13,0,13671,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749152	23948	PASS	G	C	12486	0.885712	0	6,0,12449,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gat/Cat	D796H	S	0.879747	0.913697	1	1	G>C
ERR5749152	24382	PASS	C	T	11458	0.918223	0	0,3,0,11423	LOW	SILENT	SYNONYMOUS_CODING	S	tcC/tcT	S940	S	0.002118	0.920404	2	1	C>T
ERR5749152	25276	PASS	C	A	8510	0.906933	0	0,2,2,8499	LOW	SILENT	SYNONYMOUS_CODING	S	acC/acA	T1238	S	0.005906	0.9348	2	2	C>A
ERR5749152	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	26110	0.002298	110	17519,8510,74,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749152	26319	PASS	A	G	12140	0.971582	0	3,0,12132,0	LOW	SILENT	SYNONYMOUS_CODING	E	gtA/gtG	V25	E	0.001432	0.971582	2	1	A>G
ERR5749152	26681	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11237	0.002492	0	11165,39,30,0	LOW	SILENT	SYNONYMOUS_CODING	M	ttC/ttT	F53	M	0.001297	0.074505	1	1	C>T
ERR5749152	26767	PASS	T	C	11192	0.96158	0	0,3,9,11176	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	aTc/aCc	I82T	M	0.954318	0.968313	2	1	T>C
ERR5749152	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	G	11192	8.04E-4	0	0,11182,0,9	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/	ACLVGLMWLSYFIASF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT>G
ERR5749152	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	11192	7.15E-4	0	0,11181,0,8	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749152	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	11193	8.04E-4	0	0,11178,0,9	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749152	27886	PASS	AAACGAACATGAAATT	A	8305	0.998916	0	10,0,8296,0	HIGH	NONE	GENE_FUSION	ORF7b+ORF8	.	.	.	0.997573	0.998916	1	1	AAACGAACATGAAATT>A
ERR5749152	28209	PASS	G	T	19472	0.930413	0	10,0,19451,0	HIGH	NONSENSE	STOP_GAINED	ORF8	Gaa/Taa	E106*	orf8	0.001409	0.963166	2	2	G>T
ERR5749152	28271	PASS	A	G	38756	0.923135	1	7,5,19403,19274	.	.	.	.	.	.	.	0.000482	0.924941	3	2	A>G
ERR5749152	28406	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTACCCAATA	T	19482	6.16E-4	0	6,19464,0,12	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	N	ttacccaataat/tat	LPNN45Y	N	0.00043	0.921074	3	2	TTACCCAATA>T
ERR5749152	28657	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18273	0.002463	0	0,18209,0,53	LOW	SILENT	SYNONYMOUS_CODING	N	gaC/gaT	D128	N	0.00124	0.862766	1	1	C>T
ERR5749152	28881	PASS	G	A	7728	0.745083	19	3,1,1121,6461	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749152	28882	PASS	G	A	7727	0.791899	6	2,4,1153,6457	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749152	28883	PASS	G	C	7727	0.902032	0	0,2,1158,6541	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749152	28895	PASS	GCTA	G	7761	0.850664	2147483647	1148,16,8,6594	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	N	gctaga/gga	AR208G	N	0.814516	0.850664	1	1	GCTA>G
ERR5749152	29091	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	28389	4.58E-4	0	28376,0,13,0	HIGH	NONE	FRAME_SHIFT	N	ttc/	F274	N	0.000452	0.073908	3	1	CT>C
ERR5749152	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	56355	0.001242	0	28288,27940,47,46	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749152	29386	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	7650	0.001176	0	7641,0,9,0	HIGH	NONE	FRAME_SHIFT	N	aag/aaAg	K373K?	N	0.000887	0.899197	4	2	C>CA
ERR5749152	29769	PASS	C	T	7310	0.935294	0	0,2,0,7307	.	.	.	.	.	.	.	0.001999	0.945205	1	1	C>T
ERR5749153	189	PASS	G	A	4573	0.937678	0	3,0,4569,1	.	.	.	.	.	.	.	0.926346	0.937678	1	1	G>A
ERR5749153	241	PASS	C	T	9111	0.864669	0	0,0,4525,4555	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749153	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	11285	0.001949	0	11264,0,22,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749153	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	11285	0.001063	0	11226,0,12,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749153	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	11285	0.003633	0	11226,0,41,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749153	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	11284	0.00195	0	10500,3,682,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749153	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	11284	0.001684	0	11262,3,19,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749153	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	11283	8.86E-4	0	11266,3,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749153	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	11283	8.86E-4	0	11268,3,10,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749153	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	28213	0.001063	11	16886,11291,23,7	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749153	913	PASS	C	T	16904	0.892451	0	0,9,0,16865	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749153	2453	PASS	C	T	14017	0.713705	0	0,15,1,13777	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L550F	nsp2	0.00429	0.842201	2	2	C>T
ERR5749153	3037	PASS	C	T	18174	0.804391	48	3,25,9083,8912	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749153	3267	PASS	C	T	15999	0.971811	0	2,0,15985,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749153	5388	PASS	C	A	6361	0.955196	0	1,0,6358,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749153	5986	PASS	C	T	11467	0.974972	2147483647	0,0,11459,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749153	6954	PASS	T	C	17498	0.804321	0	0,6,0,17372	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749153	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	27154	9.58E-4	72	14245,12883,26,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749153	10138	PASS	C	T	21178	0.979177	0	2,0,16041,5125	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N28	3Cpro	0.000458	0.983567	3	3	C>T
ERR5749153	11287	PASS	GTCTGGTTTT	G	15435	0.996372	0	0,56,0,15379	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749153	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	29730	8.41E-4	3	17556,12123,13,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749153	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24205	0.001281	0	12095,12055,16,16	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749153	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	13943	0.005881	2147483647	13552,124,5,254	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749153	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	26989	6.3E-4	4	13539,13450,11,6	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749153	14408	PASS	C	T	26989	0.839601	4	1,3,13486,13310	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749153	14676	PASS	C	T	10367	0.723353	0	4,0,10321,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749153	15279	PASS	C	T	17906	0.893053	0	1,0,17885,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749153	16176	PASS	T	C	17686	0.976874	0	1,1,9368,8304	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749153	18658	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	22073	5.89E-4	0	22053,6,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tgt/	C207	ExoN	0.000507	0.115741	3	2	TG>T
ERR5749153	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27200	0.00261	0	27107,1,73,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749153	20233	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22139	0.001039	0	22097,5,24,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ccc/Tcc	P205S	endoR	0.000964	0.980008	2	1	C>T
ERR5749153	21764	PASS	ATACATG	A	11472	0.994334	0	64,0,11407,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749153	21990	PASS	TTTA	T	11475	0.997647	0	0,27,4,11444	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749153	23063	PASS	A	T	11483	0.847862	0	0,5,5,11415	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749153	23271	PASS	C	A	17640	0.899547	0	2,0,17615,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749153	23403	PASS	A	G	17632	0.968693	0	0,5,0,17608	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749153	23604	PASS	C	A	14386	0.95294	0	7,0,14371,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749153	23709	PASS	C	T	14370	0.931315	0	0,4,0,14337	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749153	24506	PASS	T	G	14706	0.975384	0	9,0,14697,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749153	24914	PASS	G	C	32894	0.953639	0	0,0,16403,16468	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749153	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	20219	0.001286	408	20148,6,11,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749153	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	20371	0.001522	1310	20048,122,93,88	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749153	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	10562	0.001894	0	1,10541,0,20	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749153	27696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TCTTATTGTTGCGGCAATAGTGTTTATAACACTTTGCTTCACACTCAAAAGAAAG	T	17526	6.28E-4	0	9,17505,0,11	MODERATE	NONE	CODON_DELETION	ORF7a	cttattgttgcggcaatagtgtttataacactttgcttcacactcaaaagaaag/	LIVAAIVFITLCFTLKRK102	orf7a	0.000628	0.99631	1	1	TCTTATTGTTGCGGCAATAGTGTTTATAACACTTTGCTTCACACTCAAAAGAAAG>T
ERR5749153	27972	PASS	C	T	10589	0.90424	91	4,5,10491,56	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749153	28048	PASS	G	T	10537	0.912499	0	0,22,0,10505	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749153	28111	PASS	A	G	24666	0.976608	13	1,6,14114,10541	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749153	28270	PASS	TA	T	27088	0.995127	292	131,6,13949,13007	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749153	28280	PASS	G	C	27034	0.935267	4	7,3,13975,12987	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749153	28281	PASS	A	T	27034	0.911778	15	19,7,13958,12987	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749153	28282	PASS	T	A	27034	0.912961	13	15,5,13949,13004	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749153	28877	PASS	A	T	11429	0.888442	20	8,21,6015,5333	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Agt/Tgt	S202C	N	0.000959	0.88894	1	1	A>T
ERR5749153	28878	PASS	G	C	11425	0.90267	0	1,1,6033,5341	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGt/aCt	S202T	N	0.001	0.909986	3	2	G>C
ERR5749153	28881	PASS	G	A	11425	0.72744	23	9,0,5994,5201	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749153	28882	PASS	G	A	11425	0.774967	14	6,0,6017,5193	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749153	28883	PASS	G	C	11425	0.938293	0	0,0,6030,5352	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749153	28977	PASS	C	T	6664	0.902461	0	0,0,1,6640	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749153	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	42394	9.91E-4	0	21311,21008,23,23	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749154	241	PASS	C	T	16677	0.833063	0	1,1,8246,8333	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749154	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	9626	0.00187	0	9609,6,18,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749154	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	9627	8.31E-4	0	9563,7,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749154	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	9627	8.31E-4	0	9563,7,8,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749154	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	9627	0.003947	0	9563,7,38,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749154	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	9617	0.001872	0	9592,7,18,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749154	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	30258	4.3E-4	18	20609,9635,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749154	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	30254	3.97E-4	0	20593,9623,8,4	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749154	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	30254	8.59E-4	0	20593,9623,18,8	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749154	913	PASS	C	T	20612	0.911314	0	0,18,0,20558	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749154	2462	PASS	C	T	11805	0.408047	1	3,5648,2,6098	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L553	nsp2	0.408047	0.791388	1	1	C>T
ERR5749154	3037	PASS	C	T	13857	0.813524	41	1,17,6922,6821	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749154	3267	PASS	C	T	15727	0.967699	0	1,0,15720,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749154	3575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	8758	9.13E-4	0	8750,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/ttTa	L287F?	nsp3	0.000594	0.059126	3	1	G>GT
ERR5749154	3787	PASS	C	T	8764	0.941123	238	7,0,0,8753	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y356	nsp3	0.002354	0.956541	1	1	C>T
ERR5749154	5388	PASS	C	A	4588	0.958806	2147483647	0,0,4584,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749154	5986	PASS	C	T	9041	0.974007	2147483647	0,0,9034,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749154	6539	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8507	0.001998	0	8485,1,19,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cac/Tac	H1274Y	nsp3	0.001998	0.979821	1	1	C>T
ERR5749154	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8482	0.001651	0	6,8372,0,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749154	6954	PASS	T	C	22425	0.804013	0	0,5,1,22293	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749154	8316	PASS	C	T	32233	0.053734	1	8277,22069,505,1372	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T1866I	nsp3	0.053734	0.053734	1	1	C>T
ERR5749154	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	26706	5.62E-4	59	10681,16010,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749154	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	16851	0.001306	0	16806,1,40,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749154	11287	PASS	GTCTGGTTTT	G	16852	0.997092	0	0,49,1,16802	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749154	12357	PASS	C	T	21531	0.937903	0	0,4,0,21497	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T89I	nsp8	0.000909	0.956941	3	2	C>T
ERR5749154	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30452	0.001543	0	15205,15151,26,26	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749154	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	9876	0.005974	2147483647	9587,90,6,189	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749154	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	19051	9.97E-4	0	9570,9480,10,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749154	14408	PASS	C	T	19051	0.847672	36	0,12,9525,9385	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749154	14676	PASS	C	T	12441	0.799775	0	7,0,12397,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749154	15279	PASS	C	T	22567	0.908583	0	1,0,22537,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749154	16176	PASS	T	C	16722	0.979967	0	0,0,7060,9655	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749154	17615	PASS	A	G	10119	0.905327	0	0,0,4,10081	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749154	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	23283	4.29E-4	0	1,23272,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749154	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21558	0.002273	0	21495,1,51,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749154	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	28948	0.023698	2106	14449,13718,0,686	HIGH	NONE	FRAME_SHIFT	S	ctt/Tctt	L5S?	S	0.000394	0.091869	4	1	G>GT
ERR5749154	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GTT	28948	0.002764	249	14449,13718,0,80	HIGH	NONE	FRAME_SHIFT	S	ctt/TTctt	L5F?	S	0.000394	0.091869	4	1	G>GTT
ERR5749154	21575	PASS	C	T	27969	0.857199	11	0,5,13166,14314	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749154	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	27957	0.003899	311	13438,14402,0,109	HIGH	NONE	FRAME_SHIFT	S	gtt/Tgtt	V6C?	S	0.000619	0.877942	3	2	C>CT
ERR5749154	21764	PASS	ATACATG	A	8605	0.995816	0	36,0,8569,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749154	21990	PASS	TTTA	T	8608	0.998025	0	0,17,3,8588	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749154	23063	PASS	A	T	8498	0.853966	0	0,3,0,8436	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749154	23271	PASS	C	A	20364	0.923296	0	2,0,20341,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749154	23403	PASS	A	G	20353	0.965509	0	0,1,0,20340	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749154	23604	PASS	C	A	10904	0.949285	0	6,0,10890,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749154	23709	PASS	C	T	10902	0.942946	0	0,1,7,10879	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749154	24506	PASS	T	G	18613	0.974426	0	5,0,18608,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749154	24914	PASS	G	C	23951	0.960294	0	0,0,11927,12003	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749154	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	23234	0.001205	439	23162,14,11,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749154	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	23387	0.001283	1406	23010,131,126,97	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749154	26062	PASS	G	T	35422	0.906894	0	50,0,35313,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Ggt/Tgt	G224C	orf3a	0.001077	0.906894	1	1	G>T
ERR5749154	26065	PASS	G	T	35422	0.899102	0	101,0,35303,4	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gtt/Ttt	V225F	orf3a	0.001242	0.906322	2	1	G>T
ERR5749154	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	7663	0.001696	0	1,7648,0,13	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749154	27972	PASS	C	T	7547	0.90738	0	0,0,7486,35	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749154	28048	PASS	G	T	7518	0.911014	0	0,9,0,7503	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749154	28111	PASS	A	G	23954	0.978876	0	1,0,16427,7520	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749154	28270	PASS	TA	T	31711	0.994166	418	184,8,16192,15334	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749154	28280	PASS	G	C	31646	0.932409	16	15,4,16245,15318	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749154	28281	PASS	A	T	31646	0.913417	6	19,11,16239,15319	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749154	28282	PASS	T	A	31649	0.906253	4	21,14,16192,15325	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749154	28310	PASS	C	T	16409	0.913279	0	0,15,16,16329	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Ccc/Tcc	P13S	N	0.00095	0.92832	2	1	C>T
ERR5749154	28881	PASS	G	A	13955	0.760946	6	3,0,6911,6834	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749154	28882	PASS	G	A	13953	0.827421	2	3,1,7004,6819	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749154	28883	PASS	G	C	13954	0.943099	3	0,1,7013,6923	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749154	28977	PASS	C	T	7117	0.924828	0	0,2,1,7101	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749154	29542	PASS	A	T	14118	0.51537	6	2655,3838,3039,4576	.	.	.	.	.	.	.	0.00099	0.957487	2	1	A>T
ERR5749155	241	PASS	C	T	3198	0.858036	6	0,2,1590,1585	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749155	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	5865	0.001194	0	5854,6,7,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749155	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	5879	0.001361	0	5824,20,8,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749155	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	5879	0.004252	0	5824,20,25,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749155	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	5873	0.001703	0	5377,19,421,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749155	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	17788	8.99E-4	9	11895,5868,14,2	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749155	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	17788	5.06E-4	1	11895,5868,7,2	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749155	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11910	0.001679	0	0,11879,0,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749155	913	PASS	C	T	11910	0.917045	0	0,8,0,11885	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749155	1266	PASS	G	T	24027	0.98689	3	0,1,12356,11661	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGc/gTc	G154V	nsp2	0.00107	0.98689	2	2	G>T
ERR5749155	1960	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	G	12020	0.001414	0	11994,0,18,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcG	A385	nsp2	0.001414	0.105737	2	1	C>G
ERR5749155	2151	PASS	A	G	12016	0.971954	2147483647	0,0,0,12007	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gAt/gGt	D449G	nsp2	0.000402	0.971954	3	2	A>G
ERR5749155	2453	PASS	C	T	9758	0.737241	0	0,8,0,9627	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L550F	nsp2	0.00429	0.842201	2	2	C>T
ERR5749155	3037	PASS	C	T	11743	0.815294	33	0,11,5860,5772	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749155	3267	PASS	C	T	12262	0.971375	0	1,0,12256,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749155	3734	PASS	G	A	7326	0.968741	2147483647	0,0,0,7314	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gac/Aac	D339N	nsp3	0.00428	0.968741	2	1	G>A
ERR5749155	3877	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	8043	0.002487	0	7073,0,966,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcG	A386	nsp3	0.000588	0.960227	2	1	T>G
ERR5749155	4237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTA	T	25236	7.93E-4	0	12622,12594,10,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	ata/	I508	nsp3	0.000302	0.918634	2	2	TTA>T
ERR5749155	5388	PASS	C	A	3931	0.958789	2147483647	0,0,3930,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749155	5986	PASS	C	T	9548	0.974654	0	1,0,9539,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749155	6954	PASS	T	C	13696	0.823306	0	0,1,0,13627	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749155	8772	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8956	0.001675	0	8905,1,17,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T73I	nsp4	0.001457	0.166667	1	1	C>T
ERR5749155	9402	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	5857	0.001366	0	2927,2922,4,4	HIGH	NONE	FRAME_SHIFT	ORF1ab	ata/	I284	nsp4	0.000453	0.058824	2	2	CTA>C
ERR5749155	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	14888	6.05E-4	6	11941,2938,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749155	10165	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTG	C	15834	6.32E-4	0	15815,9,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tgt/	C38	3Cpro	0.000632	0.976163	2	2	CTG>C
ERR5749155	11082	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	16796	5.95E-4	0	16793,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000427	0.179468	2	1	TG>T
ERR5749155	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	16796	0.001429	0	16742,0,44,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749155	11287	PASS	GTCTGGTTTT	G	16785	0.996604	0	0,57,0,16728	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749155	14408	PASS	C	T	4674	0.859649	3	0,1,2341,2307	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749155	14676	PASS	C	T	8128	0.788263	0	3,0,8107,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749155	15279	PASS	C	T	11639	0.915285	0	1,0,11619,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749155	15371	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CGT	C	23210	5.6E-4	0	11612,11585,7,6	HIGH	NONE	FRAME_SHIFT	ORF1ab	tgt/	C645	RdRp	0.00056	0.786959	4	2	CGT>C
ERR5749155	16176	PASS	T	C	12966	0.980873	3	1,0,5457,7505	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749155	16508	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	16236	0.001478	0	16189,4,43,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGt/gTt	G91V	helicase	0.000561	0.074909	2	2	G>T
ERR5749155	18501	PASS	C	T	18417	0.857143	0	0,14,0,18290	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y154	ExoN	0.000336	0.857143	4	2	C>T
ERR5749155	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	22974	6.09E-4	0	22960,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749155	18984	PASS	G	A	16955	0.950929	0	8,0,16945,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atA	M315I	ExoN	0.000419	0.950929	5	2	G>A
ERR5749155	19011	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	16955	7.67E-4	0	16941,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K325	ExoN	0.000408	0.975746	4	2	CAA>C
ERR5749155	19034	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTGG	T	16952	8.26E-4	0	16939,0,14,0	MODERATE	NONE	CODON_DELETION	ORF1ab	ggt/	G333	ExoN	0.000384	0.060908	2	2	TTGG>T
ERR5749155	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22006	0.001318	0	10766,10989,18,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749155	21764	PASS	ATACATG	A	9565	0.997491	0	24,0,9541,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749155	21990	PASS	TTTA	T	9566	0.997387	0	0,25,0,9541	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749155	22019	PASS	A	G	15216	0.98035	130	6,4,15202,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Atg/Gtg	M153V	S	0.001486	0.98035	1	1	A>G
ERR5749155	22293	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TACATA	T	23921	4.18E-4	17	8711,15196,0,10	HIGH	NONE	FRAME_SHIFT	S	ttacataga/	LHR244	S	0.000308	0.160511	4	1	TACATA>T
ERR5749155	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22705	0.001013	2	10609,12050,13,11	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749155	23063	PASS	A	T	10612	0.865907	0	0,2,0,10561	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749155	23271	PASS	C	A	13401	0.920752	2147483647	0,0,13393,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749155	23403	PASS	A	G	13391	0.966171	0	0,6,0,13377	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749155	23604	PASS	C	A	11650	0.950386	0	3,0,11641,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749155	23709	PASS	C	T	11638	0.931432	0	0,3,2,11619	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749155	24506	PASS	T	G	11921	0.976344	0	1,0,11918,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749155	24914	PASS	G	C	32879	0.961069	0	0,0,16397,16466	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749155	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	19947	0.001153	25	15275,4645,25,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749155	25685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6349	0.002048	0	6331,0,13,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	gCt/gTt	A98V	orf3a	0.002048	0.964351	1	1	C>T
ERR5749155	25803	PASS	C	T	12578	0.899984	3	2,4,6288,6232	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	aaC/aaT	N137	orf3a	0.002077	0.899984	1	1	C>T
ERR5749155	25916	PASS	C	T	6348	0.964713	38	1,0,0,6343	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aCa/aTa	T175I	orf3a	0.001191	0.964713	2	2	C>T
ERR5749155	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	16255	5.54E-4	0	0,16246,0,9	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749155	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	9907	8.08E-4	0	0,9899,0,8	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749155	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	9908	0.00222	0	0,9878,0,22	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749155	27598	PASS	G	T	15315	0.958994	0	5,0,15293,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Gac/Tac	D69Y	orf7a	0.000699	0.958994	6	2	G>T
ERR5749155	27972	PASS	C	T	5583	0.904352	22	0,1,5530,28	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749155	28048	PASS	G	T	5559	0.922828	0	0,11,0,5543	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749155	28111	PASS	A	G	22208	0.977531	0	2,0,16630,5562	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749155	28270	PASS	TA	T	32253	0.995318	391	152,3,16414,15688	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749155	28280	PASS	G	C	32186	0.937675	14	8,1,16449,15666	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749155	28281	PASS	A	T	32186	0.92127	40	23,3,16437,15683	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749155	28282	PASS	T	A	32188	0.912048	12	16,6,16401,15689	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749155	28881	PASS	G	A	7302	0.761983	12	5,0,3613,3593	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749155	28882	PASS	G	A	7302	0.837853	0	1,0,3659,3579	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749155	28883	PASS	G	C	7302	0.945357	0	1,0,3658,3634	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749155	28977	PASS	C	T	3717	0.925747	0	0,2,0,3704	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749155	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	27039	0.001775	319	23296,3671,7,46	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749155	29095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23319	0.001544	0	23273,0,36,0	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F274	N	0.000792	0.961279	2	2	C>T
ERR5749155	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	46270	0.001189	0	23245,22941,38,35	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749155	29284	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23316	0.001801	0	0,23223,0,45	LOW	SILENT	SYNONYMOUS_CODING	N	atC/atT	I337	N	0.000393	0.931014	3	2	C>T
ERR5749155	29779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	5941	0.002188	0	0,5920,0,21	.	.	.	.	.	.	.	0.001489	0.975228	1	1	G>T
ERR5749156	241	PASS	C	T	13896	0.861327	3	0,2,6914,6950	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749156	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	12872	0.001088	0	12861,1,14,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749156	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	12872	0.001321	0	12847,1,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749156	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12867	0.001632	0	11951,3,864,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749156	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	35987	9.45E-4	8	23074,12875,26,8	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749156	913	PASS	C	T	23099	0.925928	0	0,13,0,23069	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749156	1510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	25548	0.003797	0	0,25245,0,105	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G235	nsp2	0.002159	0.937304	1	1	T>C
ERR5749156	1594	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25583	0.009616	0	16,25303,0,255	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S263	nsp2	0.0019	0.963177	1	1	C>T
ERR5749156	3037	PASS	C	T	20395	0.825545	35	3,20,10188,10038	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749156	3177	PASS	C	T	33410	0.897127	0	8,3,23122,10227	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P153L	nsp3	0.000773	0.96008	3	2	C>T
ERR5749156	3267	PASS	C	T	23153	0.967564	0	4,0,23128,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749156	5113	PASS	A	C	15405	0.760467	0	3030,0,12356,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K798N	nsp3	0.760467	0.766581	1	1	A>C
ERR5749156	5388	PASS	C	A	7750	0.961548	2147483647	0,0,7746,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749156	5986	PASS	C	T	14299	0.975103	0	4,0,14289,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749156	6954	PASS	T	C	26813	0.840227	0	0,3,0,26699	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749156	7528	PASS	C	T	18417	0.908943	0	0,11,36,18345	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V1603	nsp3	0.002527	0.916131	1	1	C>T
ERR5749156	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	36214	9.39E-4	107	17426,18753,34,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749156	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	22921	0.001527	0	22851,1,57,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749156	11287	PASS	GTCTGGTTTT	G	22928	0.99891	0	0,25,1,22902	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749156	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	42508	7.53E-4	0	26154,16278,21,12	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749156	11747	PASS	C	T	26181	0.728391	0	2866,1,23181,9	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L259	nsp6	0.001145	0.737282	1	1	C>T
ERR5749156	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	37020	0.001324	0	18480,18442,26,27	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749156	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10362	0.004053	2475	10102,112,2,143	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749156	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	20142	6.45E-4	0	10094,10040,7,6	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749156	14408	PASS	C	T	20142	0.84927	6	1,4,10051,9941	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749156	14676	PASS	C	T	14676	0.784274	0	5,0,14639,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749156	15279	PASS	C	T	25016	0.883355	0	3,0,24972,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749156	16176	PASS	T	C	23689	0.982017	2	2,1,11344,12334	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749156	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	25233	9.12E-4	0	25209,0,23,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749156	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30055	0.002196	0	29969,1,66,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749156	21123	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	58277	2.57E-4	5	35112,23150,7,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F156	MethTr	0.000257	0.90982	5	2	GT>G
ERR5749156	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	35975	8.62E-4	1	17725,17912,18,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749156	21622	PASS	C	T	18064	0.946634	0	0,4,0,18046	LOW	SILENT	SYNONYMOUS_CODING	S	acC/acT	T20	S	0.000846	0.946634	3	2	C>T
ERR5749156	21764	PASS	ATACATG	A	13509	0.996373	0	47,0,13460,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749156	21990	PASS	TTTA	T	13515	0.997336	0	0,36,8,13471	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749156	22450	PASS	C	T	11478	0.783586	20	1,1,11281,53	LOW	SILENT	SYNONYMOUS_CODING	S	ctC/ctT	L296	S	0.00215	0.803846	1	1	C>T
ERR5749156	23063	PASS	A	T	15258	0.870494	0	0,2,0,15190	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749156	23271	PASS	C	A	23804	0.923416	2147483647	0,0,23784,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749156	23403	PASS	A	G	23806	0.974082	0	0,4,0,23787	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749156	23604	PASS	C	A	17511	0.943807	0	14,0,17485,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749156	23709	PASS	C	T	17509	0.945285	0	0,3,1,17484	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749156	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	38193	6.02E-4	0	20666,17504,13,10	HIGH	NONE	FRAME_SHIFT	S	ttg/	L753	S	0.000334	0.080808	2	2	CT>C
ERR5749156	24506	PASS	T	G	21726	0.973304	0	13,0,21706,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749156	24914	PASS	G	C	39166	0.959991	3	1,0,19511,19628	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749156	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	28837	0.001318	52	18745,10028,40,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749156	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	25995	0.001193	0	25964,0,31,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749156	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	26225	0.001716	1298	25702,162,227,104	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749156	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	14243	0.001194	0	0,14226,0,17	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749156	27389	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19721	0.001927	0	21,19627,0,44	.	.	.	.	.	.	.	0.001157	0.899553	2	1	C>T
ERR5749156	27403	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	19712	0.001116	0	0,19663,0,39	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Att/Ttt	I4F	orf7a	0.000512	0.916	3	2	A>T
ERR5749156	27972	PASS	C	T	12761	0.897187	52	3,3,12631,81	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749156	28048	PASS	G	T	12679	0.929174	0	0,9,0,12665	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749156	28111	PASS	A	G	32134	0.979803	5	1,3,19438,12677	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749156	28270	PASS	TA	T	37847	0.995323	449	185,6,19194,18476	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749156	28280	PASS	G	C	37778	0.939912	15	16,5,19229,18453	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749156	28281	PASS	A	T	37778	0.921012	34	25,5,19229,18464	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749156	28282	PASS	T	A	37782	0.913027	10	22,11,19180,18471	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749156	28310	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	19435	0.003293	0	5,19339,0,78	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Ccc/Acc	P13T	N	0.00095	0.92832	2	1	C>A
ERR5749156	28881	PASS	G	A	23226	0.756695	33	11,0,11432,11452	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749156	28882	PASS	G	A	23225	0.834058	9	6,1,11600,11419	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749156	28883	PASS	G	C	23225	0.943767	6	0,2,11621,11584	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749156	28977	PASS	C	T	11821	0.941375	2147483647	0,0,0,11803	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749156	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	40277	9.93E-4	186	28423,11770,3,42	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749156	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	56498	8.67E-4	0	28373,28032,35,33	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749157	241	PASS	C	T	6722	0.865367	3	0,2,3340,3362	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749157	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	10483	7.63E-4	0	10470,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749157	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10478	0.001813	0	9810,0,647,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749157	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	10478	0.00105	0	10467,0,11,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttatg/gtg	VM84V	leader	0.000554	0.991848	4	1	GTTA>G
ERR5749157	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	26082	4.22E-4	23	15549,10517,11,0	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749157	913	PASS	C	T	15559	0.926216	0	0,7,0,15536	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749157	2185	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	20485	7.81E-4	0	2,20467,0,16	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L462S?	nsp2	0.000441	0.963529	4	3	G>GT
ERR5749157	3037	PASS	C	T	17425	0.833113	35	1,15,8700,8598	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749157	3267	PASS	C	T	15305	0.970663	0	4,0,15292,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749157	5170	PASS	C	T	9456	0.894036	0	0,12,2,9405	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y817	nsp3	0.000565	0.894036	2	2	C>T
ERR5749157	5388	PASS	C	A	5997	0.957479	2147483647	0,0,5993,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749157	5986	PASS	C	T	11502	0.977221	0	2,0,11491,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749157	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10992	0.001456	0	3,10844,0,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749157	6954	PASS	T	C	16456	0.81563	0	0,2,0,16372	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749157	7070	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	33612	9.82E-4	101	17071,16496,35,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggc/Agc	G1451S	nsp3	0.000698	0.101434	3	1	G>A
ERR5749157	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	22949	4.79E-4	23	13786,9152,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749157	9727	PASS	T	C	13800	0.973696	0	0,0,15,13783	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taT/taC	Y391	nsp4	0.015758	0.973696	1	1	T>C
ERR5749157	11073	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TC	T	15299	9.15E-4	0	15285,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttc/	F34	nsp6	0.000385	0.092251	6	2	TC>T
ERR5749157	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15299	0.01255	0	15062,0,205,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749157	11287	PASS	GTCTGGTTTT	G	15293	0.998496	0	0,23,0,15270	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749157	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25172	0.001986	0	12566,12526,26,26	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749157	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	6592	0.004854	1811	6421,58,5,106	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749157	14408	PASS	C	T	12780	0.85939	0	2,1,6387,6324	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749157	14676	PASS	C	T	10220	0.718591	0	8,0,10170,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749157	15279	PASS	C	T	16567	0.902095	0	1,0,16547,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749157	15654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15518	0.008055	0	15374,0,137,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D738	RdRp	0.001856	0.060658	2	2	C>T
ERR5749157	15983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	8632	0.001158	0	8623,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T850	RdRp	0.000701	0.338235	2	1	TA>T
ERR5749157	16176	PASS	T	C	17401	0.983622	0	1,0,8742,8646	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749157	16468	PASS	C	T	26037	0.977186	0	1,0,17273,8749	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ccc/Tcc	P78S	helicase	0.001077	0.977186	1	1	C>T
ERR5749157	17615	PASS	A	G	14500	0.896759	0	0,0,1,14444	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749157	17642	PASS	C	T	14511	0.955	0	0,5,1,14488	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A469V	helicase	0.949863	0.955	1	1	C>T
ERR5749157	17999	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21649	0.004111	0	11105,10443,47,45	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T588I	helicase	0.001094	0.974498	2	1	C>T
ERR5749157	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23821	0.002435	0	23748,0,60,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749157	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	22899	8.73E-4	0	11423,11458,10,10	HIGH	NONE	FRAME_SHIFT	S	ctt/Tctt	L5S?	S	0.000394	0.091869	4	1	G>GT
ERR5749157	21762	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTATACA	C	11558	0.002509	0	11526,0,29,0	MODERATE	NONE	CODON_DELETION	S	atacat/	IH68	S	0.001297	0.875707	2	2	CTATACA>C
ERR5749157	21764	PASS	ATACATG	A	11558	0.996366	0	42,0,11516,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749157	21786	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	11558	0.002423	0	11521,0,36,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gGt/gTt	G75V	S	0.001992	0.058409	1	1	G>T
ERR5749157	21990	PASS	TTTA	T	11565	0.997925	0	0,24,6,11535	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749157	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25249	9.9E-4	7	13234,11980,17,8	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749157	23063	PASS	A	T	13234	0.870258	0	0,6,0,13167	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749157	23271	PASS	C	A	17452	0.929807	0	2,0,17428,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749157	23403	PASS	A	G	17444	0.969732	0	0,6,0,17428	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749157	23604	PASS	C	A	14574	0.950871	0	7,0,14561,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749157	23664	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28908	8.99E-4	0	14361,14487,14,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCa/gTa	A701V	S	0.000837	0.918	2	2	C>T
ERR5749157	23709	PASS	C	T	14556	0.946414	0	0,2,0,14533	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749157	24506	PASS	T	G	14046	0.971309	0	3,0,14043,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749157	24914	PASS	G	C	34751	0.956606	0	0,0,17297,17423	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749157	25496	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	32883	6.69E-4	52	16114,16228,307,205	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aTa/aGa	I35R	orf3a	0.000369	0.96555	3	2	T>G
ERR5749157	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	14679	0.001771	405	14619,15,10,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749157	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	14765	0.00149	755	14535,94,70,53	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749157	27371	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17572	0.00148	0	25,17485,0,36	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF6	cCa/cTa	P57L	orf6	0.00148	0.066731	2	2	C>T
ERR5749157	27972	PASS	C	T	10513	0.903738	22	0,1,10419,57	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749157	28048	PASS	G	T	10461	0.917981	0	0,17,0,10433	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749157	28111	PASS	A	G	25071	0.976028	1	4,4,14589,10463	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749157	28270	PASS	TA	T	28377	0.995384	304	133,6,14416,13830	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749157	28280	PASS	G	C	28322	0.936869	3	5,2,14444,13820	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749157	28281	PASS	A	T	28322	0.921439	21	19,5,14447,13823	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749157	28282	PASS	T	A	28323	0.908237	21	17,4,14405,13827	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749157	28881	PASS	G	A	13498	0.747296	12	5,0,6652,6641	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749157	28882	PASS	G	A	13498	0.826345	6	3,0,6752,6613	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749157	28883	PASS	G	C	13498	0.943769	0	2,1,6761,6719	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749157	28977	PASS	C	T	6880	0.929215	2147483647	0,0,0,6869	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749157	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	53070	0.001225	0	26642,26315,41,39	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749158	241	PASS	C	T	8307	0.863007	0	0,1,4131,4136	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749158	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	7529	0.006641	0	7473,5,50,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749158	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	7528	0.001063	0	7436,5,8,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749158	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	7528	0.00983	0	7436,5,74,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749158	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	7529	0.001328	0	6910,14,443,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749158	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	7529	0.002258	0	7498,14,17,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749158	657	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7539	0.003581	0	1,7505,0,32	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A131V	leader	0.001202	0.365979	3	1	C>T
ERR5749158	673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23758	9.68E-4	30	16202,7492,9,16	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y136	leader	0.000454	0.602236	3	2	C>T
ERR5749158	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23753	9.26E-4	0	16195,7496,15,8	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L140	leader	0.000316	0.135802	3	2	C>T
ERR5749158	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	23753	8.84E-4	14	16197,7533,19,2	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749158	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	23753	5.05E-4	2	16146,7520,7,5	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749158	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	23753	0.002358	20	16146,7520,47,9	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749158	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTTG	A	23753	5.89E-4	13	16146,7520,13,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcatttgac/	KSFD141	leader	0.000303	0.999303	4	1	AAAGTCATTTG>A
ERR5749158	913	PASS	C	T	16211	0.908766	0	0,5,0,16185	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749158	3037	PASS	C	T	20664	0.835511	39	0,13,10332,10200	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749158	3267	PASS	C	T	18325	0.968622	0	1,0,18319,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749158	3877	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	16890	0.001007	0	15669,0,1216,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcG	A386	nsp3	0.000588	0.960227	2	1	T>G
ERR5749158	4255	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	36648	0.001146	0	18269,18288,24,23	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccG/ccA	P512	nsp3	0.001102	0.871853	2	1	G>A
ERR5749158	5388	PASS	C	A	5782	0.955206	2147483647	0,0,5773,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749158	5986	PASS	C	T	13538	0.972596	2147483647	0,0,13529,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749158	6525	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	35559	0.001266	1	13754,21748,19,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T1269I	nsp3	0.000813	0.968636	1	1	C>T
ERR5749158	6954	PASS	T	C	19550	0.814373	0	0,17,4,19422	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749158	7764	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20159	0.002431	0	20091,0,51,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCc/tTc	S1682F	nsp3	0.001052	0.964731	1	1	C>T
ERR5749158	7834	PASS	C	T	40000	0.86555	84	1,32,19970,19867	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N1705	nsp3	0.000523	0.86555	3	2	C>T
ERR5749158	10193	PASS	G	A	19183	0.859303	0	1,0,19143,4	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E47K	3Cpro	0.000774	0.869819	2	2	G>A
ERR5749158	10195	PASS	A	T	19183	0.958192	0	8,0,19153,5	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gaA/gaT	E47D	3Cpro	0.951998	0.969772	1	1	A>T
ERR5749158	10228	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19182	0.00537	0	19052,9,108,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ctC/ctT	L58	3Cpro	0.000533	0.961998	2	2	C>T
ERR5749158	10323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	19159	0.001827	0	4,19073,0,40	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749158	10595	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	15423	0.001297	0	18,15368,0,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F181L	3Cpro	0.000964	0.076408	1	1	T>C
ERR5749158	11104	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	20075	0.001445	0	19966,0,30,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccT/ccC	P44	nsp6	0.000866	0.675414	2	1	T>C
ERR5749158	11287	PASS	GTCTGGTTTT	G	20072	0.996214	0	0,75,0,19996	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749158	12131	PASS	G	A	19689	0.897455	35	1,4,0,19636	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gct/Act	A14T	nsp8	0.002075	0.897455	1	1	G>A
ERR5749158	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	14313	9.08E-4	0	14300,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749158	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27101	0.001033	2	13537,13493,15,18	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749158	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	7193	0.003476	1460	7018,84,3,86	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749158	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	13946	0.001506	0	7000,6940,10,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749158	14408	PASS	C	T	13946	0.848415	9	1,5,6958,6874	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749158	14676	PASS	C	T	11115	0.785425	0	3,0,11081,2	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749158	14925	PASS	C	T	17530	0.98996	36	3,1,17523,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V495	RdRp	0.002531	0.98996	1	1	C>T
ERR5749158	15279	PASS	C	T	16708	0.896217	0	1,0,16680,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749158	16176	PASS	T	C	16358	0.979398	1	3,2,7181,9169	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749158	18647	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	48743	8.62E-4	8	22508,26160,25,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P203L	ExoN	0.000283	0.970507	4	2	C>T
ERR5749158	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	22552	8.42E-4	0	22533,0,19,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749158	19343	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTTTTGTTAAT	C	21175	5.19E-4	0	21148,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tttgttaattta/	FVNL436	ExoN	0.000519	0.192257	7	2	CTTTTGTTAAT>C
ERR5749158	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24548	0.001589	0	24497,0,40,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749158	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	21371	0.001638	0	0,21330,0,35	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TA>T
ERR5749158	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	32511	8.92E-4	0	15904,16235,16,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749158	21764	PASS	ATACATG	A	14713	0.996873	0	46,0,14667,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749158	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	14713	6.8E-4	0	14703,0,10,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749158	21990	PASS	TTTA	T	14722	0.998234	0	0,26,8,14688	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749158	22716	PASS	C	A	31427	0.865911	28	38,71,15688,15585	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCt/aAt	T385N	S	0.000738	0.865911	1	1	C>A
ERR5749158	22717	PASS	T	C	31427	0.918478	3	0,1,15721,15633	LOW	SILENT	SYNONYMOUS_CODING	S	acT/acC	T385	S	0.000395	0.918478	3	2	T>C
ERR5749158	23063	PASS	A	T	14732	0.873133	0	0,4,4,14662	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749158	23271	PASS	C	A	19588	0.9199	0	1,0,19572,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749158	23403	PASS	A	G	19587	0.966866	0	0,5,0,19556	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749158	23604	PASS	C	A	16287	0.94032	0	10,0,16261,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749158	23709	PASS	C	T	16278	0.942499	0	0,4,13,16240	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749158	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	29233	8.55E-4	34	12923,16285,20,5	HIGH	NONE	FRAME_SHIFT	S	ttg/	L753	S	0.000334	0.080808	2	2	CT>C
ERR5749158	24506	PASS	T	G	14773	0.974954	0	2,0,14767,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749158	24899	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	36778	3.81E-4	0	18399,18367,7,7	HIGH	NONE	FRAME_SHIFT	S	atc/	I1114	S	0.000315	0.09021	5	3	CA>C
ERR5749158	24914	PASS	G	C	36640	0.958897	0	1,2,18242,18353	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749158	25587	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	20507	6.34E-4	0	0,20486,0,13	HIGH	NONE	FRAME_SHIFT	ORF3a	aag/	K67	orf3a	0.000598	0.813206	6	2	CA>C
ERR5749158	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	14264	0.002033	296	14174,21,16,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749158	26526	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	10301	0.001456	0	2,10277,0,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Gca/Aca	A2T	M	0.001224	0.951192	3	1	G>A
ERR5749158	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	G	13839	6.5E-4	0	9,13806,0,9	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/	ACLVGLMWLSYFIASF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT>G
ERR5749158	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	13839	0.001228	0	9,13810,0,17	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749158	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	13840	0.004335	0	7,13767,0,60	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749158	27603	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19281	0.003475	0	19177,1,71,0	LOW	SILENT	SYNONYMOUS_CODING	ORF7a	ggC/ggT	G70	orf7a	0.002411	0.959582	1	1	C>T
ERR5749158	27741	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	19317	5.18E-4	0	5,19300,0,10	HIGH	NONE	FRAME_SHIFT	ORF7a	aga/	R118	orf7a	0.000363	0.954278	3	2	CA>C
ERR5749158	27972	PASS	C	T	11359	0.907386	50	3,3,11230,84	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749158	28048	PASS	G	T	11278	0.926583	0	0,17,0,11256	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749158	28111	PASS	A	G	31003	0.977518	0	0,0,19703,11286	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749158	28113	PASS	A	G	31003	0.979486	2	3,0,19705,11281	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	Atc/Gtc	I74V	orf8	0.979486	0.979486	1	1	A>G
ERR5749158	28237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTGT	G	19712	5.58E-4	0	19698,3,11,0	MODERATE	NONE	CODON_DELETION	ORF8	gtt/	V117	orf8	0.000442	0.966707	4	2	GTGT>G
ERR5749158	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19704	0.001523	0	19569,8,31,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749158	28270	PASS	TA	T	38187	0.992956	622	261,9,19361,18557	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749158	28271	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AA	A	38181	0.001152	127	19572,18568,44,0	.	.	.	.	.	.	.	0.000482	0.924941	3	2	AA>A
ERR5749158	28280	PASS	G	C	38104	0.926412	19	16,4,19454,18542	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749158	28281	PASS	A	T	38104	0.910482	48	29,4,19448,18540	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749158	28282	PASS	T	A	38114	0.914992	13	28,14,19420,18560	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749158	28292	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	39192	4.59E-4	0	19501,19623,9,9	HIGH	NONE	FRAME_SHIFT	N	aat/	N8	N	0.000304	0.055324	4	2	CAA>C
ERR5749158	28406	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTACCCAATA	T	19725	8.62E-4	0	14,19698,0,17	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	N	ttacccaataat/tat	LPNN45Y	N	0.00043	0.921074	3	2	TTACCCAATA>T
ERR5749158	28603	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	44960	0.001179	0	22417,22291,31,32	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F110	N	0.000427	0.883357	2	2	C>T
ERR5749158	28881	PASS	G	A	13678	0.757421	9	6,1,6743,6699	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749158	28882	PASS	G	A	13677	0.820721	18	7,0,6842,6682	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749158	28883	PASS	G	C	13678	0.948092	0	1,1,6856,6814	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749158	28977	PASS	C	T	6957	0.932442	2147483647	0,0,0,6940	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749158	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	65120	0.001167	1	32685,32305,56,51	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749158	29708	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10707	0.003269	0	154,10494,0,40	.	.	.	.	.	.	.	0.003269	0.150943	1	1	C>T
ERR5749158	29738	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10569	0.001703	0	0,10539,0,21	.	.	.	.	.	.	.	0.001703	0.890671	2	1	C>T
ERR5749159	241	PASS	C	T	8325	0.861622	3	0,2,4144,4151	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749159	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	11162	0.003315	0	11125,0,37,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749159	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	11169	0.001164	0	11042,7,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749159	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	11169	0.001343	0	11042,7,15,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749159	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	11169	0.007968	0	11042,7,89,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749159	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	11163	0.002956	0	10153,7,804,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749159	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	11163	0.00206	0	11133,7,23,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749159	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	11160	0.001075	0	11137,10,12,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749159	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	31233	0.002049	1	20001,11162,43,21	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749159	913	PASS	C	T	20039	0.92315	0	0,4,0,19997	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749159	1510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	20002	0.00285	0	0,19769,0,59	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G235	nsp2	0.002159	0.937304	1	1	T>C
ERR5749159	1813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	17134	0.001109	0	2,17097,0,25	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcA	A336	nsp2	0.001022	0.152738	4	2	T>A
ERR5749159	3037	PASS	C	T	15888	0.810612	44	1,18,7939,7805	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749159	3177	PASS	C	T	27332	0.908715	0	8,3,19291,7988	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P153L	nsp3	0.000773	0.96008	3	2	C>T
ERR5749159	3267	PASS	C	T	19326	0.969212	0	0,0,19308,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749159	4582	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13738	0.010409	0	0,13565,0,150	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N621	nsp3	0.005644	0.938733	2	2	C>T
ERR5749159	5170	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	11327	8.83E-4	0	3,11314,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T819	nsp3	0.000565	0.894036	2	2	CCA>C
ERR5749159	5388	PASS	C	A	5636	0.960433	2147483647	0,0,5633,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749159	5986	PASS	C	T	11083	0.972029	0	2,0,11075,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749159	6954	PASS	T	C	19764	0.823518	0	0,1,3,19680	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749159	7070	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	34366	0.001251	99	14496,19816,40,5	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggc/Agc	G1451S	nsp3	0.000698	0.101434	3	1	G>A
ERR5749159	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	19920	0.002058	0	19339,3,41,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749159	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19920	0.001406	0	19857,3,33,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749159	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	19907	0.001407	0	19856,0,38,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749159	11287	PASS	GTCTGGTTTT	G	19907	0.995881	0	0,82,0,19825	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749159	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	18254	0.001534	0	18195,0,28,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749159	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30932	8.41E-4	0	15453,15412,13,14	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749159	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	5738	0.004531	1562	5569,69,3,95	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749159	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	11082	9.02E-4	0	5561,5523,5,5	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749159	14408	PASS	C	T	11082	0.836221	0	2,2,5531,5459	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749159	14676	PASS	C	T	12470	0.793184	0	6,0,12433,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749159	15279	PASS	C	T	20318	0.890048	0	2,0,20278,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749159	16176	PASS	T	C	18603	0.980702	0	0,0,8172,10426	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749159	17058	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	18134	0.004412	0	0,18045,0,87	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atT	M274I	helicase	0.00262	0.976037	2	1	G>T
ERR5749159	17562	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	27493	0.010075	1	13611,13552,168,160	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	cgG/cgT	R442	helicase	0.000543	0.90562	3	2	G>T
ERR5749159	17894	PASS	C	T	23414	0.598574	4	2825,2854,8636,8986	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A553V	helicase	0.00131	0.598574	1	1	C>T
ERR5749159	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23228	0.002669	0	23152,0,65,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749159	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27839	8.62E-4	0	27775,0,25,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749159	21255	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	52760	6.44E-4	0	27344,25364,20,18	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcG/gcA	A199	MethTr	0.000341	0.917425	4	2	G>A
ERR5749159	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GTT	26582	0.001806	150	13281,12526,0,48	HIGH	NONE	FRAME_SHIFT	S	ctt/TTctt	L5F?	S	0.000394	0.091869	4	1	G>GTT
ERR5749159	21575	PASS	C	T	25622	0.865038	8	1,6,12083,13143	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749159	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	25616	0.004099	298	12288,13205,0,105	HIGH	NONE	FRAME_SHIFT	S	gtt/Tgtt	V6C?	S	0.000619	0.877942	3	2	C>CT
ERR5749159	21660	PASS	C	T	13414	0.937304	110	3,1,0,13393	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T33I	S	0.008721	0.937304	1	1	C>T
ERR5749159	21764	PASS	ATACATG	A	11097	0.997477	0	28,0,11069,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749159	21990	PASS	TTTA	T	11101	0.997388	0	0,29,2,11070	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749159	23063	PASS	A	T	12766	0.872082	0	0,3,0,12713	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749159	23271	PASS	C	A	21209	0.922391	2147483647	0,0,21182,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749159	23403	PASS	A	G	21199	0.969527	0	0,4,0,21171	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749159	23604	PASS	C	A	14029	0.947252	0	11,0,14015,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749159	23709	PASS	C	T	14021	0.940161	0	0,3,9,13992	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749159	24506	PASS	T	G	16826	0.973315	0	6,0,16812,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749159	24914	PASS	G	C	36291	0.959439	0	0,0,18076,18198	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749159	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	24381	9.43E-4	22	16394,7945,31,4	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749159	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	14905	0.001476	350	14838,23,7,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749159	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	14867	9.42E-4	0	14853,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749159	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	39406	4.06E-4	0	1,39389,0,16	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749159	26571	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTTGAACAATGGAACCTAGTAATAGGTTTCCTA	C	11665	0.001114	0	11647,5,13,0	HIGH	NONE	FRAME_SHIFT	M	gaacaatggaacctagtaataggtttcctattc/	EQWNLVIGFLF18	M	0.000508	0.905823	3	2	CTTGAACAATGGAACCTAGTAATAGGTTTCCTA>C
ERR5749159	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	11653	7.72E-4	0	7,11625,0,9	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749159	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTTT	G	11653	7.72E-4	0	7,11625,0,9	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgtttgcg/gcg	ACLVGLMWLSYFIASFRLFA85A	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTTT>G
ERR5749159	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	11653	0.00103	0	7,11633,0,12	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749159	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	11657	0.002402	0	7,11617,0,28	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749159	27972	PASS	C	T	9616	0.905054	0	0,0,9523,53	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749159	28048	PASS	G	T	9571	0.917459	0	0,7,0,9558	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749159	28111	PASS	A	G	29830	0.978847	0	4,2,20238,9575	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749159	28270	PASS	TA	T	39279	0.994425	486	215,10,19949,19111	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749159	28280	PASS	G	C	39200	0.940612	23	14,2,19997,19091	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749159	28281	PASS	A	T	39200	0.917475	45	32,6,19983,19106	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749159	28282	PASS	T	A	39202	0.910362	32	35,11,19933,19111	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749159	28881	PASS	G	A	10719	0.746805	11	6,1,5258,5327	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749159	28882	PASS	G	A	10719	0.831887	0	1,1,5321,5308	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749159	28883	PASS	G	C	10719	0.947663	6	0,3,5326,5380	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749159	28977	PASS	C	T	5395	0.932901	2147483647	0,0,0,5389	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749159	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	33302	0.001051	152	27882,5351,8,28	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749159	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	55388	9.39E-4	0	27830,27470,33,32	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749160	210	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	8	1.0	2147483647	0,0,8,0	.	.	.	.	.	.	.	0.001452	1	2	1	G>T
ERR5749160	241	PASS	C	T	16	0.9375	0	0,0,8,8	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749160	913	PASS	C	T	51	0.921569	2147483647	0,0,0,51	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749160	1190	PASS	C	T	179	0.938547	2147483647	0,0,0,178	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cca/Tca	P129S	nsp2	0.002242	0.938547	1	1	C>T
ERR5749160	1415	PASS	C	T	118	0.161017	0	97,0,21,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Ttt	L204F	nsp2	0.002573	0.161017	2	2	C>T
ERR5749160	2506	PASS	TC	T	168	0.065476	0	0,157,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	ccc/	P568	nsp2	0.002339	0.065476	2	2	TC>T
ERR5749160	2890	PASS	G	A	46	0.934783	2147483647	0,0,46,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtG/gtA	V57	nsp3	0.934783	0.983505	1	1	G>A
ERR5749160	3037	PASS	C	T	92	0.858696	0	0,0,46,46	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749160	3267	PASS	C	T	149	0.979866	2147483647	0,0,149,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749160	5388	PASS	C	A	56	0.928571	2147483647	0,0,56,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749160	5986	PASS	C	T	67	0.925373	2147483647	0,0,67,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749160	6272	PASS	T	A	173	0.156069	0	145,0,28,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Aat	Y1185N	nsp3	0.001735	0.156069	2	1	T>A
ERR5749160	6954	PASS	T	C	65	0.892308	2147483647	0,0,0,65	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749160	10350	PASS	C	T	240	0.208333	0	0,189,0,51	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P99L	3Cpro	0.001438	0.208333	1	1	C>T
ERR5749160	11074	PASS	CT	C	630	0.225397	0	488,0,142,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000965	0.945355	5	2	CT>C
ERR5749160	11287	PASS	GTCTGGTTTT	G	630	1.0	2147483647	0,0,0,630	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749160	11417	PASS	G	T	51	0.882353	2147483647	0,0,51,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Ttt	V149F	nsp6	0.00274	0.951155	2	2	G>T
ERR5749160	11690	PASS	G	T	219	0.091324	0	195,0,24,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggt/Tgt	G240C	nsp6	0.000953	0.091324	4	2	G>T
ERR5749160	11750	PASS	C	T	422	0.675355	0	0,0,216,183	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L260F	nsp6	0.001019	0.70989	2	1	C>T
ERR5749160	13164	PASS	C	T	501	0.9501	2147483647	0,0,501,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T47I	nsp10	0.001249	0.952318	1	1	C>T
ERR5749160	14408	PASS	C	T	18	0.777778	0	0,0,9,9	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749160	14676	PASS	C	T	25	0.6	2147483647	0,0,25,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749160	15262	PASS	G	C	87	0.195402	0	70,0,17,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gat/Cat	D608H	RdRp	0.195402	0.195402	1	1	G>C
ERR5749160	15279	PASS	C	T	87	0.942529	2147483647	0,0,87,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749160	16176	PASS	T	C	91	0.956044	0	0,0,19,72	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749160	16575	PASS	C	T	492	0.823171	0	1,0,489,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D113	helicase	0.001088	0.827968	1	1	C>T
ERR5749160	17418	PASS	G	C	184	0.108696	6	145,19,20,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaG/aaC	K394N	helicase	0.001518	0.108696	2	1	G>C
ERR5749160	17756	PASS	GAA	G	163	0.165644	0	136,0,27,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K508	helicase	0.000865	0.165644	4	2	GAA>G
ERR5749160	21032	PASS	A	C	271	0.088561	0	0,241,0,30	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gAt/gCt	D125A	MethTr	0.000568	0.088561	2	2	A>C
ERR5749160	21334	PASS	G	T	697	0.077475	0	0,640,0,57	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gca/Tca	A226S	MethTr	0.000897	0.077475	3	1	G>T
ERR5749160	21516	PASS	C	T	225	0.871111	2147483647	0,0,225,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N286	MethTr	0.000412	0.905456	2	2	C>T
ERR5749160	21733	PASS	T	C	547	0.065814	0	509,0,38,0	LOW	SILENT	SYNONYMOUS_CODING	S	ccT/ccC	P57	S	0.001662	0.065814	2	1	T>C
ERR5749160	21764	PASS	ATACATG	A	547	0.994516	0	3,0,544,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749160	21801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	547	0.005484	0	544,0,3,0	HIGH	NONE	FRAME_SHIFT	S	gat/	D80	S	0.005484	0.946172	2	2	AT>A
ERR5749160	21990	PASS	TTTA	T	548	0.992701	0	0,4,1,543	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749160	23063	PASS	A	T	333	0.87988	0	0,1,0,329	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749160	23271	PASS	C	A	278	0.938849	2147483647	0,0,278,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749160	23403	PASS	A	G	277	0.967509	2147483647	0,0,0,277	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749160	23604	PASS	C	A	311	0.938907	2147483647	0,0,311,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749160	23709	PASS	C	T	310	0.929032	2147483647	0,0,0,310	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749160	24506	PASS	T	G	204	0.965686	0	1,0,203,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749160	24899	PASS	C	G	1430	0.09021	0	643,639,72,70	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Caa/Gaa	Q1113E	S	0.000315	0.09021	5	3	C>G
ERR5749160	24914	PASS	G	C	1426	0.951613	0	0,0,711,714	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749160	25302	PASS	G	T	2479	0.05002	7	2307,41,131,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tGt/tTt	C1247F	S	0.001121	0.05002	1	1	G>T
ERR5749160	26779	PASS	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	296	0.064189	0	0,277,0,19	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749160	26907	PASS	C	T	1539	0.055231	0	1452,0,87,0	LOW	SILENT	SYNONYMOUS_CODING	M	Ctg/Ttg	L129	M	0.000817	0.976032	1	1	C>T
ERR5749160	27078	PASS	C	T	1539	0.05783	0	0,1447,0,92	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Cgt/Tgt	R186C	M	0.000415	0.05783	2	2	C>T
ERR5749160	27972	PASS	C	T	97	0.907216	2147483647	0,0,97,0	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749160	28048	PASS	G	T	97	0.886598	2147483647	0,0,0,97	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749160	28095	PASS	A	T	97	0.907216	0	0,1,0,96	HIGH	NONSENSE	STOP_GAINED	ORF8	Aaa/Taa	K68*	orf8	0.002672	0.967672	2	2	A>T
ERR5749160	28111	PASS	A	G	97	0.927835	2147483647	0,0,0,97	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749160	28270	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	7	1.0	0	0,0,4,3	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749160	28280	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	7	1.0	0	0,0,4,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749160	28281	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	7	1.0	0	0,0,4,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749160	28282	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	7	0.857143	0	0,0,4,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749160	28881	PASS	G	A	78	0.74359	0	0,0,38,38	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749160	28882	PASS	G	A	78	0.782051	0	0,0,39,38	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749160	28883	PASS	G	C	78	0.910256	0	0,0,39,39	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749160	28977	PASS	C	T	40	0.9	2147483647	0,0,0,40	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749160	29757	PASS	G	T	254	0.933071	2147483647	0,0,0,254	.	.	.	.	.	.	.	0.840856	0.933071	1	1	G>T
ERR5749161	241	PASS	C	T	10021	0.85231	0	0,0,4988,4984	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749161	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	10817	0.001572	0	10791,11,17,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749161	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	10817	8.32E-4	0	10767,11,9,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749161	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	10817	0.002773	0	10767,11,30,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749161	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10807	0.001481	0	10050,11,674,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749161	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	10807	0.001851	112	10781,6,15,5	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749161	635	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10808	0.00148	0	0,10784,0,19	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgt/Tgt	R124C	leader	0.00148	0.880435	1	1	C>T
ERR5749161	657	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10812	0.00185	0	1,10786,0,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A131V	leader	0.001202	0.365979	3	1	C>T
ERR5749161	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	27195	0.001103	14	16362,10798,24,6	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749161	913	PASS	C	T	16382	0.888231	0	0,7,1,16338	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749161	1267	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29626	0.001789	15	17125,12420,40,15	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G154	nsp2	0.001789	0.9811	2	1	C>T
ERR5749161	1813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	16172	0.001113	0	0,16133,0,29	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcA	A336	nsp2	0.001022	0.152738	4	2	T>A
ERR5749161	1824	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16184	0.00173	0	0,16136,0,33	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCc/gTc	A340V	nsp2	0.00173	0.940138	2	1	C>T
ERR5749161	3037	PASS	C	T	15680	0.804145	47	1,19,7853,7670	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749161	3177	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	23591	0.001102	24	15658,7893,31,4	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cAt	P153H	nsp3	0.000773	0.96008	3	2	C>A
ERR5749161	3267	PASS	C	T	15693	0.970751	2147483647	0,0,15691,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749161	4578	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTAACGATC	T	11651	6.87E-4	0	2,11641,0,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	aacgatctaaat/	NDLN621	nsp3	0.000519	0.082979	2	2	TTAACGATC>T
ERR5749161	5388	PASS	C	A	4510	0.956098	2147483647	0,0,4507,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749161	5986	PASS	C	T	10979	0.976318	0	3,0,10974,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749161	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10351	0.001449	0	2,10201,0,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749161	6954	PASS	T	C	19100	0.780785	0	0,2,1,18941	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749161	7070	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	35322	8.49E-4	92	16117,19157,31,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggc/Agc	G1451S	nsp3	0.000698	0.101434	3	1	G>A
ERR5749161	8106	PASS	C	T	19826	0.89544	0	5,0,19753,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCa/gTa	A1796V	nsp3	0.014686	0.89772	1	1	C>T
ERR5749161	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	23103	9.52E-4	50	13303,9778,22,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749161	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	17756	0.001802	0	17701,0,47,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749161	11287	PASS	GTCTGGTTTT	G	17753	0.997634	0	0,42,0,17711	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749161	11750	PASS	C	T	34997	0.674172	64	3,27,18093,14932	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L260F	nsp6	0.001019	0.70989	2	1	C>T
ERR5749161	11750	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	G	34997	0.003829	13	3,27,47,1861	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Gtc	L260V	nsp6	0.001019	0.70989	2	1	C>G
ERR5749161	12109	PASS	T	C	14636	0.960235	0	0,2,2,14617	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttT/ttC	F6	nsp8	0.002176	0.963972	1	1	T>C
ERR5749161	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	7539	0.00504	2323	7329,67,2,134	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749161	14408	PASS	C	T	14608	0.836528	6	0,2,7303,7177	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749161	14676	PASS	C	T	10884	0.838387	2147483647	0,0,10860,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749161	15279	PASS	C	T	17533	0.886728	0	6,0,17513,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749161	16176	PASS	T	C	17177	0.97223	1	3,2,8206,8956	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749161	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23561	0.002165	0	23500,0,53,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749161	21764	PASS	ATACATG	A	10589	0.997261	0	29,0,10560,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749161	21990	PASS	TTTA	T	10590	0.99594	0	0,43,3,10544	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749161	22363	PASS	G	T	7773	0.955616	2147483647	0,0,7770,0	LOW	SILENT	SYNONYMOUS_CODING	S	gtG/gtT	V267	S	0.004714	0.976137	1	1	G>T
ERR5749161	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	13362	0.001347	0	0,13321,0,18	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749161	23063	PASS	A	T	11934	0.842551	0	0,5,1,11838	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749161	23271	PASS	C	A	17504	0.909449	0	2,0,17489,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749161	23311	PASS	G	T	17501	0.705903	0	180,0,17309,6	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gaG/gaT	E583D	S	0.001115	0.705903	2	1	G>T
ERR5749161	23403	PASS	A	G	17495	0.954901	0	0,3,0,17467	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749161	23604	PASS	C	A	13548	0.941246	0	7,0,13534,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749161	23709	PASS	C	T	13529	0.92468	0	0,6,0,13497	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749161	24506	PASS	T	G	14667	0.972046	0	4,0,14660,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749161	24914	PASS	G	C	32404	0.952938	0	1,2,16155,16209	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749161	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	20775	0.001492	46	14249,6483,36,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749161	25912	PASS	G	A	15585	0.979852	374	11,1,0,15570	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Ggc/Agc	G174S	orf3a	0.001337	0.979852	2	1	G>A
ERR5749161	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	10581	0.00104	0	0,10570,0,11	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749161	26985	PASS	C	T	26265	0.889358	0	9,0,26181,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Cat/Tat	H155Y	M	0.001017	0.889358	1	1	C>T
ERR5749161	27972	PASS	C	T	9070	0.90871	57	2,3,8973,50	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749161	28001	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	17981	0.001112	0	8964,8955,21,22	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ccG/ccT	P36	orf8	0.00085	0.830607	2	1	G>T
ERR5749161	28048	PASS	G	T	9001	0.901344	0	0,17,0,8982	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749161	28095	PASS	A	T	9012	0.945739	32	1,4,0,8987	HIGH	NONSENSE	STOP_GAINED	ORF8	Aaa/Taa	K68*	orf8	0.002672	0.967672	2	2	A>T
ERR5749161	28111	PASS	A	G	9012	0.961385	0	0,5,1,8997	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749161	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15998	0.002063	0	15918,1,37,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749161	28270	PASS	TA	T	14842	0.999528	0	0,7,1,14834	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749161	28280	PASS	G	C	14843	0.911676	0	0,3,1,14820	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749161	28281	PASS	A	T	14843	0.924409	0	0,7,1,14818	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749161	28282	PASS	T	A	14846	0.952715	0	0,4,1,14837	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749161	28881	PASS	G	A	13809	0.752987	3	2,0,6888,6694	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749161	28882	PASS	G	A	13809	0.817293	0	1,0,6960,6704	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749161	28883	PASS	G	C	13809	0.940039	9	0,3,6968,6826	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749161	28957	PASS	C	T	7039	0.933229	0	0,2,0,7027	LOW	SILENT	SYNONYMOUS_CODING	N	aaC/aaT	N228	N	0.01097	0.950683	1	1	C>T
ERR5749161	28977	PASS	C	T	7043	0.910975	0	0,3,0,7020	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749161	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	50495	0.001208	0	25363,25038,39,36	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749161	29272	PASS	C	T	25422	0.889938	0	0,13,0,25356	LOW	SILENT	SYNONYMOUS_CODING	N	taC/taT	Y333	N	0.001709	0.892106	1	1	C>T
ERR5749161	29793	PASS	T	C	7605	0.580539	0	0,2833,0,4759	.	.	.	.	.	.	.	0.002675	0.580539	2	1	T>C
ERR5749162	241	PASS	C	T	14114	0.866941	0	0,0,7013,7053	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749162	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	9257	0.001836	0	8618,3,619,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749162	685	PASS	AAAGTCATTT	A	35429	0.998758	1	24,10,26112,9273	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749162	841	PASS	C	T	52044	0.932538	5	5,9,26066,25889	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G12	nsp2	0.000771	0.932538	2	1	C>T
ERR5749162	913	PASS	C	T	26133	0.925229	0	0,15,3,26088	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749162	3037	PASS	C	T	18878	0.822386	48	0,16,9421,9311	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749162	3267	PASS	C	T	27034	0.97222	2147483647	0,0,27025,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749162	4237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTA	T	37420	3.21E-4	0	18740,18669,6,6	HIGH	NONE	FRAME_SHIFT	ORF1ab	ata/	I508	nsp3	0.000302	0.918634	2	2	TTA>T
ERR5749162	5388	PASS	C	A	6256	0.960198	2147483647	0,0,6254,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749162	5986	PASS	C	T	13215	0.975255	0	1,0,13205,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749162	6954	PASS	T	C	25283	0.804928	0	0,5,0,25137	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749162	7070	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	43999	0.001	153	18578,25353,45,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggc/Agc	G1451S	nsp3	0.000698	0.101434	3	1	G>A
ERR5749162	7113	PASS	C	T	18641	0.920551	261	0,7,18620,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T1465I	nsp3	0.001129	0.920551	1	1	C>T
ERR5749162	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	32358	0.001051	99	16320,16004,34,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749162	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26658	0.0015	0	26566,4,41,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749162	11287	PASS	GTCTGGTTTT	G	26643	0.998236	0	0,47,0,26596	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749162	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	44142	7.48E-4	5	29429,14643,28,9	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749162	12970	PASS	C	T	19332	0.859973	0	0,2,0,19281	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N95	nsp9	0.8352	0.861883	1	1	C>T
ERR5749162	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	38176	0.001729	0	19052,19009,36,36	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749162	14168	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	20874	4.79E-4	0	6,20858,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	atatta/	IL244	RdRp	0.000479	0.314961	1	1	CTA>C
ERR5749162	14396	PASS	C	T	9117	0.969946	0	2,0,9107,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T319I	RdRp	0.969946	0.969946	1	1	C>T
ERR5749162	14408	PASS	C	T	18112	0.857387	3	2,4,9061,8937	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749162	14415	PASS	T	C	18111	0.917398	0	1,1,9058,9021	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	agT/agC	S325	RdRp	0.917398	0.917398	1	1	T>C
ERR5749162	14676	PASS	C	T	16546	0.776985	0	4,0,16491,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749162	15279	PASS	C	T	27087	0.889172	0	4,0,27037,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749162	16176	PASS	T	C	22545	0.980838	0	0,0,9262,13275	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749162	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	25526	4.7E-4	0	25514,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749162	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	32066	4.05E-4	0	0,32053,0,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749162	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29603	0.001993	0	29526,1,64,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749162	20235	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	36332	0.00256	0	36219,3,98,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P205	endoR	0.000596	0.925795	3	2	C>T
ERR5749162	20786	PASS	A	T	11	1.0	2147483647	0,0,11,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAt/aTt	N43I	MethTr	0.001392	1	1	1	A>T
ERR5749162	21764	PASS	ATACATG	A	12768	0.997337	0	34,0,12734,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749162	21990	PASS	TTTA	T	12774	0.998121	0	0,24,4,12746	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749162	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	20648	0.001211	0	0,20612,0,25	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749162	23063	PASS	A	T	11521	0.861036	2147483647	0,0,0,11458	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749162	23271	PASS	C	A	27786	0.923307	0	4,0,27759,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749162	23403	PASS	A	G	27775	0.964464	0	0,7,0,27753	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749162	23604	PASS	C	A	16344	0.94781	0	9,0,16328,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749162	23709	PASS	C	T	16325	0.946279	0	0,2,0,16306	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749162	24506	PASS	T	G	22606	0.975139	0	8,0,22591,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749162	24914	PASS	G	C	38757	0.959904	0	0,0,19308,19425	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749162	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	27840	0.001114	52	18384,9413,37,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749162	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	27431	0.001094	495	27338,17,11,19	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749162	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	27396	5.11E-4	0	27381,1,14,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749162	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	27565	0.00127	937	27175,152,140,69	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749162	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	12778	7.83E-4	0	0,12768,0,10	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749162	27476	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	48333	7.03E-4	6	28070,20216,24,11	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	aCa/aTa	T28I	orf7a	0.000547	0.22827	4	2	C>T
ERR5749162	27972	PASS	C	T	11866	0.89609	0	0,0,11767,50	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749162	28048	PASS	G	T	11834	0.923272	0	0,11,0,11818	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749162	28111	PASS	A	G	34815	0.978314	9	6,0,22960,11838	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749162	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22961	0.007622	0	22719,5,181,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749162	28270	PASS	TA	T	44513	0.995484	492	202,6,22676,21636	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749162	28280	PASS	G	C	44424	0.938569	14	10,2,22724,21618	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749162	28281	PASS	A	T	44424	0.921686	12	23,11,22710,21613	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749162	28282	PASS	T	A	44428	0.911722	2	16,12,22649,21633	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749162	28394	PASS	C	T	22983	0.917026	0	0,8,7,22946	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Cgg/Tgg	R41W	N	0.001221	0.917026	3	2	C>T
ERR5749162	28881	PASS	G	A	24105	0.776934	0	2,1,11946,11867	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749162	28882	PASS	G	A	24104	0.829904	9	11,4,12050,11840	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749162	28883	PASS	G	C	24104	0.94391	3	0,1,12079,12012	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749162	28977	PASS	C	T	12271	0.931301	0	0,2,3,12244	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749162	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	41768	8.14E-4	76	29445,12227,11,29	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749162	29095	PASS	C	T	29493	0.961279	0	5,0,29447,0	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F274	N	0.000792	0.961279	2	2	C>T
ERR5749162	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	58599	0.001212	0	29411,29081,41,40	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749162	29642	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23258	0.001806	4	9662,13543,22,23	HIGH	NONSENSE	STOP_GAINED	ORF10	Caa/Taa	Q29*	orf10	0.001806	0.941176	2	2	C>T
ERR5749163	241	PASS	C	T	2902	0.864576	3	0,1,1445,1439	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749163	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	4411	0.003174	0	4394,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749163	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	4409	0.002495	0	4031,0,347,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749163	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	14917	0.00114	7	10486,4414,15,2	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749163	913	PASS	C	T	10495	0.915293	0	0,6,0,10476	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749163	2862	PASS	C	T	3851	0.850688	0	0,0,3810,38	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T48I	nsp3	0.000547	0.850688	4	2	C>T
ERR5749163	3037	PASS	C	T	7575	0.812145	39	0,13,3781,3716	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749163	3267	PASS	C	T	11137	0.972524	0	1,0,11125,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749163	4529	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTTTAC	T	8720	9.17E-4	0	0,8712,0,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	tacttt/	YF605	nsp3	0.000527	0.402778	3	1	TTTTAC>T
ERR5749163	5388	PASS	C	A	2444	0.954992	2147483647	0,0,2443,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749163	5986	PASS	C	T	6232	0.9724	0	1,0,6226,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749163	6035	PASS	A	C	6221	0.981193	0	4,0,6217,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Agc/Cgc	S1106R	nsp3	0.981193	0.981193	1	1	A>C
ERR5749163	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	6045	0.008933	0	3,5987,0,54	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L1328S?	nsp3	0.000731	0.14377	4	2	C>CT
ERR5749163	6954	PASS	T	C	13915	0.824075	2147483647	0,0,0,13845	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749163	7544	PASS	G	A	10049	0.875709	0	0,1,0,10004	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Att	V1609I	nsp3	0.001623	0.875709	2	1	G>A
ERR5749163	8828	PASS	G	A	7568	0.930629	2147483647	0,0,0,7558	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gct/Act	A92T	nsp4	0.930629	0.930629	1	1	G>A
ERR5749163	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	10358	0.001738	19	7829,2509,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749163	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17210	0.002092	0	17144,0,39,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749163	11287	PASS	GTCTGGTTTT	G	17203	0.997965	0	0,35,0,17168	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749163	11355	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	22956	4.79E-4	11	5746,17199,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	aga/	R129	nsp6	0.000455	0.982262	3	2	CA>C
ERR5749163	13459	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	12033	0.001496	0	12015,0,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L8	nsp11	0.000691	0.060726	5	2	GT>G
ERR5749163	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	3033	0.005605	857	2952,30,1,50	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749163	14408	PASS	C	T	5883	0.846337	0	0,0,2944,2909	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749163	14676	PASS	C	T	7689	0.832618	0	8,0,7660,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749163	15096	PASS	T	C	6829	0.962366	0	0,4,8,6814	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaT/aaC	N552	RdRp	0.941667	0.970182	1	1	T>C
ERR5749163	15279	PASS	C	T	11456	0.885126	0	5,0,11432,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749163	15289	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	11456	6.98E-4	0	11448,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gat/	D618	RdRp	0.000698	0.157576	2	1	TG>T
ERR5749163	16176	PASS	T	C	10403	0.980871	9	2,0,3471,6926	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749163	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	11601	0.001207	0	11587,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749163	18366	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	AG	17196	7.56E-4	0	17183,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggt/ggGt	G110G?	ExoN	0.000756	0.984275	2	2	A>AG
ERR5749163	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	16853	7.71E-4	0	16840,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749163	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8599	0.002442	0	8574,0,22,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749163	20031	PASS	C	T	8585	0.880489	0	1,0,8557,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A137	endoR	0.005221	0.880489	1	1	C>T
ERR5749163	21764	PASS	ATACATG	A	6981	0.995559	0	27,0,6950,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749163	21990	PASS	TTTA	T	6988	0.998426	0	0,11,6,6971	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749163	23063	PASS	A	T	8318	0.860303	2147483647	0,0,0,8275	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749163	23271	PASS	C	A	12735	0.921712	0	1,0,12720,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749163	23403	PASS	A	G	12734	0.971965	0	0,1,0,12722	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749163	23604	PASS	C	A	8106	0.947323	0	4,0,8099,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749163	23709	PASS	C	T	8099	0.943203	0	0,3,0,8086	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749163	24506	PASS	T	G	12304	0.970823	0	1,0,12300,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749163	24914	PASS	G	C	23951	0.960127	0	0,0,11934,11997	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749163	26182	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	19013	9.99E-4	0	0,18940,0,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Tat/Cat	Y264H	orf3a	0.000999	0.066002	1	1	T>C
ERR5749163	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	6605	0.001665	0	0,6594,0,11	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749163	26936	PASS	C	T	24105	0.923169	0	8,0,24071,0	LOW	SILENT	SYNONYMOUS_CODING	M	ctC/ctT	L138	M	0.001308	0.968147	2	1	C>T
ERR5749163	27078	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CGT	C	24098	4.15E-4	0	0,24088,0,10	HIGH	NONE	FRAME_SHIFT	M	gta/	V187	M	0.000415	0.05783	2	2	CGT>C
ERR5749163	27972	PASS	C	T	3934	0.906202	0	0,0,3899,27	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749163	28048	PASS	G	T	3906	0.919355	0	0,8,0,3898	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749163	28095	PASS	A	T	3912	0.957055	114	4,3,0,3890	HIGH	NONSENSE	STOP_GAINED	ORF8	Aaa/Taa	K68*	orf8	0.002672	0.967672	2	2	A>T
ERR5749163	28111	PASS	A	G	20144	0.979597	0	2,0,16223,3908	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749163	28195	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	16234	0.001417	0	16200,0,25,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	cGt/cAt	R101H	orf8	0.000851	0.926081	3	2	G>A
ERR5749163	28270	PASS	TA	T	31447	0.995166	377	156,5,16016,15279	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749163	28280	PASS	G	C	31373	0.934147	14	8,1,16044,15265	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749163	28281	PASS	A	T	31373	0.903101	25	19,4,16033,15259	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749163	28282	PASS	T	A	31375	0.917801	6	15,8,16018,15276	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749163	28396	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GC	G	16249	0.001354	0	9,16218,0,22	HIGH	NONE	FRAME_SHIFT	N	caa/	Q43	N	0.000496	0.946059	5	2	GC>G
ERR5749163	28881	PASS	G	A	6552	0.77152	12	5,0,3231,3213	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749163	28882	PASS	G	A	6552	0.832723	9	4,0,3277,3211	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749163	28883	PASS	G	C	6552	0.944292	0	0,0,3286,3263	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749163	28977	PASS	C	T	3337	0.930476	0	0,1,0,3335	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749164	241	PASS	C	T	17007	0.867172	0	1,2,8454,8476	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749164	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	12943	0.001004	0	12932,2,13,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749164	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	12945	0.001468	0	12888,4,19,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749164	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	12945	0.002472	0	12888,4,32,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749164	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12939	0.002009	0	11775,6,1076,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749164	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	12939	6.96E-4	0	12924,6,9,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749164	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	12938	6.96E-4	0	12916,6,9,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749164	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	38134	7.6E-4	29	25146,12954,27,2	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749164	913	PASS	C	T	25171	0.917723	0	0,9,0,25137	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749164	1510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	24759	0.003918	0	0,24425,0,101	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G235	nsp2	0.002159	0.937304	1	1	T>C
ERR5749164	2185	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	29345	0.011723	0	1,28976,0,344	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L462S?	nsp2	0.000441	0.963529	4	3	G>GT
ERR5749164	2189	PASS	C	T	29345	0.960061	36	1,5,0,29323	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Ttt	L462F	nsp2	0.000491	0.960061	3	2	C>T
ERR5749164	2189	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	29345	0.031079	0	1,28412,0,912	HIGH	NONE	FRAME_SHIFT+STOP_GAINED	ORF1ab	aga/Taga	R463*?	nsp2	0.000491	0.960061	3	2	C>CT
ERR5749164	3037	PASS	C	T	20677	0.821541	33	0,11,10325,10190	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749164	3267	PASS	C	T	24515	0.970793	0	3,0,24497,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749164	5388	PASS	C	A	7117	0.961079	0	2,0,7111,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749164	5986	PASS	C	T	14927	0.97662	0	1,0,14918,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749164	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14008	0.001285	0	2,13844,0,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749164	6954	PASS	T	C	27707	0.819432	0	0,3,0,27556	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749164	7564	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	18704	0.001283	0	0,18680,0,24	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/	Y1617	nsp3	0.000586	0.056194	4	2	CT>C
ERR5749164	8760	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30778	0.003379	0	30472,0,126,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A69V	nsp4	0.003379	0.892678	1	1	C>T
ERR5749164	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	34983	4.0E-4	43	17149,17820,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749164	10323	PASS	A	G	19493	0.958549	0	0,4,0,19467	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749164	11287	PASS	GTCTGGTTTT	G	22617	0.997745	0	0,51,0,22566	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749164	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	38135	0.001023	0	19056,18994,21,21	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749164	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	9733	0.004829	2519	9513,75,3,140	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749164	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	18928	5.28E-4	0	9499,9436,5,5	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749164	14408	PASS	C	T	18928	0.838969	0	3,3,9450,9355	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749164	14676	PASS	C	T	15125	0.752661	0	7,0,15071,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749164	15096	PASS	T	C	21320	0.966979	0	0,2,21,21289	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaT/aaC	N552	RdRp	0.941667	0.970182	1	1	T>C
ERR5749164	15279	PASS	C	T	25637	0.889028	0	4,0,25591,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749164	16176	PASS	T	C	22446	0.981422	1	3,2,10616,11817	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749164	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	28717	4.53E-4	0	2,28702,0,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749164	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34475	0.00145	0	34402,0,52,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749164	20786	PASS	A	T	39	0.435897	93	0,16,22,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAt/aTt	N43I	MethTr	0.001392	1	1	1	A>T
ERR5749164	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	39664	0.001563	0	19429,19764,34,36	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749164	21764	PASS	ATACATG	A	14527	0.99704	0	43,0,14484,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749164	21990	PASS	TTTA	T	14533	0.998005	0	0,29,5,14499	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749164	23063	PASS	A	T	15076	0.865283	0	0,2,1,14994	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749164	23271	PASS	C	A	25538	0.921646	0	1,0,25511,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749164	23403	PASS	A	G	25526	0.969835	2147483647	0,0,0,25511	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749164	23604	PASS	C	A	17936	0.930029	0	19,0,17907,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749164	23709	PASS	C	T	17931	0.944621	0	0,3,4,17907	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749164	23817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	39048	8.45E-4	9	21065,17924,23,11	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTt/cCt	L752P	S	0.000646	0.066832	1	1	T>C
ERR5749164	24237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14104	0.001276	0	14079,0,19,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gTt	A892V	S	0.001242	0.889739	1	1	C>T
ERR5749164	24506	PASS	T	G	20384	0.973214	0	9,0,20371,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749164	24914	PASS	G	C	40256	0.958689	3	1,0,20061,20168	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749164	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	28421	0.00285	104	19608,8711,90,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749164	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	27608	0.001413	675	27505,25,12,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749164	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	27636	0.001122	0	27605,0,31,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749164	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	27808	0.001007	1068	27427,171,102,74	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749164	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	56320	2.84E-4	0	4,56297,0,16	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749164	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	13649	0.001246	0	2,13625,0,17	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749164	27972	PASS	C	T	13065	0.902334	38	2,2,12947,63	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749164	28048	PASS	G	T	13000	0.911154	0	0,16,0,12976	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749164	28095	PASS	A	T	13017	0.956211	209	6,1,0,12998	HIGH	NONSENSE	STOP_GAINED	ORF8	Aaa/Taa	K68*	orf8	0.002672	0.967672	2	2	A>T
ERR5749164	28111	PASS	A	G	33934	0.97946	0	2,1,20909,13006	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749164	28270	PASS	TA	T	40502	0.994716	538	214,5,20631,19657	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749164	28280	PASS	G	C	40408	0.939492	26	15,2,20671,19641	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749164	28281	PASS	A	T	40408	0.919348	40	30,6,20669,19640	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749164	28282	PASS	T	A	40411	0.911979	21	29,11,20619,19649	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749164	28881	PASS	G	A	21710	0.757577	32	15,1,10737,10670	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749164	28882	PASS	G	A	21709	0.830992	24	9,0,10855,10636	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749164	28883	PASS	G	C	21709	0.945138	0	2,1,10874,10811	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749164	28977	PASS	C	T	11075	0.93228	0	0,2,0,11056	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749164	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	41867	0.001361	220	30758,11006,9,54	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749164	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	61106	0.001015	0	30691,30310,43,42	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749164	29253	PASS	C	T	30779	0.053998	0	0,28914,0,1808	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCg/tTg	S327L	N	0.000361	0.053998	4	2	C>T
ERR5749165	239	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTC	T	20079	4.98E-4	0	10021,10048,5,5	.	.	.	.	.	.	.	0.000495	0.25	4	1	TTC>T
ERR5749165	241	PASS	C	T	20076	0.858886	6	0,2,10005,9980	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749165	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	11896	0.002017	0	11027,4,842,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749165	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	42116	4.75E-4	0	30166,11928,15,5	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749165	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30164	8.62E-4	0	0,30084,0,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749165	913	PASS	C	T	30164	0.90913	0	0,11,0,30110	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749165	1510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	28309	0.002508	0	0,27927,0,76	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G235	nsp2	0.002159	0.937304	1	1	T>C
ERR5749165	2702	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	50927	9.62E-4	2147483647	50559,40,64,164	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F633V	nsp2	0.000632	0.333333	1	1	T>G
ERR5749165	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	100972	0.001634	2147483647	50385,46962,97,3255	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749165	3037	PASS	C	T	24703	0.804194	67	3,32,12345,12116	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749165	3267	PASS	C	T	29291	0.971049	0	2,0,29269,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749165	3671	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	31905	8.46E-4	0	15935,15784,13,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E318K	nsp3	0.000351	0.0625	6	2	G>A
ERR5749165	5388	PASS	C	A	8203	0.956357	2147483647	0,0,8199,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749165	5986	PASS	C	T	16832	0.974453	0	0,0,16815,2	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749165	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15935	0.001381	0	2,15763,0,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749165	6954	PASS	T	C	31695	0.814608	0	0,5,1,31520	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749165	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	39930	4.51E-4	57	19243,20670,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749165	11287	PASS	GTCTGGTTTT	G	26136	0.998737	0	0,33,0,26103	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749165	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	22711	0.001057	0	22666,0,24,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749165	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	41107	0.001216	0	20530,20479,28,27	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749165	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	14245	0.004563	2147483647	13905,104,6,220	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749165	14408	PASS	C	T	27655	0.870259	3	5,8,13832,13664	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749165	14676	PASS	C	T	17716	0.722567	0	6,0,17647,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749165	15279	PASS	C	T	30176	0.894221	0	10,0,30119,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749165	15652	PASS	G	T	20698	0.935936	0	16,0,20676,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gac/Tac	D738Y	RdRp	0.000691	0.935936	2	2	G>T
ERR5749165	15983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	13920	7.9E-4	0	13909,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T850	RdRp	0.000701	0.338235	2	1	TA>T
ERR5749165	16176	PASS	T	C	25084	0.979309	0	0,1,11134,13936	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749165	16647	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	32183	7.46E-4	0	5,31937,0,26	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acG/acA	T137	helicase	0.000746	0.885245	2	1	G>A
ERR5749165	17615	PASS	A	G	19720	0.894422	0	0,3,5,19663	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749165	18171	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29108	8.59E-4	0	14522,14495,13,13	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G44	ExoN	0.000859	0.892019	1	1	C>T
ERR5749165	18366	PASS	A	G	40827	0.984275	0	7,0,40791,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ctA/ctG	L109	ExoN	0.000756	0.984275	2	2	A>G
ERR5749165	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	29080	8.94E-4	0	29054,0,26,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749165	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	34519	3.77E-4	0	0,34506,0,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749165	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	40283	0.001514	0	40189,0,67,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749165	21764	PASS	ATACATG	A	16207	0.998087	0	31,0,16176,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749165	21990	PASS	TTTA	T	16212	0.99852	0	0,24,5,16183	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749165	23063	PASS	A	T	15876	0.861237	0	0,4,0,15790	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749165	23123	PASS	C	T	15915	0.854414	238	7,1,1,15880	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Cca/Tca	P521S	S	0.04007	0.854414	2	1	C>T
ERR5749165	23271	PASS	C	A	12	1.0	2147483647	0,0,12,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749165	23403	PASS	A	G	29723	0.966423	0	0,11,0,29679	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749165	23604	PASS	C	A	19700	0.938223	0	13,0,19676,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749165	23709	PASS	C	T	19675	0.936213	0	0,7,3,19642	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749165	24506	PASS	T	G	24186	0.974903	0	4,0,24172,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749165	24914	PASS	G	C	37264	0.953333	0	0,0,18562,18663	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749165	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	31436	0.001686	79	21995,9366,61,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749165	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	34232	9.64E-4	450	34115,22,17,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749165	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	34191	6.43E-4	0	34169,0,22,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749165	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	34405	0.001134	1484	33887,193,175,106	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749165	27390	PASS	G	T	23063	0.885357	0	0,85,10,22952	.	.	.	.	.	.	.	0.001176	0.885357	1	1	G>T
ERR5749165	27972	PASS	C	T	15369	0.899733	0	0,0,15254,67	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749165	28048	PASS	G	T	15309	0.921745	0	0,25,0,15279	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749165	28111	PASS	A	G	40712	0.975732	4	0,1,25380,15321	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749165	28247	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AGATTT	A	25375	0.001025	0	25345,4,26,0	HIGH	NONE	FRAME_SHIFT	ORF8	gatttc/	DF119	orf8	0.000374	0.998357	3	1	AGATTT>A
ERR5749165	28270	PASS	TA	T	49009	0.995144	546	231,8,25043,23728	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749165	28280	PASS	G	C	48904	0.936079	18	12,2,25092,23708	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749165	28281	PASS	A	T	48904	0.914445	29	21,4,25088,23722	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749165	28282	PASS	T	A	48905	0.914017	5	19,12,25032,23724	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749165	28881	PASS	G	A	24682	0.717041	57	19,0,12068,12125	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749165	28882	PASS	G	A	24682	0.815979	42	15,0,12328,12094	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749165	28883	PASS	G	C	24680	0.939668	0	2,2,12360,12295	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749165	28977	PASS	C	T	12602	0.931757	0	0,2,1,12582	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749165	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	45148	0.001307	249	32506,12534,5,56	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749165	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	64577	0.001053	0	32440,32018,44,41	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749166	241	PASS	C	T	15143	0.87136	0	1,1,7463,7620	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749166	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	12415	0.004994	0	12351,5,62,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749166	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	12416	0.002336	0	12282,6,29,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749166	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	12416	0.006685	0	12282,6,83,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749166	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12409	0.00137	0	11556,12,600,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749166	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	12409	0.00274	0	12363,12,34,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749166	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	12407	0.00129	0	12373,13,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749166	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	12409	8.86E-4	0	12373,16,11,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749166	673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	43451	8.06E-4	56	31001,12393,12,24	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y136	leader	0.000454	0.602236	3	2	C>T
ERR5749166	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	43446	3.68E-4	20	30999,12425,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749166	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	43447	4.37E-4	2	30919,12386,15,4	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749166	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	43447	0.002555	2	30919,12386,76,35	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749166	913	PASS	C	T	31018	0.913534	0	0,12,0,30962	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749166	1027	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	16808	0.00238	412	16722,19,22,19	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccT/ccC	P74	nsp2	0.001454	0.276316	1	1	T>C
ERR5749166	1684	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	23495	6.38E-4	0	23480,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gcc/	A294	nsp2	0.000638	0.973136	2	2	CG>C
ERR5749166	1862	PASS	C	T	23490	0.936867	0	0,20,0,23398	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Ttt	L353F	nsp2	0.000585	0.936867	4	2	C>T
ERR5749166	2702	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	51102	6.65E-4	2829	50647,130,80,143	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F633V	nsp2	0.000632	0.333333	1	1	T>G
ERR5749166	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	101160	0.001414	2147483647	50501,47243,91,3054	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749166	3037	PASS	C	T	24286	0.801326	72	2,31,12120,11929	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749166	3267	PASS	C	T	30900	0.970259	0	5,0,30869,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749166	5170	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	15929	5.65E-4	0	1,15919,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T819	nsp3	0.000565	0.894036	2	2	CCA>C
ERR5749166	5388	PASS	C	A	8367	0.964862	2147483647	0,0,8365,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749166	5986	PASS	C	T	15905	0.976611	0	1,0,15888,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749166	6954	PASS	T	C	31399	0.799038	0	0,11,11,31179	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749166	7318	PASS	C	T	23541	0.851451	180	6,5,5,23409	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1533	nsp3	0.001387	0.851451	1	1	C>T
ERR5749166	8603	PASS	T	C	15288	0.969453	506	16,3,0,15257	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Ctc	F17L	nsp4	0.002607	0.974959	2	1	T>C
ERR5749166	9198	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	20254	5.43E-4	0	0,20243,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F216	nsp4	0.000543	0.93476	4	2	CT>C
ERR5749166	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	44028	0.00109	159	20427,23550,48,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749166	10077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	9272	0.001833	404	6,9216,15,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTc/tCc	F8S	3Cpro	0.001833	0.454545	1	1	T>C
ERR5749166	10798	PASS	C	T	27777	0.955467	0	4,0,27733,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D248	3Cpro	0.003021	0.97286	1	1	C>T
ERR5749166	11082	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	28497	5.26E-4	0	28491,1,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000427	0.179468	2	1	TG>T
ERR5749166	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	28497	0.002386	0	28363,0,106,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749166	11199	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	56762	0.001163	0	28172,28336,35,36	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCc/gTc	A76V	nsp6	0.000309	0.056758	3	2	C>T
ERR5749166	11287	PASS	GTCTGGTTTT	G	28487	0.996735	24	1,93,0,28394	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749166	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	49940	0.001161	4	32536,17298,36,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749166	12125	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	21993	9.55E-4	0	8,21898,0,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y12H	nsp8	0.000847	0.113436	1	1	T>C
ERR5749166	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	24219	0.00161	0	24139,0,40,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749166	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	16365	0.0011	0	16348,0,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749166	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	42416	0.002051	0	21164,21104,46,48	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749166	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	20125	0.003627	2147483647	19639,226,8,245	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749166	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	39130	0.001431	0	19606,19488,29,27	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749166	14408	PASS	C	T	39130	0.842372	9	1,5,19518,19290	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749166	14676	PASS	C	T	18882	0.744677	0	14,0,18804,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749166	15279	PASS	C	T	31239	0.887769	2147483647	0,0,31186,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749166	16176	PASS	T	C	26379	0.98078	3	1,0,11716,14652	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749166	17615	PASS	A	G	19860	0.902115	0	0,1,2,19794	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749166	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	39723	0.002467	0	39601,0,98,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749166	20233	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	40759	0.002993	0	40599,9,127,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ccc/Tcc	P205S	endoR	0.000964	0.980008	2	1	C>T
ERR5749166	20987	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	63068	3.49E-4	0	31543,31503,11,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L111	MethTr	0.000276	0.056129	4	2	CT>C
ERR5749166	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	41944	8.58E-4	0	20590,20923,19,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749166	21762	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTATACA	C	16718	0.002333	0	16677,1,39,0	MODERATE	NONE	CODON_DELETION	S	atacat/	IH68	S	0.001297	0.875707	2	2	CTATACA>C
ERR5749166	21764	PASS	ATACATG	A	16718	0.994437	0	93,0,16624,1	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749166	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	16717	5.98E-4	0	16706,1,10,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749166	21990	PASS	TTTA	T	16723	0.99689	17	1,51,5,16666	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749166	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	40170	0.001469	0	17511,22565,25,34	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749166	23063	PASS	A	T	17535	0.875677	0	0,3,0,17460	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749166	23271	PASS	C	A	32095	0.92759	0	4,0,32056,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749166	23403	PASS	A	G	32094	0.968031	0	0,7,1,32059	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749166	23604	PASS	C	A	20027	0.941829	0	15,0,19995,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749166	23709	PASS	C	T	20013	0.944136	0	0,4,12,19970	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749166	24127	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TTTTTG	42356	4.01E-4	36	16932,25424,0,17	HIGH	NONE	FRAME_SHIFT+STOP_GAINED	S	aac/TTTTGaac	N856F*?	S	0.000324	0.111888	4	1	T>TTTTTG
ERR5749166	24506	PASS	T	G	25653	0.97435	0	6,0,25638,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749166	24914	PASS	G	C	45752	0.960876	0	2,3,22787,22931	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749166	25437	PASS	G	T	22963	0.964769	0	11,0,22920,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	ttG/ttT	L15F	orf3a	0.001128	0.971411	2	2	G>T
ERR5749166	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	35546	0.001407	678	35399,18,25,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749166	25782	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	35475	9.58E-4	0	35334,0,36,0	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	tgC/tgT	C130	orf3a	0.000916	0.955348	1	1	C>T
ERR5749166	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	35828	0.001563	1580	35134,290,243,130	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749166	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	15640	0.001982	0	5,15604,0,31	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749166	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	15640	0.004284	0	5,15563,0,67	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749166	26918	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	41108	0.001119	0	41031,2,59,0	LOW	SILENT	SYNONYMOUS_CODING	M	ccG/ccT	P132	M	0.000999	0.977086	2	1	G>T
ERR5749166	27972	PASS	C	T	16077	0.90757	0	0,0,15893,133	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749166	28048	PASS	G	T	15961	0.924441	0	0,24,0,15923	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749166	28111	PASS	A	G	41630	0.977877	0	6,3,25641,15966	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749166	28270	PASS	TA	T	49754	0.995237	541	219,6,25328,24189	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749166	28270	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAA	T	49754	3.22E-4	68	219,6,8,8	.	.	.	.	.	.	.	0.000322	1	2	1	TAA>T
ERR5749166	28280	PASS	G	C	49672	0.938799	30	19,3,25377,24171	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749166	28281	PASS	A	T	49672	0.92229	50	32,5,25369,24176	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749166	28282	PASS	T	A	49674	0.911302	25	34,12,25320,24188	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749166	28407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TACCCAATA	T	25674	5.06E-4	0	16,25646,0,13	HIGH	NONE	FRAME_SHIFT	N	cccaataat/	PNN46	N	0.000382	0.179673	1	1	TACCCAATA>T
ERR5749166	28881	PASS	G	A	25305	0.773207	21	8,0,12524,12458	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749166	28882	PASS	G	A	25305	0.829876	6	5,1,12652,12420	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749166	28883	PASS	G	C	25305	0.944082	6	3,0,12664,12610	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749166	28977	PASS	C	T	12897	0.9282	2147483647	0,0,0,12872	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749166	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	66456	9.48E-4	0	33359,32988,42,42	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749167	241	PASS	C	T	16627	0.872857	0	0,1,8268,8308	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749167	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	9429	0.001485	0	9416,0,14,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749167	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	9429	0.001167	0	9404,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749167	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	9418	0.001699	0	9401,1,16,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749167	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	32142	4.98E-4	12	22680,9443,15,1	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749167	913	PASS	C	T	22692	0.907809	0	0,8,0,22652	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749167	3037	PASS	C	T	20665	0.814566	61	1,24,10316,10162	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749167	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10432	0.001917	500	7,10388,21,12	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749167	3189	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	22188	0.001758	0	22144,1,40,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cAa/cGa	Q157R	nsp3	0.001758	0.132615	2	1	A>G
ERR5749167	3267	PASS	C	T	22185	0.971332	0	1,0,22172,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749167	5388	PASS	C	A	6339	0.958826	2147483647	0,0,6337,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749167	5986	PASS	C	T	13503	0.974524	2147483647	0,0,13496,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749167	6954	PASS	T	C	23646	0.803519	0	0,3,1,23481	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749167	8603	PASS	T	C	12682	0.966882	203	6,2,0,12664	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Ctc	F17L	nsp4	0.002607	0.974959	2	1	T>C
ERR5749167	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	32164	0.001181	119	15603,16523,38,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749167	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19754	0.001266	0	19703,1,25,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749167	11104	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	19745	0.001114	0	19667,0,23,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccT/ccC	P44	nsp6	0.000866	0.675414	2	1	T>C
ERR5749167	11287	PASS	GTCTGGTTTT	G	19744	0.998278	0	0,34,0,19710	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749167	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29375	0.001226	0	14672,14643,20,20	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749167	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10968	0.004103	3013	10713,81,2,166	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749167	14408	PASS	C	T	21313	0.860601	12	0,4,10635,10532	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749167	14676	PASS	C	T	13324	0.779796	0	4,0,13281,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749167	15279	PASS	C	T	22659	0.886447	0	9,0,22616,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749167	16176	PASS	T	C	18935	0.980037	0	1,1,8641,10286	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749167	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	19442	0.001234	0	19418,0,24,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749167	17615	PASS	A	G	15985	0.899155	0	0,1,0,15943	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749167	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	22300	8.07E-4	0	22282,0,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749167	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	32624	0.002575	0	32520,1,86,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749167	20091	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	32567	3.68E-4	0	4,32551,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	caa/Acaa	Q159T?	endoR	0.000368	0.051583	1	1	C>CA
ERR5749167	21764	PASS	ATACATG	A	13125	0.995733	0	56,0,13069,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749167	21990	PASS	TTTA	T	13133	0.998477	0	0,20,8,13105	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749167	23031	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12779	0.001096	0	3,12497,0,266	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tTt/tGt	F490C	S	0.001067	0.92095	2	1	T>G
ERR5749167	23063	PASS	A	T	12821	0.862257	0	0,2,0,12760	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749167	23271	PASS	C	A	22874	0.926467	0	1,0,22851,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749167	23403	PASS	A	G	22863	0.9745	0	0,8,0,22842	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749167	23604	PASS	C	A	15890	0.940906	0	7,0,15875,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749167	23709	PASS	C	T	15871	0.926092	0	0,4,2,15837	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749167	24331	PASS	T	A	12380	0.707916	0	0,3,0,12265	LOW	SILENT	SYNONYMOUS_CODING	S	atT/atA	I923	S	0.707916	0.817033	1	1	T>A
ERR5749167	24506	PASS	T	G	18175	0.971774	0	7,0,18161,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749167	24914	PASS	G	C	32295	0.958384	0	1,2,16088,16181	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749167	25437	PASS	G	T	17737	0.963466	0	12,0,17710,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	ttG/ttT	L15F	orf3a	0.001128	0.971411	2	2	G>T
ERR5749167	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	27190	0.001103	994	26817,141,125,70	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749167	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	12304	7.31E-4	0	0,12295,0,9	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749167	27754	PASS	G	T	21758	0.928716	0	0,24,0,21719	HIGH	NONSENSE	STOP_GAINED	ORF7a	Gaa/Taa	E121*	orf7a	0.001253	0.928716	1	1	G>T
ERR5749167	27972	PASS	C	T	12007	0.911385	56	3,3,11903,58	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749167	28048	PASS	G	T	11959	0.913622	0	0,17,0,11935	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749167	28111	PASS	A	G	31367	0.978512	1	3,3,19392,11963	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749167	28209	PASS	G	T	19399	0.584618	0	7540,0,11851,0	HIGH	NONSENSE	STOP_GAINED	ORF8	Gaa/Taa	E106*	orf8	0.001409	0.963166	2	2	G>T
ERR5749167	28270	PASS	TA	T	37505	0.994321	538	214,5,19104,18188	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749167	28271	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AA	A	37503	0.001173	126	19267,18194,44,0	.	.	.	.	.	.	.	0.000482	0.924941	3	2	AA>A
ERR5749167	28280	PASS	G	C	37417	0.934148	27	13,1,19167,18169	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749167	28281	PASS	A	T	37417	0.914611	25	23,6,19159,18173	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749167	28282	PASS	T	A	37421	0.909516	0	21,18,19125,18174	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749167	28881	PASS	G	A	18209	0.777967	18	7,0,9047,8935	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749167	28882	PASS	G	A	18209	0.82602	5	6,2,9112,8946	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749167	28883	PASS	G	C	18209	0.941842	0	1,1,9132,9062	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749167	28977	PASS	C	T	9280	0.92931	0	0,0,3,9267	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749167	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	50066	0.001079	0	25127,24847,35,34	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749168	239	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTC	T	18779	5.33E-4	0	9328,9441,5,5	.	.	.	.	.	.	.	0.000495	0.25	4	1	TTC>T
ERR5749168	241	PASS	C	T	18779	0.861547	0	0,0,9309,9381	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749168	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	12921	0.001625	0	12900,2,21,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749168	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	12921	6.19E-4	0	12857,2,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749168	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	12921	8.51E-4	0	12857,2,11,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749168	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	12921	0.002786	0	12857,2,36,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749168	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12912	0.001936	0	11819,3,986,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749168	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	12912	0.001162	54	12896,1,13,2	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749168	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	12913	6.97E-4	0	12896,4,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749168	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	32698	0.001529	7	19714,12923,35,15	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749168	913	PASS	C	T	19747	0.924697	0	0,10,0,19714	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749168	2462	PASS	C	T	16303	0.791388	0	0,47,8,16141	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L553	nsp2	0.408047	0.791388	1	1	C>T
ERR5749168	3037	PASS	C	T	20837	0.825023	42	0,14,10410,10294	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749168	3267	PASS	C	T	15223	0.970571	0	1,0,15214,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749168	3787	PASS	C	T	11298	0.956541	148	4,0,0,11286	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y356	nsp3	0.002354	0.956541	1	1	C>T
ERR5749168	5388	PASS	C	A	6132	0.95711	2147483647	0,0,6127,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749168	5986	PASS	C	T	12355	0.974585	2147483647	0,0,12350,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749168	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12020	0.001498	0	5,11897,0,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749168	6954	PASS	T	C	22977	0.81747	0	0,4,3,22833	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749168	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	30657	0.001925	203	13821,16777,59,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749168	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	14598	0.001233	0	14550,0,38,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749168	11287	PASS	GTCTGGTTTT	G	14594	0.998493	0	0,22,0,14572	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749168	12357	PASS	C	T	21877	0.956941	0	0,7,1,21847	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T89I	nsp8	0.000909	0.956941	3	2	C>T
ERR5749168	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	36874	8.95E-4	0	18431,18381,17,17	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749168	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12714	0.002596	1973	12504,90,8,107	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749168	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	24886	0.001045	0	12486,12398,13,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749168	14408	PASS	C	T	24886	0.856425	18	0,6,12418,12293	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749168	14676	PASS	C	T	12945	0.81854	0	3,0,12908,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749168	15279	PASS	C	T	21378	0.885349	0	4,0,21349,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749168	16176	PASS	T	C	18853	0.984247	0	0,1,9009,9838	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749168	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	16778	9.54E-4	0	16755,0,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749168	17615	PASS	A	G	13580	0.912813	0	0,0,2,13540	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749168	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	21689	0.00106	0	21666,0,23,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749168	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26600	0.002444	0	26512,0,67,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749168	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GTT	30738	0.002342	224	15329,14574,0,72	HIGH	NONE	FRAME_SHIFT	S	ctt/TTctt	L5F?	S	0.000394	0.091869	4	1	G>GTT
ERR5749168	21575	PASS	C	T	29689	0.862777	6	1,5,14021,15229	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749168	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	29675	0.003538	299	14252,15303,0,105	HIGH	NONE	FRAME_SHIFT	S	gtt/Tgtt	V6C?	S	0.000619	0.877942	3	2	C>CT
ERR5749168	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	29675	8.42E-4	70	14252,15303,0,25	HIGH	NONE	FRAME_SHIFT	S	gtt/TTgtt	V6L?	S	0.000619	0.877942	3	2	C>CTT
ERR5749168	21764	PASS	ATACATG	A	12486	0.995275	0	59,0,12427,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749168	21990	PASS	TTTA	T	12498	0.99816	0	0,23,12,12463	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749168	23063	PASS	A	T	10067	0.884871	2147483647	0,0,0,10027	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749168	23271	PASS	C	A	19845	0.907685	0	2,0,19822,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749168	23403	PASS	A	G	19847	0.972641	0	0,6,0,19830	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749168	23604	PASS	C	A	14573	0.941055	0	14,0,14553,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749168	23709	PASS	C	T	14553	0.939737	0	0,1,4,14528	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749168	24506	PASS	T	G	16492	0.973927	0	6,0,16484,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749168	24914	PASS	G	C	28524	0.96112	0	0,1,14206,14307	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749168	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	24884	0.001326	398	24795,13,18,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749168	26062	PASS	G	T	50415	0.895666	0	92,0,50234,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Ggt/Tgt	G224C	orf3a	0.001077	0.906894	1	1	G>T
ERR5749168	26065	PASS	G	T	50415	0.897987	0	166,0,50218,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gtt/Ttt	V225F	orf3a	0.001242	0.906322	2	1	G>T
ERR5749168	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	10280	0.001751	0	0,10256,0,18	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749168	27598	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GACGGCGTAAAACACGTCTATCAGTT	G	21473	6.99E-4	0	21455,1,15,0	HIGH	NONE	FRAME_SHIFT	ORF7a	ggcgtaaaacacgtctatcagttacgt/	GVKHVYQLR70	orf7a	0.000699	0.958994	6	2	GACGGCGTAAAACACGTCTATCAGTT>G
ERR5749168	27972	PASS	C	T	9917	0.905717	23	0,1,9849,39	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749168	28048	PASS	G	T	9883	0.941212	0	0,11,0,9863	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749168	28111	PASS	A	G	25557	0.97308	3	5,1,15651,9893	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749168	28270	PASS	TA	T	30497	0.994655	452	167,2,15443,14891	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749168	28280	PASS	G	C	30426	0.945178	9	11,4,15488,14871	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749168	28281	PASS	A	T	30426	0.929665	20	22,7,15482,14867	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749168	28282	PASS	T	A	30428	0.90982	4	17,11,15451,14877	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749168	28310	PASS	C	T	15639	0.92832	0	0,6,17,15590	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Ccc/Tcc	P13S	N	0.00095	0.92832	2	1	C>T
ERR5749168	28881	PASS	G	A	13505	0.742984	21	7,0,6628,6642	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749168	28882	PASS	G	A	13505	0.834061	5	6,2,6748,6652	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749168	28883	PASS	G	C	13504	0.944757	0	1,1,6763,6732	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749168	28977	PASS	C	T	6882	0.931561	0	0,1,4,6865	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749168	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	39519	8.35E-4	0	19838,19624,20,20	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749168	29386	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	8249	9.7E-4	0	8239,2,8,0	HIGH	NONE	FRAME_SHIFT	N	aag/aaAg	K373K?	N	0.000887	0.899197	4	2	C>CA
ERR5749168	29542	PASS	A	T	16536	0.957487	15	29,14,8281,8203	.	.	.	.	.	.	.	0.00099	0.957487	2	1	A>T
ERR5749169	241	PASS	C	T	12547	0.872479	0	0,0,6227,6271	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749169	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	10215	0.003328	0	10180,3,34,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749169	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	10214	0.001273	0	10107,3,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749169	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	10214	0.001664	0	10107,3,17,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749169	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	10214	0.006462	0	10107,3,66,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749169	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10209	0.002351	0	9301,4,738,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749169	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	10209	0.002057	0	10184,4,21,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749169	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	10209	8.82E-4	0	10188,5,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749169	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	10209	7.84E-4	0	10188,6,8,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749169	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	26360	5.31E-4	18	16117,10227,13,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749169	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	26360	4.17E-4	2	16070,10202,8,3	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749169	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	26360	0.00258	4	16070,10202,46,22	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749169	913	PASS	C	T	16121	0.909063	0	0,12,0,16083	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749169	1510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	16797	0.003632	0	0,16605,0,64	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G235	nsp2	0.002159	0.937304	1	1	T>C
ERR5749169	1813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	13515	0.001258	0	0,13480,0,24	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcA	A336	nsp2	0.001022	0.152738	4	2	T>A
ERR5749169	3037	PASS	C	T	17019	0.8108	29	2,15,8502,8361	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749169	3267	PASS	C	T	15285	0.970298	0	2,0,15273,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749169	3379	PASS	A	G	15265	0.228104	2	3,11113,0,4104	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtA/gtG	V220	nsp3	0.018231	0.228104	2	1	A>G
ERR5749169	4206	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15312	0.003069	0	15257,0,49,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCg/gTg	A496V	nsp3	0.003069	0.879444	1	1	C>T
ERR5749169	4255	PASS	G	A	30536	0.833966	38	17,1,15178,15142	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccG/ccA	P512	nsp3	0.001102	0.871853	2	1	G>A
ERR5749169	5388	PASS	C	A	6535	0.958531	2147483647	0,0,6530,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749169	5986	PASS	C	T	11515	0.975944	0	1,0,11502,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749169	6954	PASS	T	C	17646	0.814462	0	0,5,1,17529	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749169	11074	PASS	C	CT	13616	0.070138	0	12428,1,955,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CT
ERR5749169	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	13616	0.012118	0	12428,1,165,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749169	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13616	0.003452	0	13534,1,54,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749169	11082	PASS	TG	T	13561	0.08871	0	12412,0,1203,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000427	0.179468	2	1	TG>T
ERR5749169	11083	PASS	G	T	13561	0.868889	0	4,0,12295,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749169	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	13561	0.030455	0	13080,0,413,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/tTat	Y38L?	nsp6	0.000477	0.901695	5	2	G>GT
ERR5749169	11287	PASS	GTCTGGTTTT	G	13607	0.997207	0	0,38,0,13569	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749169	11507	PASS	G	A	26078	0.903559	6	8,3,13028,12950	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Att	V179I	nsp6	0.007744	0.914418	2	2	G>A
ERR5749169	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	15250	0.001443	0	15200,0,22,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749169	12756	PASS	C	T	28893	0.877514	0	0,0,13640,15243	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T24I	nsp9	0.000889	0.877514	1	1	C>T
ERR5749169	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22798	0.001886	0	11372,11342,25,25	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749169	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10662	0.00347	2474	10411,100,5,142	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749169	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	20720	0.002172	0	10378,10315,23,22	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749169	14408	PASS	C	T	20720	0.843533	0	1,1,10322,10212	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749169	14676	PASS	C	T	9636	0.765982	0	4,0,9597,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749169	15279	PASS	C	T	16744	0.884556	2147483647	0,0,16714,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749169	16176	PASS	T	C	16417	0.981239	5	3,0,8690,7717	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749169	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	21011	6.19E-4	0	20998,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749169	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27201	0.001948	0	27130,0,54,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749169	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25538	9.4E-4	0	25482,1,27,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749169	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	15156	9.9E-4	0	0,15140,0,15	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TA>T
ERR5749169	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GTT	24076	0.001869	140	12022,11438,0,45	HIGH	NONE	FRAME_SHIFT	S	ctt/TTctt	L5F?	S	0.000394	0.091869	4	1	G>GTT
ERR5749169	21575	PASS	C	T	23285	0.860812	2	1,3,11005,11893	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749169	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	23275	0.003781	251	11208,11975,0,88	HIGH	NONE	FRAME_SHIFT	S	gtt/Tgtt	V6C?	S	0.000619	0.877942	3	2	C>CT
ERR5749169	21764	PASS	ATACATG	A	11046	0.997375	0	29,0,11017,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749169	21990	PASS	TTTA	T	11050	0.998009	0	0,22,4,11024	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749169	23063	PASS	A	T	10374	0.866782	0	0,1,1,10332	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749169	23271	PASS	C	A	15930	0.920465	0	2,0,15911,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749169	23403	PASS	A	G	15924	0.965273	0	0,2,0,15908	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749169	23604	PASS	C	A	13529	0.948777	0	16,0,13507,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749169	23709	PASS	C	T	13517	0.944884	0	0,6,2,13499	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749169	24506	PASS	T	G	13643	0.976105	0	5,0,13635,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749169	24914	PASS	G	C	29194	0.958896	0	1,1,14532,14639	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749169	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	20791	0.002453	78	14996,5731,57,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749169	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	18770	0.001811	492	18683,20,14,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749169	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	18730	8.01E-4	0	18714,1,15,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749169	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	18883	0.001218	793	18578,136,90,59	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749169	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	45467	6.16E-4	0	0,45434,0,28	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749169	26509	PASS	C	T	8991	0.946613	0	0,1,0,8981	.	.	.	.	.	.	.	0.000852	0.946613	3	1	C>T
ERR5749169	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	9936	0.003019	0	0,9903,0,30	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749169	27972	PASS	C	T	9898	0.903415	60	2,3,9820,43	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749169	28048	PASS	G	T	9863	0.927811	0	0,15,0,9841	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749169	28111	PASS	A	G	24165	0.97844	2	1,2,14288,9864	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749169	28270	PASS	TA	T	27659	0.995228	268	127,8,14102,13425	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749169	28280	PASS	G	C	27604	0.937147	16	11,2,14128,13410	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749169	28281	PASS	A	T	27604	0.917113	32	15,1,14128,13414	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749169	28282	PASS	T	A	27604	0.910339	10	16,7,14095,13427	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749169	28292	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	28413	6.69E-4	0	14159,14236,10,9	HIGH	NONE	FRAME_SHIFT	N	aat/	N8	N	0.000304	0.055324	4	2	CA>C
ERR5749169	28881	PASS	G	A	12701	0.76679	16	11,2,6286,6243	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749169	28882	PASS	G	A	12698	0.833281	0	1,0,6355,6218	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749169	28883	PASS	G	C	12698	0.939597	3	0,1,6364,6316	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749169	28977	PASS	C	T	6486	0.926149	2147483647	0,0,0,6477	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749169	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	27995	8.22E-4	85	21485,6458,4,19	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749169	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	42645	7.74E-4	1	21432,21163,23,19	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749170	241	PASS	C	T	11749	0.859052	9	1,6,5835,5858	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749170	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	11022	0.001542	0	10991,14,17,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749170	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	11024	0.001905	0	10921,16,21,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749170	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	11024	0.00508	0	10921,16,56,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749170	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	11010	0.001635	2	10200,19,658,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749170	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	11010	0.001544	0	10974,19,17,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749170	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	11009	9.08E-4	0	10969,13,10,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttatg/gtg	VM84V	leader	0.000554	0.991848	4	1	GTTA>G
ERR5749170	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	11009	0.001544	128	10969,13,11,6	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749170	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	11010	9.99E-4	16	10976,20,10,1	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749170	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	32370	0.001545	3	21309,11001,36,14	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749170	913	PASS	C	T	21344	0.921242	0	0,13,0,21294	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749170	3037	PASS	C	T	19025	0.813088	16	2,10,9500,9358	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749170	3267	PASS	C	T	21144	0.970346	0	3,0,21131,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749170	5388	PASS	C	A	5905	0.957832	2147483647	0,0,5900,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749170	5730	PASS	C	T	19305	0.721782	0	4336,0,14942,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T1004I	nsp3	0.001601	0.721782	1	1	C>T
ERR5749170	5986	PASS	C	T	12911	0.973433	0	1,0,12899,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749170	6472	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23517	0.002764	0	7,23406,0,67	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acC/acT	T1251	nsp3	0.00083	0.966307	2	2	C>T
ERR5749170	6954	PASS	T	C	24568	0.820539	0	0,6,3,24419	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749170	8240	PASS	C	T	26372	0.104353	0	0,23353,0,3000	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cat/Tat	H1841Y	nsp3	0.001345	0.104353	1	1	C>T
ERR5749170	8603	PASS	T	C	12204	0.97214	128	4,5,0,12182	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Ctc	F17L	nsp4	0.002607	0.974959	2	1	T>C
ERR5749170	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	31250	0.00112	102	15659,15556,35,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749170	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21017	0.001285	0	20959,0,30,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749170	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	21012	0.001333	0	20943,0,56,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749170	11287	PASS	GTCTGGTTTT	G	21003	0.997762	0	0,47,0,20956	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749170	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	32914	0.00158	1	16434,16400,28,31	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749170	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10485	0.004101	2629	10236,91,5,150	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749170	14408	PASS	C	T	20333	0.838735	14	3,11,10175,9999	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749170	14676	PASS	C	T	13723	0.765576	0	9,0,13666,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749170	15279	PASS	C	T	23016	0.896594	0	4,0,22979,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749170	15708	PASS	G	T	15943	0.095967	0	0,14192,0,1747	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atT	M756I	RdRp	0.001488	0.095967	1	1	G>T
ERR5749170	16176	PASS	T	C	20849	0.983165	0	0,1,9880,10962	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749170	16524	PASS	A	G	24289	0.924575	0	1,0,24249,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acA/acG	T96	helicase	0.00047	0.926983	2	2	A>G
ERR5749170	17615	PASS	A	G	14888	0.918995	0	0,0,6,14843	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749170	17762	PASS	C	T	14144	0.912542	0	2,0,14119,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A509V	helicase	0.000697	0.912542	2	2	C>T
ERR5749170	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	23086	5.2E-4	0	23074,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749170	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29289	0.001536	0	29222,0,48,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749170	21764	PASS	ATACATG	A	12402	0.99742	0	31,0,12370,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749170	21990	PASS	TTTA	T	12413	0.997422	0	0,32,9,12372	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749170	22690	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	17189	0.001164	0	16897,6,23,0	LOW	SILENT	SYNONYMOUS_CODING	S	acT/acC	T376	S	0.000815	0.051311	2	1	T>C
ERR5749170	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29737	9.08E-4	22	12486,17206,19,8	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749170	23063	PASS	A	T	12497	0.863087	0	0,3,1,12448	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749170	23271	PASS	C	A	22839	0.916634	0	3,0,22811,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749170	23403	PASS	A	G	22832	0.966713	0	0,5,3,22810	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749170	23604	PASS	C	A	15404	0.946572	0	14,0,15381,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749170	23709	PASS	C	T	15395	0.937252	0	0,8,9,15355	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749170	24506	PASS	T	G	19283	0.974226	0	10,0,19270,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749170	24914	PASS	G	C	34920	0.961312	0	0,0,17406,17501	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749170	25437	PASS	G	T	16729	0.964194	0	6,0,16690,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	ttG/ttT	L15F	orf3a	0.001128	0.971411	2	2	G>T
ERR5749170	25496	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	33348	7.2E-4	9	16309,16369,342,303	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aTa/aGa	I35R	orf3a	0.000369	0.96555	3	2	T>G
ERR5749170	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	26465	0.001511	354	26359,23,27,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749170	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	11763	6.8E-4	0	6,11748,0,8	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749170	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	11761	0.003061	0	3,11720,0,36	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749170	27382	PASS	G	C	17061	0.927964	0	0,2,21,17024	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF6	Gat/Cat	D61H	orf6	0.001236	0.927964	2	2	G>C
ERR5749170	27383	PASS	A	T	17061	0.923217	0	0,14,21,17016	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF6	gAt/gTt	D61V	orf6	0.001454	0.928985	1	1	A>T
ERR5749170	27384	PASS	T	C	17061	0.893383	0	0,0,21,17012	LOW	SILENT	SYNONYMOUS_CODING	ORF6	gaT/gaC	D61	orf6	0.00154	0.931035	3	3	T>C
ERR5749170	27972	PASS	C	T	11246	0.903077	35	2,2,11116,77	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749170	28048	PASS	G	T	11181	0.927645	0	0,12,1,11160	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749170	28111	PASS	A	G	31002	0.97884	5	3,4,19801,11182	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749170	28270	PASS	TA	T	38389	0.994582	448	205,11,19530,18651	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749170	28280	PASS	G	C	38313	0.940046	21	13,2,19580,18637	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749170	28281	PASS	A	T	38313	0.911492	21	21,6,19575,18639	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749170	28282	PASS	T	A	38316	0.906227	2	16,12,19528,18650	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749170	28406	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTACCCAATA	T	19836	5.04E-4	0	23,19804,0,10	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	N	ttacccaataat/tat	LPNN45Y	N	0.00043	0.921074	3	2	TTACCCAATA>T
ERR5749170	28881	PASS	G	A	16741	0.764411	9	6,1,8267,8230	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749170	28882	PASS	G	A	16740	0.835245	3	2,0,8370,8219	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749170	28883	PASS	G	C	16740	0.942832	2	1,2,8387,8334	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749170	28977	PASS	C	T	8527	0.935382	0	0,1,2,8506	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749170	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	45265	0.001149	0	22711,22456,35,34	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749171	241	PASS	C	T	40	0.9	0	0,0,20,20	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749171	657	PASS	C	T	194	0.365979	0	0,113,0,81	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A131V	leader	0.001202	0.365979	3	1	C>T
ERR5749171	913	PASS	C	T	620	0.925806	2147483647	0,0,0,620	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749171	1652	PASS	A	G	1046	0.98088	0	1,0,1045,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Att/Gtt	I283V	nsp2	0.001057	0.98088	2	2	A>G
ERR5749171	2722	PASS	A	G	1927	0.920083	0	0,0,963,961	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcA/gcG	A1	nsp3	0.003728	0.9625	1	1	A>G
ERR5749171	2823	PASS	T	C	969	0.069143	0	0,898,0,69	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cTt/cCt	L35P	nsp3	0.035733	0.069143	1	1	T>C
ERR5749171	2862	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1181	0.017782	16	212,946,0,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T48I	nsp3	0.000547	0.850688	4	2	C>T
ERR5749171	3037	PASS	C	T	420	0.795238	0	0,0,210,207	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749171	3114	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	212	0.028302	0	0,206,0,6	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGt/gTt	G132V	nsp3	0.028302	0.941088	2	1	G>T
ERR5749171	5388	PASS	C	A	125	0.968	2147483647	0,0,125,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749171	5986	PASS	C	T	581	0.975904	2147483647	0,0,580,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749171	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	451	0.035477	0	0,435,0,16	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L1328S?	nsp3	0.000731	0.14377	4	2	C>CT
ERR5749171	6954	PASS	T	C	856	0.808411	2147483647	0,0,0,850	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749171	8208	PASS	C	T	347	0.84438	2147483647	0,0,0,347	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T1830I	nsp3	0.001142	0.84438	1	1	C>T
ERR5749171	9198	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTT	C	2400	0.027917	0	0,2333,0,67	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F216	nsp4	0.000543	0.93476	4	2	CTT>C
ERR5749171	9541	PASS	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	803	0.057285	2	739,18,46,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749171	11074	PASS	C	CT	1392	0.057471	0	1311,0,80,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CT
ERR5749171	11287	PASS	GTCTGGTTTT	G	1391	0.998562	0	0,2,0,1389	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749171	11750	PASS	C	T	1257	0.703262	0	0,0,647,553	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L260F	nsp6	0.001019	0.70989	2	1	C>T
ERR5749171	11991	PASS	A	G	4681	0.05063	0	4428,0,250,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gAa/gGa	E50G	nsp7	0.003937	0.05063	1	1	A>G
ERR5749171	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	1104	0.026268	0	1050,0,29,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749171	12676	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	1103	0.018132	0	0,1083,0,20	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K196	nsp8	0.000716	0.87302	3	2	CA>C
ERR5749171	13995	PASS	T	C	637	0.050235	0	602,0,35,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcC	A185	RdRp	0.000877	0.050235	2	2	T>C
ERR5749171	14408	PASS	C	T	71	0.901408	0	0,0,36,35	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749171	14676	PASS	C	T	300	0.743333	2147483647	0,0,299,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749171	15279	PASS	C	T	648	0.915123	2147483647	0,0,648,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749171	16176	PASS	T	C	551	0.985481	0	0,0,91,460	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749171	16293	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	91	0.076923	0	84,0,7,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C19	helicase	0.001538	0.968351	1	1	C>T
ERR5749171	18032	PASS	C	T	998	0.973948	0	0,0,391,607	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T599I	helicase	0.000604	0.973948	2	2	C>T
ERR5749171	18457	PASS	C	T	470	0.948936	2147483647	0,0,470,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cca/Tca	P140S	ExoN	0.001253	0.951352	2	1	C>T
ERR5749171	18647	PASS	CTG	C	6502	0.054906	118	5672,473,357,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctgag/	PE203	ExoN	0.000283	0.970507	4	2	CTG>C
ERR5749171	20235	PASS	C	T	1981	0.925795	0	1,0,1976,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P205	endoR	0.000596	0.925795	3	2	C>T
ERR5749171	20245	PASS	A	G	1981	0.060575	0	1840,0,138,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Atg/Gtg	M209V	endoR	0.001027	0.060575	3	2	A>G
ERR5749171	21764	PASS	ATACATG	A	1348	0.999258	0	1,0,1347,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749171	21990	PASS	TTTA	T	1347	0.997773	0	0,3,0,1344	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749171	23063	PASS	A	T	1079	0.883225	2147483647	0,0,0,1074	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749171	23271	PASS	C	A	1062	0.921846	2147483647	0,0,1062,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749171	23403	PASS	A	G	1062	0.977401	2147483647	0,0,0,1062	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749171	23593	PASS	G	T	901	0.851276	0	2,0,899,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	caG/caT	Q677H	S	0.021779	0.924148	3	2	G>T
ERR5749171	23604	PASS	C	A	901	0.948946	2147483647	0,0,901,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749171	23709	PASS	C	T	900	0.935556	2147483647	0,0,0,900	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749171	24166	PASS	A	G	920	0.054348	0	870,0,50,0	LOW	SILENT	SYNONYMOUS_CODING	S	gaA/gaG	E868	S	0.002854	0.054348	2	2	A>G
ERR5749171	24237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	920	0.006522	0	913,0,7,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gTt	A892V	S	0.001242	0.889739	1	1	C>T
ERR5749171	24506	PASS	T	G	835	0.985629	2147483647	0,0,835,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749171	24914	PASS	G	C	14	1.0	0	0,0,7,7	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749171	25587	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	5995	0.039366	0	0,5758,0,236	HIGH	NONE	FRAME_SHIFT	ORF3a	aag/	K67	orf3a	0.000598	0.813206	6	2	CAA>C
ERR5749171	26532	PASS	T	C	679	0.05891	0	1,636,0,42	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Tcc/Ccc	S4P	M	0.001836	0.05891	2	2	T>C
ERR5749171	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	906	0.024283	0	0,884,0,22	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749171	27972	PASS	C	T	229	0.908297	0	0,0,228,1	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749171	28048	PASS	G	T	228	0.929825	0	0,1,0,227	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749171	28095	PASS	A	T	228	0.942982	2147483647	0,0,0,228	HIGH	NONSENSE	STOP_GAINED	ORF8	Aaa/Taa	K68*	orf8	0.002672	0.967672	2	2	A>T
ERR5749171	28111	PASS	A	G	228	0.982456	2147483647	0,0,0,228	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749171	28270	PASS	TA	T	3231	0.999381	0	0,2,0,3229	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749171	28280	PASS	G	C	3231	0.922006	0	0,1,0,3226	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749171	28281	PASS	A	T	3231	0.917673	0	0,2,0,3227	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749171	28282	PASS	T	A	3233	0.943087	0	0,3,0,3228	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749171	28292	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	6871	0.001164	0	3427,3436,4,4	HIGH	NONE	FRAME_SHIFT	N	aat/	N8	N	0.000304	0.055324	4	2	CA>C
ERR5749171	28881	PASS	G	A	114	0.798246	0	0,0,56,54	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749171	28882	PASS	G	A	114	0.815789	0	0,0,58,55	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749171	28883	PASS	G	C	114	0.964912	0	0,0,58,56	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749171	28977	PASS	C	T	58	0.862069	2147483647	0,0,0,58	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749172	241	PASS	C	T	473	0.906977	0	0,0,237,236	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749172	913	PASS	C	T	3060	0.925817	2147483647	0,0,0,3057	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749172	1390	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	4242	0.0033	0	4213,0,15,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaT/aaC	N195	nsp2	0.0033	0.968424	1	1	T>C
ERR5749172	2185	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	2157	0.003245	0	2,2148,0,7	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L462S?	nsp2	0.000441	0.963529	4	3	G>GT
ERR5749172	3037	PASS	C	T	2746	0.824472	9	0,3,1371,1357	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749172	3177	PASS	C	T	4093	0.92084	0	0,0,2711,1379	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P153L	nsp3	0.000773	0.96008	3	2	C>T
ERR5749172	3267	PASS	C	T	2713	0.970512	2147483647	0,0,2712,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749172	3832	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	2941	0.00306	0	2932,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L373	nsp3	0.000689	0.327273	4	2	CT>C
ERR5749172	5388	PASS	C	A	1255	0.961753	0	1,0,1254,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749172	5986	PASS	C	T	4305	0.974913	0	1,0,4299,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749172	6516	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	8273	0.001209	33	4450,3813,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	att/aAtt	I1268N?	nsp3	0.000479	0.186047	4	2	T>TA
ERR5749172	6954	PASS	T	C	7774	0.81541	2147483647	0,0,0,7726	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749172	8084	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	4939	0.004657	0	4909,0,26,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E1789K	nsp3	0.000543	0.923413	4	2	G>A
ERR5749172	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	6196	0.00226	0	5827,355,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749172	10386	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15537	0.001995	53	5128,10374,0,32	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T111I	3Cpro	0.000642	0.160456	4	2	C>T
ERR5749172	10642	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	5127	0.002536	0	0,5109,0,17	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acG/acT	T196	3Cpro	0.001264	0.951979	3	1	G>T
ERR5749172	11287	PASS	GTCTGGTTTT	G	13631	0.999046	0	0,13,0,13618	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749172	11337	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	16293	0.00626	79	2654,13532,0,104	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTa/tCa	L122S	nsp6	0.00626	0.987619	1	1	T>C
ERR5749172	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	7599	0.001711	22	4927,2654,13,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749172	11750	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9678	0.001963	0	4910,4731,13,12	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L260F	nsp6	0.001019	0.70989	2	1	C>T
ERR5749172	12459	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11083	0.001624	33	5888,5174,2,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T123I	nsp8	0.000658	0.986093	1	1	C>T
ERR5749172	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9723	0.002057	0	4850,4841,11,11	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749172	13665	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1965	0.005089	0	1955,0,10,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H75	RdRp	0.002046	0.977554	1	1	C>T
ERR5749172	14408	PASS	C	T	1320	0.853788	1	3,4,656,647	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749172	14676	PASS	C	T	1903	0.802417	0	2,0,1895,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749172	14688	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	1903	0.002627	0	1898,0,5,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K417	RdRp	0.000534	0.979772	2	2	CA>C
ERR5749172	15042	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	3982	0.002511	0	3960,0,14,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaT/aaG	N534K	RdRp	0.002424	0.901818	2	2	T>G
ERR5749172	15279	PASS	C	T	4459	0.894147	2147483647	0,0,4455,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749172	15493	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GC	G	4459	0.002467	0	0,4448,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	gcc/	A685	RdRp	0.001408	0.076816	3	2	GC>G
ERR5749172	15960	PASS	C	T	2170	0.793548	2147483647	0,0,2161,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A840	RdRp	0.001581	0.81574	1	1	C>T
ERR5749172	16176	PASS	T	C	3596	0.980534	0	0,0,1426,2169	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749172	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	8341	0.002158	0	8323,0,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749172	17756	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	4647	0.001722	0	4639,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K508	helicase	0.000865	0.165644	4	2	GA>G
ERR5749172	18086	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4254	0.004466	0	4234,0,19,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T16I	ExoN	0.001699	0.075758	1	1	C>T
ERR5749172	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	19106	0.001308	0	19081,0,25,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749172	18756	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	19104	0.002774	0	19039,0,55,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccG/ccA	P239	ExoN	0.000392	0.942688	3	2	G>A
ERR5749172	21234	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	13667	0.00139	0	13650,0,19,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/Tgtt	V194C?	MethTr	0.000472	0.857572	5	2	C>CT
ERR5749172	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9810	0.004587	0	4777,4880,24,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749172	21597	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4934	0.004054	0	0,4903,0,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCt/tTt	S12F	S	0.00218	0.901607	2	1	C>T
ERR5749172	21764	PASS	ATACATG	A	6433	0.997979	0	13,0,6420,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749172	21990	PASS	TTTA	T	6433	0.998912	0	0,7,1,6425	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749172	22706	PASS	G	T	25162	0.623003	9	369,399,12405,11978	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gtg/Ttg	V382L	S	0.001622	0.623003	2	1	G>T
ERR5749172	22717	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	25536	0.00188	2	12697,12714,40,35	LOW	SILENT	SYNONYMOUS_CODING	S	acT/acA	T385	S	0.000395	0.918478	3	2	T>A
ERR5749172	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	12814	0.001249	0	0,12795,0,16	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749172	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18650	0.001984	38	5828,12778,2,36	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749172	23063	PASS	A	T	5820	0.87835	0	0,1,0,5787	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749172	23271	PASS	C	A	3087	0.933269	2147483647	0,0,3086,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749172	23403	PASS	A	G	3089	0.97572	0	0,1,0,3086	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749172	23575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6078	0.003784	0	6047,0,27,0	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C671	S	0.001569	0.894896	2	2	C>T
ERR5749172	23604	PASS	C	A	6078	0.944883	0	7,0,6066,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749172	23709	PASS	C	T	6069	0.944142	2147483647	0,0,0,6057	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749172	23712	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	6069	0.002636	0	0,6053,0,16	HIGH	NONE	FRAME_SHIFT	S	ttt/	F718	S	0.000679	0.958955	3	2	AT>A
ERR5749172	24432	PASS	A	T	12542	0.944666	4	4,1,6719,5813	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cAa/cTa	Q957L	S	0.935743	0.949489	1	1	A>T
ERR5749172	24506	PASS	T	G	6725	0.972491	0	4,0,6720,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749172	24914	PASS	G	C	20400	0.960294	0	0,0,10172,10223	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749172	25350	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13702	0.004233	0	13642,0,59,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCa/cTa	P1263L	S	0.000626	0.97904	4	2	C>T
ERR5749172	25495	PASS	A	G	27213	0.899644	0	2,2,13526,13646	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Ata/Gta	I35V	orf3a	0.000735	0.911134	2	1	A>G
ERR5749172	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	1198	0.010017	202	1176,8,1,11	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749172	26013	PASS	C	T	12498	0.961434	0	2,0,12493,0	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	ttC/ttT	F207	orf3a	0.000839	0.974528	1	1	C>T
ERR5749172	27145	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	16329	0.002082	0	8,16287,0,34	HIGH	NONE	FRAME_SHIFT	M	gac/	D209	M	0.000476	0.863895	2	2	CAG>C
ERR5749172	27459	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	11366	0.002024	0	2,11338,0,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	gaG/gaT	E22D	orf7a	0.002024	0.943812	1	1	G>T
ERR5749172	27494	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24060	9.56E-4	69	12664,11361,25,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	cCt/cTt	P34L	orf7a	0.000672	0.961447	2	2	C>T
ERR5749172	27494	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	24060	8.31E-4	50	12695,11345,1,19	HIGH	NONE	FRAME_SHIFT	ORF7a	tgc/	C35	orf7a	0.000672	0.961447	2	2	CT>C
ERR5749172	27506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	24060	0.001953	3	12670,11334,22,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	gGa/gAa	G38E	orf7a	0.000715	0.985435	4	2	G>A
ERR5749172	27765	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12696	0.00252	0	0,12608,0,33	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7b	Ctt/Ttt	L4F	orf7b	0.00109	0.970449	1	1	C>T
ERR5749172	27879	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1954	0.038895	0	1878,0,76,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7b	Cac/Tac	H42Y	orf7b	0.038895	0.983329	1	1	C>T
ERR5749172	27972	PASS	C	T	2038	0.91315	13	0,1,1949,83	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749172	28048	PASS	G	T	1954	0.923746	0	0,2,0,1950	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749172	28111	PASS	A	G	15071	0.979563	2	5,1,13105,1953	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749172	28270	PASS	TA	T	25529	0.995143	275	118,5,12951,12454	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749172	28271	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AA	A	25527	8.23E-4	46	13048,12460,20,1	.	.	.	.	.	.	.	0.000482	0.924941	3	2	AA>A
ERR5749172	28280	PASS	G	C	25486	0.944165	14	8,1,12988,12449	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749172	28281	PASS	A	T	25486	0.921879	10	16,7,12983,12447	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749172	28282	PASS	T	A	25487	0.912622	2	10,7,12950,12455	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749172	28396	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	13123	0.001143	0	6,13102,0,15	HIGH	NONE	FRAME_SHIFT	N	caa/cCaa	Q43P?	N	0.000496	0.946059	5	2	G>GC
ERR5749172	28881	PASS	G	A	1047	0.710602	0	0,0,515,515	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749172	28882	PASS	G	A	1047	0.856734	0	0,0,522,517	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749172	28883	PASS	G	C	1047	0.949379	0	0,0,523,524	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749172	28977	PASS	C	T	532	0.932331	2147483647	0,0,0,532	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749172	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	17507	0.001828	1	8773,8691,20,17	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749172	29386	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	3751	0.001866	0	3744,0,7,0	HIGH	NONE	FRAME_SHIFT	N	aag/aaAg	K373K?	N	0.000887	0.899197	4	2	C>CA
ERR5749173	241	PASS	C	T	23254	0.865873	0	0,0,11559,11613	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749173	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	13234	0.003174	0	13188,5,42,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749173	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	13228	6.8E-4	0	13125,5,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749173	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	13228	0.001436	0	13125,5,19,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749173	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	13228	0.005443	0	13125,5,72,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749173	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	13227	0.002495	0	11993,10,1041,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749173	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	13227	0.002419	0	13185,10,32,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749173	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	13225	0.001059	0	13198,11,14,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttatg/gtg	VM84V	leader	0.000554	0.991848	4	1	GTTA>G
ERR5749173	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	13224	0.001891	0	13176,11,25,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749173	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	36935	5.41E-4	17	23670,13241,18,2	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749173	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	36934	0.002193	19	23621,13226,63,18	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749173	913	PASS	C	T	23669	0.909586	0	0,17,0,23622	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749173	1027	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	12475	0.002405	413	12410,23,11,19	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccT/ccC	P74	nsp2	0.001454	0.276316	1	1	T>C
ERR5749173	3037	PASS	C	T	19919	0.810482	39	0,13,9954,9798	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749173	3267	PASS	C	T	20869	0.96986	0	0,0,20847,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749173	5388	PASS	C	A	5531	0.960947	2147483647	0,0,5529,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749173	5986	PASS	C	T	12444	0.976454	2147483647	0,0,12434,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749173	6954	PASS	T	C	24810	0.825232	0	0,3,2,24675	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749173	7843	PASS	C	T	41222	0.916161	0	5,6,20339,20801	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N1708	nsp3	0.000845	0.916161	2	2	C>T
ERR5749173	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	33870	6.79E-4	83	14720,19127,23,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749173	11082	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	17009	7.64E-4	0	17001,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000427	0.179468	2	1	TG>T
ERR5749173	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	17009	0.002704	0	16927,0,67,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749173	11287	PASS	GTCTGGTTTT	G	17001	0.996824	0	0,54,0,16947	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749173	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	34757	9.49E-4	1	22744,11960,23,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749173	12125	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	12942	0.001236	0	9,12869,0,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y12H	nsp8	0.000847	0.113436	1	1	T>C
ERR5749173	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	14605	0.001438	0	14560,0,21,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749173	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	33295	0.001261	0	16635,16569,23,23	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749173	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	13405	0.004924	2147483647	13040,117,11,229	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749173	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	25967	0.001964	1	13018,12912,27,24	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749173	14408	PASS	C	T	25967	0.826125	7	2,6,12959,12756	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749173	14676	PASS	C	T	14548	0.829874	0	11,0,14505,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749173	15279	PASS	C	T	24418	0.903309	0	1,0,24386,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749173	16176	PASS	T	C	20069	0.979571	0	1,1,9173,10877	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749173	18079	PASS	G	T	11319	0.944695	0	10,0,11294,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gta/Tta	V14L	ExoN	0.003215	0.944695	2	1	G>T
ERR5749173	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	23374	6.42E-4	0	23359,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749173	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30268	0.001883	0	30192,0,60,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749173	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25911	8.88E-4	0	25854,0,23,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749173	20825	PASS	C	T	48289	0.202489	2	17699,20436,4674,5465	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T56I	MethTr	0.001237	0.202489	2	1	C>T
ERR5749173	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34590	8.09E-4	0	16989,17241,17,19	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749173	21764	PASS	ATACATG	A	12480	0.996474	0	44,0,12436,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749173	21990	PASS	TTTA	T	12489	0.997438	0	0,32,13,12444	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749173	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	15987	0.001188	0	0,15956,0,21	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749173	23063	PASS	A	T	10497	0.856816	0	0,5,0,10442	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749173	23271	PASS	C	A	23157	0.926027	0	2,0,23134,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749173	23403	PASS	A	G	23149	0.965225	0	0,3,0,23125	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749173	23604	PASS	C	A	14836	0.948234	0	6,0,14823,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749173	23709	PASS	C	T	14822	0.943058	0	0,1,3,14803	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749173	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	35657	5.89E-4	2	20803,14833,14,7	HIGH	NONE	FRAME_SHIFT	S	ttg/	L753	S	0.000334	0.080808	2	2	CT>C
ERR5749173	24370	PASS	C	T	11542	0.899498	0	0,2,0,11511	LOW	SILENT	SYNONYMOUS_CODING	S	gaC/gaT	D936	S	0.004751	0.899498	1	1	C>T
ERR5749173	24506	PASS	T	G	19025	0.975716	0	4,0,19019,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749173	24914	PASS	G	C	33107	0.959102	0	1,2,16503,16571	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749173	25019	PASS	G	T	24756	0.981297	2	1,1,8088,16649	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gat/Tat	D1153Y	S	0.00048	0.981297	3	2	G>T
ERR5749173	25496	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	33510	7.76E-4	195	16648,16468,99,273	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aTa/aGa	I35R	orf3a	0.000369	0.96555	3	2	T>G
ERR5749173	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	29183	0.001679	534	29068,15,27,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749173	25782	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29150	0.001029	0	29040,0,32,0	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	tgC/tgT	C130	orf3a	0.000916	0.955348	1	1	C>T
ERR5749173	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	52933	0.002154	0	0,52817,0,114	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749173	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	10193	7.85E-4	0	3,10179,0,8	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749173	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	10193	0.003434	0	2,10156,0,35	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749173	27467	PASS	G	C	17064	0.953528	2147483647	479,2,396,16179	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	aGa/aCa	R25T	orf7a	0.003204	0.953528	2	1	G>C
ERR5749173	27493	PASS	C	T	28905	0.971493	0	1,2,12707,16180	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Cct/Tct	P34S	orf7a	0.000794	0.971493	2	1	C>T
ERR5749173	27599	PASS	A	G	11843	0.959723	0	1,0,11801,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	gAc/gGc	D69G	orf7a	0.950072	0.959723	1	1	A>G
ERR5749173	27696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TCTTATTGTTGCGGCAATAGTGTTTATAACACTTTGCTTCACACTCAAAAGAAAG	T	12692	7.09E-4	0	20,12663,0,9	MODERATE	NONE	CODON_DELETION	ORF7a	cttattgttgcggcaatagtgtttataacactttgcttcacactcaaaagaaag/	LIVAAIVFITLCFTLKRK102	orf7a	0.000628	0.99631	1	1	TCTTATTGTTGCGGCAATAGTGTTTATAACACTTTGCTTCACACTCAAAAGAAAG>T
ERR5749173	27972	PASS	C	T	10353	0.906694	16	2,1,10242,76	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749173	28048	PASS	G	T	10272	0.910923	0	0,16,0,10248	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749173	28111	PASS	A	G	31633	0.97942	6	1,2,21340,10277	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749173	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	21343	7.03E-4	0	21323,8,15,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749173	28270	PASS	TA	T	41315	0.995425	496	195,4,21093,20033	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749173	28280	PASS	G	C	41226	0.940474	20	8,0,21135,20014	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749173	28281	PASS	A	T	41227	0.920343	25	23,6,21110,20003	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749173	28282	PASS	T	A	41231	0.913075	4	24,16,21058,20023	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749173	28881	PASS	G	A	16631	0.778065	9	8,2,8240,8167	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749173	28882	PASS	G	A	16628	0.831549	4	8,4,8326,8138	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749173	28883	PASS	G	C	16628	0.947919	3	2,0,8333,8269	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749173	28960	PASS	G	T	8455	0.913661	0	0,6,0,8436	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	caG/caT	Q229H	N	0.00273	0.921139	2	2	G>T
ERR5749173	28977	PASS	C	T	8459	0.932971	30	1,3,1,8432	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749173	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	31635	8.85E-4	160	23159,8420,0,28	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749173	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	46004	7.83E-4	0	23099,22841,23,23	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749174	241	PASS	C	T	953	0.881427	0	0,0,474,477	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749174	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6078	0.002797	0	0,6051,0,19	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749174	913	PASS	C	T	6078	0.916091	0	0,2,0,6071	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749174	2185	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	5743	0.00209	0	2,5729,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L462S?	nsp2	0.000441	0.963529	4	3	G>GT
ERR5749174	2494	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	4955	0.002624	0	0,4937,0,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gaG/gaT	E563D	nsp2	0.002624	0.951457	2	2	G>T
ERR5749174	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	21713	0.001013	1590	10847,10198,17,607	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749174	3037	PASS	C	T	3435	0.819796	3	0,1,1712,1696	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749174	3267	PASS	C	T	5644	0.969702	2147483647	0,0,5642,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749174	3734	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	2804	0.00428	0	0,2792,0,12	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gac/Tac	D339Y	nsp3	0.00428	0.968741	2	1	G>T
ERR5749174	4255	PASS	G	A	8837	0.825506	9	4,0,4395,4366	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccG/ccA	P512	nsp3	0.001102	0.871853	2	1	G>A
ERR5749174	4423	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	5299	0.003208	0	5280,2,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K569	nsp3	0.00063	0.953796	2	2	CA>C
ERR5749174	4578	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTAACGATC	T	5294	0.0051	0	0,5267,0,27	HIGH	NONE	FRAME_SHIFT	ORF1ab	aacgatctaaat/	NDLN621	nsp3	0.000519	0.082979	2	2	TTAACGATC>T
ERR5749174	5388	PASS	C	A	1130	0.957522	2147483647	0,0,1129,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749174	5986	PASS	C	T	4450	0.97573	0	1,0,4445,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749174	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	4416	0.007699	0	0,4381,0,34	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L1328S?	nsp3	0.000731	0.14377	4	2	C>CT
ERR5749174	6954	PASS	T	C	10489	0.820193	2147483647	0,0,0,10423	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749174	7735	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	9301	0.002473	0	9278,0,23,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/	V1673	nsp3	0.000658	0.954659	3	2	CG>C
ERR5749174	8015	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	7980	0.005764	0	7930,0,48,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gcg/Tcg	A1766S	nsp3	0.00385	0.392265	3	2	G>T
ERR5749174	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	6041	0.002152	4	5385,643,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749174	9968	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	2812	0.004267	0	2795,0,14,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gca/Tca	A472S	nsp4	0.003141	0.078014	2	1	G>T
ERR5749174	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	17057	0.002345	0	16580,0,40,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749174	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTTT	17057	0.002755	0	16580,0,47,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_INSERTION	ORF1ab	ttg/ttTTTg	L37FL	nsp6	0.000965	0.945355	5	2	C>CTTT
ERR5749174	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17057	0.002404	0	16988,0,43,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749174	11287	PASS	GTCTGGTTTT	G	17046	0.997829	0	0,37,0,17009	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749174	11507	PASS	G	A	6043	0.909979	0	1,0,3039,2991	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Att	V179I	nsp6	0.007744	0.914418	2	2	G>A
ERR5749174	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	9107	0.001977	0	9089,0,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749174	13308	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	9111	0.001976	0	3,9077,0,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aTg	K95M	nsp10	0.001976	0.928707	2	1	A>T
ERR5749174	13459	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	7793	0.002053	0	7777,0,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/ttTa	L8F?	nsp11	0.000691	0.060726	5	2	G>GT
ERR5749174	14408	PASS	C	T	499	0.867735	0	0,0,250,247	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749174	14676	PASS	C	T	4143	0.891866	0	5,0,4132,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749174	14724	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4128	0.002422	0	4108,1,11,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F428	RdRp	0.000952	0.789267	3	2	C>T
ERR5749174	15279	PASS	C	T	6601	0.888653	2147483647	0,0,6592,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749174	15379	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	13168	0.001519	14	6535,6569,22,10	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Agc/Ggc	S647G	RdRp	0.000745	0.947742	2	2	A>G
ERR5749174	16176	PASS	T	C	6407	0.98408	0	0,0,1435,4969	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749174	16792	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CGTG	C	23549	6.37E-4	62	8974,14560,15,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	cgtgta/cta	RV186L	helicase	0.000335	0.072562	5	2	CGTG>C
ERR5749174	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	8989	8.9E-4	0	8981,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749174	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	18215	5.49E-4	0	18205,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749174	19011	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	11897	0.002522	0	11867,0,30,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttc/Attc	F326I?	ExoN	0.000408	0.975746	4	2	C>CA
ERR5749174	19113	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	23676	0.001478	102	11843,11814,0,35	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K359	ExoN	0.000461	0.125	4	3	CA>C
ERR5749174	19186	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	G	11897	0.002942	0	0,11852,0,38	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cta/Gta	L383V	ExoN	0.000709	0.96164	4	3	C>G
ERR5749174	19329	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	6766	0.001921	0	6749,0,13,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcC	A430	ExoN	0.001217	0.228916	1	1	T>C
ERR5749174	19343	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	6766	0.001626	0	6755,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/Tgtt	V437C?	ExoN	0.000519	0.192257	7	2	C>CT
ERR5749174	19656	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	8812	0.001929	0	8777,0,34,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaG/aaT	K12N	endoR	0.001929	0.189573	1	1	G>T
ERR5749174	20853	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	15683	0.001212	13	11908,3746,25,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atT	M65I	MethTr	0.000856	0.198276	2	1	G>T
ERR5749174	21305	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	14490	0.001656	0	0,14454,0,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cGc/cAc	R216H	MethTr	0.000727	0.703943	1	1	G>A
ERR5749174	21764	PASS	ATACATG	A	6032	0.998342	0	10,0,6022,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749174	21809	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	6031	0.00315	0	6008,0,21,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gtc/Ttc	V83F	S	0.00315	0.889163	2	1	G>T
ERR5749174	21987	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	6032	0.002653	0	0,6014,0,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gGt/gTt	G142V	S	0.000998	0.922156	5	2	G>T
ERR5749174	21990	PASS	TTTA	T	6032	0.998674	0	0,8,0,6024	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749174	21998	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19660	0.002747	88	13567,6031,56,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Cac/Tac	H146Y	S	0.002747	0.657088	1	1	C>T
ERR5749174	22290	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	13630	0.001687	0	2,13605,0,23	HIGH	NONE	FRAME_SHIFT	S	tta/	L244	S	0.000389	0.578006	2	2	CT>C
ERR5749174	22690	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	14423	0.001248	0	14190,0,25,0	LOW	SILENT	SYNONYMOUS_CODING	S	acT/acC	T376	S	0.000815	0.051311	2	1	T>C
ERR5749174	23063	PASS	A	T	5301	0.865874	0	0,1,0,5279	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749174	23271	PASS	C	A	7572	0.926572	2147483647	0,0,7562,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749174	23403	PASS	A	G	7567	0.971719	2147483647	0,0,0,7562	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749174	23525	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAT	C	6345	0.001418	0	6336,0,9,0	HIGH	NONE	FRAME_SHIFT	S	cat/	H655	S	0.001101	0.97751	2	2	CAT>C
ERR5749174	23604	PASS	C	A	6342	0.938663	0	2,0,6332,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749174	23709	PASS	C	T	6330	0.940916	0	0,5,0,6315	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749174	24506	PASS	T	G	8372	0.972289	0	1,0,8369,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749174	24914	PASS	G	C	19541	0.96254	0	0,0,9734,9797	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749174	25302	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	16445	0.001277	12	13688,2724,22,10	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tGt/tTt	C1247F	S	0.001121	0.05002	1	1	G>T
ERR5749174	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	1667	0.005399	76	1630,22,7,6	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749174	25710	PASS	C	T	1639	0.776693	2147483647	0,0,1631,0	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	ctC/ctT	L106	orf3a	0.002127	0.789778	2	2	C>T
ERR5749174	26208	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	12741	7.85E-4	0	0,12731,0,10	HIGH	NONE	FRAME_SHIFT	ORF3a	gtg/	V273	orf3a	0.000315	0.922222	2	2	CG>C
ERR5749174	26257	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	19609	6.63E-4	22	6865,12731,0,13	HIGH	NONE	FRAME_SHIFT	E	tcg/	S6	E	0.000247	0.948926	4	2	GT>G
ERR5749174	26493	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	6864	0.002185	0	0,6849,0,15	.	.	.	.	.	.	.	0.001082	0.069277	3	1	GT>G
ERR5749174	26509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	6864	0.002331	0	0,6848,0,16	.	.	.	.	.	.	.	0.000852	0.946613	3	1	CT>C
ERR5749174	27312	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	10958	0.001825	0	10938,0,20,0	HIGH	NONE	FRAME_SHIFT	ORF6	aat/aaAt	N39K?	orf6	0.000911	0.088458	4	2	T>TA
ERR5749174	27389	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10958	0.002373	0	0,10917,0,30	.	.	.	.	.	.	.	0.001157	0.899553	2	1	C>T
ERR5749174	27527	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12293	0.001708	0	12262,2,21,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	cCa/cTa	P45L	orf7a	0.001708	0.973593	1	1	C>T
ERR5749174	27641	PASS	C	T	12254	0.911213	0	1,0,12225,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	tCa/tTa	S83L	orf7a	0.000983	0.911213	2	2	C>T
ERR5749174	27670	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	12228	0.002944	0	1,12128,0,96	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Gtt/Ttt	V93F	orf7a	0.002392	0.990588	3	2	G>T
ERR5749174	27972	PASS	C	T	1751	0.908053	0	0,0,1737,8	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749174	28048	PASS	G	T	1747	0.919863	0	0,2,0,1743	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749174	28111	PASS	A	G	20391	0.980727	1	15,0,18621,1748	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749174	28198	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	18642	0.001556	0	18601,0,38,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tGt/tTt	C102F	orf8	0.000718	0.94386	4	2	G>T
ERR5749174	28270	PASS	TA	T	36184	0.995633	373	158,6,18406,17620	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749174	28280	PASS	G	C	36122	0.942002	9	6,1,18449,17614	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749174	28281	PASS	A	T	36122	0.9229	21	19,5,18445,17613	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749174	28282	PASS	T	A	36126	0.916597	0	12,11,18410,17619	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749174	28292	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	37085	5.93E-4	0	18484,18579,11,11	HIGH	NONE	FRAME_SHIFT	N	aat/	N8	N	0.000304	0.055324	4	2	CA>C
ERR5749174	28378	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	18643	0.001609	0	0,18591,0,33	LOW	SILENT	SYNONYMOUS_CODING	N	gcG/gcC	A35	N	0.001609	0.060482	3	1	G>C
ERR5749174	28881	PASS	G	A	2253	0.778961	3	2,0,1117,1108	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749174	28882	PASS	G	A	2253	0.834443	0	0,0,1129,1109	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749174	28883	PASS	G	C	2253	0.938304	0	1,0,1129,1123	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749174	28977	PASS	C	T	1146	0.93281	2147483647	0,0,0,1146	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749174	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	17292	0.001735	0	8679,8565,21,20	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749174	29386	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	3268	0.003672	0	3256,0,12,0	HIGH	NONE	FRAME_SHIFT	N	aag/	K373	N	0.000887	0.899197	4	2	CA>C
ERR5749175	241	PASS	C	T	18273	0.866634	0	3,3,9081,9122	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749175	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	10058	9.94E-4	0	10043,1,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749175	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10051	0.00199	0	9203,1,819,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749175	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23445	0.001024	0	0,23404,0,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749175	913	PASS	C	T	23446	0.922759	0	0,12,0,23402	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749175	1510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	21945	0.002871	0	0,21668,0,72	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G235	nsp2	0.002159	0.937304	1	1	T>C
ERR5749175	3037	PASS	C	T	15374	0.806231	48	0,16,7687,7551	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749175	3267	PASS	C	T	20489	0.971936	0	2,0,20477,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749175	5388	PASS	C	A	5488	0.959184	2147483647	0,0,5486,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749175	5986	PASS	C	T	10379	0.976298	2147483647	0,0,10371,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749175	6670	PASS	G	T	9612	0.921348	0	16,0,9590,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tgG/tgT	W1317C	nsp3	0.005523	0.921348	2	2	G>T
ERR5749175	6954	PASS	T	C	24020	0.817985	0	0,11,1,23884	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749175	8123	PASS	C	T	26663	0.765818	0	4,0,26411,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Ttt	L1802F	nsp3	0.001144	0.778589	1	1	C>T
ERR5749175	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	27143	5.89E-4	55	12187,14940,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749175	11287	PASS	GTCTGGTTTT	G	17795	0.998426	0	0,28,0,17767	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749175	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	36067	0.001054	0	18016,17972,22,22	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749175	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10009	0.005295	2941	9777,63,4,162	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749175	14408	PASS	C	T	19465	0.841716	5	2,5,9720,9613	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749175	14676	PASS	C	T	14227	0.777747	0	4,0,14183,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749175	15279	PASS	C	T	25474	0.876816	0	2,0,25430,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749175	16176	PASS	T	C	18891	0.983272	0	0,0,7867,11019	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749175	17615	PASS	A	G	11505	0.920817	0	0,0,2,11466	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749175	17626	PASS	C	T	11504	0.94428	0	0,4,0,11485	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cat/Tat	H464Y	helicase	0.001039	0.946125	2	2	C>T
ERR5749175	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	19628	9.17E-4	0	19610,0,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749175	19296	PASS	G	A	15427	0.972386	247	1,7,15415,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttG/ttA	L419	ExoN	0.000586	0.977017	2	2	G>A
ERR5749175	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25697	0.002257	0	25621,0,61,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749175	21764	PASS	ATACATG	A	10037	0.997509	0	24,0,10012,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749175	21817	PASS	A	G	10029	0.959019	0	4,0,10013,0	LOW	SILENT	SYNONYMOUS_CODING	S	ccA/ccG	P85	S	0.000689	0.961354	3	2	A>G
ERR5749175	21990	PASS	TTTA	T	10042	0.998805	0	0,12,4,10026	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749175	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	15591	0.001347	0	0,15566,0,21	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749175	23063	PASS	A	T	9060	0.866004	0	0,2,0,9022	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749175	23271	PASS	C	A	23505	0.918826	0	1,0,23477,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749175	23403	PASS	A	G	23500	0.97217	0	0,7,0,23479	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749175	23604	PASS	C	A	12524	0.940913	0	14,0,12504,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749175	23709	PASS	C	T	12509	0.935327	0	0,9,0,12481	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749175	24506	PASS	T	G	19574	0.974252	0	12,0,19557,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749175	24914	PASS	G	C	27893	0.962213	3	1,0,13873,13998	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749175	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	22795	0.001667	93	13755,8988,44,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749175	25690	PASS	G	T	26549	0.979849	2147483647	0,0,26534,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Ggc/Tgc	G100C	orf3a	0.971091	0.979849	1	1	G>T
ERR5749175	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	26549	5.65E-4	0	26534,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749175	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	26751	0.001308	1410	26301,172,153,103	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749175	26526	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	13222	0.001588	0	2,13179,0,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Gca/Aca	A2T	M	0.001224	0.951192	3	1	G>A
ERR5749175	27513	PASS	C	T	23417	0.980655	40	1,1,23403,0	LOW	SILENT	SYNONYMOUS_CODING	ORF7a	taC/taT	Y40	orf7a	0.001863	0.982462	2	2	C>T
ERR5749175	27972	PASS	C	T	8448	0.905185	19	1,1,8379,42	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749175	28048	PASS	G	T	8411	0.927952	0	0,15,0,8393	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749175	28111	PASS	A	G	28857	0.978099	1	5,1,20425,8413	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749175	28270	PASS	TA	T	39671	0.995059	460	198,8,20159,19316	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749175	28280	PASS	G	C	39590	0.941324	13	13,4,20198,19295	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749175	28281	PASS	A	T	39590	0.919904	11	17,7,20188,19302	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749175	28282	PASS	T	A	39593	0.913318	0	16,16,20163,19303	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749175	28881	PASS	G	A	23525	0.76017	31	17,2,11601,11601	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749175	28882	PASS	G	A	23524	0.830471	11	9,2,11741,11569	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749175	28883	PASS	G	C	23522	0.941374	0	1,0,11756,11742	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749175	28977	PASS	C	T	12016	0.934088	0	0,1,8,11985	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749175	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	29926	0.00127	118	17910,11950,2,36	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749175	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	35576	9.56E-4	0	17862,17661,21,20	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749175	29686	PASS	C	T	11798	0.786574	18	0,6,5885,5773	.	.	.	.	.	.	.	0.001045	0.802514	2	1	C>T
ERR5749175	29688	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	11811	0.003048	0	5873,5874,20,20	.	.	.	.	.	.	.	0.002374	0.664502	2	1	G>A
ERR5749176	241	PASS	C	T	12543	0.868134	3	0,2,6245,6244	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749176	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	12165	0.001891	0	12132,13,23,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749176	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	12166	0.001069	0	12065,15,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749176	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	12166	0.001397	0	12065,15,17,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749176	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	12166	0.003863	0	12065,15,47,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749176	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12168	0.00189	0	11126,24,873,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749176	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	12168	0.00189	13	12121,24,22,1	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749176	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	12170	0.001315	33	12113,23,14,2	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttatg/gtg	VM84V	leader	0.000554	0.991848	4	1	GTTA>G
ERR5749176	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	12170	0.001397	32	12113,23,15,2	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749176	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	12169	7.4E-4	0	12126,27,9,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749176	635	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12175	0.0023	0	0,12138,0,33	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgt/Tgt	R124C	leader	0.00148	0.880435	1	1	C>T
ERR5749176	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	32000	7.81E-4	11	19810,12163,20,5	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749176	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	32000	7.19E-4	0	19777,12157,15,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749176	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	32000	0.001187	35	19777,12157,34,4	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749176	913	PASS	C	T	19824	0.908848	0	0,14,0,19787	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749176	1573	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	21119	0.001231	698	0,21058,22,4	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acA/acG	T256	nsp2	0.001231	0.75	1	1	A>G
ERR5749176	2232	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	38128	0.001757	8	14788,23238,34,38	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A476V	nsp2	0.000499	0.381237	2	2	C>T
ERR5749176	3037	PASS	C	T	18522	0.813519	57	0,19,9258,9129	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749176	3267	PASS	C	T	20200	0.970297	0	2,0,20191,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749176	4255	PASS	G	A	36310	0.871853	64	34,4,18040,18089	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccG/ccA	P512	nsp3	0.001102	0.871853	2	1	G>A
ERR5749176	5388	PASS	C	A	5950	0.956807	2147483647	0,0,5941,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749176	5986	PASS	C	T	12397	0.973945	0	3,0,12385,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749176	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11693	0.001625	0	7,11552,0,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749176	6954	PASS	T	C	23254	0.817924	0	0,3,0,23117	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749176	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	28667	0.001081	82	15144,13492,31,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749176	10323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	17211	0.001743	0	0,17134,0,31	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749176	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	19725	0.001622	0	19676,1,45,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749176	11287	PASS	GTCTGGTTTT	G	19720	0.997312	0	0,53,1,19666	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749176	11507	PASS	G	A	27573	0.902368	6	5,1,13803,13688	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Att	V179I	nsp6	0.007744	0.914418	2	2	G>A
ERR5749176	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	36938	7.85E-4	4	23036,13853,22,9	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749176	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	35778	0.001453	2	17862,17806,28,33	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749176	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	7754	0.004127	2058	7552,78,1,118	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749176	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	15036	0.00153	0	7535,7488,12,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749176	14408	PASS	C	T	15036	0.844374	6	0,2,7499,7414	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749176	14676	PASS	C	T	12773	0.749472	0	4,0,12735,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749176	15279	PASS	C	T	21081	0.890802	2147483647	0,0,21052,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749176	16176	PASS	T	C	19366	0.982185	0	0,0,9165,10194	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749176	18674	PASS	G	A	23717	0.056921	0	22277,0,1416,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aGa/aAa	R212K	ExoN	0.000413	0.056921	3	2	G>A
ERR5749176	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	23717	6.32E-4	0	23702,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749176	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	24361	4.1E-4	0	0,24351,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749176	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28020	0.002034	0	27945,0,59,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749176	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34109	0.001085	1	16739,17008,23,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749176	21764	PASS	ATACATG	A	12086	0.998014	0	24,0,12062,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749176	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	12086	7.45E-4	0	12077,0,9,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749176	21990	PASS	TTTA	T	12090	0.997932	0	0,25,3,12062	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749176	23063	PASS	A	T	13167	0.871573	0	0,2,0,13114	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749176	23271	PASS	C	A	21838	0.914415	0	2,0,21805,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749176	23403	PASS	A	G	21835	0.968079	0	0,1,0,21818	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749176	23426	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	21845	0.001785	0	0,21792,0,45	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gtt/Ttt	V622F	S	0.000428	0.916192	4	2	G>T
ERR5749176	23604	PASS	C	A	15660	0.940549	0	12,0,15643,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749176	23664	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	31049	8.37E-4	0	15414,15557,14,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCa/gTa	A701V	S	0.000837	0.918	2	2	C>T
ERR5749176	23709	PASS	C	T	15647	0.928868	0	0,7,3,15603	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749176	24127	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	29240	4.1E-4	14	12012,17217,9,3	HIGH	NONE	FRAME_SHIFT	S	aac/	N856	S	0.000324	0.111888	4	1	TA>T
ERR5749176	24127	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAACGGCCTTACTG	T	29240	3.76E-4	42	12012,17217,11,0	HIGH	NONE	FRAME_SHIFT	S	aacggccttactgtt/	NGLTV856	S	0.000324	0.111888	4	1	TAACGGCCTTACTG>T
ERR5749176	24506	PASS	T	G	17338	0.97566	0	6,0,17330,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749176	24914	PASS	G	C	36196	0.958034	0	0,0,18024,18132	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749176	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	24222	0.001115	39	16851,7330,33,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749176	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	21826	0.001375	362	21745,15,16,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749176	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	21796	6.88E-4	0	21781,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749176	25710	PASS	C	T	21796	0.789778	0	2,0,21713,0	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	ctC/ctT	L106	orf3a	0.002127	0.789778	2	2	C>T
ERR5749176	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	21939	0.001367	887	21589,127,136,67	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749176	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	12088	0.002068	0	0,12059,0,25	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749176	27641	PASS	C	T	21453	0.902018	0	7,0,21370,7	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	tCa/tTa	S83L	orf7a	0.000983	0.911213	2	2	C>T
ERR5749176	27972	PASS	C	T	10755	0.885821	39	2,2,10676,45	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749176	28001	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	21398	0.001495	0	10661,10674,18,18	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ccG/ccA	P36	orf8	0.00085	0.830607	2	1	G>A
ERR5749176	28048	PASS	G	T	10713	0.926911	0	0,9,0,10697	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749176	28111	PASS	A	G	30402	0.978653	2	2,2,19669,10721	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749176	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19668	0.001424	0	19583,5,30,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749176	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	19662	0.001933	0	19625,5,38,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749176	28270	PASS	TA	T	38236	0.995031	498	189,3,19423,18623	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749176	28280	PASS	G	C	38159	0.939359	15	14,4,19459,18607	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749176	28281	PASS	A	T	38159	0.924736	11	20,9,19461,18596	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749176	28282	PASS	T	A	38162	0.91371	6	24,15,19414,18610	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749176	28881	PASS	G	A	17991	0.778222	11	9,2,8929,8837	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749176	28882	PASS	G	A	17991	0.82847	0	3,2,9006,8834	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749176	28883	PASS	G	C	17991	0.944083	0	2,1,9023,8948	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749176	28977	PASS	C	T	9159	0.929687	0	0,1,0,9140	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749176	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	53484	8.6E-4	0	26851,26555,30,29	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749177	241	PASS	C	T	572	0.865385	0	0,0,285,284	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749177	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	1781	0.006738	0	1769,0,12,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749177	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	1781	0.002807	0	1771,0,5,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749177	635	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1781	0.006738	0	0,1766,0,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgt/Tgt	R124C	leader	0.00148	0.880435	1	1	C>T
ERR5749177	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	8627	8.11E-4	4	6838,1782,7,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749177	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	8627	0.001391	8	6769,1776,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749177	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	8627	0.008114	19	6769,1776,64,6	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749177	913	PASS	C	T	6841	0.922526	0	0,3,0,6825	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749177	1191	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	6028	9.95E-4	0	0,6022,0,6	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N130	nsp2	0.000749	0.916048	3	2	CA>C
ERR5749177	1594	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6234	0.004652	0	1,6176,0,29	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S263	nsp2	0.0019	0.963177	1	1	C>T
ERR5749177	2151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATTGGCTTGAAGAGAAG	A	6893	0.001886	0	0,6880,0,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	tggcttgaagagaagttt/	WLEEKF450	nsp2	0.000402	0.971954	3	2	ATTGGCTTGAAGAGAAG>A
ERR5749177	2185	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	6897	0.00174	0	3,6882,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F461	nsp2	0.000441	0.963529	4	3	GT>G
ERR5749177	2232	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11084	0.001534	23	4189,6870,1,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A476V	nsp2	0.000499	0.381237	2	2	C>T
ERR5749177	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	23591	0.001017	1657	11783,11098,17,629	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749177	3037	PASS	C	T	3918	0.840225	15	0,5,1958,1933	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749177	3096	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1972	0.005071	0	0,1956,0,11	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCa/tTa	S126L	nsp3	0.001801	0.932094	1	1	C>T
ERR5749177	3253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	7599	0.004343	0	7566,0,33,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N179	nsp3	0.000764	0.07578	1	1	CA>C
ERR5749177	3267	PASS	C	T	7599	0.972233	2147483647	0,0,7596,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749177	3741	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	3172	0.002837	0	0,3151,0,9	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I341T	nsp3	0.000648	0.968922	2	2	T>C
ERR5749177	3832	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	2856	0.006303	0	2836,2,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L373	nsp3	0.000689	0.327273	4	2	CT>C
ERR5749177	4255	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	11927	0.002935	4	5936,5933,24,32	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccG/ccT	P512	nsp3	0.001102	0.871853	2	1	G>T
ERR5749177	5230	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	5130	0.003119	0	0,5105,0,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaG/aaT	K837N	nsp3	0.002515	0.902519	1	1	G>T
ERR5749177	5388	PASS	C	A	1107	0.969286	2147483647	0,0,1107,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749177	5986	PASS	C	T	4076	0.974975	2147483647	0,0,4072,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749177	6573	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3816	0.003931	0	3801,0,15,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S1285F	nsp3	0.001862	0.957014	1	1	C>T
ERR5749177	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	3804	0.01551	0	0,3745,0,59	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L1328S?	nsp3	0.000731	0.14377	4	2	C>CT
ERR5749177	6954	PASS	T	C	8546	0.829511	0	0,2,0,8498	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749177	6990	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8564	0.002335	0	0,8431,0,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S1424F	nsp3	0.000504	0.101156	4	2	C>T
ERR5749177	7564	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTT	C	6523	0.001686	0	0,6511,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttttat/	FY1616	nsp3	0.000586	0.056194	4	2	CTT>C
ERR5749177	8917	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10665	0.004594	22	7722,2891,44,5	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F121	nsp4	0.004594	0.201937	1	1	C>T
ERR5749177	9165	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7765	0.001803	0	0,7743,0,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCc/aTc	T204I	nsp4	0.00112	0.253438	1	1	C>T
ERR5749177	9198	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	7768	0.001931	0	0,7753,0,15	HIGH	NONE	FRAME_SHIFT+STOP_GAINED	ORF1ab	gat/Tgat	D217*?	nsp4	0.000543	0.93476	4	2	C>CT
ERR5749177	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	5563	0.001079	0	4868,689,6,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749177	10228	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAT	C	8895	0.001911	0	8878,0,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	att/	I59	3Cpro	0.000533	0.961998	2	2	CAT>C
ERR5749177	10369	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8898	0.002023	0	0,8877,0,18	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	cgC/cgT	R105	3Cpro	0.001225	0.120075	1	1	C>T
ERR5749177	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	15712	0.005474	0	15315,0,86,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749177	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	15704	0.004012	0	15616,0,81,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749177	11095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15698	0.001529	0	15649,0,27,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A41	nsp6	0.000515	0.887707	7	2	C>T
ERR5749177	11173	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15656	0.00115	0	15557,1,40,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ctC/ctT	L67	nsp6	0.00115	0.587518	1	1	C>T
ERR5749177	11185	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	30624	0.001012	204	15570,14981,70,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L71F	nsp6	0.000356	0.883658	3	3	G>T
ERR5749177	11287	PASS	GTCTGGTTTT	G	15706	0.994779	0	0,82,0,15624	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749177	11507	PASS	G	A	4703	0.911333	0	2,1,2360,2326	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Att	V179I	nsp6	0.007744	0.914418	2	2	G>A
ERR5749177	12125	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	12177	0.002382	0	1,12117,0,30	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y12H	nsp8	0.000847	0.113436	1	1	T>C
ERR5749177	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	6999	0.002143	0	6977,0,18,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749177	12741	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10045	0.00229	3	3041,6976,5,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T19I	nsp9	0.000486	0.962552	2	2	C>T
ERR5749177	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13917	0.00194	0	6938,6933,14,14	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749177	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	2417	0.004137	0	1205,1200,5,5	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749177	14408	PASS	C	T	2417	0.859743	3	0,1,1198,1188	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749177	14676	PASS	C	T	5067	0.827314	0	3,0,5051,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749177	15240	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5727	0.003667	0	5693,9,21,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N600	RdRp	0.000934	0.931284	2	2	C>T
ERR5749177	15279	PASS	C	T	5716	0.889608	0	1,0,5708,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749177	16176	PASS	T	C	6805	0.982366	0	0,0,1230,5572	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749177	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	7737	0.00168	0	7724,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749177	17167	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5017	0.003189	0	5001,0,16,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cat/Tat	H311Y	helicase	0.001728	0.238095	1	1	C>T
ERR5749177	17502	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6302	0.009203	0	6243,0,58,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F422	helicase	0.000611	0.9865	2	2	C>T
ERR5749177	18304	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	15825	0.003096	30	12397,3372,49,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Ctc	F89L	ExoN	0.003096	0.071597	1	1	T>C
ERR5749177	18357	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	12451	0.002731	0	12399,0,36,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccT/ccC	P106	ExoN	0.001226	0.057597	1	1	T>C
ERR5749177	18501	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	12405	0.003628	0	0,12360,0,45	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K155	ExoN	0.000336	0.857143	4	2	CA>C
ERR5749177	18636	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	30594	0.001406	115	18132,12402,7,47	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtG/gtT	V199	ExoN	0.00055	0.963467	3	2	G>T
ERR5749177	18761	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	18132	0.001048	0	18107,0,22,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTg/aAg	M241K	ExoN	0.001048	0.251353	3	1	T>A
ERR5749177	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4340	0.004147	0	4320,0,18,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749177	20544	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	6954	0.001869	0	6927,6,21,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcA	S308	endoR	0.000834	0.975334	2	1	C>A
ERR5749177	20719	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6922	0.002023	0	0,6830,0,16	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L21	MethTr	0.000341	0.209091	2	2	C>T
ERR5749177	20825	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	19787	0.001668	62	12805,6947,34,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aAa	T56K	MethTr	0.001237	0.202489	2	1	C>A
ERR5749177	21034	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12829	0.001871	0	0,12776,0,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L126F	MethTr	0.001871	0.915185	1	1	C>T
ERR5749177	21516	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	6413	0.002183	0	6399,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	agagtt/	RV287	MethTr	0.000412	0.905456	2	2	CAG>C
ERR5749177	21597	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6407	0.002966	0	0,6367,0,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCt/tTt	S12F	S	0.00218	0.901607	2	1	C>T
ERR5749177	21655	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	6412	0.001871	0	0,6390,0,16	LOW	SILENT	SYNONYMOUS_CODING	S	tcT/tcC	S31	S	0.001481	0.110354	1	1	T>C
ERR5749177	21764	PASS	ATACATG	A	5825	0.992275	0	45,0,5780,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749177	21990	PASS	TTTA	T	5826	0.997769	0	0,13,1,5812	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749177	22206	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	11304	0.002035	0	0,11250,0,28	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gTt	D215V	S	0.002035	0.950097	2	1	A>T
ERR5749177	22227	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11309	0.001326	0	0,11245,0,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gTt	A222V	S	0.000419	0.824305	2	2	C>T
ERR5749177	22280	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ACTTTACTTG	A	11315	8.84E-4	0	2,11303,0,10	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	cttgctttacat/cat	LALH242H	S	0.00046	0.997799	1	1	ACTTTACTTG>A
ERR5749177	22290	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	11315	0.001768	0	2,11293,0,20	HIGH	NONE	FRAME_SHIFT	S	tta/	L244	S	0.000389	0.578006	2	2	CT>C
ERR5749177	22690	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	11358	0.001761	0	11135,0,28,0	LOW	SILENT	SYNONYMOUS_CODING	S	acT/acC	T376	S	0.000815	0.051311	2	1	T>C
ERR5749177	23043	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAT	C	5223	0.001915	0	0,5213,0,10	HIGH	NONE	FRAME_SHIFT	S	tat/	Y495	S	0.000881	0.056585	2	2	CAT>C
ERR5749177	23063	PASS	A	T	5228	0.873565	2147483647	0,0,0,5201	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749177	23271	PASS	C	A	10375	0.921928	0	1,0,10370,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749177	23403	PASS	A	G	10378	0.970996	0	0,1,0,10371	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749177	23426	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTT	G	10383	0.002697	0	0,10355,0,28	HIGH	NONE	FRAME_SHIFT	S	gtt/	V622	S	0.000428	0.916192	4	2	GTT>G
ERR5749177	23525	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5562	0.002337	0	5548,0,13,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Cat/Tat	H655Y	S	0.001101	0.97751	2	2	C>T
ERR5749177	23604	PASS	C	A	5561	0.943356	0	2,0,5556,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749177	23709	PASS	C	T	5558	0.948183	0	0,1,0,5551	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749177	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	8725	0.00149	24	3163,5549,0,13	HIGH	NONE	FRAME_SHIFT	S	ttg/	L753	S	0.000334	0.080808	2	2	CT>C
ERR5749177	24010	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATTTATTGAAGATCTAC	A	3175	0.002205	0	15,3153,0,7	HIGH	NONE	FRAME_SHIFT	S	attgaagatctacttttc/	IEDLLF818	S	0.000455	0.926398	4	2	ATTTATTGAAGATCTAC>A
ERR5749177	24127	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TTTTTG	8201	8.54E-4	29	5045,3156,0,7	HIGH	NONE	FRAME_SHIFT+STOP_GAINED	S	aac/TTTTGaac	N856F*?	S	0.000324	0.111888	4	1	T>TTTTTG
ERR5749177	24127	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	8201	0.001341	20	5034,3163,11,0	HIGH	NONE	FRAME_SHIFT	S	aac/	N856	S	0.000324	0.111888	4	1	TA>T
ERR5749177	24506	PASS	T	G	7447	0.974352	0	2,0,7445,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749177	24914	PASS	G	C	25444	0.96003	0	0,1,12681,12744	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749177	24998	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	12790	0.002815	0	0,12749,0,36	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1146H	S	0.001186	0.846993	3	1	G>C
ERR5749177	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	1353	0.008869	208	1332,8,1,11	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749177	26256	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16114	0.001738	58	6340,9736,0,28	LOW	SILENT	SYNONYMOUS_CODING	E	ttC/ttT	F4	E	0.000748	0.969561	2	2	C>T
ERR5749177	26257	PASS	G	A	16114	0.948926	2	2,1,6317,9763	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	Gtt/Att	V5I	E	0.000247	0.948926	4	2	G>A
ERR5749177	26270	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16114	0.001117	2	6334,9757,7,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	aCa/aTa	T9I	E	0.000586	0.930791	3	2	C>T
ERR5749177	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	4596	0.003916	0	14,4564,0,18	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749177	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	4596	0.001523	0	14,4575,0,7	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749177	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	4582	0.003492	0	0,4566,0,16	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749177	26958	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17215	0.002846	0	17160,0,52,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Cgt/Tgt	R146C	M	0.00096	0.122326	1	1	C>T
ERR5749177	27972	PASS	C	T	1964	0.891039	0	0,0,1944,11	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749177	28048	PASS	G	T	1950	0.922051	0	0,1,0,1948	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749177	28111	PASS	A	G	18711	0.977874	0	7,0,16748,1951	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749177	28192	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	16759	0.001134	0	16735,0,22,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	gTg/gAg	V100E	orf8	0.001134	0.980889	2	1	T>A
ERR5749177	28250	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TG	16741	0.001971	0	16713,0,33,0	HIGH	NONE	FRAME_SHIFT	ORF8	ttc/Gttc	F120V?	orf8	0.000494	0.993968	5	3	T>TG
ERR5749177	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16737	0.00472	0	16576,0,81,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749177	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	16734	0.001972	0	16704,0,33,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749177	28270	PASS	TA	T	32481	0.994828	437	168,3,16516,15797	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749177	28280	PASS	G	C	32425	0.939429	9	6,1,16580,15781	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749177	28281	PASS	A	T	32425	0.917625	12	11,3,16591,15785	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749177	28282	PASS	T	A	32425	0.912629	4	6,10,16540,15788	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749177	28292	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	33346	3.6E-4	0	16619,16715,6,6	HIGH	NONE	FRAME_SHIFT	N	aat/	N8	N	0.000304	0.055324	4	2	CA>C
ERR5749177	28406	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTA	T	16760	0.00179	0	0,16730,0,30	HIGH	NONE	FRAME_SHIFT	N	tta/	L45	N	0.00043	0.921074	3	2	TTA>T
ERR5749177	28412	PASS	A	T	16760	0.965453	0	0,2,0,16749	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Aat/Tat	N47Y	N	0.00198	0.965453	2	1	A>T
ERR5749177	28881	PASS	G	A	3205	0.786583	0	1,0,1593,1579	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749177	28882	PASS	G	A	3205	0.842434	0	0,0,1610,1573	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749177	28883	PASS	G	C	3205	0.948518	0	1,1,1609,1592	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749177	28977	PASS	C	T	1623	0.93284	2147483647	0,0,0,1620	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749177	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	23696	0.001013	0	11887,11775,15,13	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749177	29386	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	3130	0.001917	0	3124,0,6,0	HIGH	NONE	FRAME_SHIFT	N	aag/aaAg	K373K?	N	0.000887	0.899197	4	2	C>CA
ERR5749177	29421	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3128	0.003197	0	3117,0,11,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	cCg/cTg	P383L	N	0.002705	0.052892	2	2	C>T
ERR5749178	241	PASS	C	T	17477	0.860846	0	1,2,8688,8735	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749178	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	11658	0.002745	0	11628,1,32,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749178	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	11656	0.00103	0	11619,2,12,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749178	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	11656	0.001373	0	11619,2,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749178	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	11654	0.001802	0	10807,6,742,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749178	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	11654	0.001888	0	11626,6,22,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749178	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	11655	7.72E-4	0	11633,7,9,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttatg/gtg	VM84V	leader	0.000554	0.991848	4	1	GTTA>G
ERR5749178	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	30426	0.001643	24	18707,11658,41,9	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749178	913	PASS	C	T	18748	0.917004	0	0,9,0,18718	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749178	3037	PASS	C	T	15794	0.800747	48	0,16,7893,7723	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749178	3095	PASS	T	C	7954	0.944179	0	0,4,0,7944	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tca/Cca	S126P	nsp3	0.937591	0.970297	1	1	T>C
ERR5749178	3177	PASS	C	T	26094	0.913697	0	5,2,18113,7944	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P153L	nsp3	0.000773	0.96008	3	2	C>T
ERR5749178	3267	PASS	C	T	18134	0.968623	0	4,0,18120,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749178	4578	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTAACGATC	T	13138	6.09E-4	0	0,13130,0,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	aacgatctaaat/	NDLN621	nsp3	0.000519	0.082979	2	2	TTAACGATC>T
ERR5749178	5170	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	10483	7.63E-4	0	1,10474,0,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T819	nsp3	0.000565	0.894036	2	2	CCA>C
ERR5749178	5388	PASS	C	A	5506	0.958409	2147483647	0,0,5502,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749178	5986	PASS	C	T	11000	0.977182	2147483647	0,0,10984,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749178	6954	PASS	T	C	21380	0.81174	0	0,8,2,21224	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749178	7834	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	37086	0.031953	0	17782,17809,672,675	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N1705	nsp3	0.000523	0.86555	3	2	C>T
ERR5749178	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	28089	8.54E-4	78	13251,14814,24,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749178	10156	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15167	0.001978	0	15113,16,32,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D34	3Cpro	0.001207	0.949463	1	1	C>T
ERR5749178	10369	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15154	0.002574	0	5,15099,0,40	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	cgC/cgT	R105	3Cpro	0.001225	0.120075	1	1	C>T
ERR5749178	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	17003	0.002176	0	16936,0,57,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749178	11287	PASS	GTCTGGTTTT	G	16999	0.997412	0	0,44,0,16955	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749178	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25820	0.00151	1	12893,12851,20,22	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749178	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	9993	0.003302	2207	9778,83,5,124	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749178	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	19459	9.25E-4	0	9763,9693,10,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749178	14408	PASS	C	T	19459	0.839252	4	1,3,9724,9583	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749178	14676	PASS	C	T	11722	0.813172	0	1,0,11702,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749178	15279	PASS	C	T	19747	0.886818	0	1,0,19713,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749178	15960	PASS	C	T	8921	0.802937	0	1,0,8876,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A840	RdRp	0.001581	0.81574	1	1	C>T
ERR5749178	16176	PASS	T	C	17545	0.980906	0	1,1,8613,8922	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749178	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	21460	5.13E-4	0	3,21446,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749178	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26545	0.002675	0	26452,1,73,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749178	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30599	8.82E-4	7	14963,15260,14,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749178	21762	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTATACA	C	10462	0.001912	0	10441,1,20,0	MODERATE	NONE	CODON_DELETION	S	atacat/	IH68	S	0.001297	0.875707	2	2	CTATACA>C
ERR5749178	21764	PASS	ATACATG	A	10462	0.996463	0	36,0,10424,1	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749178	21990	PASS	TTTA	T	10466	0.996178	0	0,40,6,10420	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749178	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	14100	0.001489	0	0,14067,0,23	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749178	23063	PASS	A	T	11086	0.870828	0	0,4,0,11023	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749178	23271	PASS	C	A	19461	0.923899	0	1,0,19429,4	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749178	23403	PASS	A	G	19449	0.970538	0	0,2,0,19429	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749178	23604	PASS	C	A	13430	0.940953	0	12,0,13413,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749178	23709	PASS	C	T	13427	0.936695	0	0,3,4,13405	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749178	24432	PASS	A	T	26823	0.938747	12	9,1,15945,10845	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cAa/cTa	Q957L	S	0.935743	0.949489	1	1	A>T
ERR5749178	24506	PASS	T	G	15952	0.976116	0	6,0,15943,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749178	24914	PASS	G	C	31492	0.957608	3	1,0,15697,15776	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749178	25495	PASS	A	G	29151	0.893348	1	4,3,14489,14625	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Ata/Gta	I35V	orf3a	0.000735	0.911134	2	1	A>G
ERR5749178	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	22084	0.001177	339	22003,19,12,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749178	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	22047	6.35E-4	0	22033,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749178	26013	PASS	C	T	42182	0.96444	0	4,0,42144,0	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	ttC/ttT	F207	orf3a	0.000839	0.974528	1	1	C>T
ERR5749178	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	42116	4.99E-4	0	2,42093,0,21	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749178	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	9678	0.002273	0	0,9656,0,22	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749178	27972	PASS	C	T	9566	0.904767	48	0,2,9498,35	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749178	28048	PASS	G	T	9544	0.92456	0	0,8,0,9530	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749178	28111	PASS	A	G	28351	0.976791	1	4,3,18791,9545	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749178	28250	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TCTG	18803	5.85E-4	0	18783,7,11,0	MODERATE	NONE	CODON_INSERTION	ORF8	ttc/CTGttc	F120LF	orf8	0.000494	0.993968	5	3	T>TCTG
ERR5749178	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	18798	0.001064	0	18775,7,20,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749178	28270	PASS	TA	T	36405	0.994314	542	211,4,18535,17663	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749178	28280	PASS	G	C	36322	0.937118	29	14,1,18592,17648	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749178	28281	PASS	A	T	36322	0.918865	39	25,4,18587,17653	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749178	28282	PASS	T	A	36324	0.908876	19	18,5,18556,17659	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749178	28881	PASS	G	A	16072	0.77383	0	1,0,7990,7902	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749178	28882	PASS	G	A	16072	0.832815	6	3,0,8046,7889	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749178	28883	PASS	G	C	16074	0.944507	2	1,2,8057,7995	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749178	28977	PASS	C	T	8174	0.920724	0	0,1,0,8158	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749178	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	44458	0.001485	0	22331,22037,38,36	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749178	29739	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7651	0.001961	0	0,7617,0,25	.	.	.	.	.	.	.	0.001961	0.706433	1	1	C>T
ERR5749179	241	PASS	C	T	225	0.906667	0	0,0,112,113	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749179	635	PASS	C	T	368	0.880435	2147483647	0,0,0,368	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgt/Tgt	R124C	leader	0.00148	0.880435	1	1	C>T
ERR5749179	913	PASS	C	T	4420	0.926244	2147483647	0,0,0,4416	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749179	2779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	4884	0.007985	0	0,4836,0,46	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	agT/agA	S20R	nsp3	0.003967	0.16	2	2	T>A
ERR5749179	3037	PASS	C	T	1090	0.806422	0	1,1,547,535	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749179	3267	PASS	C	T	3846	0.971399	2147483647	0,0,3845,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749179	5388	PASS	C	A	262	0.942748	2147483647	0,0,261,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749179	5986	PASS	C	T	1615	0.978328	2147483647	0,0,1615,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749179	6543	PASS	C	T	1689	0.955595	2147483647	0,0,1688,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T1275I	nsp3	0.001888	0.955595	1	1	C>T
ERR5749179	6813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4710	0.008068	75	2980,1688,40,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T1365I	nsp3	0.001082	0.95799	2	1	C>T
ERR5749179	6954	PASS	T	C	3015	0.825207	2147483647	0,0,0,3001	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749179	7067	PASS	G	A	3293	0.059217	2605	71,3020,201,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E1450K	nsp3	0.000274	0.059217	5	3	G>A
ERR5749179	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	7873	0.037724	0	7549,0,297,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CT
ERR5749179	11082	PASS	TG	T	7851	0.179468	0	6464,0,1409,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000427	0.179468	2	1	TG>T
ERR5749179	11083	PASS	G	T	7851	0.782575	0	2,0,6414,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749179	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	7851	0.018214	0	7697,0,143,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/tTat	Y38L?	nsp6	0.000477	0.901695	5	2	G>GT
ERR5749179	11287	PASS	GTCTGGTTTT	G	7872	0.998857	0	0,9,0,7863	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749179	12125	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	7698	0.016238	0	2,7548,0,133	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y12H	nsp8	0.000847	0.113436	1	1	T>C
ERR5749179	12784	PASS	C	T	627	0.966507	2147483647	0,0,627,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N33	nsp9	0.005814	0.966507	2	2	C>T
ERR5749179	12970	PASS	C	T	625	0.8352	2147483647	0,0,0,622	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N95	nsp9	0.8352	0.861883	1	1	C>T
ERR5749179	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7940	0.002015	0	3963,3953,8,8	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749179	14408	PASS	C	T	122	0.877049	0	0,0,61,60	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749179	14676	PASS	C	T	2163	0.738789	0	3,0,2156,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749179	15279	PASS	C	T	2238	0.89008	2147483647	0,0,2234,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749179	15774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	5094	0.008049	0	0,5048,0,46	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	agC/agA	S778R	RdRp	0.006387	0.078608	2	2	C>A
ERR5749179	16176	PASS	T	C	1571	0.98154	0	0,0,313,1258	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749179	18131	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1010	0.007921	0	1001,0,9,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T31I	ExoN	0.0025	0.853992	1	1	C>T
ERR5749179	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	13705	7.3E-4	0	13695,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749179	18788	PASS	C	T	27331	0.51652	5	4773,4784,8886,8678	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T250I	ExoN	0.000792	0.51652	2	1	C>T
ERR5749179	20925	PASS	G	T	7009	0.136967	0	6027,0,982,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L89F	MethTr	0.001064	0.136967	2	1	G>T
ERR5749179	21764	PASS	ATACATG	A	2895	0.997927	0	6,0,2889,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749179	21990	PASS	TTTA	T	2897	0.997584	0	0,7,2,2888	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749179	22981	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	2119	0.010854	0	2086,0,33,0	HIGH	NONSENSE	STOP_GAINED	S	taT/taG	Y473*	S	0.001557	0.861194	3	2	T>G
ERR5749179	23063	PASS	A	T	2120	0.873113	2147483647	0,0,0,2114	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749179	23271	PASS	C	A	6330	0.921801	2147483647	0,0,6323,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749179	23403	PASS	A	G	6329	0.972665	0	0,2,0,6325	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749179	23604	PASS	C	A	1980	0.955051	0	1,0,1979,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749179	23709	PASS	C	T	1978	0.948433	2147483647	0,0,0,1977	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749179	24506	PASS	T	G	3058	0.972858	0	4,0,3054,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749179	24914	PASS	G	C	18197	0.961587	0	0,0,9064,9120	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749179	24949	PASS	A	G	9149	0.963384	2147483647	0,0,0,9143	LOW	SILENT	SYNONYMOUS_CODING	S	gtA/gtG	V1129	S	0.001446	0.963384	2	2	A>G
ERR5749179	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	232	0.038793	128	219,4,0,9	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749179	26416	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	5866	0.00375	63	2952,2940,0,22	HIGH	NONE	FRAME_SHIFT	E	tac/	Y59	E	0.000457	0.913418	2	2	GT>G
ERR5749179	26510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	2986	0.009712	0	0,2948,0,34	.	.	.	.	.	.	.	0.001235	0.933642	2	1	T>C
ERR5749179	27346	PASS	T	C	16043	0.888737	0	0,0,8002,7992	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF6	Tat/Cat	Y49H	orf6	0.000895	0.888737	2	1	T>C
ERR5749179	27506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	15829	0.001958	89	7727,8068,33,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	gGa/gTa	G38V	orf7a	0.000715	0.985435	4	2	G>T
ERR5749179	27552	PASS	ATTTGCACTGACTTGCTTTAGCACTCAATTTGCTTTTGCTTGTCCTGACGGCGTAAAACACGTCTATCAGTTACGTGCCAGATCAGTTTCACC	A	7747	0.985801	0	114,0,7637,0	HIGH	NONE	FRAME_SHIFT	ORF7a	tttgcactgacttgctttagcactcaatttgcttttgcttgtcctgacggcgtaaaacacgtctatcagttacgtgccagatcagtttcacct/	FALTCFSTQFAFACPDGVKHVYQLRARSVSP54	orf7a	0.000563	0.985801	6	1	ATTTGCACTGACTTGCTTTAGCACTCAATTTGCTTTTGCTTGTCCTGACGGCGTAAAACACGTCTATCAGTTACGTGCCAGATCAGTTTCACC>A
ERR5749179	27972	PASS	C	T	826	0.889831	0	0,0,823,3	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749179	28048	PASS	G	T	822	0.930657	2147483647	0,0,0,822	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749179	28111	PASS	A	G	14789	0.98012	0	4,0,13954,824	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749179	28270	PASS	TA	T	27104	0.994798	325	137,5,13771,13192	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749179	28280	PASS	G	C	27047	0.935113	21	8,0,13799,13175	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749179	28281	PASS	A	T	27047	0.915665	23	20,5,13796,13184	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749179	28282	PASS	T	A	27047	0.911155	12	19,8,13774,13186	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749179	28881	PASS	G	A	1954	0.783009	15	0,5,967,954	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749179	28882	PASS	G	A	1954	0.837769	0	1,0,973,951	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749179	28883	PASS	G	C	1954	0.942682	0	0,0,979,970	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749179	28977	PASS	C	T	996	0.940763	2147483647	0,0,0,994	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749179	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	17754	0.001464	0	8911,8806,16,15	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749180	241	PASS	C	T	377	0.859416	0	0,0,188,187	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749180	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	379	0.029024	0	368,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749180	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	4626	0.006485	7	4217,379,30,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749180	913	PASS	C	T	4243	0.916568	0	0,3,0,4240	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749180	1230	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AGT	A	3084	0.003243	0	0,3074,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	tgtgat/	CD143	nsp2	0.00129	0.969658	2	2	AGT>A
ERR5749180	1820	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	3990	0.005013	0	0,3960,0,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggt/Agt	G339S	nsp2	0.001189	0.949024	2	2	G>A
ERR5749180	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	16456	0.001337	1100	8207,7735,20,452	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749180	3037	PASS	C	T	1815	0.824242	3	0,1,910,894	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749180	3267	PASS	C	T	4933	0.970606	2147483647	0,0,4927,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749180	3575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	1407	0.007107	0	1397,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/ttTa	L287F?	nsp3	0.000594	0.059126	3	1	G>GT
ERR5749180	3817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2645	0.003781	33	1227,1407,10,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D366	nsp3	0.000777	0.972816	2	2	C>T
ERR5749180	4206	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2989	0.006357	0	2964,0,22,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCg/gTg	A496V	nsp3	0.003069	0.879444	1	1	C>T
ERR5749180	4693	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	1741	0.002872	0	1736,0,5,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/	V659	nsp3	0.000654	0.078873	1	1	TG>T
ERR5749180	4752	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1741	0.009765	0	1721,0,19,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T678I	nsp3	0.009765	0.938482	1	1	C>T
ERR5749180	5184	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTAG	C	3468	0.017301	0	0,3408,0,60	MODERATE	NONE	CODON_DELETION	ORF1ab	agt/	S823	nsp3	0.004643	0.894684	2	2	CTAG>C
ERR5749180	5388	PASS	C	A	466	0.95279	2147483647	0,0,466,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749180	5986	PASS	C	T	1991	0.975892	2147483647	0,0,1988,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749180	6336	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4827	0.003108	0	4807,0,17,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCg/tTg	S1206L	nsp3	0.001317	0.951419	1	1	C>T
ERR5749180	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	1200	0.014167	0	0,1183,0,17	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L1328S?	nsp3	0.000731	0.14377	4	2	C>CT
ERR5749180	6813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7035	0.006112	3	5794,1189,37,10	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T1365I	nsp3	0.001082	0.95799	2	1	C>T
ERR5749180	6954	PASS	T	C	5815	0.829063	0	0,1,0,5781	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749180	6990	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	5833	0.005143	0	0,5704,0,124	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tAt	S1424Y	nsp3	0.000504	0.101156	4	2	C>A
ERR5749180	7488	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3729	0.002682	0	3702,0,10,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T1590I	nsp3	0.001403	0.889265	2	1	C>T
ERR5749180	7600	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3732	0.008307	0	0,3698,0,32	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C1627	nsp3	0.001321	0.973632	1	1	C>T
ERR5749180	7691	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5814	0.003784	0	5791,0,22,0	HIGH	NONSENSE	STOP_GAINED	ORF1ab	Cag/Tag	Q1658*	nsp3	0.003784	0.095012	1	1	C>T
ERR5749180	7834	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11583	0.002935	0	5752,5753,19,19	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N1705	nsp3	0.000523	0.86555	3	2	C>T
ERR5749180	8137	PASS	G	T	3356	0.762515	0	39,0,3315,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtG/gtT	V1806	nsp3	0.002602	0.762515	2	1	G>T
ERR5749180	10323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	5546	0.006671	0	0,5495,0,40	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749180	10387	PASS	T	C	12335	0.973895	0	1,1,6784,5544	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T111	3Cpro	0.00094	0.973895	1	1	T>C
ERR5749180	11287	PASS	GTCTGGTTTT	G	26	0.961538	0	0,1,0,25	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749180	11575	PASS	C	T	1191	0.915197	30	1,0,0,1189	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F201	nsp6	0.912731	0.921085	1	1	C>T
ERR5749180	11674	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	3133	0.018513	0	3075,0,58,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F235	nsp6	0.00054	0.985782	3	2	CT>C
ERR5749180	11935	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATG	A	7950	0.003396	0	7922,1,27,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtc/	V33	nsp7	0.000833	0.976236	2	2	ATG>A
ERR5749180	12125	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	7943	0.005791	0	0,7865,0,50	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y12H	nsp8	0.000847	0.113436	1	1	T>C
ERR5749180	12676	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	3165	0.001896	0	0,3159,0,6	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K196	nsp8	0.000716	0.87302	3	2	CA>C
ERR5749180	12854	PASS	C	T	1310	0.948855	0	1,0,1308,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cct/Tct	P57S	nsp9	0.028995	0.95209	1	1	C>T
ERR5749180	13115	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5908	0.003216	0	5885,0,20,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L31	nsp10	0.001806	0.922167	1	1	C>T
ERR5749180	14408	PASS	C	T	353	0.866856	0	0,0,177,175	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749180	14676	PASS	C	T	2373	0.815423	2147483647	0,0,2365,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749180	15279	PASS	C	T	2870	0.884321	2147483647	0,0,2868,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749180	15493	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	2870	0.007666	0	0,2834,0,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gcc/Ccc	A685P	RdRp	0.001408	0.076816	3	2	G>C
ERR5749180	15493	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	2870	0.00453	0	0,2834,0,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gcc/Tcc	A685S	RdRp	0.001408	0.076816	3	2	G>T
ERR5749180	15720	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5708	0.002628	0	0,5686,0,19	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D760	RdRp	0.001002	0.917823	1	1	C>T
ERR5749180	15983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	3194	0.005009	0	3178,0,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T850	RdRp	0.000701	0.338235	2	1	TA>T
ERR5749180	16176	PASS	T	C	3785	0.982827	0	0,0,585,3198	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749180	16794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	13617	6.61E-4	44	4316,9292,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gta/	V187	helicase	0.000354	0.077626	2	2	TG>T
ERR5749180	17615	PASS	A	G	3426	0.908348	2147483647	0,0,0,3417	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749180	18457	PASS	C	A	4436	0.770965	2147483647	0,0,4413,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cca/Aca	P140T	ExoN	0.001253	0.951352	2	1	C>A
ERR5749180	18642	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	16081	0.001928	46	11603,4443,34,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atA/atG	I201M	ExoN	0.000464	0.078253	3	2	A>G
ERR5749180	18642	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AG	A	16081	0.00342	76	11582,4444,55,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gga/	G202	ExoN	0.000464	0.078253	3	2	AG>A
ERR5749180	18756	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	11636	0.003352	0	11598,0,39,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F240	ExoN	0.000392	0.942688	3	2	GT>G
ERR5749180	18803	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	23239	0.007014	1	11480,11470,96,91	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aGc/aCc	S255T	ExoN	0.000786	0.897116	2	1	G>C
ERR5749180	19023	PASS	T	A	8736	0.951351	0	1,0,8730,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtT/gtA	V328	ExoN	0.001259	0.951351	2	1	T>A
ERR5749180	19029	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8736	0.003777	0	8693,0,36,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H330	ExoN	0.003777	0.923016	1	1	C>T
ERR5749180	19188	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	8736	0.005151	0	0,8691,0,45	HIGH	NONE	FRAME_SHIFT	ORF1ab	tgg/	W385	ExoN	0.000427	0.06319	2	1	AT>A
ERR5749180	20148	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1451	0.005513	0	0,1440,0,8	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F176	endoR	0.000513	0.969223	2	2	C>T
ERR5749180	21004	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	16184	0.004078	0	8046,8028,35,36	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gca/Cca	A116P	MethTr	0.000749	0.857814	3	1	G>C
ERR5749180	21255	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	14183	0.002538	122	7300,6833,43,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcG/gcT	A199	MethTr	0.000341	0.917425	4	2	G>T
ERR5749180	21595	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTCTA	C	4000	0.008	0	0,3968,0,32	HIGH	NONE	FRAME_SHIFT	S	tctagt/	SS12	S	0.001296	0.918559	3	2	CTCTA>C
ERR5749180	21604	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	4000	0.00775	0	0,3960,0,39	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	caG/caT	Q14H	S	0.00775	0.878713	1	1	G>T
ERR5749180	21658	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4005	0.005743	21	0,3978,1,25	LOW	SILENT	SYNONYMOUS_CODING	S	ttC/ttT	F32	S	0.001649	0.937508	2	2	C>T
ERR5749180	21733	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	3353	0.00507	0	3330,4,17,0	LOW	SILENT	SYNONYMOUS_CODING	S	ccT/ccC	P57	S	0.001662	0.065814	2	1	T>C
ERR5749180	21764	PASS	ATACATG	A	3349	0.997611	0	8,0,3341,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749180	21990	PASS	TTTA	T	3355	0.995529	0	0,15,5,3335	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749180	22706	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	19117	0.001622	8	9544,9503,15,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gtg/Atg	V382M	S	0.001622	0.623003	2	1	G>A
ERR5749180	22817	PASS	G	T	9612	0.100291	0	0,8596,0,1014	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gct/Tct	A419S	S	0.100291	0.100291	1	1	G>T
ERR5749180	22907	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	2418	0.004549	0	2405,0,12,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tat/Cat	Y449H	S	0.004549	0.976342	1	1	T>C
ERR5749180	23063	PASS	A	T	2416	0.866308	2147483647	0,0,0,2407	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749180	23086	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2417	0.00662	0	0,2398,0,18	LOW	SILENT	SYNONYMOUS_CODING	S	taC/taT	Y508	S	0.00176	0.131707	2	2	C>T
ERR5749180	23271	PASS	C	A	6851	0.918406	2147483647	0,0,6819,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749180	23403	PASS	A	G	6848	0.976782	2147483647	0,0,0,6846	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749180	23424	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6854	0.004085	0	0,6821,0,30	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cTt	P621L	S	0.004085	0.067721	2	1	C>T
ERR5749180	23604	PASS	C	A	2979	0.944948	0	14,0,2964,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749180	23709	PASS	C	T	2977	0.951965	0	0,1,0,2973	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749180	23780	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATG	A	2979	0.002014	0	0,2973,0,6	HIGH	NONE	FRAME_SHIFT	S	atgtac/	MY740	S	0.002014	0.967596	3	2	ATG>A
ERR5749180	24506	PASS	T	G	6079	0.970719	0	3,0,6074,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749180	24914	PASS	G	C	17819	0.961838	0	1,1,8845,8966	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749180	25553	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9991	0.002602	0	0,9965,0,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	gCt/gTt	A54V	orf3a	0.001165	0.868131	3	2	C>T
ERR5749180	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	897	0.018952	251	868,12,1,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749180	26065	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	6508	0.002151	0	6490,0,17,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gtt/Ttt	V225F	orf3a	0.001242	0.906322	2	1	G>T
ERR5749180	26256	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	11082	0.002256	66	4543,6504,27,4	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	ttC/ttA	F4L	E	0.000748	0.969561	2	2	C>A
ERR5749180	26257	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	11082	0.001354	37	4554,6509,16,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	Gtt/Ttt	V5F	E	0.000247	0.948926	4	2	G>T
ERR5749180	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	2957	0.002367	0	0,2950,0,7	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749180	26895	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14243	0.005055	0	14166,1,74,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Cat/Tat	H125Y	M	0.000874	0.97046	1	1	C>T
ERR5749180	27312	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	6551	0.005343	0	6516,0,35,0	HIGH	NONE	FRAME_SHIFT	ORF6	aat/aaAt	N39K?	orf6	0.000911	0.088458	4	2	T>TA
ERR5749180	27467	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	6555	0.003204	0	1,6530,0,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	aGa/aTa	R25I	orf7a	0.003204	0.953528	2	1	G>T
ERR5749180	27476	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	15999	0.001313	97	9445,6517,0,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	aCa/aAa	T28K	orf7a	0.000547	0.22827	4	2	C>A
ERR5749180	27493	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15998	0.001438	0	9428,6542,13,10	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Cct/Tct	P34S	orf7a	0.000794	0.971493	2	1	C>T
ERR5749180	27532	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9450	0.002857	0	9415,5,27,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Cat/Tat	H47Y	orf7a	0.001165	0.982473	2	1	C>T
ERR5749180	27638	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	9437	0.001695	0	9403,0,16,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	gTt/gCt	V82A	orf7a	0.001695	0.96066	1	1	T>C
ERR5749180	27741	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9442	0.002965	0	0,9398,0,29	LOW	SILENT	SYNONYMOUS_CODING	ORF7a	ctC/ctT	L116	orf7a	0.000363	0.954278	3	2	C>T
ERR5749180	27745	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AG	A	9442	0.001695	0	0,9426,0,16	HIGH	NONE	FRAME_SHIFT	ORF7a	aga/	R118	orf7a	0.000941	0.082742	2	2	AG>A
ERR5749180	27746	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	9442	0.00233	0	0,9391,0,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	aGa/aAa	R118K	orf7a	0.000528	0.94095	3	2	G>A
ERR5749180	27972	PASS	C	T	1086	0.895028	0	0,0,1063,16	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749180	28048	PASS	G	T	1068	0.893258	0	0,3,0,1064	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749180	28057	PASS	C	T	1068	0.051498	0	0,1007,0,61	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	gCa/gTa	A55V	orf8	0.001401	0.051498	1	1	C>T
ERR5749180	28096	PASS	A	T	1073	0.650513	26	5,318,0,746	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aAa/aTa	K68I	orf8	0.650513	0.650513	1	1	A>T
ERR5749180	28111	PASS	A	G	1073	0.982293	0	0,0,5,1068	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749180	28195	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	12721	0.00283	0	12672,0,47,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	cGt/cTt	R101L	orf8	0.000851	0.926081	3	2	G>T
ERR5749180	28227	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12719	0.004481	0	12649,0,61,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	Cat/Tat	H112Y	orf8	0.000906	0.951206	2	2	C>T
ERR5749180	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12707	0.004092	0	12631,0,54,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749180	28270	PASS	TA	T	12055	0.999834	0	0,2,5,12048	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749180	28280	PASS	G	C	12056	0.920123	0	0,1,5,12025	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749180	28281	PASS	A	T	12056	0.92427	0	0,2,5,12040	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749180	28282	PASS	T	A	12056	0.957283	0	0,5,5,12046	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749180	28290	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	12699	0.001339	0	5,12667,0,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	cCc/cAc	P6H	N	0.001339	0.943901	2	1	C>A
ERR5749180	28310	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12716	0.001416	0	0,12689,0,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Ccc/Tcc	P13S	N	0.00095	0.92832	2	1	C>T
ERR5749180	28396	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	12730	0.002278	0	8,12673,0,30	LOW	SILENT	SYNONYMOUS_CODING	N	cgG/cgC	R41	N	0.000496	0.946059	5	2	G>C
ERR5749180	28674	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9616	0.003744	0	0,9573,0,38	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gCa/gTa	A134V	N	0.001338	0.958634	1	1	C>T
ERR5749180	28881	PASS	G	A	2312	0.771626	6	3,0,1149,1134	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749180	28882	PASS	G	A	2309	0.821135	0	0,0,1156,1128	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749180	28883	PASS	G	C	2309	0.944998	0	0,0,1158,1147	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749180	28977	PASS	C	T	1184	0.920608	2147483647	0,0,0,1183	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749180	29095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9483	0.001687	0	9461,0,16,0	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F274	N	0.000792	0.961279	2	2	C>T
ERR5749180	29096	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	9483	0.003164	0	9449,0,32,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Ggc/Tgc	G275C	N	0.003164	0.051234	2	1	G>T
ERR5749180	29253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	G	9483	0.002109	0	0,9422,0,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCg/tGg	S327W	N	0.000361	0.053998	4	2	C>G
ERR5749180	29253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9483	0.002425	0	0,9422,0,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCg/tTg	S327L	N	0.000361	0.053998	4	2	C>T
ERR5749181	180	PASS	C	T	5269	0.949706	0	1,0,5259,0	.	.	.	.	.	.	.	0.949706	0.949706	1	1	C>T
ERR5749181	241	PASS	C	T	10510	0.866698	0	0,0,5230,5224	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749181	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	12247	0.002041	0	12219,3,25,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749181	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	12247	9.8E-4	0	12173,3,12,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749181	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	12247	0.004409	0	12173,3,54,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749181	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	12240	0.001797	43	12214,4,20,2	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749181	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	12238	7.35E-4	0	12217,6,9,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749181	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	31796	0.001856	10	19489,12242,43,16	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749181	913	PASS	C	T	19525	0.922151	0	0,5,0,19498	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749181	3037	PASS	C	T	20910	0.810665	41	1,17,10441,10314	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749181	3267	PASS	C	T	18968	0.971847	0	1,0,18958,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749181	5170	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	12344	6.48E-4	0	2,12334,0,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T819	nsp3	0.000565	0.894036	2	2	CCA>C
ERR5749181	5388	PASS	C	A	6816	0.957453	0	1,0,6809,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749181	5784	PASS	C	T	39025	0.070519	0	17764,18227,1485,1511	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T1022I	nsp3	0.001294	0.919357	2	1	C>T
ERR5749181	5986	PASS	C	T	13403	0.973588	0	2,0,13392,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749181	6651	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12598	0.008493	0	12437,2,121,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A1311V	nsp3	0.008493	0.857717	1	1	C>T
ERR5749181	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12581	0.00151	0	2,12449,0,28	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749181	6954	PASS	T	C	21319	0.821708	0	0,5,1,21214	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749181	7070	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	40921	8.31E-4	40	19457,21376,36,11	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggc/Tgc	G1451C	nsp3	0.000698	0.101434	3	1	G>T
ERR5749181	8603	PASS	T	C	12779	0.974959	379	12,3,0,12750	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Ctc	F17L	nsp4	0.002607	0.974959	2	1	T>C
ERR5749181	10244	PASS	C	T	18573	0.074194	0	17121,0,1436,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cat/Tat	H64Y	3Cpro	0.001845	0.074194	2	2	C>T
ERR5749181	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	20513	0.002096	0	19955,2,43,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749181	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	20504	0.002097	0	20416,0,78,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749181	11287	PASS	GTCTGGTTTT	G	20500	0.997902	0	0,43,0,20457	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749181	11782	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	20114	0.001094	0	20,19905,0,27	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaA/aaG	K270	nsp6	0.001073	0.917917	2	2	A>G
ERR5749181	12741	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	36706	0.001062	5	16537,20115,22,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T19I	nsp9	0.000486	0.962552	2	2	C>T
ERR5749181	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34802	0.001092	0	17379,17320,22,22	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749181	13665	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20483	0.004199	0	20380,1,86,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H75	RdRp	0.002046	0.977554	1	1	C>T
ERR5749181	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	9324	0.00311	2033	9113,88,4,116	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749181	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	18148	9.92E-4	0	9103,9034,9,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749181	14408	PASS	C	T	18148	0.837062	6	0,2,9062,8941	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749181	14676	PASS	C	T	13318	0.780072	0	2,0,13283,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749181	15279	PASS	C	T	21723	0.888597	0	1,0,21694,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749181	16176	PASS	T	C	21395	0.981351	3	14,10,10404,10960	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749181	17615	PASS	A	G	16561	0.914075	0	0,1,1,16527	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749181	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	25516	0.001058	0	25489,0,27,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749181	19269	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	44454	0.001282	1	19976,24412,27,30	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N410	ExoN	0.000773	0.954777	2	2	C>T
ERR5749181	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29824	0.001643	0	29736,0,54,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749181	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	20547	6.81E-4	0	0,20532,0,14	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TA>T
ERR5749181	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30538	0.001768	0	14949,15245,31,32	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749181	21764	PASS	ATACATG	A	13456	0.997473	0	34,0,13422,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749181	21990	PASS	TTTA	T	13458	0.997548	0	0,33,2,13423	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749181	22690	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	15428	9.72E-4	0	15239,4,19,0	LOW	SILENT	SYNONYMOUS_CODING	S	acT/acC	T376	S	0.000815	0.051311	2	1	T>C
ERR5749181	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	15461	0.001294	0	0,15432,0,21	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749181	23063	PASS	A	T	14330	0.87083	0	0,4,2,14257	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749181	23271	PASS	C	A	21337	0.91892	0	1,0,21316,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749181	23403	PASS	A	G	21336	0.973144	0	0,2,0,21320	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749181	23604	PASS	C	A	16439	0.936493	0	21,0,16409,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749181	23709	PASS	C	T	16421	0.945131	0	0,5,3,16388	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749181	24506	PASS	T	G	18430	0.974932	0	11,0,18419,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749181	24914	PASS	G	C	40029	0.960703	0	0,0,19938,20065	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749181	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	27159	0.001215	59	18336,8773,44,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749181	25437	PASS	G	T	18526	0.965346	0	8,0,18473,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	ttG/ttT	L15F	orf3a	0.001128	0.971411	2	2	G>T
ERR5749181	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	19391	6.7E-4	0	19378,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749181	26163	PASS	T	C	48757	0.962816	0	0,18,0,48689	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	aaT/aaC	N257	orf3a	0.962816	0.962816	1	1	T>C
ERR5749181	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	13639	8.8E-4	0	1,13620,0,12	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749181	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	13639	7.33E-4	0	0,13629,0,10	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749181	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	13640	0.003299	0	0,13593,0,45	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749181	27476	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	42246	0.001444	3	21889,20285,35,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	aCa/aTa	T28I	orf7a	0.000547	0.22827	4	2	C>T
ERR5749181	27972	PASS	C	T	11409	0.897362	20	1,1,11317,55	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749181	28048	PASS	G	T	11359	0.927458	0	0,16,0,11338	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749181	28111	PASS	A	G	31369	0.974943	10	6,0,19988,11364	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749181	28270	PASS	TA	T	38878	0.994624	523	207,5,19710,18959	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749181	28280	PASS	G	C	38780	0.941723	21	13,2,19764,18943	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749181	28281	PASS	A	T	38780	0.917122	12	19,8,19748,18944	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749181	28282	PASS	T	A	38780	0.918515	0	12,12,19715,18945	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749181	28881	PASS	G	A	15001	0.788414	1	5,3,7441,7382	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749181	28882	PASS	G	A	15001	0.843344	3	2,0,7496,7374	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749181	28883	PASS	G	C	15001	0.944804	2	1,2,7505,7479	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749181	28977	PASS	C	T	7613	0.931302	0	0,4,2,7597	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749181	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	37941	9.49E-4	164	30292,7564,7,33	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749181	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	60211	9.8E-4	0	30239,29877,37,37	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749182	241	PASS	C	T	9583	0.85996	3	0,1,4787,4761	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749182	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	8091	0.004326	0	8049,10,35,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749182	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	8091	0.00136	0	7987,10,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749182	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	8091	0.001607	0	7987,10,13,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749182	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	8091	0.008157	0	7987,10,66,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749182	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	8083	0.001361	0	7478,7,433,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749182	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	8083	0.003835	49	8043,9,28,3	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749182	520	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTT	G	8094	0.001235	0	8059,25,10,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttgag/gag	VE86E	leader	0.000583	0.051154	1	1	GGTT>G
ERR5749182	635	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8094	0.004695	0	0,8049,0,41	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgt/Tgt	R124C	leader	0.00148	0.880435	1	1	C>T
ERR5749182	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29102	0.002955	21	20922,8060,77,14	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L140	leader	0.000316	0.135802	3	2	C>T
ERR5749182	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	29102	0.0011	44	20969,8093,32,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749182	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	29102	5.5E-4	20	20920,8078,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749182	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	29102	0.002474	6	20920,8078,57,15	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749182	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTTGACTT	A	29102	5.5E-4	20	20920,8078,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcatttgactta/	KSFDL141	leader	0.000303	0.999303	4	1	AAAGTCATTTGACTT>A
ERR5749182	913	PASS	C	T	20998	0.920802	0	0,6,0,20964	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749182	1652	PASS	A	G	19374	0.975792	114	1,3,19363,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Att/Gtt	I283V	nsp2	0.001057	0.98088	2	2	A>G
ERR5749182	2722	PASS	A	G	160	0.9625	0	0,0,78,82	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcA/gcG	A1	nsp3	0.003728	0.9625	1	1	A>G
ERR5749182	3037	PASS	C	T	19433	0.822158	44	1,18,9713,9584	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749182	3096	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9778	0.002148	0	0,9742,0,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCa/tTa	S126L	nsp3	0.001801	0.932094	1	1	C>T
ERR5749182	4529	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTTTAC	T	16336	6.73E-4	0	7,16316,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	tacttt/	YF605	nsp3	0.000527	0.402778	3	1	TTTTAC>T
ERR5749182	5388	PASS	C	A	5124	0.961944	0	0,0,5121,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749182	5986	PASS	C	T	12816	0.975421	0	2,0,12806,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749182	6954	PASS	T	C	24318	0.815157	0	0,4,0,24178	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749182	7067	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	36689	0.001281	131	12148,24406,50,13	HIGH	NONSENSE	STOP_GAINED	ORF1ab	Gaa/Taa	E1450*	nsp3	0.000274	0.059217	5	3	G>T
ERR5749182	7070	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	36689	0.001908	244	12191,24414,72,9	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggc/Tgc	G1451C	nsp3	0.000698	0.101434	3	1	G>T
ERR5749182	7318	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12261	0.001387	0	0,12236,0,18	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1533	nsp3	0.001387	0.851451	1	1	C>T
ERR5749182	7735	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19149	0.004596	0	19037,0,93,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I1672	nsp3	0.000658	0.954659	3	2	C>T
ERR5749182	8207	PASS	A	G	25404	0.940954	0	0,6,0,25347	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Act/Gct	T1830A	nsp3	0.001457	0.940954	2	2	A>G
ERR5749182	8208	PASS	C	T	25405	0.801574	0	0,11,0,25318	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T1830I	nsp3	0.001142	0.84438	1	1	C>T
ERR5749182	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	25234	0.001427	85	14329,10869,36,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749182	11082	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	22694	5.29E-4	0	22691,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000427	0.179468	2	1	TG>T
ERR5749182	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	22694	0.003305	0	22592,0,89,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749182	11287	PASS	GTCTGGTTTT	G	22686	0.996694	0	0,74,0,22611	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749182	11750	PASS	C	T	48978	0.688289	46	3,22,25095,21618	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L260F	nsp6	0.001019	0.70989	2	1	C>T
ERR5749182	11750	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	G	48978	0.002675	14	3,22,62,2143	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Gtc	L260V	nsp6	0.001019	0.70989	2	1	C>G
ERR5749182	13458	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15705	0.002101	0	15659,1,36,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCg/tTg	S6L	nsp11	0.001017	0.058608	4	2	C>T
ERR5749182	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	31359	0.001212	0	15663,15613,19,20	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749182	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	6994	0.004003	1880	6815,66,3,109	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749182	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	13580	8.84E-4	1	6807,6769,7,5	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749182	14408	PASS	C	T	13581	0.843384	1	3,4,6773,6701	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749182	14676	PASS	C	T	13644	0.762973	0	2,0,13597,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749182	14724	PASS	C	T	13655	0.783962	0	1,0,13419,46	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F428	RdRp	0.000952	0.789267	3	2	C>T
ERR5749182	14724	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	13655	0.02446	1	13262,48,334,0	HIGH	NONE	FRAME_SHIFT+STOP_GAINED	ORF1ab	aag/Taag	K430*?	RdRp	0.000952	0.789267	3	2	C>CT
ERR5749182	15279	PASS	C	T	21236	0.89353	2147483647	0,0,21216,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749182	16176	PASS	T	C	18352	0.981582	0	1,2,7046,11296	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749182	16508	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	27643	0.001338	0	27577,4,61,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGt/gTt	G91V	helicase	0.000561	0.074909	2	2	G>T
ERR5749182	17167	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15110	0.002052	0	15077,0,32,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cat/Tat	H311Y	helicase	0.001728	0.238095	1	1	C>T
ERR5749182	18032	PASS	C	T	26193	0.947238	0	2,3,10496,15671	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T599I	helicase	0.000604	0.973948	2	2	C>T
ERR5749182	18457	PASS	C	T	31468	0.936094	0	4,0,31400,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cca/Tca	P140S	ExoN	0.001253	0.951352	2	1	C>T
ERR5749182	20080	PASS	T	G	45	0.866667	0	0,1,0,44	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tct/Gct	S154A	endoR	0.866667	0.866667	1	1	T>G
ERR5749182	20235	PASS	C	T	34992	0.920953	0	12,0,34938,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P205	endoR	0.000596	0.925795	3	2	C>T
ERR5749182	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26856	0.001154	0	26794,0,31,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749182	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	25004	7.6E-4	0	0,24982,0,19	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TA>T
ERR5749182	21764	PASS	ATACATG	A	13685	0.995981	0	53,0,13630,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749182	21990	PASS	TTTA	T	13695	0.997225	0	0,38,10,13647	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749182	22227	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	23850	4.19E-4	0	0,23840,0,10	HIGH	NONE	FRAME_SHIFT	S	tta/	L223	S	0.000419	0.824305	2	2	CT>C
ERR5749182	22280	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ACTTTACTTG	A	23862	5.87E-4	0	2,23846,0,14	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	cttgctttacat/cat	LALH242H	S	0.00046	0.997799	1	1	ACTTTACTTG>A
ERR5749182	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	33138	9.35E-4	3	13914,19166,11,21	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749182	22995	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	13908	0.00151	0	13866,0,40,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aAa	T478K	S	0.000881	0.67268	2	2	C>A
ERR5749182	23063	PASS	A	T	13907	0.864672	0	0,2,0,13836	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749182	23191	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23624	0.001736	0	23569,2,45,0	LOW	SILENT	SYNONYMOUS_CODING	S	ttC/ttT	F543	S	0.000538	0.973337	2	2	C>T
ERR5749182	23271	PASS	C	A	23617	0.925858	0	2,0,23586,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749182	23277	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23616	0.008342	0	23312,2,262,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCt/aTt	T572I	S	0.001007	0.74768	1	1	C>T
ERR5749182	23403	PASS	A	G	23604	0.968988	0	0,3,0,23578	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749182	23593	PASS	G	T	15756	0.883663	0	24,0,15726,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	caG/caT	Q677H	S	0.021779	0.924148	3	2	G>T
ERR5749182	23604	PASS	C	A	15756	0.943958	0	9,0,15736,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749182	23664	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	31227	0.001025	0	15510,15651,17,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCa/gTa	A701V	S	0.000837	0.918	2	2	C>T
ERR5749182	23709	PASS	C	T	15744	0.944042	0	0,5,7,15716	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749182	23817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	32475	0.001139	2	16681,15729,22,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTt/cCt	L752P	S	0.000646	0.066832	1	1	T>C
ERR5749182	24010	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATTTATTGAAGATCTAC	A	16845	5.34E-4	0	160,16680,0,9	HIGH	NONE	FRAME_SHIFT	S	attgaagatctacttttc/	IEDLLF818	S	0.000455	0.926398	4	2	ATTTATTGAAGATCTAC>A
ERR5749182	24506	PASS	T	G	19252	0.975951	0	8,0,19233,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749182	24914	PASS	G	C	31275	0.956355	0	0,0,15579,15669	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749182	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	16760	0.001909	404	16683,21,15,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749182	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	16721	5.98E-4	0	16711,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749182	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	44993	5.78E-4	0	2,44960,0,26	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749182	26158	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	44993	6.22E-4	0	2,44962,0,28	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF3a	gttaat/gat	VN256D	orf3a	0.000297	0.905181	6	2	GTTA>G
ERR5749182	26526	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	12079	0.002235	0	1,12030,0,35	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Gca/Tca	A2S	M	0.001224	0.951192	3	1	G>T
ERR5749182	26768	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13527	0.001479	0	25,13470,0,25	LOW	SILENT	SYNONYMOUS_CODING	M	atC/atT	I82	M	0.001479	0.055024	1	1	C>T
ERR5749182	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	13507	0.001555	0	3,13476,0,21	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749182	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	13507	0.001555	0	3,13483,0,21	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749182	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	13507	0.002517	0	3,13465,0,34	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749182	26958	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	33332	9.6E-4	0	33276,0,33,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Cgt/Tgt	R146C	M	0.00096	0.122326	1	1	C>T
ERR5749182	27297	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21402	0.01869	0	20946,0,431,0	LOW	SILENT	SYNONYMOUS_CODING	ORF6	atC/atT	I32	orf6	0.000978	0.91266	1	1	C>T
ERR5749182	27972	PASS	C	T	10491	0.908588	0	0,0,10388,76	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749182	28048	PASS	G	T	10422	0.916235	0	0,13,0,10400	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749182	28095	PASS	A	T	10443	0.954228	295	9,1,0,10399	HIGH	NONSENSE	STOP_GAINED	ORF8	Aaa/Taa	K68*	orf8	0.002672	0.967672	2	2	A>T
ERR5749182	28111	PASS	A	G	30682	0.977381	0	1,0,20235,10432	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749182	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20218	0.006331	0	20020,2,143,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749182	28270	PASS	TA	T	39243	0.994904	443	192,8,19973,19070	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749182	28280	PASS	G	C	39175	0.937358	38	17,1,20024,19048	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749182	28281	PASS	A	T	39175	0.919413	60	31,3,20013,19048	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749182	28282	PASS	T	A	39177	0.909232	5	27,18,19973,19060	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749182	28406	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTACCCAATA	T	20258	6.42E-4	0	12,20231,0,13	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	N	ttacccaataat/tat	LPNN45Y	N	0.00043	0.921074	3	2	TTACCCAATA>T
ERR5749182	28881	PASS	G	A	20511	0.749793	19	9,1,10081,10098	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749182	28882	PASS	G	A	20507	0.829034	21	13,2,10231,10056	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749182	28883	PASS	G	C	20506	0.94387	3	0,1,10263,10218	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749182	28977	PASS	C	T	10465	0.929384	0	0,2,0,10439	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749182	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	65190	9.82E-4	0	32738,32333,46,44	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749183	239	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTC	T	15935	6.28E-4	0	7919,8008,5,5	.	.	.	.	.	.	.	0.000495	0.25	4	1	TTC>T
ERR5749183	241	PASS	C	T	15933	0.841587	5	2,6,7898,7931	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749183	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	10808	0.002776	0	10779,0,30,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749183	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	10808	0.00148	0	10730,0,16,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749183	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	10808	0.005459	0	10730,0,59,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749183	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10809	0.00185	0	10039,3,640,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749183	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	10809	7.4E-4	0	10798,3,8,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749183	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	10809	7.4E-4	0	10792,3,8,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749183	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	33008	0.001575	8	22140,10810,40,12	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749183	913	PASS	C	T	22173	0.885266	0	0,17,1,22101	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749183	1510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	21703	0.003318	0	0,21349,0,79	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G235	nsp2	0.002159	0.937304	1	1	T>C
ERR5749183	2453	PASS	C	T	17210	0.724695	0	0,17,4,16873	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L550F	nsp2	0.00429	0.842201	2	2	C>T
ERR5749183	3037	PASS	C	T	21372	0.815881	46	3,24,10688,10486	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749183	3267	PASS	C	T	20756	0.969166	0	4,0,20734,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749183	5388	PASS	C	A	6380	0.957524	2147483647	0,0,6378,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749183	5986	PASS	C	T	13666	0.975926	2147483647	0,0,13659,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749183	6954	PASS	T	C	25143	0.802689	0	0,4,3,24962	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749183	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	32028	4.37E-4	46	14823,17191,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749183	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16214	0.002467	0	16143,2,43,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749183	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	16203	0.001296	0	16155,0,35,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749183	11287	PASS	GTCTGGTTTT	G	16211	0.997101	0	0,47,0,16164	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749183	12269	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	24870	4.83E-4	0	24858,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aag/	K61	nsp8	0.000434	0.213333	2	1	GA>G
ERR5749183	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29702	0.001111	1	14842,14773,19,21	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749183	14097	PASS	C	T	14387	0.975533	0	4,0,14353,8	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F219	RdRp	0.000613	0.981481	2	2	C>T
ERR5749183	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12477	0.006492	2147483647	12149,69,2,252	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749183	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	24192	9.09E-4	0	12133,12038,11,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749183	14408	PASS	C	T	24192	0.834739	4	1,3,12093,11869	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749183	14676	PASS	C	T	13347	0.692141	0	5,0,13269,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749183	15279	PASS	C	T	22554	0.895628	0	3,0,22524,2	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749183	15983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	10152	8.87E-4	0	10144,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T850	RdRp	0.000701	0.338235	2	1	TA>T
ERR5749183	16176	PASS	T	C	18789	0.975784	0	0,0,8621,10160	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749183	18501	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29122	0.002816	0	1,28926,0,96	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y154	ExoN	0.000336	0.857143	4	2	C>T
ERR5749183	18504	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	29135	7.89E-4	0	1,28632,0,451	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K155N	ExoN	0.000518	0.094148	4	3	A>C
ERR5749183	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	22841	8.32E-4	0	22822,0,19,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749183	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24158	0.001863	0	24099,0,46,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749183	20481	PASS	A	G	31030	0.956461	103	3,9,0,30963	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcA/tcG	S287	endoR	0.001272	0.966106	1	1	A>G
ERR5749183	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34207	0.001228	3	16754,17047,22,28	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749183	21764	PASS	ATACATG	A	13658	0.997145	0	39,0,13619,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749183	21990	PASS	TTTA	T	13658	0.997657	0	0,32,6,13620	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749183	23063	PASS	A	T	10823	0.848563	0	0,3,0,10774	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749183	23271	PASS	C	A	21640	0.920564	0	1,0,21614,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749183	23403	PASS	A	G	21626	0.957921	0	0,5,0,21599	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749183	23604	PASS	C	A	15506	0.944344	0	12,0,15484,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749183	23709	PASS	C	T	15483	0.919395	0	0,6,3,15437	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749183	24506	PASS	T	G	16803	0.974409	0	9,0,16790,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749183	24914	PASS	G	C	29779	0.956446	0	0,0,14844,14910	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749183	25217	PASS	G	T	7161	0.80324	0	0,43,0,7113	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ggt/Tgt	G1219C	S	0.002444	0.80324	1	1	G>T
ERR5749183	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	24120	0.001907	74	16874,7185,59,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749183	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	28557	0.001086	0	28526,0,31,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749183	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	28795	0.001285	1682	28363,188,106,112	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749183	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	56995	3.33E-4	0	3,56969,0,19	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749183	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	8401	0.001786	0	84,8301,0,15	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749183	26895	PASS	C	T	27285	0.97046	57	8,2,27239,4	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Cat/Tat	H125Y	M	0.000874	0.97046	1	1	C>T
ERR5749183	27461	PASS	G	T	18083	0.916386	2147483647	922,7,551,16599	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	tGt/tTt	C23F	orf7a	0.002221	0.974441	1	1	G>T
ERR5749183	27972	PASS	C	T	10889	0.90045	71	3,4,10767,70	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749183	28048	PASS	G	T	10819	0.909696	0	0,17,1,10795	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749183	28111	PASS	A	G	29588	0.975801	1	4,3,18747,10826	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749183	28270	PASS	TA	T	36066	0.995481	325	161,11,18531,17372	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749183	28280	PASS	G	C	36009	0.933322	11	12,4,18563,17357	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749183	28281	PASS	A	T	36009	0.9113	11	22,10,18554,17358	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749183	28282	PASS	T	A	36011	0.908334	1	13,10,18515,17370	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749183	28881	PASS	G	A	15618	0.744782	6	5,1,7740,7637	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749183	28882	PASS	G	A	15618	0.816558	3	5,2,7829,7612	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749183	28883	PASS	G	C	15617	0.939297	1	4,2,7835,7757	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749183	28977	PASS	C	T	7950	0.915975	0	0,1,5,7922	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749183	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	42736	8.42E-4	0	21478,21201,21,21	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749183	29384	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	8969	0.021407	0	8763,1,199,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gac/Aac	D371N	N	0.009923	0.099057	2	2	G>A
ERR5749183	29384	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GA	8969	0.009923	0	8867,1,89,0	HIGH	NONE	FRAME_SHIFT	N	gac/gaAc	D371E?	N	0.009923	0.099057	2	2	G>GA
ERR5749183	29386	PASS	C	A	8968	0.899197	0	12,0,8915,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaC/gaA	D371E	N	0.000887	0.899197	4	2	C>A
ERR5749183	29386	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	8968	0.005798	0	8907,1,52,0	HIGH	NONE	FRAME_SHIFT	N	aag/aaAg	K373K?	N	0.000887	0.899197	4	2	C>CA
ERR5749184	241	PASS	C	T	46	0.891304	0	0,0,23,23	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749184	645	PASS	G	A	81	0.185185	0	0,66,0,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGt/gAt	G127D	leader	0.004011	0.185185	1	1	G>A
ERR5749184	683	PASS	C	T	81	0.135802	0	0,67,0,14	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L140	leader	0.000316	0.135802	3	2	C>T
ERR5749184	913	PASS	C	T	157	0.910828	2147483647	0,0,0,157	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749184	1676	PASS	G	T	222	0.13964	0	191,0,31,0	HIGH	NONSENSE	STOP_GAINED	ORF1ab	Gaa/Taa	E291*	nsp2	0.13964	0.13964	1	1	G>T
ERR5749184	3037	PASS	C	T	267	0.835206	0	0,0,134,133	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749184	3230	PASS	G	A	384	0.979167	2147483647	0,0,384,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggt/Agt	G171S	nsp3	0.001231	0.979167	2	1	G>A
ERR5749184	3267	PASS	C	T	384	0.966146	2147483647	0,0,383,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749184	5629	PASS	G	T	412	0.917476	2147483647	0,0,412,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acG/acT	T970	nsp3	0.917476	0.917476	1	1	G>T
ERR5749184	5986	PASS	C	T	144	0.986111	2147483647	0,0,144,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749184	6274	PASS	T	C	406	0.990148	2147483647	0,0,406,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taT/taC	Y1185	nsp3	0.000755	0.990148	2	2	T>C
ERR5749184	6954	PASS	T	C	432	0.810185	2147483647	0,0,0,430	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749184	10369	PASS	C	T	814	0.104423	0	0,726,0,88	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	cgC/cgT	R105	3Cpro	0.001225	0.120075	1	1	C>T
ERR5749184	11287	PASS	GTCTGGTTTT	G	751	1.0	2147483647	0,0,0,751	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749184	11674	PASS	C	T	211	0.985782	2147483647	0,0,210,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y234	nsp6	0.00054	0.985782	3	2	C>T
ERR5749184	13356	PASS	C	T	896	0.091518	0	1,809,0,85	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T111I	nsp10	0.000806	0.091518	1	1	C>T
ERR5749184	13665	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13	0.461538	0	7,0,6,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H75	RdRp	0.002046	0.977554	1	1	C>T
ERR5749184	13994	PASS	CT	C	367	0.114441	0	325,0,42,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L186	RdRp	0.000427	0.114441	3	2	CT>C
ERR5749184	14408	PASS	C	T	125	0.832	0	0,0,63,62	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749184	14676	PASS	C	T	96	0.78125	2147483647	0,0,96,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749184	15029	PASS	A	G	45	0.266667	0	33,0,12,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tAt/tGt	Y530C	RdRp	0.00483	0.266667	1	1	A>G
ERR5749184	15279	PASS	C	T	181	0.878453	2147483647	0,0,181,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749184	15396	PASS	CTA	C	180	0.116667	0	0,159,0,21	HIGH	NONE	FRAME_SHIFT	ORF1ab	tataga/	YR653	RdRp	0.000524	0.116667	1	1	CTA>C
ERR5749184	15493	PASS	G	T	181	0.060773	0	0,170,0,11	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gcc/Tcc	A685S	RdRp	0.001408	0.076816	3	2	G>T
ERR5749184	15720	PASS	C	T	669	0.09417	0	0,599,0,70	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D760	RdRp	0.001002	0.917823	1	1	C>T
ERR5749184	15839	PASS	G	T	671	0.074516	0	0,618,0,53	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tGg/tTg	W800L	RdRp	0.001405	0.074516	2	1	G>T
ERR5749184	15983	PASS	TA	T	68	0.338235	0	45,0,23,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T850	RdRp	0.000701	0.338235	2	1	TA>T
ERR5749184	16176	PASS	T	C	27	0.962963	2147483647	0,0,27,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749184	18647	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1348	0.017062	129	952,372,0,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P203L	ExoN	0.000283	0.970507	4	2	C>T
ERR5749184	19113	PASS	C	CT	192	0.125	76	97,73,0,24	HIGH	NONE	FRAME_SHIFT+STOP_GAINED	ORF1ab	aaa/Taaa	K359*?	ExoN	0.000461	0.125	4	3	C>CT
ERR5749184	19114	PASS	A	T	192	0.098958	61	73,96,22,1	HIGH	NONSENSE	STOP_GAINED	ORF1ab	Aaa/Taa	K359*	ExoN	0.00119	0.098958	2	2	A>T
ERR5749184	19151	PASS	CCA	C	97	0.247423	0	0,73,0,24	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749184	19521	PASS	T	C	166	0.957831	2147483647	0,0,0,166	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taT/taC	Y494	ExoN	0.001343	0.957831	1	1	T>C
ERR5749184	19983	PASS	C	CT	22	0.545455	0	10,0,12,0	HIGH	NONE	FRAME_SHIFT+STOP_GAINED	ORF1ab	gat/Tgat	D124*?	endoR	0.000884	0.981982	5	2	C>CT
ERR5749184	21764	PASS	ATACATG	A	570	0.998246	0	1,0,569,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749184	21990	PASS	TTTA	T	570	1.0	2147483647	0,0,0,570	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749184	22344	PASS	G	A	359	0.103064	0	304,0,54,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gGt/gAt	G261D	S	0.003588	0.103064	2	1	G>A
ERR5749184	22771	PASS	AG	A	1419	0.112051	0	0,1260,0,159	HIGH	NONE	FRAME_SHIFT	S	ggt/	G404	S	0.000511	0.112051	3	3	AG>A
ERR5749184	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1729	0.015616	206	282,1420,27,0	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749184	23063	PASS	A	T	309	0.851133	2147483647	0,0,0,309	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749184	23183	PASS	T	C	309	0.135922	0	0,267,0,42	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ttc/Ctc	F541L	S	0.000388	0.135922	2	2	T>C
ERR5749184	23271	PASS	C	A	401	0.9202	2147483647	0,0,400,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749184	23403	PASS	A	G	400	0.975	2147483647	0,0,0,400	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749184	23519	PASS	G	T	288	0.104167	0	256,1,31,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gct/Tct	A653S	S	0.104167	0.104167	1	1	G>T
ERR5749184	23604	PASS	C	A	287	0.923345	2147483647	0,0,287,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749184	23709	PASS	C	T	287	0.944251	0	0,1,0,286	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749184	24506	PASS	T	G	237	0.978903	0	1,0,236,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749184	24914	PASS	G	C	4745	0.964805	0	0,1,2366,2377	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749184	26182	PASS	T	C	803	0.066002	0	0,747,0,55	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Tat/Cat	Y264H	orf3a	0.000999	0.066002	1	1	T>C
ERR5749184	27312	PASS	TA	T	1277	0.081441	0	1173,0,104,0	HIGH	NONE	FRAME_SHIFT	ORF6	aat/	N39	orf6	0.000911	0.088458	4	2	TA>T
ERR5749184	27972	PASS	C	T	117	0.91453	2147483647	0,0,117,0	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749184	28048	PASS	G	T	118	0.940678	2147483647	0,0,0,117	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749184	28095	PASS	A	T	118	0.940678	2147483647	0,0,0,117	HIGH	NONSENSE	STOP_GAINED	ORF8	Aaa/Taa	K68*	orf8	0.002672	0.967672	2	2	A>T
ERR5749184	28111	PASS	A	G	118	0.957627	2147483647	0,0,0,118	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749184	28270	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	5	1.0	0	0,0,3,2	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749184	28280	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	5	1.0	0	0,0,3,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749184	28281	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	5	1.0	0	0,0,3,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749184	28282	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	5	0.8	0	0,0,3,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749184	28881	PASS	G	A	121	0.760331	0	0,0,61,58	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749184	28882	PASS	G	A	121	0.818182	0	0,0,61,60	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749184	28883	PASS	G	C	121	0.950413	0	0,0,61,60	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749184	28977	PASS	C	T	62	0.967742	2147483647	0,0,0,62	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749184	29179	PASS	G	T	568	0.913732	0	1,0,565,1	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccT	P302	N	0.000713	0.913732	2	1	G>T
ERR5749185	186	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7984	0.002255	0	7956,0,18,0	.	.	.	.	.	.	.	0.002255	0.966959	1	1	C>T
ERR5749185	222	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15931	0.002134	0	7935,7918,20,20	.	.	.	.	.	.	.	0.002134	0.864859	1	1	C>T
ERR5749185	241	PASS	C	T	15908	0.86139	0	2,3,7921,7924	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749185	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	10086	9.91E-4	0	10071,3,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749185	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10080	0.00129	0	9475,3,576,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749185	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	10080	0.003968	0	10037,3,40,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749185	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	34422	4.36E-4	2	24309,10093,12,3	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749185	913	PASS	C	T	24306	0.908582	0	0,32,0,24239	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749185	2574	PASS	C	T	40225	0.057651	0	37680,1,2529,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T590I	nsp2	0.000817	0.057651	1	1	C>T
ERR5749185	2702	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	40351	7.93E-4	2471	40013,42,84,116	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F633V	nsp2	0.000632	0.333333	1	1	T>G
ERR5749185	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	80009	0.001525	2147483647	39935,37246,82,2554	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749185	2815	PASS	T	C	40221	0.067104	0	0,37449,0,2745	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaT/gaC	D32	nsp3	0.001668	0.067104	2	2	T>C
ERR5749185	3037	PASS	C	T	20341	0.80822	76	0,25,10176,10003	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749185	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10265	0.001851	512	4,10232,19,4	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749185	3267	PASS	C	T	24811	0.969046	0	2,0,24793,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749185	4280	PASS	G	A	17633	0.87393	0	0,2,2,17554	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gta/Ata	V521I	nsp3	0.002822	0.896067	2	1	G>A
ERR5749185	5388	PASS	C	A	5763	0.954191	2147483647	0,0,5761,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749185	5986	PASS	C	T	13866	0.975552	2147483647	0,0,13860,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749185	6954	PASS	T	C	26007	0.814665	0	0,1,2,25831	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749185	8084	PASS	G	A	28939	0.91375	0	24,0,28867,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E1789K	nsp3	0.000543	0.923413	4	2	G>A
ERR5749185	8084	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GA	28938	0.020423	0	28341,0,591,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctc/Actc	L1791T?	nsp3	0.000543	0.923413	4	2	G>GA
ERR5749185	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	16455	9.12E-4	0	16431,9,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749185	9559	PASS	C	T	16455	0.062899	0	15283,9,1135,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y335	nsp4	0.001348	0.062899	2	2	C>T
ERR5749185	10323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	19445	0.00108	0	0,19378,0,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749185	10595	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	19283	0.001348	0	2,19218,0,29	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F181L	3Cpro	0.000964	0.076408	1	1	T>C
ERR5749185	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	23832	0.00235	0	23185,4,56,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749185	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	23823	0.002057	0	23739,0,70,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749185	11104	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	23816	9.66E-4	0	23670,0,25,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccT/ccC	P44	nsp6	0.000866	0.675414	2	1	T>C
ERR5749185	11287	PASS	GTCTGGTTTT	G	23817	0.998446	0	0,37,0,23780	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749185	12459	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	48717	0.002484	28	19768,28814,67,54	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T123I	nsp8	0.000658	0.986093	1	1	C>T
ERR5749185	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34046	0.001498	0	16996,16952,30,31	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749185	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10561	0.004734	2777	10300,95,2,157	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749185	14408	PASS	C	T	20508	0.848303	6	0,2,10248,10132	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749185	14676	PASS	C	T	15180	0.773452	0	3,0,15136,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749185	15279	PASS	C	T	23846	0.822779	0	4,0,23777,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749185	16176	PASS	T	C	21090	0.980133	0	0,0,9234,11849	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749185	17615	PASS	A	G	17001	0.874537	0	0,1,0,16940	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749185	18171	PASS	C	T	24106	0.892019	0	2,3,11986,12037	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G44	ExoN	0.000859	0.892019	1	1	C>T
ERR5749185	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	25816	5.04E-4	0	25803,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749185	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30535	0.001965	0	30445,0,66,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749185	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	40468	0.002595	0	19813,20155,58,61	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749185	21764	PASS	ATACATG	A	13617	0.996181	0	52,0,13565,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749185	21990	PASS	TTTA	T	13621	0.997284	0	0,37,1,13583	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749185	22388	PASS	C	T	10124	0.949921	2147483647	0,0,10080,0	LOW	SILENT	SYNONYMOUS_CODING	S	Cta/Tta	L276	S	0.003317	0.950604	1	1	C>T
ERR5749185	23063	PASS	A	T	52	0.865385	2147483647	0,0,0,51	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749185	23271	PASS	C	A	25782	0.919052	0	2,0,25748,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749185	23403	PASS	A	G	25756	0.964241	0	0,2,0,25730	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749185	23604	PASS	C	A	16712	0.940163	0	18,0,16684,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749185	23709	PASS	C	T	16693	0.938178	0	0,5,0,16665	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749185	23817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	36579	9.02E-4	34	19820,16699,30,6	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTt/cCt	L752P	S	0.000646	0.066832	1	1	T>C
ERR5749185	24506	PASS	T	G	20030	0.973689	0	8,0,20013,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749185	24914	PASS	G	C	38731	0.960135	0	0,0,19310,19402	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749185	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	27171	0.001141	52	19564,7558,39,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749185	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	24345	0.001191	1070	23983,136,124,76	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749185	26228	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	66238	6.49E-4	13	13890,52258,9,67	.	.	.	.	.	.	.	0.000649	0.94873	2	1	C>A
ERR5749185	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	13300	9.02E-4	0	0,13288,0,12	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749185	27128	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	35035	9.99E-4	0	0,34987,0,35	LOW	SILENT	SYNONYMOUS_CODING	M	ggC/ggT	G202	M	0.000719	0.147659	1	1	C>T
ERR5749185	27384	PASS	T	C	20914	0.063307	0	6,19384,0,1458	LOW	SILENT	SYNONYMOUS_CODING	ORF6	gaT/gaC	D61	orf6	0.00154	0.931035	3	3	T>C
ERR5749185	27476	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	45452	0.017139	0	24056,20565,440,375	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	aCa/aTa	T28I	orf7a	0.000547	0.22827	4	2	C>T
ERR5749185	27643	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24480	0.002206	0	24401,7,59,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Cct/Tct	P84S	orf7a	0.00166	0.858006	2	1	C>T
ERR5749185	27972	PASS	C	T	11600	0.902672	0	0,0,11496,62	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749185	28001	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	23045	0.001041	0	11502,11496,15,15	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ccG/ccA	P36	orf8	0.00085	0.830607	2	1	G>A
ERR5749185	28048	PASS	G	T	11538	0.924424	0	0,17,0,11514	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749185	28111	PASS	A	G	37348	0.977375	0	6,2,25785,11540	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749185	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25785	0.001435	0	25674,8,39,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749185	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	25781	8.15E-4	0	25756,8,21,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749185	28270	PASS	TA	T	49990	0.994839	533	251,15,25455,24277	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749185	28280	PASS	G	C	49895	0.938431	18	14,3,25511,24252	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749185	28281	PASS	A	T	49895	0.91434	40	34,8,25492,24253	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749185	28282	PASS	T	A	49903	0.91259	5	38,27,25440,24267	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749185	28881	PASS	G	A	20479	0.778456	3	2,0,10183,10054	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749185	28882	PASS	G	A	20479	0.822257	24	12,1,10245,10010	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749185	28883	PASS	G	C	20479	0.946579	9	0,3,10265,10194	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749185	28977	PASS	C	T	10414	0.926157	0	0,5,0,10393	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749185	29095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	32106	0.00109	0	32044,2,35,0	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F274	N	0.000792	0.961279	2	2	C>T
ERR5749185	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	63712	8.32E-4	0	32009,31605,34,34	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749185	29402	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	11391	0.002634	0	11352,0,37,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Tat	D377Y	N	0.002634	0.94235	1	1	G>T
ERR5749185	29733	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9499	0.004527	0	2,9437,0,49	.	.	.	.	.	.	.	0.001821	0.915943	2	1	C>T
ERR5749185	29774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9505	0.002525	0	0,9471,0,24	.	.	.	.	.	.	.	0.002525	0.973955	1	1	C>T
ERR5749186	241	PASS	C	T	23970	0.872549	0	2,2,11924,11955	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749186	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	14592	0.004592	0	14512,10,67,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749186	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	14595	9.59E-4	0	14412,15,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749186	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	14595	0.001576	0	14412,15,23,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749186	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	14595	0.008428	0	14412,15,123,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749186	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	14583	0.001509	2	13340,17,934,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749186	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	14583	0.002537	0	14526,19,37,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749186	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	14582	0.001029	0	14518,16,15,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttatg/gtg	VM84V	leader	0.000554	0.991848	4	1	GTTA>G
ERR5749186	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	14582	0.001852	52	14518,16,24,3	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749186	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	14583	0.001234	0	14539,21,18,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749186	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	44989	4.45E-4	21	30380,14589,19,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749186	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	44990	7.33E-4	14	30277,14559,28,5	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749186	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	44990	0.002467	18	30277,14559,87,24	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749186	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30376	0.00135	0	3,30288,0,45	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749186	913	PASS	C	T	30377	0.921618	0	0,20,3,30312	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749186	2305	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTAAATAAATTTTTGGCTTTGTGTGCTGACTCTATCATTATTGGTGGAGCTAAACTTAAAGC	G	18586	5.38E-4	0	18576,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtaaataaatttttggctttgtgtgctgactctatcattattggtggagctaaacttaaagccttg/	VNKFLALCADSIIIGGAKLKAL502	nsp2	0.000443	0.070409	4	3	GCTTGTAAATAAATTTTTGGCTTTGTGTGCTGACTCTATCATTATTGGTGGAGCTAAACTTAAAGC>G
ERR5749186	2702	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	47514	6.95E-4	2507	47177,50,68,113	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F633V	nsp2	0.000632	0.333333	1	1	T>G
ERR5749186	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	94312	0.001272	2147483647	47053,44019,90,2901	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749186	3037	PASS	C	T	25452	0.810467	70	0,23,12728,12523	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749186	3267	PASS	C	T	31132	0.96971	0	1,0,31110,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749186	3671	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	31499	8.89E-4	0	15722,15562,15,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E318K	nsp3	0.000351	0.0625	6	2	G>A
ERR5749186	4255	PASS	G	A	53126	0.827674	37	28,6,26427,26256	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccG/ccA	P512	nsp3	0.001102	0.871853	2	1	G>A
ERR5749186	4578	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTAACGATC	T	21996	5.91E-4	0	0,21983,0,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	aacgatctaaat/	NDLN621	nsp3	0.000519	0.082979	2	2	TTAACGATC>T
ERR5749186	4980	PASS	C	T	38661	0.977652	0	0,1,15947,22708	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T754I	nsp3	0.005479	0.982571	1	1	C>T
ERR5749186	5388	PASS	C	A	8295	0.956118	2147483647	0,0,8293,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749186	5986	PASS	C	T	16054	0.973714	2147483647	0,0,16039,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749186	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15483	0.001163	0	9,15307,0,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749186	6954	PASS	T	C	28814	0.818942	0	0,5,3,28662	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749186	7070	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	51967	8.47E-4	92	22994,28916,43,6	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggc/Tgc	G1451C	nsp3	0.000698	0.101434	3	1	G>T
ERR5749186	7113	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23058	0.014312	0	22660,16,357,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T1465I	nsp3	0.001129	0.920551	1	1	C>T
ERR5749186	8218	PASS	T	C	35400	0.947345	0	0,17,0,35368	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtT/gtC	V1833	nsp3	0.939174	0.947345	1	1	T>C
ERR5749186	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	44355	0.002345	297	22871,21378,104,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749186	10642	PASS	G	A	24177	0.951979	0	0,6,0,24130	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acG/acA	T196	3Cpro	0.001264	0.951979	3	1	G>A
ERR5749186	11073	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TC	T	31195	3.85E-4	0	31181,2,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttc/	F34	nsp6	0.000385	0.092251	6	2	TC>T
ERR5749186	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	31176	0.001957	0	31065,0,97,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749186	11287	PASS	GTCTGGTTTT	G	31171	0.995252	69	3,148,0,31023	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749186	11355	PASS	C	T	49893	0.982262	6	4,2,18688,31195	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCa/gTa	A128V	nsp6	0.000455	0.982262	3	2	C>T
ERR5749186	11507	PASS	G	A	37149	0.906135	5	9,4,18573,18424	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Att	V179I	nsp6	0.007744	0.914418	2	2	G>A
ERR5749186	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	51504	7.77E-4	0	32758,18673,26,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749186	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	48997	0.001408	0	24469,24392,40,41	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749186	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	13880	0.004755	2147483647	13498,149,4,223	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749186	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	26866	0.002531	0	13460,13356,35,33	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749186	14408	PASS	C	T	26866	0.841175	1	2,3,13397,13232	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749186	14676	PASS	C	T	18562	0.73268	0	4,0,18488,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749186	15279	PASS	C	T	28841	0.89397	0	3,0,28800,2	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749186	15411	PASS	T	C	28782	0.952192	0	0,3,0,28763	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaT/aaC	N657	RdRp	0.00222	0.952192	2	2	T>C
ERR5749186	16176	PASS	T	C	27768	0.981417	10	3,0,12551,15202	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749186	16647	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	34246	7.59E-4	0	7,34016,0,28	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acG/acA	T137	helicase	0.000746	0.885245	2	1	G>A
ERR5749186	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	32034	7.8E-4	0	32008,0,25,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749186	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	36265	0.004026	0	36069,7,156,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749186	20091	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	36182	3.87E-4	0	9,36159,0,14	HIGH	NONE	FRAME_SHIFT	ORF1ab	caa/Acaa	Q159T?	endoR	0.000368	0.051583	1	1	C>CA
ERR5749186	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	38289	7.84E-4	0	38202,0,31,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749186	20844	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	71006	3.38E-4	1	32691,38281,10,14	HIGH	NONE	FRAME_SHIFT	ORF1ab	tataat/	YN63	MethTr	0.000293	0.905571	5	2	CTA>C
ERR5749186	20987	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	65208	2.76E-4	0	32616,32575,9,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L111	MethTr	0.000276	0.056129	4	2	CT>C
ERR5749186	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	47759	0.001131	0	23323,23817,30,31	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749186	21764	PASS	ATACATG	A	17808	0.995676	0	76,0,17731,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749186	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	17807	6.74E-4	0	17795,0,12,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749186	21990	PASS	TTTA	T	17819	0.998372	0	0,29,8,17782	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749186	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	22363	0.001655	0	0,22312,0,38	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749186	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	40419	8.16E-4	0	18017,22342,15,19	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749186	23063	PASS	A	T	18015	0.864002	0	0,4,1,17920	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749186	23271	PASS	C	A	32129	0.925675	0	3,0,32096,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749186	23403	PASS	A	G	32113	0.970386	0	0,3,0,32087	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749186	23604	PASS	C	A	21113	0.922891	0	26,0,21074,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749186	23709	PASS	C	T	21101	0.935738	0	0,2,12,21052	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749186	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	44123	4.53E-4	25	22987,21116,17,3	HIGH	NONE	FRAME_SHIFT	S	ttg/	L753	S	0.000334	0.080808	2	2	CT>C
ERR5749186	24127	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	40493	3.95E-4	2	17499,22995,8,8	HIGH	NONE	FRAME_SHIFT	S	aac/	N856	S	0.000324	0.111888	4	1	TA>T
ERR5749186	24506	PASS	T	G	25494	0.971523	0	11,0,25478,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749186	24794	PASS	G	T	26902	0.957884	2147483647	0,0,26878,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gct/Tct	A1078S	S	0.001791	0.957884	1	1	G>T
ERR5749186	24914	PASS	G	C	53422	0.958388	0	0,1,26599,26770	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749186	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	35939	0.001169	65	25947,9937,48,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749186	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	29074	0.001376	477	28966,22,21,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749186	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	29031	7.58E-4	0	29009,0,22,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749186	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	66008	4.24E-4	0	0,65980,0,28	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749186	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	17752	0.001183	0	5,17715,0,21	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749186	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	17752	9.58E-4	0	4,17730,0,17	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749186	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	17754	0.003492	0	3,17681,0,62	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749186	26936	PASS	C	T	44315	0.956087	0	10,0,44246,2	LOW	SILENT	SYNONYMOUS_CODING	M	ctC/ctT	L138	M	0.001308	0.968147	2	1	C>T
ERR5749186	27972	PASS	C	T	13692	0.914841	19	1,1,13577,72	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749186	28048	PASS	G	T	13637	0.918164	0	0,21,0,13605	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749186	28111	PASS	A	G	47595	0.978296	18	5,8,33917,13641	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749186	28270	PASS	TA	T	65689	0.994748	838	348,11,33439,31905	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749186	28280	PASS	G	C	65549	0.93797	23	20,5,33487,31872	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749186	28281	PASS	A	T	65549	0.911806	109	67,9,33475,31876	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749186	28282	PASS	T	A	65560	0.906223	14	52,31,33386,31888	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749186	28406	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTACCCAATA	T	33978	4.41E-4	0	36,33923,0,15	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	N	ttacccaataat/tat	LPNN45Y	N	0.00043	0.921074	3	2	TTACCCAATA>T
ERR5749186	28407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TACCCAATA	T	33982	5.3E-4	0	36,33928,0,18	HIGH	NONE	FRAME_SHIFT	N	cccaataat/	PNN46	N	0.000382	0.179673	1	1	TACCCAATA>T
ERR5749186	28881	PASS	G	A	27745	0.740314	66	26,1,13618,13654	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749186	28882	PASS	G	A	27743	0.822081	51	18,0,13845,13621	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749186	28883	PASS	G	C	27744	0.941357	1	3,4,13880,13831	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749186	28977	PASS	C	T	14167	0.928708	0	0,3,0,14123	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749186	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	59367	9.77E-4	278	45143,14102,8,59	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749186	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	89677	0.001327	0	45043,44459,75,73	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749187	71	PASS	C	T	465	0.092473	0	422,0,43,0	.	.	.	.	.	.	.	0.002088	0.926791	2	1	C>T
ERR5749187	210	PASS	G	T	262	0.759542	0	4,0,254,4	.	.	.	.	.	.	.	0.001452	1	2	1	G>T
ERR5749187	241	PASS	C	T	513	0.875244	0	0,0,256,256	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749187	913	PASS	C	T	1571	0.910885	2147483647	0,0,0,1567	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749187	1190	PASS	C	T	1606	0.879826	2147483647	0,0,0,1602	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cca/Tca	P129S	nsp2	0.002242	0.938547	1	1	C>T
ERR5749187	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	3982	0.002511	245	1983,1881,6,105	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749187	2890	PASS	G	A	485	0.983505	2147483647	0,0,485,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtG/gtA	V57	nsp3	0.934783	0.983505	1	1	G>A
ERR5749187	3037	PASS	C	T	964	0.824689	3	0,1,481,476	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749187	3267	PASS	C	T	1434	0.966527	0	1,0,1432,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749187	5388	PASS	C	A	258	0.957364	2147483647	0,0,258,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749187	5986	PASS	C	T	1127	0.974268	2147483647	0,0,1127,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749187	6741	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGT	G	923	0.008667	0	0,915,0,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	tgt/	C1342	nsp3	0.001093	0.204082	3	2	GGT>G
ERR5749187	6954	PASS	T	C	2792	0.825573	2147483647	0,0,0,2775	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749187	10386	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5535	0.00813	101	2278,3211,0,45	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T111I	3Cpro	0.000642	0.160456	4	2	C>T
ERR5749187	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	6284	0.012094	0	5970,0,76,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749187	11287	PASS	GTCTGGTTTT	G	6284	0.999045	0	0,6,0,6278	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749187	11417	PASS	G	T	550	0.943636	2147483647	0,0,550,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Ttt	V149F	nsp6	0.00274	0.951155	2	2	G>T
ERR5749187	11750	PASS	C	T	6598	0.701576	3	0,1,3397,2910	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L260F	nsp6	0.001019	0.70989	2	1	C>T
ERR5749187	13164	PASS	C	T	3754	0.952318	0	1,0,3751,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T47I	nsp10	0.001249	0.952318	1	1	C>T
ERR5749187	14408	PASS	C	T	253	0.841897	0	0,0,126,126	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749187	14676	PASS	C	T	1026	0.765107	2147483647	0,0,1025,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749187	15279	PASS	C	T	1491	0.865191	2147483647	0,0,1487,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749187	16176	PASS	T	C	1482	0.981107	0	0,0,295,1187	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749187	16575	PASS	C	T	6069	0.806723	2147483647	0,0,6044,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D113	helicase	0.001088	0.827968	1	1	C>T
ERR5749187	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	9058	0.001435	0	9045,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749187	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	722	0.018006	0	708,0,14,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749187	21516	PASS	C	T	3226	0.905456	2147483647	0,0,3220,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N286	MethTr	0.000412	0.905456	2	2	C>T
ERR5749187	21764	PASS	ATACATG	A	2155	0.996288	0	8,0,2147,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749187	21990	PASS	TTTA	T	2158	0.987488	0	0,27,3,2128	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749187	23063	PASS	A	T	1732	0.860277	2147483647	0,0,0,1725	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749187	23271	PASS	C	A	1557	0.938343	2147483647	0,0,1554,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749187	23403	PASS	A	G	1556	0.969794	2147483647	0,0,0,1555	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749187	23604	PASS	C	A	1874	0.94397	0	2,0,1872,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749187	23709	PASS	C	T	1874	0.935432	2147483647	0,0,0,1870	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749187	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	2774	0.003244	14	899,1866,0,9	HIGH	NONE	FRAME_SHIFT	S	ttg/	L753	S	0.000334	0.080808	2	2	CT>C
ERR5749187	24506	PASS	T	G	3835	0.970795	0	2,0,3832,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749187	24712	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	3842	0.005726	0	5,3808,0,28	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	atG/atA	M1050I	S	0.005726	0.796995	2	1	G>A
ERR5749187	24914	PASS	G	C	7606	0.959243	0	0,0,3789,3815	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749187	25350	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	7519	0.007847	0	7458,1,60,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCa/cAa	P1263Q	S	0.000626	0.97904	4	2	C>A
ERR5749187	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	533	0.02439	185	507,13,0,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749187	27798	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	5965	0.006538	0	0,5917,0,41	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7b	Gcc/Acc	A15T	orf7b	0.002041	0.051256	2	1	G>A
ERR5749187	27916	PASS	G	A	462	0.101732	0	411,0,51,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	gGa/gAa	G8E	orf8	0.101732	0.101732	1	1	G>A
ERR5749187	27972	PASS	C	T	460	0.915217	0	0,0,459,1	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749187	28048	PASS	G	T	461	0.904555	2147483647	0,0,0,461	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749187	28095	PASS	A	T	464	0.967672	50	2,0,0,462	HIGH	NONSENSE	STOP_GAINED	ORF8	Aaa/Taa	K68*	orf8	0.002672	0.967672	2	2	A>T
ERR5749187	28111	PASS	A	G	10751	0.978607	0	2,0,10284,462	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749187	28270	PASS	TA	T	19945	0.995036	191	94,7,10151,9695	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749187	28280	PASS	G	C	19906	0.934542	21	8,0,10135,9656	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749187	28280	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	19906	0.001608	11	10189,9681,11,21	HIGH	NONE	FRAME_SHIFT	N	gat/	D3	N	0.001608	1	2	2	GA>G
ERR5749187	28281	PASS	A	T	19906	0.909726	10	10,3,10114,9637	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749187	28282	PASS	T	A	19908	0.906671	0	58,58,10094,9644	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749187	28881	PASS	G	A	655	0.754198	0	0,0,324,317	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749187	28882	PASS	G	A	655	0.850382	0	0,0,328,325	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749187	28883	PASS	G	C	655	0.937405	3	0,1,330,324	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749187	28977	PASS	C	T	332	0.951807	2147483647	0,0,0,331	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749187	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	6485	0.003855	0	3246,3210,15,13	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749187	29555	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2440	0.006557	22	722,1698,0,17	.	.	.	.	.	.	.	0.000611	0.957048	3	1	C>T
ERR5749187	29757	PASS	G	T	723	0.881051	0	0,1,0,721	.	.	.	.	.	.	.	0.840856	0.933071	1	1	G>T
ERR5749188	241	PASS	C	T	27646	0.862584	3	0,2,13765,13775	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749188	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	8451	0.002367	0	7811,2,632,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749188	913	PASS	C	T	26391	0.90709	0	0,14,0,26350	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749188	1368	PASS	T	C	25865	0.940189	0	4,0,25818,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTt/aCt	I188T	nsp2	0.925045	0.945837	1	1	T>C
ERR5749188	1510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	25843	0.00236	0	0,25520,0,70	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G235	nsp2	0.002159	0.937304	1	1	T>C
ERR5749188	3037	PASS	C	T	16700	0.812156	36	0,12,8345,8204	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749188	3267	PASS	C	T	24932	0.968514	0	1,0,24920,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749188	3877	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	31374	0.001243	0	28600,0,2761,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcG	A386	nsp3	0.000588	0.960227	2	1	T>G
ERR5749188	5388	PASS	C	A	4603	0.971758	2147483647	0,0,4600,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749188	5497	PASS	C	T	4597	0.888623	0	0,5,0,4583	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C926	nsp3	0.000964	0.897745	3	2	C>T
ERR5749188	5784	PASS	C	T	47110	0.903566	5	4,9,23300,23732	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T1022I	nsp3	0.001294	0.919357	2	1	C>T
ERR5749188	5986	PASS	C	T	11284	0.975895	0	1,0,11278,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749188	6954	PASS	T	C	24855	0.820801	0	0,1,0,24720	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749188	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	34604	0.001243	171	13749,20812,43,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749188	9661	PASS	C	T	27058	0.912004	40	4,24,13737,13222	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F369	nsp4	0.000584	0.920378	2	2	C>T
ERR5749188	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23756	0.001263	0	23704,1,31,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749188	11287	PASS	GTCTGGTTTT	G	23746	0.998189	0	0,43,0,23703	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749188	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	15073	0.001725	0	15027,0,26,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749188	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	39799	0.001281	0	19880,19826,28,30	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749188	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10526	0.004465	2147483647	10252,86,3,184	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749188	14408	PASS	C	T	20404	0.840963	0	0,0,10196,10051	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749188	14676	PASS	C	T	15794	0.724642	0	11,0,15726,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749188	15279	PASS	C	T	27964	0.879309	0	4,0,27919,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749188	16176	PASS	T	C	19822	0.981031	0	0,0,7383,12433	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749188	18403	PASS	A	G	35674	0.978191	0	16,0,35637,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Aca/Gca	T122A	ExoN	0.975463	0.978459	1	1	A>G
ERR5749188	18756	PASS	G	T	20775	0.928905	0	25,0,20713,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccG/ccT	P239	ExoN	0.000392	0.942688	3	2	G>T
ERR5749188	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26790	0.002277	0	26713,0,63,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749188	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26843	8.57E-4	0	26783,0,23,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749188	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GTT	36739	0.001606	182	18337,17571,0,59	HIGH	NONE	FRAME_SHIFT	S	ctt/TTctt	L5F?	S	0.000394	0.091869	4	1	G>GTT
ERR5749188	21575	PASS	C	T	35651	0.858433	3	0,2,16922,18181	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749188	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	35634	0.003368	344	17220,18295,0,120	HIGH	NONE	FRAME_SHIFT	S	gtt/Tgtt	V6C?	S	0.000619	0.877942	3	2	C>CT
ERR5749188	21764	PASS	ATACATG	A	10613	0.995948	0	43,0,10570,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749188	21990	PASS	TTTA	T	10619	0.997928	0	0,22,7,10590	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749188	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	17293	0.001157	0	1,17259,0,20	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749188	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29354	8.52E-4	12	12049,17273,6,21	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749188	23063	PASS	A	T	12028	0.850765	0	0,2,0,11961	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749188	23271	PASS	C	A	26737	0.921906	0	3,0,26715,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749188	23403	PASS	A	G	26722	0.969201	0	0,5,0,26703	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749188	23604	PASS	C	A	13421	0.93771	0	13,0,13398,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749188	23709	PASS	C	T	13405	0.937934	0	0,6,0,13382	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749188	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	35747	3.92E-4	0	22316,13417,9,5	HIGH	NONE	FRAME_SHIFT	S	ttg/	L753	S	0.000334	0.080808	2	2	CT>C
ERR5749188	23817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	35747	8.11E-4	0	22292,13400,18,12	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTt/cCt	L752P	S	0.000646	0.066832	1	1	T>C
ERR5749188	24382	PASS	C	T	10269	0.90856	0	0,3,0,10243	LOW	SILENT	SYNONYMOUS_CODING	S	tcC/tcT	S940	S	0.002118	0.920404	2	1	C>T
ERR5749188	24506	PASS	T	G	21933	0.974924	0	4,0,21925,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749188	24914	PASS	G	C	29755	0.955033	0	0,0,14828,14899	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749188	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	23827	9.65E-4	42	15140,8643,28,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749188	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	32655	0.001194	455	32536,13,24,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749188	25685	PASS	C	T	32624	0.964351	0	1,0,32601,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	gCt/gTt	A98V	orf3a	0.002048	0.964351	1	1	C>T
ERR5749188	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	32841	0.001462	1578	32339,174,177,111	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749188	26461	PASS	C	T	14679	0.920907	0	0,9,0,14630	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	Ctt/Ttt	L73F	E	0.001401	0.928597	1	1	C>T
ERR5749188	27972	PASS	C	T	9758	0.904899	40	2,2,9680,35	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749188	28048	PASS	G	T	9725	0.91126	0	0,18,0,9706	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749188	28111	PASS	A	G	34954	0.979773	3	7,1,25205,9731	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749188	28270	PASS	TA	T	48677	0.994926	535	243,12,24871,23559	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749188	28271	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AA	A	48670	5.34E-4	74	25076,23573,26,0	.	.	.	.	.	.	.	0.000482	0.924941	3	2	AA>A
ERR5749188	28280	PASS	G	C	48587	0.93842	10	13,5,24957,23543	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749188	28281	PASS	A	T	48587	0.907074	25	29,9,24920,23543	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749188	28282	PASS	T	A	48587	0.910182	43	29,5,24888,23560	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749188	28881	PASS	G	A	21726	0.779711	15	6,0,10821,10667	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749188	28882	PASS	G	A	21725	0.82771	16	9,1,10882,10619	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749188	28883	PASS	G	C	21727	0.942698	0	1,1,10896,10812	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749188	28977	PASS	C	T	11065	0.927429	0	0,3,0,11039	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749188	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	33459	0.001166	122	22366,11031,5,36	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749188	29140	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	22382	9.83E-4	28	22344,0,31,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	caG/caT	Q289H	N	0.000955	0.888232	2	1	G>T
ERR5749188	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	44405	0.001126	0	22315,22018,29,29	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749189	241	PASS	C	T	1711	0.845704	0	0,1,853,853	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749189	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	6439	0.004814	0	6408,0,31,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749189	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	6439	0.001398	0	6373,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749189	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	6439	0.001398	0	6373,0,9,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749189	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	6439	0.007144	0	6373,0,46,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749189	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	6434	0.002331	0	5853,0,456,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749189	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	6434	0.001865	0	6422,0,12,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749189	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	6433	0.001865	0	6417,0,12,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749189	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	18480	6.49E-4	19	12020,6448,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749189	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	18480	0.002706	28	11980,6440,43,7	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749189	913	PASS	C	T	12024	0.890136	0	0,6,0,11982	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749189	2706	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	33238	9.03E-4	0	16690,16496,21,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T634I	nsp2	0.000591	0.821437	1	1	C>T
ERR5749189	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	33264	0.002225	2147483647	16593,15271,33,1269	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749189	3037	PASS	C	T	7597	0.796235	18	0,6,3798,3734	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749189	3267	PASS	C	T	10104	0.967439	2147483647	0,0,10097,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749189	5100	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6785	0.002948	0	6754,1,20,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCa/tTa	S794L	nsp3	0.001443	0.071429	2	2	C>T
ERR5749189	5388	PASS	C	A	2807	0.952618	0	2,0,2802,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749189	5986	PASS	C	T	6842	0.972523	0	1,0,6836,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749189	6091	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6820	0.002493	0	8,6776,0,17	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N1124	nsp3	0.002493	0.918485	2	2	C>T
ERR5749189	6954	PASS	T	C	9076	0.85985	0	0,1,0,9037	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749189	7674	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CGA	C	13310	0.001127	0	13293,2,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gac/	D1654	nsp3	0.000682	0.109264	3	2	CGA>C
ERR5749189	8137	PASS	G	T	10519	0.760909	0	118,0,10391,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtG/gtT	V1806	nsp3	0.002602	0.762515	2	1	G>T
ERR5749189	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	13203	8.33E-4	11	9830,3362,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749189	10323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	12396	0.004276	0	0,12313,0,56	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749189	10387	PASS	T	C	22971	0.97375	2	7,6,10558,12391	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T111	3Cpro	0.00094	0.973895	1	1	T>C
ERR5749189	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12227	0.001636	0	12184,1,22,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749189	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	12222	0.0018	0	12189,0,31,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749189	11287	PASS	GTCTGGTTTT	G	12220	0.99689	0	0,38,0,12182	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749189	11575	PASS	C	T	7093	0.912731	32	1,3,0,7064	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F201	nsp6	0.912731	0.921085	1	1	C>T
ERR5749189	12854	PASS	C	T	8015	0.95209	0	1,0,8005,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cct/Tct	P57S	nsp9	0.028995	0.95209	1	1	C>T
ERR5749189	13459	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTT	G	11426	7.88E-4	0	11410,0,9,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ttttta/tta	FL7L	nsp11	0.000691	0.060726	5	2	GTTT>G
ERR5749189	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22813	9.64E-4	0	11395,11372,12,13	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749189	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	2495	0.006012	742	2431,19,1,42	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749189	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	4820	0.001245	1	2424,2392,4,2	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749189	14408	PASS	C	T	4820	0.846888	12	0,4,2408,2362	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749189	14676	PASS	C	T	7946	0.762019	0	2,0,7923,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749189	15279	PASS	C	T	10255	0.879571	0	1,0,10236,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749189	15983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	6768	0.001625	0	6757,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T850	RdRp	0.000701	0.338235	2	1	TA>T
ERR5749189	16176	PASS	T	C	11556	0.979664	18	0,9,4777,6765	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749189	17356	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GATGAAATT	G	10343	8.7E-4	0	0,10334,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	gatgaaatt/	DEI374	helicase	0.00087	0.057034	1	1	GATGAAATT>G
ERR5749189	17562	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	18279	0.002024	4	9127,9097,28,21	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	cgG/cgT	R442	helicase	0.000543	0.90562	3	2	G>T
ERR5749189	17615	PASS	A	G	9149	0.917805	2147483647	0,0,0,9133	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749189	18457	PASS	C	A	16750	0.738806	0	2,0,16630,6	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cca/Aca	P140T	ExoN	0.001253	0.951352	2	1	C>A
ERR5749189	18658	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	19249	5.2E-4	0	19229,8,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tgt/	C207	ExoN	0.000507	0.115741	3	2	TG>T
ERR5749189	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	19237	9.88E-4	0	19218,0,19,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749189	18803	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	38388	0.001172	3	19113,19076,81,90	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aGc/aTc	S255I	ExoN	0.000786	0.897116	2	1	G>T
ERR5749189	19023	PASS	T	A	13348	0.951004	0	2,0,13343,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtT/gtA	V328	ExoN	0.001259	0.951351	2	1	T>A
ERR5749189	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11228	0.001425	0	11205,0,16,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749189	20951	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	11864	9.27E-4	0	11853,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gat/	D99	MethTr	0.000431	0.138667	3	3	CAG>C
ERR5749189	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	11863	7.59E-4	0	0,11853,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TA>T
ERR5749189	21305	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	18301	0.001202	0	0,18264,0,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cGc/cAc	R216H	MethTr	0.000727	0.703943	1	1	G>A
ERR5749189	21658	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	6719	0.002084	25	0,6700,1,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	ttC/ttA	F32L	S	0.001649	0.937508	2	2	C>A
ERR5749189	21764	PASS	ATACATG	A	8383	0.996779	0	26,0,8356,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749189	21990	PASS	TTTA	T	8385	0.997615	0	0,20,2,8363	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749189	23063	PASS	A	T	8454	0.839957	0	0,2,0,8405	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749189	23271	PASS	C	A	13354	0.915756	0	3,0,13336,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749189	23277	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13354	0.001647	0	13310,0,26,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCt/aTt	T572I	S	0.001007	0.74768	1	1	C>T
ERR5749189	23294	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	13354	0.001797	0	13320,0,33,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gat/Tat	D578Y	S	0.001754	0.102649	2	1	G>T
ERR5749189	23403	PASS	A	G	13355	0.973867	0	0,0,5,13343	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749189	23604	PASS	C	A	9464	0.935651	0	6,0,9453,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749189	23709	PASS	C	T	9454	0.937593	0	0,3,0,9437	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749189	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	15980	8.14E-4	0	6508,9459,5,8	HIGH	NONE	FRAME_SHIFT	S	ttg/	L753	S	0.000334	0.080808	2	2	CT>C
ERR5749189	24506	PASS	T	G	10032	0.972687	0	5,0,10024,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749189	24914	PASS	G	C	29488	0.959204	0	0,0,14696,14761	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749189	25019	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	20836	0.004127	0	5970,14770,27,68	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gat/Tat	D1153Y	S	0.00048	0.981297	3	2	G>T
ERR5749189	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	5673	0.004054	386	5632,12,6,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749189	25710	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5642	0.002127	0	5622,0,15,0	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	ctC/ctT	L106	orf3a	0.002127	0.789778	2	2	C>T
ERR5749189	26060	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGG	C	23967	4.59E-4	0	23957,0,11,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF3a	ggtgtt/gtt	GV224V	orf3a	0.000459	0.822477	2	2	CTGG>C
ERR5749189	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	23908	6.27E-4	0	0,23893,0,15	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749189	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	8943	7.83E-4	0	3,8928,0,7	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749189	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	8945	7.83E-4	0	3,8935,0,7	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749189	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	8947	0.003241	0	3,8908,0,29	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749189	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	G	8947	7.82E-4	0	3,8908,0,7	HIGH	NONE	FRAME_SHIFT	M	cttgtaggcttgatgtggctcagctacttcattgcttctttc/	LVGLMWLSYFIASF87	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT>G
ERR5749189	27391	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	AGTCGGTGCCG	14246	7.02E-4	0	34,14203,0,10	.	.	.	.	.	.	.	0.000702	0.938682	3	1	A>AGTCGGTGCCG
ERR5749189	27972	PASS	C	T	5211	0.898292	18	1,1,5156,33	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749189	28048	PASS	G	T	5185	0.901061	0	0,9,0,5174	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749189	28111	PASS	A	G	16457	0.977821	5	0,1,11257,5186	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749189	28270	PASS	TA	T	21710	0.993874	301	133,6,11088,10489	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749189	28280	PASS	G	C	21653	0.943195	36	19,2,11115,10481	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749189	28281	PASS	A	T	21653	0.917425	34	25,5,11108,10475	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749189	28282	PASS	T	A	21653	0.899275	29	21,4,11080,10480	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749189	28292	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	22378	6.7E-4	0	11151,11213,7,8	HIGH	NONE	FRAME_SHIFT	N	aat/	N8	N	0.000304	0.055324	4	2	CA>C
ERR5749189	28881	PASS	G	A	9040	0.763717	2	3,1,4488,4451	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749189	28882	PASS	G	A	9040	0.826881	2	3,1,4523,4431	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749189	28883	PASS	G	C	9040	0.945575	0	1,1,4522,4500	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749189	28977	PASS	C	T	4591	0.922457	0	0,1,0,4580	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749189	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	26462	9.45E-4	166	21848,4562,2,25	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749189	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	43384	0.001613	0	21769,21497,42,41	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749190	199	PASS	G	T	39	0.615385	2147483647	0,0,39,0	.	.	.	.	.	.	.	0.615385	0.766141	1	1	G>T
ERR5749190	241	PASS	C	T	78	0.884615	0	0,0,37,39	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749190	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	1816	0.004405	65	1541,267,0,8	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749190	823	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1538	0.019506	0	1502,0,36,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V6	nsp2	0.001213	0.901722	1	1	C>T
ERR5749190	913	PASS	C	T	1540	0.909091	0	0,1,0,1533	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749190	1190	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1288	0.006211	0	0,1277,0,11	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cca/Tca	P129S	nsp2	0.002242	0.938547	1	1	C>T
ERR5749190	1912	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3139	0.009557	96	1514,1594,31,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S369	nsp2	0.000681	0.08802	2	1	C>T
ERR5749190	1968	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	1545	0.02589	0	1505,0,40,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ata/	I389	nsp2	0.001009	0.95	2	2	CA>C
ERR5749190	2453	PASS	C	T	423	0.728132	2147483647	0,0,0,413	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L550F	nsp2	0.00429	0.842201	2	2	C>T
ERR5749190	2779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	2160	0.031019	0	0,2090,0,70	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	agT/agA	S20R	nsp3	0.003967	0.16	2	2	T>A
ERR5749190	3037	PASS	C	T	517	0.816248	0	0,0,258,254	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749190	3177	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2130	0.006103	6	1853,260,16,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P153L	nsp3	0.000773	0.96008	3	2	C>T
ERR5749190	3267	PASS	C	T	1869	0.970037	2147483647	0,0,1869,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749190	3379	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	1865	0.018231	0	0,1826,0,39	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtA/gtT	V220	nsp3	0.018231	0.228104	2	1	A>T
ERR5749190	3671	PASS	GA	G	896	0.0625	0	420,420,28,28	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N319	nsp3	0.000351	0.0625	6	2	GA>G
ERR5749190	3817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	713	0.01683	52	251,450,12,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D366	nsp3	0.000777	0.972816	2	2	C>T
ERR5749190	4136	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	1210	0.015702	16	927,262,19,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Ctt	V473L	nsp3	0.00075	0.974623	4	2	G>C
ERR5749190	4675	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	2048	0.015625	0	2015,0,33,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaT	K652N	nsp3	0.015625	0.967819	2	2	A>T
ERR5749190	5388	PASS	C	A	194	0.979381	2147483647	0,0,194,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749190	5392	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	194	0.025773	0	189,0,5,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N891	nsp3	0.012876	0.944629	2	2	C>T
ERR5749190	5392	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	194	0.046392	0	185,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tgt/	C893	nsp3	0.012876	0.944629	2	2	CT>C
ERR5749190	5497	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	193	0.015544	0	0,190,0,3	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaaaga/	KR927	nsp3	0.000964	0.897745	3	2	CAA>C
ERR5749190	5724	PASS	C	T	1560	0.866667	2147483647	0,0,1553,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T1002I	nsp3	0.001553	0.866667	1	1	C>T
ERR5749190	5892	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1560	0.012179	0	0,1537,0,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCc/aTc	T1058I	nsp3	0.012179	0.912046	1	1	C>T
ERR5749190	5986	PASS	C	T	699	0.971388	2147483647	0,0,696,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749190	6954	PASS	T	C	1191	0.801008	2147483647	0,0,0,1186	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749190	7564	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1259	0.030183	0	0,1217,0,40	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S1615	nsp3	0.000586	0.056194	4	2	C>T
ERR5749190	7926	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	2197	0.022758	0	0,2147,0,50	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1737	nsp3	0.000531	0.97019	5	2	CA>C
ERR5749190	8669	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	321	0.040498	0	308,0,13,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F39L	nsp4	0.000973	0.22449	1	1	T>C
ERR5749190	9060	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	2308	0.043328	0	2198,0,105,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tAt/tGt	Y169C	nsp4	0.000621	0.433333	5	2	A>G
ERR5749190	10323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	2499	0.019608	0	0,2439,0,56	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aTg	K90M	3Cpro	0.000946	0.965046	2	1	A>T
ERR5749190	11075	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	4897	0.020421	0	4746,0,122,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F35L	nsp6	0.000555	0.885796	4	2	T>C
ERR5749190	11287	PASS	GTCTGGTTTT	G	4897	0.974678	0	0,124,0,4773	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749190	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	2371	0.008013	150	1978,373,0,19	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749190	12439	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	487	0.036961	0	0,469,0,18	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L117	nsp8	0.000666	0.637117	2	2	CT>C
ERR5749190	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	1840	0.013587	0	1815,0,25,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749190	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	3555	0.01519	0	3501,0,54,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749190	14408	PASS	C	T	48	0.791667	0	0,0,24,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749190	14676	PASS	C	T	893	0.721165	2147483647	0,0,886,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749190	15279	PASS	C	T	743	0.928668	0	1,0,740,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749190	15720	PASS	C	T	3827	0.915077	2147483647	0,0,0,3819	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D760	RdRp	0.001002	0.917823	1	1	C>T
ERR5749190	16176	PASS	T	C	1461	0.982888	0	0,0,83,1378	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749190	16559	PASS	C	T	1731	0.051993	0	1634,0,93,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCa/gTa	A108V	helicase	0.000644	0.051993	3	2	C>T
ERR5749190	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAA	G	1221	0.030303	0	1182,0,37,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GAA>G
ERR5749190	17747	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1395	0.022939	0	1362,0,33,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P504L	helicase	0.000839	0.968462	2	2	C>T
ERR5749190	17795	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1395	0.020072	0	1366,0,29,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A520V	helicase	0.00111	0.966723	2	2	C>T
ERR5749190	18029	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1912	0.01046	26	517,1374,0,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCa/gTa	A598V	helicase	0.001444	0.063613	1	1	C>T
ERR5749190	18232	PASS	C	T	517	0.056093	0	0,488,0,29	HIGH	NONSENSE	STOP_GAINED	ORF1ab	Caa/Taa	Q65*	ExoN	0.002195	0.056093	1	1	C>T
ERR5749190	19164	PASS	CA	C	2390	0.075732	0	0,2209,0,181	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K376	ExoN	0.000358	0.075732	4	2	CA>C
ERR5749190	19320	PASS	C	T	1174	0.955707	2147483647	0,0,1173,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H427	ExoN	0.004154	0.957053	2	2	C>T
ERR5749190	20125	PASS	GGA	G	359	0.058496	0	0,338,0,21	HIGH	NONE	FRAME_SHIFT	ORF1ab	gaa/	E170	endoR	0.003053	0.058496	1	1	GGA>G
ERR5749190	20445	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	4579	0.029046	0	0,4446,0,133	HIGH	NONE	FRAME_SHIFT	ORF1ab	aac/aaAc	N277K?	endoR	0.000518	0.059736	4	2	T>TA
ERR5749190	21077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	2972	0.030283	0	0,2882,0,90	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K141	MethTr	0.000492	0.955529	4	2	CAA>C
ERR5749190	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1455	0.011684	0	711,714,9,9	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749190	21655	PASS	T	C	734	0.110354	0	0,649,0,84	LOW	SILENT	SYNONYMOUS_CODING	S	tcT/tcC	S31	S	0.001481	0.110354	1	1	T>C
ERR5749190	21657	PASS	TCA	T	734	0.06812	0	0,684,0,50	HIGH	NONE	FRAME_SHIFT	S	acacgt/	TR33	S	0.000702	0.06812	2	2	TCA>T
ERR5749190	21764	PASS	ATACATG	A	1685	0.997626	0	4,0,1681,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749190	21990	PASS	TTTA	T	1686	0.969751	0	0,51,0,1635	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749190	21991	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTA	T	1686	0.016014	0	0,1659,0,27	HIGH	NONE	FRAME_SHIFT	S	tat/	Y144	S	0.00078	0.991378	2	1	TTA>T
ERR5749190	22712	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8415	0.01331	0	4136,4125,68,68	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Cct/Tct	P384S	S	0.001254	0.842266	2	2	C>T
ERR5749190	23063	PASS	A	T	998	0.893788	2147483647	0,0,0,994	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749190	23271	PASS	C	A	3863	0.925964	2147483647	0,0,3860,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749190	23403	PASS	A	G	3862	0.968151	2147483647	0,0,0,3860	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749190	23604	PASS	C	A	1272	0.939465	0	2,0,1270,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749190	23625	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1272	0.011792	0	1254,0,16,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gTt	A688V	S	0.002362	0.901054	2	2	C>T
ERR5749190	23709	PASS	C	T	1272	0.944182	0	0,1,0,1271	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749190	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1755	0.006268	15	482,1260,0,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L752F	S	0.000334	0.080808	2	2	C>T
ERR5749190	23855	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	482	0.026971	0	469,0,13,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Cgt/Tgt	R765C	S	0.000815	0.181818	2	2	C>T
ERR5749190	24506	PASS	T	G	1597	0.969317	2147483647	0,0,1597,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749190	24512	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1597	0.016907	0	1570,0,27,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L984F	S	0.001476	0.154545	1	1	C>T
ERR5749190	24914	PASS	G	C	15283	0.956815	0	0,0,7608,7668	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749190	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8804	0.021127	78	7795,816,188,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tTc	S1252F	S	0.000828	0.956514	4	2	C>T
ERR5749190	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	247	0.036437	71	228,10,2,7	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749190	26044	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	2986	0.012391	0	2949,0,37,0	HIGH	NONE	FRAME_SHIFT	ORF3a	caa/	Q218	orf3a	0.000469	0.102679	3	3	CA>C
ERR5749190	26091	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	2980	0.007047	0	2959,0,21,0	HIGH	NONE	FRAME_SHIFT	ORF3a	aat/	N234	orf3a	0.000569	0.128212	4	2	CA>C
ERR5749190	26256	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5006	0.007591	150	1982,2981,38,0	LOW	SILENT	SYNONYMOUS_CODING	E	ttC/ttT	F4	E	0.000748	0.969561	2	2	C>T
ERR5749190	26333	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2020	0.008911	0	1998,0,20,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	aCa/aTa	T30I	E	0.00158	0.943221	1	1	C>T
ERR5749190	26510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	2020	0.020297	0	0,1970,0,46	.	.	.	.	.	.	.	0.001235	0.933642	2	1	T>C
ERR5749190	26571	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	1324	0.006798	0	1314,1,9,0	HIGH	NONE	FRAME_SHIFT	M	ctt/	L17	M	0.000508	0.905823	3	2	CT>C
ERR5749190	26801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1323	0.010582	0	0,1302,0,18	LOW	SILENT	SYNONYMOUS_CODING	M	ctC/ctT	L93	M	0.002753	0.954545	3	1	C>T
ERR5749190	26907	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6484	0.023288	0	6330,0,153,0	LOW	SILENT	SYNONYMOUS_CODING	M	Ctg/Ttg	L129	M	0.000817	0.976032	1	1	C>T
ERR5749190	26918	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	6484	0.010642	0	6410,0,71,0	LOW	SILENT	SYNONYMOUS_CODING	M	ccG/ccA	P132	M	0.000999	0.977086	2	1	G>A
ERR5749190	27816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	585	0.008547	0	579,1,5,0	HIGH	NONE	FRAME_SHIFT	ORF7b	tta/	L22	orf7b	0.000423	0.053007	1	1	GT>G
ERR5749190	27972	PASS	C	T	591	0.903553	0	0,0,581,8	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749190	28048	PASS	G	T	584	0.924658	0	0,1,0,583	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749190	28111	PASS	A	G	659	0.971168	0	0,2,75,581	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749190	28270	PASS	TA	T	81	1.0	0	0,0,75,6	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749190	28280	PASS	G	C	142	0.915493	0	0,0,75,67	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749190	28281	PASS	A	T	142	0.866197	0	0,0,75,67	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749190	28282	PASS	T	A	142	0.887324	0	0,0,74,67	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749190	28396	PASS	G	A	78	0.897436	42	3,1,0,72	LOW	SILENT	SYNONYMOUS_CODING	N	cgG/cgA	R41	N	0.000496	0.946059	5	2	G>A
ERR5749190	28434	PASS	C	CTACTGGGT	78	0.871795	28	3,7,0,68	HIGH	NONE	FRAME_SHIFT	N	acc/acTACTGGGTc	T54TTG?	N	0.000815	0.871795	4	2	C>CTACTGGGT
ERR5749190	28603	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5217	0.003834	0	3,5150,0,21	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F110	N	0.000427	0.883357	2	2	C>T
ERR5749190	28881	PASS	G	A	802	0.769327	3	1,0,393,396	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749190	28882	PASS	G	A	802	0.820449	0	0,0,399,394	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749190	28883	PASS	G	C	802	0.950125	0	0,0,402,400	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749190	28977	PASS	C	T	407	0.943489	2147483647	0,0,0,407	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749190	29095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4674	0.006632	0	4640,0,31,0	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F274	N	0.000792	0.961279	2	2	C>T
ERR5749190	29370	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	1141	0.007888	0	1130,2,9,0	HIGH	NONE	FRAME_SHIFT	N	aca/	T366	N	0.007888	0.893443	2	2	CA>C
ERR5749190	29421	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1138	0.007909	0	1127,0,9,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	cCg/cTg	P383L	N	0.002705	0.052892	2	2	C>T
ERR5749190	29543	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	1966	0.004578	21	827,1125,0,10	.	.	.	.	.	.	.	0.001058	0.973475	3	1	G>C
ERR5749190	29555	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1966	0.005086	8	824,1128,2,9	.	.	.	.	.	.	.	0.000611	0.957048	3	1	C>T
ERR5749190	29642	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1967	0.005592	45	814,1138,12,0	HIGH	NONSENSE	STOP_GAINED	ORF10	Caa/Taa	Q29*	orf10	0.001806	0.941176	2	2	C>T
ERR5749190	29675	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	1653	0.00605	0	823,820,5,5	.	.	.	.	.	.	.	0.000624	0.883495	2	1	CA>C
ERR5749190	29774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	828	0.01087	0	0,819,0,9	.	.	.	.	.	.	.	0.002525	0.973955	1	1	C>T
ERR5749190	29779	PASS	G	T	828	0.966184	0	0,1,0,827	.	.	.	.	.	.	.	0.001489	0.975228	1	1	G>T
ERR5749191	92	PASS	C	T	5206	0.960238	0	1,0,5205,0	.	.	.	.	.	.	.	0.960238	0.960238	1	1	C>T
ERR5749191	241	PASS	C	T	10210	0.838883	0	0,0,5014,5121	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749191	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	10837	0.004983	0	10782,2,54,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749191	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	10839	0.001384	0	10685,4,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749191	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	10839	0.002122	0	10685,4,23,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749191	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	10839	0.009687	0	10685,4,105,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749191	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	10838	0.002399	0	10803,9,26,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749191	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	10841	0.002029	0	10793,13,22,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749191	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATGGTTG	T	10841	0.001015	0	10793,13,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	atggttgag/	MVE85	leader	0.000587	0.476744	4	1	TATGGTTG>T
ERR5749191	520	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTT	G	10866	9.2E-4	14	10819,37,9,1	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttgag/gag	VE86E	leader	0.000583	0.051154	1	1	GGTT>G
ERR5749191	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	27186	8.46E-4	26	16317,10843,21,2	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749191	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	27185	6.99E-4	5	16254,10809,14,5	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749191	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	27185	0.003421	10	16254,10809,64,29	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749191	913	PASS	C	T	16327	0.914681	0	0,15,0,16286	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749191	3037	PASS	C	T	14929	0.789001	45	0,15,7461,7311	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749191	3267	PASS	C	T	13651	0.9685	0	2,0,13639,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749191	3638	PASS	G	T	9363	0.896828	0	6,0,9336,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggt/Tgt	G307C	nsp3	0.003698	0.896828	1	1	G>T
ERR5749191	5170	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	9098	8.79E-4	0	1,9089,0,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T819	nsp3	0.000565	0.894036	2	2	CCA>C
ERR5749191	5388	PASS	C	A	5078	0.961796	2147483647	0,0,5076,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749191	5986	PASS	C	T	9187	0.976053	2147483647	0,0,9181,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749191	6954	PASS	T	C	16488	0.811014	0	0,6,0,16389	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749191	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	24475	7.76E-4	65	11105,13351,19,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749191	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	11770	0.001699	0	11727,2,37,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749191	11287	PASS	GTCTGGTTTT	G	11757	0.996002	0	0,46,0,11710	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749191	11300	PASS	C	T	11758	0.873873	0	0,3,0,11716	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L110	nsp6	0.001087	0.873873	1	1	C>T
ERR5749191	11956	PASS	C	T	10886	0.936616	0	2,0,10879,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D38	nsp7	0.00119	0.936616	1	1	C>T
ERR5749191	13424	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11874	0.039582	0	11379,0,484,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgc/Tgc	R134C	nsp10	0.039582	0.967209	1	1	C>T
ERR5749191	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23713	0.001265	0	11838,11821,17,17	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749191	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	9687	0.003716	2702	9432,84,2,153	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749191	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	18809	0.001435	0	9429,9366,14,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749191	14408	PASS	C	T	18809	0.840555	7	2,6,9390,9271	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749191	14676	PASS	C	T	8096	0.797801	2147483647	0,0,8069,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749191	15279	PASS	C	T	17768	0.884793	0	1,0,17747,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749191	16176	PASS	T	C	14545	0.977999	0	0,0,7397,7136	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749191	16629	PASS	G	A	14479	0.891084	0	10,0,14426,11	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaG/aaA	K131	helicase	0.891084	0.891084	1	1	G>A
ERR5749191	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23087	0.001863	0	23022,1,50,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749191	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21343	8.9E-4	0	10448,10630,11,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749191	21764	PASS	ATACATG	A	8520	0.996244	72	30,3,8488,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749191	21990	PASS	TTTA	T	8522	0.998123	0	0,16,3,8503	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749191	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17867	0.001231	12	7551,10271,5,18	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749191	23063	PASS	A	T	7554	0.859412	0	0,2,0,7516	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749191	23271	PASS	C	A	14655	0.921733	0	1,0,14632,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749191	23403	PASS	A	G	14650	0.964027	0	0,2,0,14636	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749191	23604	PASS	C	A	12124	0.963378	0	7,0,12113,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749191	23709	PASS	C	T	12124	0.93286	0	0,5,15,12078	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749191	24506	PASS	T	G	13672	0.974985	0	7,0,13663,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749191	24914	PASS	G	C	23194	0.954428	0	0,0,11558,11618	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749191	25496	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	26938	7.42E-4	11	13210,13253,246,208	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aTa/aGa	I35R	orf3a	0.000369	0.96555	3	2	T>G
ERR5749191	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	38661	5.17E-4	0	4,38635,0,20	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749191	26395	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15687	0.002996	5	7878,7319,31,38	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	Ctt/Ttt	L51F	E	0.000707	0.745829	2	1	C>T
ERR5749191	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	G	7669	9.13E-4	0	0,7645,0,7	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/	ACLVGLMWLSYFIASF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT>G
ERR5749191	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	7669	0.001174	0	0,7645,0,9	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749191	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	7669	0.001434	0	0,7656,0,11	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749191	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	7669	0.005085	0	0,7624,0,39	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749191	27972	PASS	C	T	6327	0.906749	23	0,1,6282,28	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749191	28048	PASS	G	T	6310	0.931537	0	0,6,1,6299	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749191	28111	PASS	A	G	17758	0.976011	2	2,2,11434,6312	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749191	28270	PASS	TA	T	22068	0.994472	288	124,5,11254,10692	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749191	28280	PASS	G	C	22019	0.933557	19	10,1,11282,10679	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749191	28281	PASS	A	T	22019	0.912394	23	14,2,11283,10682	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749191	28282	PASS	T	A	22022	0.907956	0	10,11,11265,10686	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749191	28881	PASS	G	A	8500	0.713412	9	3,0,4162,4182	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749191	28882	PASS	G	A	8499	0.807036	6	5,1,4253,4154	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749191	28883	PASS	G	C	8499	0.939875	3	0,1,4260,4232	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749191	28977	PASS	C	T	4344	0.929328	0	0,0,1,4337	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749191	29095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13914	0.008624	0	13779,3,123,0	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F274	N	0.000792	0.961279	2	2	C>T
ERR5749191	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	27560	0.001197	0	13848,13654,24,22	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749191	29555	PASS	C	T	11897	0.957048	0	1,1,6295,5583	.	.	.	.	.	.	.	0.000611	0.957048	3	1	C>T
ERR5749192	241	PASS	C	T	18347	0.860686	0	1,2,9095,9190	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749192	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	10328	8.71E-4	0	10322,0,9,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749192	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	10328	0.001162	0	10312,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749192	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10322	0.001259	0	9603,0,684,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749192	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	10322	8.72E-4	0	10313,0,9,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749192	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	29818	8.72E-4	5	19459,10333,20,6	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749192	913	PASS	C	T	19465	0.924069	0	0,6,0,19441	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749192	3037	PASS	C	T	14936	0.829539	27	0,9,7468,7385	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749192	3267	PASS	C	T	16731	0.969518	0	1,0,16721,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749192	5388	PASS	C	A	4426	0.961817	0	2,0,4423,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749192	5986	PASS	C	T	9758	0.976635	2147483647	0,0,9749,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749192	6670	PASS	G	T	9423	0.65043	0	2947,0,6469,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tgG/tgT	W1317C	nsp3	0.005523	0.921348	2	2	G>T
ERR5749192	6954	PASS	T	C	20825	0.832845	0	0,1,0,20714	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749192	8123	PASS	C	T	22999	0.768642	0	1,0,22745,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Ttt	L1802F	nsp3	0.001144	0.778589	1	1	C>T
ERR5749192	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	26051	5.37E-4	56	10299,15738,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749192	10748	PASS	C	T	15376	0.100416	0	13787,7,1569,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Ttt	L232F	3Cpro	0.100416	0.100416	1	1	C>T
ERR5749192	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13297	0.002106	0	13250,2,29,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749192	11287	PASS	GTCTGGTTTT	G	13292	0.998571	0	0,19,0,13273	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749192	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26141	0.00153	0	13052,13014,22,23	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749192	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	9153	0.004261	2217	8967,55,5,120	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749192	14408	PASS	C	T	17854	0.851406	0	1,1,8912,8841	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749192	14676	PASS	C	T	11280	0.832801	0	6,0,11249,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749192	15279	PASS	C	T	20208	0.878711	0	1,0,20175,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749192	16176	PASS	T	C	15564	0.981496	0	0,1,6436,9116	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749192	17615	PASS	A	G	10578	0.910664	2147483647	0,0,0,10546	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749192	17626	PASS	C	T	10580	0.946125	0	0,5,0,10566	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cat/Tat	H464Y	helicase	0.001039	0.946125	2	2	C>T
ERR5749192	17678	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10594	0.019445	0	1,10366,0,216	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aTg	T481M	helicase	0.001162	0.968704	2	1	C>T
ERR5749192	19296	PASS	G	A	14042	0.975787	110	1,3,14036,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttG/ttA	L419	ExoN	0.000586	0.977017	2	2	G>A
ERR5749192	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21443	0.001819	0	21389,0,41,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749192	21764	PASS	ATACATG	A	10142	0.998225	0	18,0,10124,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749192	21817	PASS	A	G	10142	0.956616	0	0,0,10125,2	LOW	SILENT	SYNONYMOUS_CODING	S	ccA/ccG	P85	S	0.000689	0.961354	3	2	A>G
ERR5749192	21990	PASS	TTTA	T	10155	0.997538	0	0,25,9,10121	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749192	23063	PASS	A	T	7352	0.87636	0	0,2,0,7323	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749192	23271	PASS	C	A	18731	0.923816	2147483647	0,0,18720,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749192	23403	PASS	A	G	18733	0.97427	0	0,1,0,18717	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749192	23604	PASS	C	A	10981	0.939532	0	6,0,10971,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749192	23709	PASS	C	T	10970	0.946399	0	0,1,1,10957	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749192	24506	PASS	T	G	14857	0.975769	0	11,0,14845,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749192	24914	PASS	G	C	20793	0.960131	0	0,0,10345,10423	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749192	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	24063	0.001247	375	23985,14,15,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749192	25690	PASS	G	T	24034	0.977365	0	1,0,24023,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Ggc/Tgc	G100C	orf3a	0.971091	0.979849	1	1	G>T
ERR5749192	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	24033	7.07E-4	0	24016,0,17,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749192	25782	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24018	9.16E-4	0	23934,0,22,0	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	tgC/tgT	C130	orf3a	0.000916	0.955348	1	1	C>T
ERR5749192	27513	PASS	C	T	18613	0.982163	39	1,1,18600,0	LOW	SILENT	SYNONYMOUS_CODING	ORF7a	taC/taT	Y40	orf7a	0.001863	0.982462	2	2	C>T
ERR5749192	27972	PASS	C	T	6544	0.911064	0	1,0,6501,22	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749192	28048	PASS	G	T	6527	0.928911	0	0,9,0,6517	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749192	28111	PASS	A	G	22256	0.979376	0	0,0,15720,6531	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749192	28270	PASS	TA	T	30630	0.995756	375	135,1,15530,14970	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749192	28280	PASS	G	C	30566	0.939639	12	11,3,15552,14949	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749192	28281	PASS	A	T	30566	0.920042	1	12,9,15559,14948	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749192	28282	PASS	T	A	30569	0.909451	4	16,10,15514,14963	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749192	28881	PASS	G	A	19441	0.791935	4	4,1,9659,9547	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749192	28882	PASS	G	A	19441	0.838228	3	5,2,9743,9537	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749192	28883	PASS	G	C	19441	0.945219	0	1,1,9751,9660	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749192	28977	PASS	C	T	9875	0.935696	0	0,1,0,9860	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749192	29686	PASS	C	T	10839	0.782544	11	1,6,5394,5320	.	.	.	.	.	.	.	0.001045	0.802514	2	1	C>T
ERR5749192	29688	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	10852	0.002764	0	5379,5404,17,17	.	.	.	.	.	.	.	0.002374	0.664502	2	1	G>A
ERR5749193	241	PASS	C	T	13781	0.862202	0	1,1,6845,6887	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749193	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	10425	0.003741	0	10384,2,39,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749193	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	10429	0.001247	0	10322,6,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749193	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	10429	0.001247	0	10322,6,13,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749193	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	10429	0.007096	0	10322,6,74,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749193	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10427	0.001822	0	9649,12,604,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749193	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	10427	0.003644	0	10377,12,38,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749193	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	10425	0.001055	18	10398,11,10,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749193	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	10426	0.001439	0	10390,13,15,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749193	520	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTT	G	10438	9.58E-4	0	10403,25,10,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttgag/gag	VE86E	leader	0.000583	0.051154	1	1	GGTT>G
ERR5749193	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	29481	5.77E-4	20	19030,10432,16,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749193	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	29481	0.002103	14	18991,10418,48,14	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749193	913	PASS	C	T	19036	0.909015	0	0,11,0,18994	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749193	3037	PASS	C	T	15310	0.812476	33	1,14,7657,7518	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749193	3267	PASS	C	T	18405	0.96941	0	2,0,18389,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749193	4255	PASS	G	A	29488	0.839697	51	32,5,14644,14640	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccG/ccA	P512	nsp3	0.001102	0.871853	2	1	G>A
ERR5749193	4980	PASS	C	T	23779	0.978637	0	2,3,11170,12596	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T754I	nsp3	0.005479	0.982571	1	1	C>T
ERR5749193	5388	PASS	C	A	4674	0.954001	2147483647	0,0,4671,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749193	5986	PASS	C	T	10393	0.975657	0	2,0,10385,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749193	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	9532	0.005455	0	11,9468,0,52	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L1328S?	nsp3	0.000731	0.14377	4	2	C>CT
ERR5749193	6954	PASS	T	C	21229	0.805125	0	0,4,5,21090	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749193	8218	PASS	T	C	22885	0.939174	0	0,3,0,22865	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtT/gtC	V1833	nsp3	0.939174	0.947345	1	1	T>C
ERR5749193	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	27456	5.46E-4	51	12512,14929,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749193	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	17428	0.002525	0	16879,3,44,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749193	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17428	0.001434	0	17374,3,28,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749193	11082	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	17416	5.74E-4	0	17415,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000427	0.179468	2	1	TG>T
ERR5749193	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	17416	0.004536	0	17301,0,98,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749193	11287	PASS	GTCTGGTTTT	G	17417	0.996153	0	0,67,0,17350	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749193	11355	PASS	C	T	29232	0.979269	0	1,1,11802,17423	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCa/gTa	A128V	nsp6	0.000455	0.982262	3	2	C>T
ERR5749193	11507	PASS	G	A	23466	0.902327	3	2,0,11738,11640	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Att	V179I	nsp6	0.007744	0.914418	2	2	G>A
ERR5749193	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	32159	8.71E-4	16	20314,11794,25,5	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749193	12025	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12536	0.003829	0	12462,3,55,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S61	nsp7	0.001295	0.948026	1	1	C>T
ERR5749193	12961	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	14848	0.00128	0	2,14749,0,19	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaA/aaG	K92	nsp9	0.00128	0.923934	1	1	A>G
ERR5749193	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10213	0.002742	2280	9998,77,6,127	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749193	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	19906	0.001758	1	9972,9909,19,16	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749193	14408	PASS	C	T	19906	0.845122	3	0,1,9935,9830	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749193	14676	PASS	C	T	12386	0.708623	0	4,0,12333,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749193	15279	PASS	C	T	20734	0.886804	0	2,0,20712,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749193	15411	PASS	T	C	20700	0.948696	0	0,4,1,20679	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaT/aaC	N657	RdRp	0.00222	0.952192	2	2	T>C
ERR5749193	16176	PASS	T	C	17746	0.979432	0	0,0,8091,9648	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749193	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	19482	7.7E-4	0	19467,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749193	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24514	0.001958	0	24443,0,48,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749193	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	19093	6.81E-4	0	0,19080,0,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TA>T
ERR5749193	21764	PASS	ATACATG	A	9709	0.996292	0	36,0,9671,2	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749193	21990	PASS	TTTA	T	9710	0.997219	0	0,27,3,9680	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749193	22225	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	20163	0.003521	0	0,20080,0,81	LOW	SILENT	SYNONYMOUS_CODING	S	tcG/tcT	S221	S	0.001195	0.94526	3	1	G>T
ERR5749193	23063	PASS	A	T	10388	0.863785	0	0,2,4,10325	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749193	23271	PASS	C	A	20189	0.926396	0	2,0,20172,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749193	23403	PASS	A	G	20180	0.968285	0	0,2,0,20157	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749193	23604	PASS	C	A	12351	0.942515	0	9,0,12335,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749193	23709	PASS	C	T	12347	0.941686	0	0,2,4,12325	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749193	24506	PASS	T	G	17393	0.976197	0	4,0,17388,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749193	24914	PASS	G	C	29692	0.95551	0	0,0,14770,14894	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749193	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	21152	5.2E-4	0	21140,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749193	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	39544	4.55E-4	0	3,39520,0,18	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749193	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	9567	0.001254	0	5,9550,0,12	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749193	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	9563	0.003033	0	1,9530,0,29	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749193	26895	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29621	0.001114	0	29568,6,35,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Cat/Tat	H125Y	M	0.000874	0.97046	1	1	C>T
ERR5749193	26936	PASS	C	T	29605	0.968147	0	9,0,29567,0	LOW	SILENT	SYNONYMOUS_CODING	M	ctC/ctT	L138	M	0.001308	0.968147	2	1	C>T
ERR5749193	27513	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20014	0.002448	0	19944,6,49,0	LOW	SILENT	SYNONYMOUS_CODING	ORF7a	taC/taT	Y40	orf7a	0.001863	0.982462	2	2	C>T
ERR5749193	27972	PASS	C	T	8818	0.906215	19	1,1,8727,54	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749193	28048	PASS	G	T	8766	0.915925	0	0,12,1,8747	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749193	28111	PASS	A	G	8778	0.972317	0	0,3,4,8766	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749193	28270	PASS	TA	T	17819	0.999551	0	0,7,3,17808	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749193	28280	PASS	G	C	17822	0.911402	0	0,0,3,17792	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749193	28281	PASS	A	T	17822	0.921614	0	0,5,3,17792	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749193	28282	PASS	T	A	17825	0.951809	0	0,8,3,17812	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749193	28456	PASS	G	T	11592	0.070307	0	10750,12,824,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aaG/aaT	K61N	N	0.001535	0.070307	3	2	G>T
ERR5749193	28881	PASS	G	A	16255	0.775085	11	7,1,8065,7989	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749193	28882	PASS	G	A	16252	0.829436	6	5,1,8126,7949	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749193	28883	PASS	G	C	16252	0.940561	0	1,1,8144,8080	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749193	28977	PASS	C	T	8259	0.922388	0	0,2,0,8240	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749193	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	42043	9.51E-4	0	21133,20844,26,24	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749194	241	PASS	C	T	4927	0.855693	0	0,0,2448,2468	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749194	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	8715	0.001492	0	8704,0,13,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749194	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	8715	0.001033	0	8673,0,9,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749194	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	8715	0.002869	0	8673,0,25,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749194	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	8708	0.001263	0	8068,0,560,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749194	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	8705	8.04E-4	0	8693,0,7,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749194	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	8705	0.001149	0	8689,0,10,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749194	657	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8726	0.001948	0	1,8704,0,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A131V	leader	0.001202	0.365979	3	1	C>T
ERR5749194	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	29134	0.001236	41	20369,8723,35,1	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749194	913	PASS	C	T	20402	0.922361	0	0,10,0,20361	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749194	1820	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	15351	0.001629	0	0,15299,0,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggt/Agt	G339S	nsp2	0.001189	0.949024	2	2	G>A
ERR5749194	3037	PASS	C	T	12471	0.823591	24	0,8,6226,6159	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749194	3247	PASS	T	C	20677	0.200222	0	16436,0,4233,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	agT/agC	S176	nsp3	0.001502	0.200222	2	2	T>C
ERR5749194	3267	PASS	C	T	20677	0.969483	0	2,0,20658,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749194	3802	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	25688	0.001051	1	17458,8203,20,7	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N363	nsp3	0.000554	0.064198	4	2	TA>T
ERR5749194	5388	PASS	C	A	3916	0.958376	2147483647	0,0,3915,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749194	5986	PASS	C	T	9255	0.97396	2147483647	0,0,9248,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749194	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8599	0.001512	0	2,8504,0,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749194	6954	PASS	T	C	21104	0.819513	0	0,2,0,20973	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749194	7070	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	32202	0.001987	291	10964,21158,66,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggc/Agc	G1451S	nsp3	0.000698	0.101434	3	1	G>A
ERR5749194	7318	PASS	C	T	11037	0.84561	70	2,2,0,10990	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1533	nsp3	0.001387	0.851451	1	1	C>T
ERR5749194	8603	PASS	T	C	8505	0.967901	63	2,4,0,8493	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Ctc	F17L	nsp4	0.002607	0.974959	2	1	T>C
ERR5749194	8964	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	13237	7.55E-4	0	13219,4,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K138	nsp4	0.000553	0.981649	4	2	CA>C
ERR5749194	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	19648	6.11E-4	27	11309,8327,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749194	10798	PASS	C	T	3832	0.97286	2147483647	0,0,3824,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D248	3Cpro	0.003021	0.97286	1	1	C>T
ERR5749194	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21515	0.002231	0	21413,1,53,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749194	11082	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	21508	4.65E-4	0	21504,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000427	0.179468	2	1	TG>T
ERR5749194	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	21508	0.001488	0	21442,0,55,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749194	11287	PASS	GTCTGGTTTT	G	21503	0.997721	0	0,48,0,21454	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749194	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	10952	9.13E-4	0	10942,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749194	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28535	0.001998	0	14234,14203,32,32	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749194	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	7870	0.001017	0	3952,3909,4,4	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749194	14408	PASS	C	T	7870	0.85108	7	4,9,3935,3868	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749194	14676	PASS	C	T	12649	0.7097	0	6,0,12595,3	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749194	15279	PASS	C	T	19082	0.898858	0	5,0,19041,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749194	16176	PASS	T	C	16456	0.982073	4	3,2,6078,10361	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749194	17615	PASS	A	G	11799	0.907704	0	0,0,3,11762	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749194	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18413	0.002172	0	18358,0,42,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749194	20930	PASS	C	T	22786	0.95585	0	2,0,22756,4	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aTg	T91M	MethTr	0.000902	0.95585	2	2	C>T
ERR5749194	21764	PASS	ATACATG	A	9519	0.997479	0	22,0,9495,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749194	21990	PASS	TTTA	T	9525	0.998005	0	0,19,5,9501	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749194	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28251	8.5E-4	2	11520,16688,12,13	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749194	23063	PASS	A	T	11526	0.865261	0	0,4,0,11476	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749194	23271	PASS	C	A	22912	0.929513	0	1,0,22890,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749194	23403	PASS	A	G	22901	0.976027	0	0,2,0,22885	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749194	23604	PASS	C	A	12119	0.940507	0	9,0,12106,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749194	23709	PASS	C	T	12112	0.946087	0	0,2,3,12093	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749194	23817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	27161	8.47E-4	11	15011,12107,18,6	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTt/cCt	L752P	S	0.000646	0.066832	1	1	T>C
ERR5749194	24506	PASS	T	G	16321	0.975124	0	1,0,16316,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749194	24914	PASS	G	C	31577	0.950914	0	0,1,15733,15826	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749194	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	22155	0.001083	41	14648,7471,30,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749194	25437	PASS	G	T	14720	0.966236	0	3,0,14696,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	ttG/ttT	L15F	orf3a	0.001128	0.971411	2	2	G>T
ERR5749194	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	15874	0.001638	264	15798,9,15,11	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749194	25855	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	15840	0.001326	0	0,15806,0,30	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gac/Tac	D155Y	orf3a	0.001326	0.969697	1	1	G>T
ERR5749194	26526	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	10347	0.001643	0	4,10306,0,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Gca/Tca	A2S	M	0.001224	0.951192	3	1	G>T
ERR5749194	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	10248	8.78E-4	0	0,10233,0,9	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749194	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	10249	0.001561	0	0,10233,0,16	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749194	27972	PASS	C	T	8608	0.901836	37	2,2,8529,47	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749194	28048	PASS	G	T	8570	0.928471	0	0,8,0,8557	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749194	28111	PASS	A	G	27360	0.977266	1	3,2,18776,8569	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749194	28270	PASS	TA	T	36574	0.995051	383	176,10,18540,17853	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749194	28280	PASS	G	C	36503	0.941238	16	13,3,18572,17843	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749194	28281	PASS	A	T	36503	0.92039	34	27,6,18569,17843	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749194	28282	PASS	T	A	36506	0.912918	7	23,14,18538,17850	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749194	28739	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	25035	0.005353	0	9760,15116,59,87	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gca/Tca	A156S	N	0.005353	0.951077	1	1	G>T
ERR5749194	28878	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	19448	0.001285	2	9782,9605,13,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGt/aCt	S202T	N	0.001	0.909986	3	2	G>C
ERR5749194	28881	PASS	G	A	19339	0.774652	9	4,0,9559,9523	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749194	28882	PASS	G	A	19339	0.828998	27	10,0,9661,9509	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749194	28883	PASS	G	C	19338	0.944151	3	0,1,9678,9629	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749194	28977	PASS	C	T	9821	0.936157	0	0,2,0,9812	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749194	29171	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24787	0.00121	0	24727,9,38,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Cat/Tat	H300Y	N	0.00121	0.854685	2	2	C>T
ERR5749194	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	49253	0.001117	0	24723,24448,34,32	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749195	241	PASS	C	T	72	0.930556	0	0,0,36,36	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749195	657	PASS	C	T	112	0.125	0	0,97,0,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A131V	leader	0.001202	0.365979	3	1	C>T
ERR5749195	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	947	0.015839	6	820,112,15,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L140	leader	0.000316	0.135802	3	2	C>T
ERR5749195	823	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	834	0.029976	0	808,0,26,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V6	nsp2	0.001213	0.901722	1	1	C>T
ERR5749195	913	PASS	C	T	834	0.922062	0	0,1,0,832	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749195	2084	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	801	0.036205	0	385,383,16,16	HIGH	NONSENSE	STOP_GAINED	ORF1ab	Cag/Tag	Q427*	nsp2	0.001943	0.253112	1	1	C>T
ERR5749195	3037	PASS	C	T	240	0.8375	0	0,0,120,120	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749195	3117	PASS	C	T	121	0.950413	2147483647	0,0,0,121	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T133I	nsp3	0.013158	0.950413	1	1	C>T
ERR5749195	3267	PASS	C	T	993	0.971803	2147483647	0,0,993,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749195	5388	PASS	C	A	99	0.929293	2147483647	0,0,99,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749195	5986	PASS	C	T	573	0.975567	2147483647	0,0,572,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749195	6472	PASS	C	T	742	0.966307	2147483647	0,0,0,742	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acC/acT	T1251	nsp3	0.00083	0.966307	2	2	C>T
ERR5749195	6954	PASS	T	C	1570	0.819745	2147483647	0,0,0,1563	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749195	7564	PASS	CT	C	783	0.056194	0	0,739,0,44	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/	Y1617	nsp3	0.000586	0.056194	4	2	CT>C
ERR5749195	8697	PASS	CTA	C	194	0.072165	0	180,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	att/	I49	nsp4	0.000737	0.072165	1	1	CTA>C
ERR5749195	11287	PASS	GTCTGGTTTT	G	5267	0.999051	0	0,5,0,5262	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749195	12343	PASS	T	C	685	0.064234	0	0,635,0,46	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T84	nsp8	0.003533	0.064234	1	1	T>C
ERR5749195	12503	PASS	T	C	506	0.108696	0	449,0,56,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749195	14408	PASS	C	T	44	0.931818	0	0,0,22,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749195	14676	PASS	C	T	407	0.719902	0	1,0,404,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749195	15279	PASS	C	T	576	0.902778	2147483647	0,0,575,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749195	16176	PASS	T	C	886	0.972912	0	0,1,82,802	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749195	18432	PASS	A	C	1002	0.115768	0	877,0,125,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acA/acC	T131	ExoN	0.115768	0.115768	1	1	A>C
ERR5749195	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	192	0.020833	0	188,0,4,0	HIGH	NONE	FRAME_SHIFT+STOP_GAINED	ORF1ab	gat/Tgat	D124*?	endoR	0.000884	0.981982	5	2	C>CT
ERR5749195	21066	PASS	TA	T	1601	0.081824	0	0,1470,0,131	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TA>T
ERR5749195	21101	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	1601	0.016864	0	0,1573,0,27	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttc/ttTc	F150F?	MethTr	0.001498	0.083467	2	2	G>GT
ERR5749195	21764	PASS	ATACATG	A	748	1.0	2147483647	0,0,748,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749195	21889	PASS	T	C	745	0.065772	0	0,691,0,52	LOW	SILENT	SYNONYMOUS_CODING	S	acT/acC	T109	S	0.00091	0.065772	2	2	T>C
ERR5749195	21990	PASS	TTTA	T	748	1.0	2147483647	0,0,0,748	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749195	23063	PASS	A	T	502	0.850598	2147483647	0,0,0,500	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749195	23271	PASS	C	A	1186	0.919899	0	1,0,1183,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749195	23403	PASS	A	G	1185	0.974684	2147483647	0,0,0,1182	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749195	23604	PASS	C	A	675	0.937778	2147483647	0,0,675,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749195	23709	PASS	C	T	673	0.939079	2147483647	0,0,0,673	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749195	24320	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	665	0.007519	0	0,660,0,5	HIGH	NONE	FRAME_SHIFT	S	ttg/Attg	L922I?	S	0.000763	0.138365	4	2	C>CA
ERR5749195	24320	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	665	0.018045	0	0,653,0,12	HIGH	NONE	FRAME_SHIFT	S	aaa/	K921	S	0.000763	0.138365	4	2	CAA>C
ERR5749195	24506	PASS	T	G	1324	0.978097	2147483647	0,0,1324,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749195	24914	PASS	G	C	3024	0.962632	0	0,0,1506,1518	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749195	27598	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GACGGCGTAAAACACGTCTATCAGTTA	G	2483	0.026581	0	2417,0,66,0	HIGH	NONE	FRAME_SHIFT	ORF7a	gacggcgtaaaacacgtctatcagtta/	DGVKHVYQL69	orf7a	0.000699	0.958994	6	2	GACGGCGTAAAACACGTCTATCAGTTA>G
ERR5749195	27643	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2479	0.022186	0	2394,0,84,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Cct/Tct	P84S	orf7a	0.00166	0.858006	2	1	C>T
ERR5749195	27670	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	2539	0.011422	2	67,2428,0,43	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Gtt/Ttt	V93F	orf7a	0.002392	0.990588	3	2	G>T
ERR5749195	27972	PASS	C	T	110	0.954545	2147483647	0,0,109,0	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749195	28048	PASS	G	T	110	0.936364	2147483647	0,0,0,110	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749195	28111	PASS	A	G	122	0.983607	0	0,1,12,109	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749195	28270	PASS	TA	T	22	1.0	0	0,0,12,10	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749195	28280	PASS	G	C	22	0.909091	0	0,0,12,10	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749195	28281	PASS	A	T	22	0.909091	0	0,0,12,10	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749195	28282	PASS	T	A	22	0.863636	0	0,0,12,10	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749195	28881	PASS	G	A	198	0.792929	0	0,0,99,98	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749195	28882	PASS	G	A	198	0.848485	0	0,0,100,97	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749195	28883	PASS	G	C	198	0.944444	0	0,0,100,98	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749195	28977	PASS	C	T	100	0.93	2147483647	0,0,0,100	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749195	29451	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	571	0.024518	0	556,0,15,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aCt/aTt	T393I	N	0.007675	0.757685	2	2	C>T
ERR5749196	241	PASS	C	T	22224	0.862311	0	0,0,11056,11094	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749196	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	11637	0.001719	0	11615,3,20,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749196	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	11639	0.003265	0	11583,5,38,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749196	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	11633	0.002665	0	10669,12,861,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749196	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	11633	0.001461	0	11604,12,17,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749196	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	11635	6.88E-4	0	11604,14,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749196	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	11634	9.46E-4	0	11597,14,11,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749196	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	35258	4.54E-4	2	23595,11643,12,4	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749196	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	35258	0.00173	9	23547,11634,47,14	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749196	913	PASS	C	T	23591	0.909796	0	0,10,0,23552	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749196	3037	PASS	C	T	15445	0.807122	19	1,9,7716,7601	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749196	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	7802	0.002179	420	9,7770,17,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749196	3267	PASS	C	T	21801	0.96913	0	3,0,21785,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749196	5388	PASS	C	A	4106	0.959084	0	0,0,4102,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749196	5986	PASS	C	T	9982	0.971649	2147483647	0,0,9970,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749196	6432	PASS	C	T	23699	0.936031	0	0,12,0,23660	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCc/aTc	T1238I	nsp3	0.931716	0.936031	1	1	C>T
ERR5749196	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9538	0.001468	0	8,9428,0,19	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749196	6954	PASS	T	C	25351	0.812394	0	0,8,3,25195	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749196	8151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	54292	6.08E-4	1166	26656,27141,454,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gTc/gGc	V1811G	nsp3	0.00055	0.34	2	1	T>G
ERR5749196	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	28492	5.26E-4	53	12615,15862,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749196	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	20301	0.001231	0	20251,0,44,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749196	11287	PASS	GTCTGGTTTT	G	20293	0.996945	0	0,61,0,20231	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749196	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	33510	9.25E-4	0	16741,16691,17,17	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749196	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	8736	0.004121	2432	8508,80,5,142	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749196	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	16931	7.09E-4	0	8498,8440,6,6	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749196	14408	PASS	C	T	16931	0.839525	0	1,1,8461,8353	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749196	14676	PASS	C	T	14642	0.829395	0	8,0,14598,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749196	14829	PASS	G	T	14664	0.868726	0	0,29,24,14607	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atT	M463I	RdRp	0.220233	0.868726	1	1	G>T
ERR5749196	15279	PASS	C	T	25276	0.882299	0	2,0,25229,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749196	16176	PASS	T	C	19497	0.980612	0	0,0,8003,11490	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749196	16391	PASS	C	T	8003	0.71923	0	0,1,2,7980	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A52V	helicase	0.71923	0.732678	1	1	C>T
ERR5749196	17615	PASS	A	G	11778	0.902445	0	0,1,4,11747	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749196	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	19935	5.52E-4	0	19924,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749196	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24426	0.001269	0	24367,0,32,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749196	21764	PASS	ATACATG	A	9499	0.997052	0	28,0,9471,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749196	21990	PASS	TTTA	T	9504	0.99737	0	0,25,5,9474	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749196	23063	PASS	A	T	10009	0.854631	0	0,4,0,9960	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749196	23271	PASS	C	A	23858	0.919692	0	3,0,23834,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749196	23403	PASS	A	G	23854	0.966714	0	0,1,0,23833	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749196	23604	PASS	C	A	12454	0.931428	0	10,0,12435,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749196	23709	PASS	C	T	12447	0.940468	0	0,3,4,12427	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749196	24127	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	29493	3.73E-4	16	9443,20048,0,11	HIGH	NONE	FRAME_SHIFT	S	aac/	N856	S	0.000324	0.111888	4	1	TA>T
ERR5749196	24506	PASS	T	G	20239	0.973368	0	11,0,20223,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749196	24646	PASS	A	G	20222	0.957967	0	0,3,11,20191	LOW	SILENT	SYNONYMOUS_CODING	S	aaA/aaG	K1028	S	0.001283	0.957967	1	1	A>G
ERR5749196	24914	PASS	G	C	29787	0.956693	3	1,0,14830,14936	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749196	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	22721	0.002421	75	13671,8979,61,6	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749196	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	26601	5.26E-4	0	26587,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749196	26730	PASS	G	C	18487	0.912317	0	4,4,9203,9244	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Gtt/Ctt	V70L	M	0.000371	0.919543	3	2	G>C
ERR5749196	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	9333	0.001821	0	0,9316,0,17	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749196	27972	PASS	C	T	8501	0.908011	0	0,0,8444,28	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749196	28048	PASS	G	T	8485	0.910784	0	0,7,0,8468	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749196	28111	PASS	A	G	31064	0.978271	7	6,5,22564,8482	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749196	28270	PASS	TA	T	43492	0.995355	459	200,8,22275,21015	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749196	28280	PASS	G	C	43417	0.936983	16	9,1,22327,20991	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749196	28281	PASS	A	T	43417	0.912039	40	31,6,22309,20990	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749196	28282	PASS	T	A	43420	0.911423	7	24,14,22272,21006	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749196	28881	PASS	G	A	18808	0.784666	18	7,0,9354,9233	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749196	28882	PASS	G	A	18807	0.824321	15	6,0,9417,9216	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749196	28883	PASS	G	C	18808	0.939122	3	0,1,9432,9352	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749196	28977	PASS	C	T	9594	0.925266	0	0,1,5,9573	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749196	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	30783	0.001494	138	21182,9518,8,42	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749196	29109	PASS	C	A	21204	0.936144	0	13,0,21186,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	cCa/cAa	P279Q	N	0.004059	0.940585	2	2	C>A
ERR5749196	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	42063	7.61E-4	0	21136,20862,19,18	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749196	29642	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16598	0.002711	1	6623,9915,21,28	HIGH	NONSENSE	STOP_GAINED	ORF10	Caa/Taa	Q29*	orf10	0.001806	0.941176	2	2	C>T
ERR5749197	241	PASS	C	T	3145	0.855962	3	0,1,1568,1563	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749197	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	8012	0.001248	0	8006,0,10,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749197	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	8012	0.001248	0	7973,0,10,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749197	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	8012	0.003495	0	7973,0,28,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749197	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	7999	0.002125	0	7354,0,575,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749197	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	7999	0.002	0	7983,0,16,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749197	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	7998	0.001	0	7986,0,8,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749197	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	22103	0.001131	35	14047,8029,24,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749197	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	22103	5.88E-4	3	14030,8003,10,3	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749197	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	22103	0.002534	4	14030,8003,32,24	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749197	913	PASS	C	T	14064	0.921217	0	0,15,0,14033	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749197	3037	PASS	C	T	11981	0.822302	48	0,16,5990,5920	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749197	3267	PASS	C	T	14606	0.971176	0	1,0,14593,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749197	4529	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTTTAC	T	10557	0.001326	0	4,10530,0,14	HIGH	NONE	FRAME_SHIFT	ORF1ab	tacttt/	YF605	nsp3	0.000527	0.402778	3	1	TTTTAC>T
ERR5749197	4529	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTTTACTTTTACACCAGTAAAACAAC	T	10557	8.53E-4	0	4,10530,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttttacttttacaccagtaaaacaact/	FYFYTSKTT604	nsp3	0.000527	0.402778	3	1	TTTTACTTTTACACCAGTAAAACAAC>T
ERR5749197	5051	PASS	C	T	8116	0.973139	2147483647	0,0,8115,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cca/Tca	P778S	nsp3	0.973139	0.973139	1	1	C>T
ERR5749197	5074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	8114	9.86E-4	0	8106,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/	V786	nsp3	0.000986	0.967824	2	2	TG>T
ERR5749197	5388	PASS	C	A	3845	0.955006	0	0,0,3842,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749197	5986	PASS	C	T	9536	0.977349	2147483647	0,0,9527,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749197	6579	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	8873	0.00958	0	8785,0,85,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cTt/cCt	L1287P	nsp3	0.003451	0.968477	2	1	T>C
ERR5749197	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8845	0.002261	0	7,8738,0,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749197	6954	PASS	T	C	14912	0.828058	0	0,2,3,14827	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749197	6990	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14953	0.001873	0	0,14675,0,30	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S1424F	nsp3	0.000504	0.101156	4	2	C>T
ERR5749197	8389	PASS	C	T	8907	0.058493	0	8315,0,588,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N1890	nsp3	0.058493	0.058493	1	1	C>T
ERR5749197	8697	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	12212	7.37E-4	0	12203,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	att/	I49	nsp4	0.000737	0.072165	1	1	CTA>C
ERR5749197	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	10615	0.002355	0	10575,0,34,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749197	11287	PASS	GTCTGGTTTT	G	10617	0.996515	0	0,37,0,10580	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749197	11674	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	16668	5.4E-4	0	16647,12,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F235	nsp6	0.00054	0.985782	3	2	CT>C
ERR5749197	11750	PASS	C	T	32436	0.70989	39	0,12,16552,14560	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L260F	nsp6	0.001019	0.70989	2	1	C>T
ERR5749197	11824	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	16645	5.41E-4	0	4,16632,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K285	nsp6	0.000465	0.922016	2	2	CA>C
ERR5749197	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	15833	0.001832	0	15774,0,29,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749197	12513	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15833	0.001137	0	15803,0,18,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aTg	T141M	nsp8	0.000794	0.984064	2	2	C>T
ERR5749197	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22042	0.001543	0	11006,10970,18,18	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749197	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	5099	0.004118	1351	4961,56,1,79	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749197	14408	PASS	C	T	9867	0.833384	3	0,1,4927,4878	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749197	14676	PASS	C	T	9295	0.730715	0	4,0,9251,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749197	15279	PASS	C	T	13067	0.897375	0	1,0,13047,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749197	16176	PASS	T	C	13296	0.982025	0	0,0,5344,7946	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749197	18086	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9101	0.002307	0	9074,0,23,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T16I	ExoN	0.001699	0.075758	1	1	C>T
ERR5749197	18647	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	45285	0.012035	4	22840,21871,276,285	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P203L	ExoN	0.000283	0.970507	4	2	C>T
ERR5749197	19188	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	19338	5.17E-4	0	0,19328,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	tgg/	W385	ExoN	0.000427	0.06319	2	1	AT>A
ERR5749197	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16074	0.002986	0	16015,0,51,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749197	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	16229	8.01E-4	0	0,16210,0,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TA>T
ERR5749197	21094	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGAGGGTTTTTT	A	16239	5.54E-4	0	7,16223,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaagagggttttttc/	KEGFF146	MethTr	0.000554	0.211111	5	2	AAAGAGGGTTTTTT>A
ERR5749197	21145	PASS	C	T	39413	0.921396	0	5,4,23157,16217	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Ttt	L163F	MethTr	0.001379	0.921396	3	2	C>T
ERR5749197	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23050	0.001258	1	11315,11489,19,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749197	21764	PASS	ATACATG	A	10196	0.996567	0	35,0,10161,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749197	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	10196	8.83E-4	0	10187,0,9,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749197	21990	PASS	TTTA	T	10199	0.997157	19	1,28,3,10167	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749197	23063	PASS	A	T	11589	0.879886	0	0,1,3,11536	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749197	23271	PASS	C	A	11141	0.938336	0	1,0,11133,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749197	23403	PASS	A	G	11136	0.976473	0	0,2,0,11124	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749197	23522	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTA	G	12312	6.5E-4	0	12304,0,8,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	gaacatgtcaacaactcatatgagtgtgacatacccattggtgcaggtata/gta	EHVNNSYECDIPIGAGI654V	S	0.00053	0.959726	5	2	GAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTA>G
ERR5749197	23604	PASS	C	A	12309	0.948493	0	12,0,12287,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749197	23709	PASS	C	T	12297	0.948117	0	0,7,8,12269	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749197	24506	PASS	T	G	12167	0.977234	0	3,0,12163,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749197	24914	PASS	G	C	33721	0.962308	3	1,0,16810,16891	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749197	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	21607	0.001435	41	16507,5057,39,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749197	25624	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24475	0.003677	4	7831,16552,34,58	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Cac/Tac	H78Y	orf3a	0.00089	0.983312	1	1	C>T
ERR5749197	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	7915	0.002401	311	7856,27,5,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749197	25803	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15892	0.002077	0	7905,7916,18,18	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	aaC/aaT	N137	orf3a	0.002077	0.899984	1	1	C>T
ERR5749197	26013	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30812	0.001136	0	30763,0,36,0	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	ttC/ttT	F207	orf3a	0.000839	0.974528	1	1	C>T
ERR5749197	26526	PASS	G	T	8769	0.951192	0	0,1,0,8764	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Gca/Tca	A2S	M	0.001224	0.951192	3	1	G>T
ERR5749197	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	9549	9.43E-4	0	0,9539,0,9	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749197	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	9550	0.002094	0	0,9530,0,20	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749197	27816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	22808	7.45E-4	5	7308,15483,3,14	HIGH	NONE	FRAME_SHIFT	ORF7b	tta/	L22	orf7b	0.000423	0.053007	1	1	GT>G
ERR5749197	27972	PASS	C	T	7345	0.902927	37	2,2,7269,38	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749197	28048	PASS	G	T	7305	0.926352	0	0,11,0,7290	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749197	28111	PASS	A	G	23118	0.979453	10	1,3,15802,7305	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749197	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15794	0.00152	0	15719,5,29,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749197	28270	PASS	TA	T	30689	0.994363	331	157,10,15586,14930	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749197	28280	PASS	G	C	30625	0.939559	29	14,1,15631,14914	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749197	28281	PASS	A	T	30625	0.915298	25	21,5,15630,14918	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749197	28282	PASS	T	A	30627	0.912136	20	22,7,15599,14931	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749197	28292	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	31428	9.86E-4	11	15649,15698,26,42	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Caa/Aaa	Q7K	N	0.000304	0.055324	4	2	C>A
ERR5749197	28881	PASS	G	A	10866	0.739555	27	9,0,5303,5361	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749197	28882	PASS	G	A	10861	0.834822	11	7,1,5409,5348	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749197	28883	PASS	G	C	10861	0.944296	0	0,0,5424,5424	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749197	28977	PASS	C	T	5521	0.939323	0	0,2,0,5511	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749197	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	32381	0.001791	334	26823,5458,8,55	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749197	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	53365	9.37E-4	0	26795,26487,29,29	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749198	241	PASS	C	T	12586	0.858732	3	0,2,6257,6280	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749198	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	10399	0.00375	21	10359,1,38,1	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749198	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	10401	8.65E-4	0	10300,4,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749198	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	10401	0.007499	0	10300,4,78,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749198	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10397	0.001924	0	9491,6,721,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749198	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	10397	0.002308	0	10366,7,24,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749198	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	10397	8.66E-4	0	10376,6,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749198	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	10395	0.001539	0	10360,8,16,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749198	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATGGTTG	T	10395	7.7E-4	0	10360,8,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	atggttgag/	MVE85	leader	0.000587	0.476744	4	1	TATGGTTG>T
ERR5749198	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	29278	8.2E-4	33	18848,10403,23,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749198	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	29278	4.1E-4	0	18795,10384,8,4	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749198	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	29278	0.002596	20	18795,10384,60,16	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749198	913	PASS	C	T	18864	0.920006	0	0,5,0,18839	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749198	1420	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18583	0.006673	0	18424,0,131,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A205	nsp2	0.006673	0.870681	1	1	C>T
ERR5749198	1510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	18573	0.004307	0	0,18331,0,91	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G235	nsp2	0.002159	0.937304	1	1	T>C
ERR5749198	3037	PASS	C	T	15034	0.819808	27	0,9,7513,7425	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749198	3267	PASS	C	T	17551	0.969802	2147483647	0,0,17540,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749198	3483	PASS	G	T	25075	0.962114	3	1,7,7517,17543	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGa/gTa	G255V	nsp3	0.001819	0.962114	2	1	G>T
ERR5749198	3671	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	14986	0.001201	0	7472,7417,9,9	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E318K	nsp3	0.000351	0.0625	6	2	G>A
ERR5749198	5388	PASS	C	A	5162	0.960868	2147483647	0,0,5162,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749198	5986	PASS	C	T	10329	0.974441	2147483647	0,0,10325,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749198	6954	PASS	T	C	20256	0.804552	0	0,5,0,20121	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749198	9712	PASS	C	T	12592	0.893027	0	0,15,15,12532	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S386	nsp4	0.002641	0.893027	2	1	C>T
ERR5749198	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	16946	0.001711	0	16890,0,44,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749198	11287	PASS	GTCTGGTTTT	G	16939	0.996576	0	0,58,0,16881	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749198	11747	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20963	0.001145	0	20913,1,29,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L259	nsp6	0.001145	0.737282	1	1	C>T
ERR5749198	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	7895	0.002787	1531	7730,70,5,87	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749198	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	15408	0.001558	0	7719,7673,12,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749198	14408	PASS	C	T	15408	0.848585	6	0,2,7695,7598	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749198	14676	PASS	C	T	11628	0.700206	0	6,0,11569,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749198	15279	PASS	C	T	19191	0.910896	0	1,0,19163,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749198	16176	PASS	T	C	16903	0.980004	9	3,0,7991,8904	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749198	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	19876	6.54E-4	0	19863,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749198	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	21783	4.59E-4	0	1,21772,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749198	19269	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	36664	0.005155	4	14777,21682,86,109	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N410	ExoN	0.000773	0.954777	2	2	C>T
ERR5749198	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24305	0.002304	0	24230,1,57,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749198	21762	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTATACA	C	9830	0.002848	0	9802,0,28,0	MODERATE	NONE	CODON_DELETION	S	atacat/	IH68	S	0.001297	0.875707	2	2	CTATACA>C
ERR5749198	21764	PASS	ATACATG	A	9830	0.995829	0	41,0,9789,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749198	21990	PASS	TTTA	T	9836	0.99756	0	0,24,5,9807	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749198	23063	PASS	A	T	10395	0.865993	0	0,2,0,10347	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749198	23271	PASS	C	A	19425	0.925302	0	1,0,19406,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749198	23403	PASS	A	G	19420	0.970391	0	0,2,0,19406	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749198	23604	PASS	C	A	12704	0.948363	0	11,0,12687,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749198	23709	PASS	C	T	12700	0.940157	0	0,2,2,12672	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749198	24506	PASS	T	G	15028	0.973782	0	7,0,15016,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749198	24616	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	15010	0.004863	0	15,14900,0,92	LOW	SILENT	SYNONYMOUS_CODING	S	atC/atA	I1018	S	0.001268	0.127917	3	2	C>A
ERR5749198	24914	PASS	G	C	30757	0.957083	3	1,0,15317,15408	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749198	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	20456	0.002786	89	14049,6335,65,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749198	25531	PASS	A	G	14296	0.975378	0	0,2,2,14277	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Att/Gtt	I47V	orf3a	0.000473	0.975891	5	2	A>G
ERR5749198	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	20113	0.001094	0	20091,0,22,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749198	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	20277	0.001381	842	19908,141,135,67	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749198	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	40056	5.24E-4	0	3,40022,0,21	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749198	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	9470	8.45E-4	0	1,9455,0,8	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749198	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	9470	0.001056	0	1,9459,0,10	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749198	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	9471	0.001795	0	1,9450,0,17	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749198	27384	PASS	T	C	15129	0.913081	0	0,5,33,15070	LOW	SILENT	SYNONYMOUS_CODING	ORF6	gaT/gaC	D61	orf6	0.00154	0.931035	3	3	T>C
ERR5749198	27604	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	18175	0.001486	0	18116,1,30,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Gta/Tta	V71L	orf7a	0.001008	0.967671	3	2	G>T
ERR5749198	27972	PASS	C	T	8582	0.904102	0	0,0,8515,40	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749198	28048	PASS	G	T	8551	0.932055	0	0,12,0,8531	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749198	28111	PASS	A	G	26008	0.965818	5	4,0,17436,8555	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749198	28270	PASS	TA	T	33922	0.994871	456	179,4,17213,16535	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749198	28280	PASS	G	C	33854	0.941602	21	11,1,17269,16530	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749198	28281	PASS	A	T	33854	0.920541	20	20,6,17265,16524	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749198	28282	PASS	T	A	33858	0.913876	17	17,5,17216,16534	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749198	28881	PASS	G	A	15836	0.774122	30	11,0,7830,7812	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749198	28882	PASS	G	A	15832	0.828891	2	3,1,7897,7783	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749198	28883	PASS	G	C	15832	0.94189	9	4,0,7906,7903	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749198	28960	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	8060	0.00273	0	0,8022,0,35	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	caG/caT	Q229H	N	0.00273	0.921139	2	2	G>T
ERR5749198	28977	PASS	C	T	8061	0.930406	2147483647	0,0,0,8044	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749198	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	30622	0.001012	132	22530,8023,4,30	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749198	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	44783	0.001116	0	22482,22211,34,34	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749198	29386	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	8483	0.001061	0	8474,0,9,0	HIGH	NONE	FRAME_SHIFT	N	aag/aaAg	K373K?	N	0.000887	0.899197	4	2	C>CA
ERR5749199	241	PASS	C	T	22195	0.853661	0	4,4,11042,11048	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749199	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	12424	0.002254	0	12396,3,28,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749199	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	12424	8.85E-4	0	12348,3,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749199	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	12424	0.001449	0	12348,3,18,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749199	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	12424	0.003139	0	12348,3,39,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749199	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12416	0.002577	0	11392,4,879,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749199	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	12416	0.002175	0	12385,4,27,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749199	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	12416	6.44E-4	0	12394,4,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749199	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	12417	0.003866	0	12355,5,48,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749199	520	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTT	G	12428	7.24E-4	0	12403,16,9,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttgag/gag	VE86E	leader	0.000583	0.051154	1	1	GGTT>G
ERR5749199	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	33415	6.28E-4	29	20956,12437,20,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749199	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	33415	0.001676	6	20928,12423,40,16	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749199	913	PASS	C	T	20970	0.910873	0	0,14,0,20924	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749199	1820	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	18856	0.004932	0	0,18732,0,98	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggt/Agt	G339S	nsp2	0.001189	0.949024	2	2	G>A
ERR5749199	3037	PASS	C	T	21353	0.820681	24	1,11,10671,10530	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749199	3267	PASS	C	T	19681	0.972308	0	1,0,19671,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749199	5388	PASS	C	A	7050	0.958014	2147483647	0,0,7047,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749199	5497	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	7041	0.00142	0	0,7030,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	aga/	R928	nsp3	0.000964	0.897745	3	2	CA>C
ERR5749199	5986	PASS	C	T	13152	0.974605	0	1,0,13137,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749199	6954	PASS	T	C	21031	0.821882	0	0,5,0,20903	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749199	7488	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	14969	0.001403	0	14879,5,80,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aAt	T1590N	nsp3	0.001403	0.889265	2	1	C>A
ERR5749199	8106	PASS	C	T	24863	0.89772	0	2,0,24772,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCa/gTa	A1796V	nsp3	0.014686	0.89772	1	1	C>T
ERR5749199	9165	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16076	0.00112	0	0,16050,0,19	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCc/aTc	T204I	nsp4	0.00112	0.253438	1	1	C>T
ERR5749199	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	33792	6.21E-4	58	17791,15980,21,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749199	9561	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17821	0.008249	0	17621,9,166,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCa/tTa	S336L	nsp4	0.00171	0.161742	2	2	C>T
ERR5749199	11082	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	18613	5.37E-4	0	18603,5,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000427	0.179468	2	1	TG>T
ERR5749199	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	18613	0.003438	0	18504,5,91,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749199	11104	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	18605	0.001612	0	18508,3,35,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccT/ccC	P44	nsp6	0.000866	0.675414	2	1	T>C
ERR5749199	11287	PASS	GTCTGGTTTT	G	18604	0.996721	0	0,61,0,18543	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749199	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	36679	0.001009	8	21666,14942,18,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749199	11750	PASS	C	T	42079	0.689584	49	3,23,21588,18512	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L260F	nsp6	0.001019	0.70989	2	1	C>T
ERR5749199	11750	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	G	42079	0.00259	12	3,23,61,1863	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Gtc	L260V	nsp6	0.001019	0.70989	2	1	C>G
ERR5749199	12109	PASS	T	C	17542	0.963972	0	0,3,1,17524	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttT/ttC	F6	nsp8	0.002176	0.963972	1	1	T>C
ERR5749199	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	20084	0.001145	0	20020,0,23,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749199	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	12474	0.001283	0	12458,0,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749199	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27528	0.001235	0	13744,13714,18,19	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749199	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	16695	0.00563	2147483647	16269,106,4,307	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749199	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	32378	7.72E-4	0	16251,16136,12,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749199	14408	PASS	C	T	32378	0.846285	10	3,9,16157,15961	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749199	14676	PASS	C	T	12338	0.78392	0	6,0,12297,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749199	15279	PASS	C	T	22142	0.882847	2147483647	0,0,22099,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749199	16176	PASS	T	C	19923	0.978467	0	1,0,10459,9459	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749199	17795	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12406	0.002579	0	12367,0,33,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A520V	helicase	0.00111	0.966723	2	2	C>T
ERR5749199	18501	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29138	0.002814	0	2,28942,0,97	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y154	ExoN	0.000336	0.857143	4	2	C>T
ERR5749199	18576	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29249	0.016445	0	0,28679,0,548	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D179	ExoN	0.005404	0.876866	2	2	C>T
ERR5749199	19011	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22675	0.004542	0	22551,0,108,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D324	ExoN	0.000408	0.975746	4	2	C>T
ERR5749199	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	22657	4.41E-4	0	0,22647,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749199	19188	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	22674	5.73E-4	0	0,22660,0,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	tgg/	W385	ExoN	0.000427	0.06319	2	1	AT>A
ERR5749199	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	33100	0.001662	0	33018,0,56,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749199	21764	PASS	ATACATG	A	13662	0.997585	0	33,0,13629,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749199	21990	PASS	TTTA	T	13666	0.996707	0	0,45,4,13617	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749199	22225	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	19638	0.004787	0	0,19532,0,104	LOW	SILENT	SYNONYMOUS_CODING	S	tcG/tcT	S221	S	0.001195	0.94526	3	1	G>T
ERR5749199	22363	PASS	G	T	9764	0.976137	2147483647	0,0,9763,0	LOW	SILENT	SYNONYMOUS_CODING	S	gtG/gtT	V267	S	0.004714	0.976137	1	1	G>T
ERR5749199	22690	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	14382	0.001252	0	14261,3,20,0	LOW	SILENT	SYNONYMOUS_CODING	S	acT/acC	T376	S	0.000815	0.051311	2	1	T>C
ERR5749199	23063	PASS	A	T	13506	0.857989	0	0,6,2,13429	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749199	23271	PASS	C	A	21340	0.920993	0	2,0,21311,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749199	23311	PASS	G	T	21323	0.698119	0	253,0,21055,7	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gaG/gaT	E583D	S	0.001115	0.705903	2	1	G>T
ERR5749199	23403	PASS	A	G	21333	0.969812	0	0,2,0,21320	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749199	23604	PASS	C	A	16345	0.95026	0	8,0,16334,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749199	23709	PASS	C	T	16335	0.937741	0	0,3,1,16316	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749199	24506	PASS	T	G	16464	0.97534	0	4,0,16457,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749199	24914	PASS	G	C	39656	0.959476	0	0,0,19753,19877	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749199	25572	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	15840	6.31E-4	0	0,15829,0,10	HIGH	NONE	FRAME_SHIFT	ORF3a	atc/	I62	orf3a	0.000543	0.959687	4	2	CA>C
ERR5749199	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	23772	0.001178	377	23702,13,15,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749199	25912	PASS	G	A	23755	0.97651	437	13,4,0,23728	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Ggc/Agc	G174S	orf3a	0.001337	0.979852	2	1	G>A
ERR5749199	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	13371	0.002468	0	0,13337,0,33	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749199	26822	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13381	0.001495	0	0,13341,0,24	LOW	SILENT	SYNONYMOUS_CODING	M	ttC/ttT	F100	M	0.001495	0.855211	1	1	C>T
ERR5749199	26985	PASS	C	T	28531	0.8693	0	8,0,28418,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Cat/Tat	H155Y	M	0.001017	0.889358	1	1	C>T
ERR5749199	27532	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	19109	0.00157	0	19070,2,36,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Cat/Aat	H47N	orf7a	0.001165	0.982473	2	1	C>A
ERR5749199	27972	PASS	C	T	11723	0.89849	16	1,1,11543,136	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749199	28048	PASS	G	T	11593	0.921677	0	0,18,0,11567	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749199	28095	PASS	A	T	11602	0.955525	114	3,0,0,11534	HIGH	NONSENSE	STOP_GAINED	ORF8	Aaa/Taa	K68*	orf8	0.002672	0.967672	2	2	A>T
ERR5749199	28095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AA	A	11602	0.002672	0	3,11568,0,31	HIGH	NONE	FRAME_SHIFT	ORF8	aaa/	K68	orf8	0.002672	0.967672	2	2	AA>A
ERR5749199	28111	PASS	A	G	30992	0.974703	0	3,1,19384,11595	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749199	28147	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	19396	6.19E-4	0	19379,4,12,0	HIGH	NONE	FRAME_SHIFT	ORF8	ttt/	F86	orf8	0.000438	0.981624	4	2	CT>C
ERR5749199	28270	PASS	TA	T	37633	0.995802	372	158,6,19164,18311	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749199	28280	PASS	G	C	37574	0.937404	14	10,2,19196,18284	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749199	28281	PASS	A	T	37574	0.917603	40	32,7,19182,18288	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749199	28282	PASS	T	A	37575	0.909647	15	22,9,19157,18305	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749199	28881	PASS	G	A	18216	0.792929	4	4,1,9049,8928	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749199	28882	PASS	G	A	18216	0.820652	6	5,1,9118,8894	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749199	28883	PASS	G	C	18216	0.942468	0	1,0,9134,9062	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749199	28957	PASS	C	T	9255	0.942626	0	0,2,0,9239	LOW	SILENT	SYNONYMOUS_CODING	N	aaC/aaT	N228	N	0.01097	0.950683	1	1	C>T
ERR5749199	28977	PASS	C	T	9256	0.921889	0	0,2,0,9239	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749199	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	39627	0.001035	159	30337,9206,8,37	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749199	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	60333	7.13E-4	0	30304,29951,26,26	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749199	29272	PASS	C	T	30363	0.892106	0	0,4,0,30299	LOW	SILENT	SYNONYMOUS_CODING	N	taC/taT	Y333	N	0.001709	0.892106	1	1	C>T
ERR5749199	29779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	9592	0.011989	0	0,9454,0,137	.	.	.	.	.	.	.	0.001489	0.975228	1	1	G>T
ERR5749200	71	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	3049	0.003608	0	3027,0,14,0	.	.	.	.	.	.	.	0.002088	0.926791	2	1	C>A
ERR5749200	241	PASS	C	T	5539	0.883372	1	2,3,2763,2749	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749200	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	11273	7.98E-4	0	11269,0,9,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749200	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	11273	0.001064	0	11249,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749200	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	11264	0.002397	0	10380,0,836,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749200	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	11264	0.001332	0	11249,0,15,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749200	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	11263	7.1E-4	0	11256,0,8,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttatg/gtg	VM84V	leader	0.000554	0.991848	4	1	GTTA>G
ERR5749200	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	32301	7.12E-4	0	20992,11283,15,8	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749200	913	PASS	C	T	21002	0.913104	0	0,11,0,20955	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749200	1813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	19143	0.001201	0	0,19087,0,32	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcA	A336	nsp2	0.001022	0.152738	4	2	T>A
ERR5749200	2146	PASS	C	T	25193	0.933672	0	0,8,0,25151	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V447	nsp2	0.007119	0.933672	1	1	C>T
ERR5749200	3037	PASS	C	T	16514	0.822151	19	2,11,8254,8149	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749200	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	8336	0.002279	369	5,8295,16,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749200	3267	PASS	C	T	21457	0.971105	0	1,0,21444,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749200	5170	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	10169	8.85E-4	0	0,10160,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T819	nsp3	0.000565	0.894036	2	2	CCA>C
ERR5749200	5388	PASS	C	A	5183	0.954852	0	1,0,5178,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749200	5986	PASS	C	T	12094	0.975442	2147483647	0,0,12081,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749200	6954	PASS	T	C	18844	0.802484	0	0,1,0,18736	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749200	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	23106	6.06E-4	24	14938,8154,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749200	10138	PASS	C	T	25079	0.982934	5	0,1,18262,6804	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N28	3Cpro	0.000458	0.983567	3	3	C>T
ERR5749200	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21754	9.65E-4	0	21699,3,23,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749200	11287	PASS	GTCTGGTTTT	G	21742	0.998206	0	0,39,0,21703	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749200	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	35665	9.53E-4	9	22831,12770,28,8	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749200	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	19198	0.001094	0	19153,0,21,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749200	14408	PASS	C	T	11119	0.859879	12	0,4,5556,5505	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749200	14676	PASS	C	T	12224	0.799575	2147483647	0,0,12191,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749200	15279	PASS	C	T	19135	0.895584	0	15,0,19094,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749200	16176	PASS	T	C	18789	0.981106	3	1,0,7971,10804	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749200	17615	PASS	A	G	15118	0.899259	0	0,2,5,15069	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749200	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	26489	5.66E-4	0	26473,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749200	19188	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	25738	4.27E-4	0	0,25727,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	tgg/	W385	ExoN	0.000427	0.06319	2	1	AT>A
ERR5749200	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23046	0.00256	0	22971,0,60,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749200	20628	PASS	C	T	27487	0.968531	0	5,0,27466,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749200	21764	PASS	ATACATG	A	12619	0.996989	0	34,0,12581,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749200	21990	PASS	TTTA	T	12627	0.997783	0	0,28,6,12593	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749200	22227	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	20399	4.9E-4	0	0,20389,0,10	HIGH	NONE	FRAME_SHIFT	S	tta/	L223	S	0.000419	0.824305	2	2	CT>C
ERR5749200	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	15849	0.001199	0	0,15820,0,21	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749200	23063	PASS	A	T	13823	0.870361	0	0,3,0,13769	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749200	23271	PASS	C	A	22255	0.922444	0	5,0,22230,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749200	23403	PASS	A	G	22246	0.978378	0	0,2,0,22233	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749200	23604	PASS	C	A	15364	0.941096	0	10,0,15345,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749200	23709	PASS	C	T	15339	0.943869	0	0,2,1,15317	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749200	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	29237	4.1E-4	8	13867,15358,3,9	HIGH	NONE	FRAME_SHIFT	S	ttg/	L753	S	0.000334	0.080808	2	2	CT>C
ERR5749200	24506	PASS	T	G	16691	0.97286	0	6,0,16683,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749200	24914	PASS	G	C	39651	0.961766	0	0,0,19759,19874	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749200	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	25356	0.002248	78	18432,6839,68,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749200	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	11081	0.002888	599	11019,10,9,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749200	26159	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTAATCCAG	T	41077	5.84E-4	0	6,41049,0,24	HIGH	NONE	FRAME_SHIFT	ORF3a	ccagtaatg/	PVM258	orf3a	0.000311	0.053032	2	2	TTAATCCAG>T
ERR5749200	26730	PASS	G	C	25119	0.919543	5	5,2,12512,12556	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Gtt/Ctt	V70L	M	0.000371	0.919543	3	2	G>C
ERR5749200	27294	PASS	C	T	19523	0.875122	0	6,0,19467,0	LOW	SILENT	SYNONYMOUS_CODING	ORF6	taC/taT	Y31	orf6	0.000651	0.875122	2	2	C>T
ERR5749200	27384	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	19540	0.005425	0	25,19334,0,127	LOW	SILENT	SYNONYMOUS_CODING	ORF6	gaT/gaC	D61	orf6	0.00154	0.931035	3	3	T>C
ERR5749200	27746	PASS	G	T	18696	0.94095	0	0,21,1,18665	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	aGa/aTa	R118I	orf7a	0.000528	0.94095	3	2	G>T
ERR5749200	27972	PASS	C	T	8189	0.905117	0	0,0,8117,49	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749200	28048	PASS	G	T	8145	0.919337	0	0,9,0,8128	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749200	28111	PASS	A	G	29608	0.977135	0	3,1,21444,8153	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749200	28270	PASS	TA	T	41626	0.995339	423	192,10,21179,20253	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749200	28280	PASS	G	C	41546	0.942449	12	19,8,21216,20238	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749200	28281	PASS	A	T	41546	0.916887	20	20,6,21208,20231	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749200	28282	PASS	T	A	41548	0.912751	6	15,8,21172,20246	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749200	28881	PASS	G	A	15355	0.771931	15	6,0,7612,7540	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749200	28882	PASS	G	A	15355	0.831911	0	1,1,7685,7528	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749200	28883	PASS	G	C	15355	0.945099	0	0,0,7697,7646	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749200	28977	PASS	C	T	7808	0.930072	0	0,4,0,7789	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749200	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	61236	0.001306	0	30753,30374,45,42	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749201	241	PASS	C	T	9820	0.850407	0	0,1,4882,4899	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749201	412	PASS	C	T	10844	0.968277	37	1,1,10838,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G49	leader	0.968277	0.983986	1	1	C>T
ERR5749201	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	10826	7.39E-4	0	10799,0,8,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749201	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	10826	0.001386	0	10799,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749201	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10819	0.001756	0	10017,0,756,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749201	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	10819	8.32E-4	0	10810,0,9,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749201	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATGGTTG	T	10817	8.32E-4	0	10806,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	atggttgag/	MVE85	leader	0.000587	0.476744	4	1	TATGGTTG>T
ERR5749201	913	PASS	C	T	15713	0.910965	0	0,12,0,15677	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749201	1652	PASS	A	G	18575	0.975989	0	1,0,18562,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Att/Gtt	I283V	nsp2	0.001057	0.98088	2	2	A>G
ERR5749201	3037	PASS	C	T	15728	0.803535	69	0,23,7858,7732	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749201	3267	PASS	C	T	16146	0.970829	0	1,0,16122,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749201	5388	PASS	C	A	5883	0.959204	2147483647	0,0,5881,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749201	5986	PASS	C	T	11831	0.974643	0	1,0,11821,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749201	6185	PASS	C	T	11830	0.933221	0	0,2,0,11822	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cac/Tac	H1156Y	nsp3	0.910265	0.954999	1	1	C>T
ERR5749201	6954	PASS	T	C	17006	0.816477	0	0,1,0,16930	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749201	9286	PASS	C	T	7300	0.950548	0	2,0,7291,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N244	nsp4	0.949239	0.971567	1	1	C>T
ERR5749201	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	22982	0.001262	46	15652,7300,29,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749201	11287	PASS	GTCTGGTTTT	G	17648	0.998527	0	0,25,0,17622	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749201	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	31246	0.00144	1	17864,13314,27,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749201	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	9106	0.004722	2591	8875,75,4,148	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749201	14408	PASS	C	T	17685	0.846593	3	0,1,8839,8732	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749201	14676	PASS	C	T	10053	0.814881	0	6,0,10020,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749201	15279	PASS	C	T	15769	0.881793	0	4,0,15739,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749201	16176	PASS	T	C	17402	0.97937	0	2,1,9085,8304	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749201	17615	PASS	A	G	15438	0.909833	0	0,0,7,15396	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749201	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	25202	5.56E-4	0	25187,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749201	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24557	0.002158	0	24482,0,59,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749201	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25524	9.79E-4	0	25463,0,25,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749201	21764	PASS	ATACATG	A	12362	0.995146	0	60,0,12302,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749201	21990	PASS	TTTA	T	12370	0.997656	0	0,29,3,12338	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749201	22432	PASS	C	T	9359	0.654557	0	0,0,9189,1	LOW	SILENT	SYNONYMOUS_CODING	S	gaC/gaT	D290	S	0.002959	0.755028	1	1	C>T
ERR5749201	23063	PASS	A	T	13717	0.858278	0	0,5,0,13656	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749201	23271	PASS	C	A	17203	0.925246	0	2,0,17188,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749201	23403	PASS	A	G	17197	0.970402	0	0,3,0,17183	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749201	23604	PASS	C	A	15023	0.94129	0	9,0,15004,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749201	23709	PASS	C	T	15006	0.940224	0	0,3,3,14985	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749201	24506	PASS	T	G	13964	0.973002	0	9,0,13951,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749201	24914	PASS	G	C	39357	0.959855	0	0,0,19611,19718	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749201	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	12940	0.0017	330	12883,13,10,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749201	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	12479	7.21E-4	0	0,12470,0,9	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749201	26918	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	25015	9.99E-4	0	24977,0,26,0	LOW	SILENT	SYNONYMOUS_CODING	M	ccG/ccA	P132	M	0.000999	0.977086	2	1	G>A
ERR5749201	27065	PASS	G	A	24957	0.746083	0	0,6,0,24629	LOW	SILENT	SYNONYMOUS_CODING	M	ttG/ttA	L181	M	0.001008	0.897124	3	2	G>A
ERR5749201	27972	PASS	C	T	9566	0.905603	22	0,1,9476,49	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749201	28048	PASS	G	T	9517	0.922349	0	0,11,0,9499	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749201	28111	PASS	A	G	27998	0.978213	0	3,2,18458,9521	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749201	28198	PASS	G	T	18471	0.935304	0	13,0,18404,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tGt/tTt	C102F	orf8	0.000718	0.94386	4	2	G>T
ERR5749201	28270	PASS	TA	T	35785	0.993712	538	226,8,18156,17404	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749201	28271	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AA	A	35783	0.001202	124	18327,17413,43,0	.	.	.	.	.	.	.	0.000482	0.924941	3	2	AA>A
ERR5749201	28280	PASS	G	C	35703	0.93572	29	11,0,18224,17385	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749201	28281	PASS	A	T	35703	0.913789	45	25,3,18217,17402	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749201	28282	PASS	T	A	35708	0.908088	5	23,15,18168,17398	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749201	28321	PASS	G	T	18447	0.947634	0	0,9,0,18399	LOW	SILENT	SYNONYMOUS_CODING	N	acG/acT	T16	N	0.00045	0.947809	3	2	G>T
ERR5749201	28881	PASS	G	A	10666	0.726702	24	8,0,5206,5239	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749201	28882	PASS	G	A	10666	0.811457	27	10,0,5323,5231	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749201	28883	PASS	G	C	10666	0.94234	6	3,0,5335,5320	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749201	28977	PASS	C	T	5420	0.931365	0	0,1,0,5412	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749201	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	59128	0.001116	0	29706,29323,42,40	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749201	29492	PASS	T	C	7063	0.91052	0	10,0,7011,8	LOW	SILENT	SYNONYMOUS_CODING	N	Ttg/Ctg	L407	N	0.029032	0.925	1	1	T>C
ERR5749201	29642	PASS	C	T	7074	0.922109	0	0,0,9,7057	HIGH	NONSENSE	STOP_GAINED	ORF10	Caa/Taa	Q29*	orf10	0.001806	0.941176	2	2	C>T
ERR5749202	241	PASS	C	T	14690	0.871749	0	3,4,7309,7329	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749202	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	11988	8.34E-4	0	11984,0,10,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749202	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	11991	0.001001	0	11974,4,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749202	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	11993	0.002001	0	11047,10,892,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749202	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	11993	0.001751	0	11960,10,21,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749202	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	11988	0.001168	0	11963,10,14,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749202	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	39828	7.78E-4	0	27786,11977,23,10	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L140	leader	0.000316	0.135802	3	2	C>T
ERR5749202	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	39828	3.52E-4	20	27796,12013,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749202	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	39828	7.53E-4	18	27787,12010,27,3	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749202	913	PASS	C	T	27794	0.910808	0	0,9,0,27745	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749202	1510	PASS	T	C	27817	0.937304	0	0,16,0,27760	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G235	nsp2	0.002159	0.937304	1	1	T>C
ERR5749202	2574	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	39156	8.17E-4	0	39098,2,37,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T590I	nsp2	0.000817	0.057651	1	1	C>T
ERR5749202	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	77893	0.001759	2147483647	38884,36326,76,2415	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749202	3037	PASS	C	T	19654	0.816882	60	0,20,9818,9676	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749202	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	9920	0.002319	646	3,9890,23,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749202	3177	PASS	C	T	36694	0.906906	21	2,6,26775,9866	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P153L	nsp3	0.000773	0.96008	3	2	C>T
ERR5749202	3267	PASS	C	T	26802	0.968995	0	6,0,26783,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749202	4255	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	41845	0.001553	2	20846,20861,61,68	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccG/ccT	P512	nsp3	0.001102	0.871853	2	1	G>T
ERR5749202	4752	PASS	C	T	18970	0.938482	2147483647	0,0,18951,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T678I	nsp3	0.009765	0.938482	1	1	C>T
ERR5749202	4754	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18970	0.001054	0	18935,0,20,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cct/Tct	P679S	nsp3	0.001054	0.947507	1	1	C>T
ERR5749202	5388	PASS	C	A	6213	0.958796	2147483647	0,0,6211,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749202	5730	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29025	0.001792	0	28958,0,57,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T1004I	nsp3	0.001601	0.721782	1	1	C>T
ERR5749202	5986	PASS	C	T	12846	0.977113	0	2,0,12837,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749202	6954	PASS	T	C	24109	0.824837	0	0,12,0,23977	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749202	7070	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	38860	0.00175	305	14586,24185,72,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggc/Agc	G1451S	nsp3	0.000698	0.101434	3	1	G>A
ERR5749202	9430	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14963	0.003141	0	7,14874,0,48	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I292	nsp4	0.001411	0.960894	1	1	C>T
ERR5749202	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	33591	0.001548	131	18566,14973,52,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749202	9712	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18640	0.006223	0	50,18448,0,136	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S386	nsp4	0.002641	0.893027	2	1	C>T
ERR5749202	11082	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	29984	4.67E-4	0	29981,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000427	0.179468	2	1	TG>T
ERR5749202	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	29984	0.001434	0	29878,0,78,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749202	11104	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	29977	0.001401	0	29814,0,46,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccT/ccC	P44	nsp6	0.000866	0.675414	2	1	T>C
ERR5749202	11287	PASS	GTCTGGTTTT	G	29978	0.997665	0	0,70,0,29908	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749202	12125	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	21564	0.00102	0	7,21464,0,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y12H	nsp8	0.000847	0.113436	1	1	T>C
ERR5749202	12459	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	51570	8.73E-4	1	22748,28761,19,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T123I	nsp8	0.000658	0.986093	1	1	C>T
ERR5749202	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	22770	0.00123	0	22712,0,28,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749202	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	46001	9.57E-4	0	22979,22929,25,25	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749202	14168	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	19936	6.02E-4	0	5,19919,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	atatta/	IL244	RdRp	0.000479	0.314961	1	1	CTA>C
ERR5749202	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	17213	0.004531	2147483647	16809,142,5,254	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749202	14408	PASS	C	T	33470	0.854347	16	1,8,16694,16555	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749202	14599	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18721	0.001335	0	18689,2,26,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L387	RdRp	0.000639	0.922766	3	2	C>T
ERR5749202	14676	PASS	C	T	18711	0.802148	0	3,0,18661,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749202	15279	PASS	C	T	30565	0.883461	0	5,0,30507,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749202	15983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	15696	7.01E-4	0	15688,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T850	RdRp	0.000701	0.338235	2	1	TA>T
ERR5749202	16176	PASS	T	C	25555	0.980004	8	2,0,9831,15710	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749202	16468	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	38990	0.001077	0	29115,9827,31,11	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ccc/Tcc	P78S	helicase	0.001077	0.977186	1	1	C>T
ERR5749202	18501	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	36952	5.68E-4	0	10,36921,0,21	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K155	ExoN	0.000336	0.857143	4	2	CA>C
ERR5749202	18681	PASS	C	T	29644	0.923661	0	3,0,29629,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A214	ExoN	0.028796	0.923661	1	1	C>T
ERR5749202	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	29644	9.45E-4	0	29616,0,28,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749202	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23924	0.001797	0	23867,0,44,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749202	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	29084	4.47E-4	0	0,29054,0,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TA>T
ERR5749202	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAA	T	29084	4.47E-4	0	0,29054,0,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TAA>T
ERR5749202	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	37826	0.003199	0	18496,18820,71,74	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749202	21764	PASS	ATACATG	A	14383	0.992561	0	107,0,14276,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749202	21812	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14382	0.004659	0	14295,0,68,0	LOW	SILENT	SYNONYMOUS_CODING	S	Cta/Tta	L84	S	0.001506	0.06449	1	1	C>T
ERR5749202	21990	PASS	TTTA	T	14393	0.997082	0	0,42,7,14344	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749202	22484	PASS	G	T	11931	0.765485	9	1,15,91,11716	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gta/Tta	V308L	S	0.003485	0.765485	2	1	G>T
ERR5749202	23063	PASS	A	T	16178	0.865002	0	0,2,2,16089	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749202	23086	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16187	0.004695	0	0,16083,0,96	LOW	SILENT	SYNONYMOUS_CODING	S	taC/taT	Y508	S	0.00176	0.131707	2	2	C>T
ERR5749202	23271	PASS	C	A	32202	0.921496	0	1,0,32172,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749202	23403	PASS	A	G	32191	0.971607	0	0,12,0,32149	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749202	23604	PASS	C	A	16698	0.94155	0	12,0,16671,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749202	23709	PASS	C	T	16674	0.941226	0	0,5,0,16649	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749202	24506	PASS	T	G	26154	0.972471	0	14,0,26133,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749202	24914	PASS	G	C	44452	0.958472	0	1,2,22134,22273	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749202	25572	PASS	C	T	22598	0.959687	0	0,10,0,22577	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	tcC/tcT	S60	orf3a	0.000543	0.959687	4	2	C>T
ERR5749202	25573	PASS	A	C	22598	0.954465	0	0,11,0,22517	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Aaa/Caa	K61Q	orf3a	0.001796	0.954465	3	2	A>C
ERR5749202	25573	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	22598	0.002788	0	0,11,0,69	HIGH	NONSENSE	STOP_GAINED	ORF3a	Aaa/Taa	K61*	orf3a	0.001796	0.954465	3	2	A>T
ERR5749202	25574	PASS	A	T	22598	0.932074	0	0,9,0,22561	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aAa/aTa	K61I	orf3a	0.899143	0.932074	1	1	A>T
ERR5749202	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	18515	0.001566	395	18437,22,12,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749202	26013	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	47685	8.39E-4	0	47613,0,43,0	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	ttC/ttT	F207	orf3a	0.000839	0.974528	1	1	C>T
ERR5749202	26208	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	47675	3.15E-4	0	0,47659,0,15	HIGH	NONE	FRAME_SHIFT	ORF3a	gtg/	V273	orf3a	0.000315	0.922222	2	2	CG>C
ERR5749202	26228	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	47686	7.34E-4	0	0,47629,0,39	.	.	.	.	.	.	.	0.000649	0.94873	2	1	C>T
ERR5749202	26270	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	47691	7.76E-4	0	5,47625,0,41	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	aCa/aTa	T9I	E	0.000586	0.930791	3	2	C>T
ERR5749202	26571	PASS	C	T	15662	0.905823	0	4,0,15645,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Ctt/Ttt	L17F	M	0.000508	0.905823	3	2	C>T
ERR5749202	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	15646	7.67E-4	0	0,15634,0,12	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749202	27676	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAACTTTACTCTCCAATTTTT	G	29533	6.09E-4	0	17,29498,0,18	HIGH	NONE	FRAME_SHIFT	ORF7a	gaactttactctccaattttt/	ELYSPIF95	orf7a	0.000609	0.877803	2	2	GAACTTTACTCTCCAATTTTT>G
ERR5749202	27972	PASS	C	T	11034	0.902574	0	0,0,10935,64	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749202	28048	PASS	G	T	10974	0.920539	0	0,12,0,10948	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749202	28111	PASS	A	G	38949	0.978921	9	8,0,27948,10982	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749202	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27946	0.001396	0	27820,0,42,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749202	28270	PASS	TA	T	54270	0.994988	641	264,8,27597,26401	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749202	28271	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AA	A	54267	4.98E-4	62	27827,26414,26,1	.	.	.	.	.	.	.	0.000482	0.924941	3	2	AA>A
ERR5749202	28280	PASS	G	C	54167	0.937914	17	17,5,27658,26369	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749202	28281	PASS	A	T	54167	0.917828	32	30,8,27649,26380	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749202	28282	PASS	T	A	54171	0.912481	9	25,14,27606,26392	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749202	28881	PASS	G	A	25761	0.775319	27	10,0,12746,12673	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749202	28882	PASS	G	A	25761	0.826521	11	7,1,12885,12633	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749202	28883	PASS	G	C	25761	0.943015	9	1,5,12908,12822	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749202	28977	PASS	C	T	13114	0.931371	0	0,5,0,13091	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749202	29095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34424	9.59E-4	0	34365,0,37,0	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F274	N	0.000792	0.961279	2	2	C>T
ERR5749202	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	68370	0.001126	0	34310,33932,48,47	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749202	29675	PASS	C	T	20497	0.883495	6	1,4,10278,10125	.	.	.	.	.	.	.	0.000624	0.883495	2	1	C>T
ERR5749203	241	PASS	C	T	13456	0.869724	0	0,0,6695,6717	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749203	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	8445	0.002368	0	8423,0,20,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749203	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	8435	0.002608	0	7747,0,654,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749203	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	8435	9.48E-4	0	8427,0,8,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749203	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATGGTTG	T	8432	8.3E-4	0	8422,0,7,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	atggttgag/	MVE85	leader	0.000587	0.476744	4	1	TATGGTTG>T
ERR5749203	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	28143	5.33E-4	12	19660,8455,14,1	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749203	892	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	19670	5.08E-4	0	0,19660,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K30	nsp2	0.000495	0.082222	2	2	TA>T
ERR5749203	913	PASS	C	T	19674	0.91288	0	0,7,0,19646	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749203	3037	PASS	C	T	14472	0.826009	19	1,9,7234,7143	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749203	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	7321	0.002322	408	13,7285,17,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749203	3267	PASS	C	T	20641	0.971561	0	1,0,20626,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749203	4764	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATT	A	14039	7.84E-4	0	14027,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F683	nsp3	0.000673	0.93404	4	2	ATT>A
ERR5749203	5170	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	10248	7.81E-4	0	0,10240,0,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T819	nsp3	0.000565	0.894036	2	2	CCA>C
ERR5749203	5388	PASS	C	A	3750	0.954133	2147483647	0,0,3748,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749203	5986	PASS	C	T	9165	0.97665	2147483647	0,0,9162,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749203	6954	PASS	T	C	18910	0.827234	0	0,5,0,18823	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749203	7070	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	29236	0.002189	296	10197,18967,65,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggc/Agc	G1451S	nsp3	0.000698	0.101434	3	1	G>A
ERR5749203	9402	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	21604	4.63E-4	0	10799,10782,5,5	HIGH	NONE	FRAME_SHIFT	ORF1ab	ata/	I284	nsp4	0.000453	0.058824	2	2	CTA>C
ERR5749203	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	23855	0.001425	89	12991,10827,34,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749203	11104	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	22479	0.001335	0	22385,0,32,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccT/ccC	P44	nsp6	0.000866	0.675414	2	1	T>C
ERR5749203	11199	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	44809	6.47E-4	0	22271,22370,15,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCc/gTc	A76V	nsp6	0.000309	0.056758	3	2	C>T
ERR5749203	11287	PASS	GTCTGGTTTT	G	22479	0.998087	0	0,43,0,22436	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749203	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	31816	0.001194	10	22693,9048,25,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749203	12125	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	17318	0.001039	0	2,17239,0,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y12H	nsp8	0.000847	0.113436	1	1	T>C
ERR5749203	13459	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTT	G	14479	6.91E-4	0	14452,0,10,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ttttta/tta	FL7L	nsp11	0.000691	0.060726	5	2	GTTT>G
ERR5749203	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28919	0.001245	0	14431,14399,21,21	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749203	13994	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	16697	6.59E-4	0	16686,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L186	RdRp	0.000427	0.114441	3	2	CT>C
ERR5749203	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	13748	0.00371	2147483647	13403,123,6,205	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749203	14408	PASS	C	T	26689	0.84739	11	1,6,13320,13203	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749203	14676	PASS	C	T	12628	0.798781	0	3,0,12585,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749203	15279	PASS	C	T	19496	0.884899	0	3,0,19465,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749203	15379	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	38907	7.45E-4	18	19340,19426,32,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Agc/Ggc	S647G	RdRp	0.000745	0.947742	2	2	A>G
ERR5749203	16176	PASS	T	C	17430	0.980838	8	2,0,6395,11030	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749203	16647	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	24088	9.13E-4	0	1,23932,0,23	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acG/acA	T137	helicase	0.000746	0.885245	2	1	G>A
ERR5749203	17795	PASS	C	T	13042	0.966723	2147483647	0,0,13029,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A520V	helicase	0.00111	0.966723	2	2	C>T
ERR5749203	18079	PASS	G	T	8538	0.934996	0	10,0,8521,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gta/Tta	V14L	ExoN	0.003215	0.944695	2	1	G>T
ERR5749203	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17867	0.002127	0	17818,0,39,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749203	20987	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	47985	4.17E-4	0	23994,23977,11,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L111	MethTr	0.000276	0.056129	4	2	CT>C
ERR5749203	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	24053	6.65E-4	0	0,24033,0,16	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TA>T
ERR5749203	21123	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	45026	0.028695	1	20264,23273,696,786	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggG/ggT	G155	MethTr	0.000257	0.90982	5	2	G>T
ERR5749203	21764	PASS	ATACATG	A	10764	0.995169	0	47,0,10712,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749203	21990	PASS	TTTA	T	10768	0.998143	0	0,20,2,10746	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749203	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	16926	0.001477	0	0,16889,0,26	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749203	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29685	8.42E-4	9	12737,16916,15,10	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749203	23063	PASS	A	T	12727	0.881355	0	0,4,0,12668	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749203	23271	PASS	C	A	23757	0.922381	0	1,0,23729,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749203	23403	PASS	A	G	23753	0.970951	0	0,1,0,23733	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749203	23604	PASS	C	A	12874	0.940889	0	8,0,12854,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749203	23709	PASS	C	T	12853	0.946627	0	0,3,0,12839	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749203	24506	PASS	T	G	16226	0.976827	0	9,0,16211,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749203	24914	PASS	G	C	35201	0.961251	2	2,1,17526,17641	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749203	25496	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	35211	3.69E-4	0	17600,17611,6,7	HIGH	NONE	FRAME_SHIFT	ORF3a	ataccg/	IP35	orf3a	0.000369	0.96555	3	2	TAC>T
ERR5749203	25626	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	30593	4.25E-4	2	12932,17643,4,9	HIGH	NONE	FRAME_SHIFT	ORF3a	ttt/	F79	orf3a	0.000403	0.915633	3	2	CT>C
ERR5749203	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	12972	0.002467	479	12906,15,13,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749203	26918	PASS	G	T	31596	0.977086	0	5,0,31583,0	LOW	SILENT	SYNONYMOUS_CODING	M	ccG/ccT	P132	M	0.000999	0.977086	2	1	G>T
ERR5749203	27599	PASS	A	G	18827	0.950072	0	6,0,18786,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	gAc/gGc	D69G	orf7a	0.950072	0.959723	1	1	A>G
ERR5749203	27972	PASS	C	T	7729	0.902963	0	0,0,7661,38	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749203	28048	PASS	G	T	7695	0.926706	0	0,8,0,7682	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749203	28111	PASS	A	G	30407	0.978031	1	6,1,22691,7697	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749203	28270	PASS	TA	T	44105	0.995057	513	217,8,22411,21476	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749203	28280	PASS	G	C	44012	0.937358	10	10,3,22466,21448	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749203	28281	PASS	A	T	44012	0.919386	20	27,10,22448,21454	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749203	28282	PASS	T	A	44014	0.914618	1	23,19,22414,21463	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749203	28406	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTACCCAATA	T	22715	4.4E-4	0	8,22697,0,10	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	N	ttacccaataat/tat	LPNN45Y	N	0.00043	0.921074	3	2	TTACCCAATA>T
ERR5749203	28881	PASS	G	A	16752	0.77937	11	7,1,8296,8248	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749203	28882	PASS	G	A	16752	0.836318	9	4,0,8371,8233	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749203	28883	PASS	G	C	16752	0.946514	0	3,3,8384,8347	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749203	28977	PASS	C	T	8512	0.936208	2147483647	0,0,0,8502	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749203	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	34498	9.57E-4	81	25963,8480,10,25	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749203	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	51587	9.3E-4	0	25900,25601,30,30	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749203	29394	PASS	A	G	9341	0.969596	0	1,0,9327,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aAg/aGg	K374R	N	0.969596	0.969596	1	1	A>G
ERR5749204	71	PASS	C	T	642	0.926791	0	38,0,604,0	.	.	.	.	.	.	.	0.002088	0.926791	2	1	C>T
ERR5749204	241	PASS	C	T	75	0.853333	0	0,0,37,37	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749204	913	PASS	C	T	8117	0.911667	0	0,4,0,8102	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749204	2306	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1453	0.01927	0	1421,0,29,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Ttt	L501F	nsp2	0.01927	0.915753	1	1	C>T
ERR5749204	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	9810	0.001427	918	4900,4500,16,370	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749204	2779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	4936	0.006686	0	0,4893,0,36	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	agT/agA	S20R	nsp3	0.003967	0.16	2	2	T>A
ERR5749204	3037	PASS	C	T	703	0.812233	6	0,2,350,347	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749204	3267	PASS	C	T	4965	0.969184	2147483647	0,0,4963,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749204	5388	PASS	C	A	189	0.968254	2147483647	0,0,189,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749204	5849	PASS	C	T	3357	0.830206	0	0,1,0,3356	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cct/Tct	P1044S	nsp3	0.00146	0.830206	2	1	C>T
ERR5749204	5986	PASS	C	T	1238	0.978191	0	1,0,1236,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749204	6411	PASS	A	T	2737	0.820972	2147483647	0,0,0,2730	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gAa/gTa	E1231V	nsp3	0.820972	0.820972	1	1	A>T
ERR5749204	6675	PASS	C	T	2536	0.80205	0	0,0,1291,1225	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T1319I	nsp3	0.80205	0.80205	1	1	C>T
ERR5749204	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	1298	0.03775	0	0,1249,0,49	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L1328S?	nsp3	0.000731	0.14377	4	2	C>CT
ERR5749204	6954	PASS	T	C	3218	0.815724	2147483647	0,0,0,3198	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749204	7926	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	6140	0.003909	0	0,6116,0,24	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1737	nsp3	0.000531	0.97019	5	2	CA>C
ERR5749204	8603	PASS	T	C	965	0.966839	2147483647	0,0,0,964	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Ctc	F17L	nsp4	0.002607	0.974959	2	1	T>C
ERR5749204	9402	PASS	C	T	170	0.058824	0	80,78,5,5	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S283F	nsp4	0.000453	0.058824	2	2	C>T
ERR5749204	9727	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	1523	0.015758	0	0,1492,0,26	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taT/taC	Y391	nsp4	0.015758	0.973696	1	1	T>C
ERR5749204	10116	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4379	0.031057	139	3373,858,147,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T21I	3Cpro	0.001266	0.952096	1	1	C>T
ERR5749204	11287	PASS	GTCTGGTTTT	G	7229	0.998063	0	0,14,0,7215	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749204	11572	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	592	0.015203	0	0,583,0,9	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F200	nsp6	0.005575	0.918642	2	2	C>T
ERR5749204	11750	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11883	0.02533	4	5840,5579,229,198	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L260F	nsp6	0.001019	0.70989	2	1	C>T
ERR5749204	13424	PASS	C	T	4239	0.967209	2147483647	0,0,4235,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgc/Tgc	R134C	nsp10	0.039582	0.967209	1	1	C>T
ERR5749204	14408	PASS	C	T	116	0.827586	0	0,0,58,57	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749204	14676	PASS	C	T	3479	0.808853	0	1,0,3468,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749204	15279	PASS	C	T	2106	0.869421	2147483647	0,0,2102,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749204	16176	PASS	T	C	4696	0.977428	0	0,0,130,4564	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749204	17615	PASS	A	G	1808	0.919248	2147483647	0,0,0,1804	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749204	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	746	0.025469	0	727,0,19,0	HIGH	NONE	FRAME_SHIFT+STOP_GAINED	ORF1ab	gat/Tgat	D124*?	endoR	0.000884	0.981982	5	2	C>CT
ERR5749204	20987	PASS	CT	C	13469	0.056129	0	6365,6348,377,379	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L111	MethTr	0.000276	0.056129	4	2	CT>C
ERR5749204	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	6753	0.016437	0	0,6642,0,111	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TA>T
ERR5749204	21101	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	6756	0.019094	0	1,6590,0,165	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGt/gTt	G148V	MethTr	0.001498	0.083467	2	2	G>T
ERR5749204	21764	PASS	ATACATG	A	1896	0.996835	0	6,0,1890,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749204	21781	PASS	C	T	1895	0.104485	0	1692,0,203,0	LOW	SILENT	SYNONYMOUS_CODING	S	acC/acT	T73	S	0.000512	0.104485	2	2	C>T
ERR5749204	21990	PASS	TTTA	T	1897	0.974697	0	0,48,1,1848	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749204	22185	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9855	0.001725	0	4865,4970,9,9	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCg/aTg	T208M	S	0.001725	0.919834	1	1	C>T
ERR5749204	22388	PASS	C	T	1822	0.950604	2147483647	0,0,1822,0	LOW	SILENT	SYNONYMOUS_CODING	S	Cta/Tta	L276	S	0.003317	0.950604	1	1	C>T
ERR5749204	23063	PASS	A	T	1806	0.841085	2147483647	0,0,0,1801	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749204	23271	PASS	C	A	10845	0.916644	0	1,0,10828,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749204	23403	PASS	A	G	10839	0.966694	0	0,1,0,10829	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749204	23593	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	1653	0.021779	0	1615,0,37,0	LOW	SILENT	SYNONYMOUS_CODING	S	caG/caA	Q677	S	0.021779	0.924148	3	2	G>A
ERR5749204	23604	PASS	C	A	1653	0.946159	2147483647	0,0,1651,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749204	23709	PASS	C	T	1651	0.937614	2147483647	0,0,0,1647	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749204	23758	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1654	0.004837	0	0,1646,0,8	LOW	SILENT	SYNONYMOUS_CODING	S	acC/acT	T732	S	0.001489	0.964055	1	1	C>T
ERR5749204	24506	PASS	T	G	2783	0.974488	0	1,0,2780,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749204	24850	PASS	T	G	12356	0.980819	0	7,0,12349,0	LOW	SILENT	SYNONYMOUS_CODING	S	gtT/gtG	V1096	S	0.002228	0.980819	2	1	T>G
ERR5749204	24914	PASS	G	C	24580	0.958869	0	1,1,12261,12301	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749204	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	11414	0.001665	15	9632,1756,26,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749204	25437	PASS	G	T	9676	0.965482	0	6,0,9664,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	ttG/ttT	L15F	orf3a	0.001128	0.971411	2	2	G>T
ERR5749204	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	243	0.032922	113	230,5,0,8	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749204	26493	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	3114	0.035645	0	0,3003,0,111	.	.	.	.	.	.	.	0.001082	0.069277	3	1	G>GT
ERR5749204	27294	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5114	0.01623	0	5007,0,94,0	LOW	SILENT	SYNONYMOUS_CODING	ORF6	taC/taT	Y31	orf6	0.000651	0.875122	2	2	C>T
ERR5749204	27972	PASS	C	T	466	0.924893	2147483647	0,0,466,0	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749204	28048	PASS	G	T	465	0.907527	0	0,2,0,463	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749204	28111	PASS	A	G	13543	0.978587	0	1,0,13072,465	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749204	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13064	0.008497	0	12905,0,119,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749204	28270	PASS	TA	T	25192	0.994601	344	136,3,12874,12182	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749204	28280	PASS	G	C	25129	0.935413	14	12,3,12901,12163	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749204	28281	PASS	A	T	25129	0.911815	23	20,5,12895,12164	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749204	28282	PASS	T	A	25131	0.911862	2	8,5,12885,12180	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749204	28881	PASS	G	A	807	0.804213	0	0,0,400,399	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749204	28882	PASS	G	A	807	0.843866	0	0,0,404,395	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749204	28883	PASS	G	C	807	0.945477	0	0,0,405,402	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749204	28977	PASS	C	T	410	0.931707	2147483647	0,0,0,409	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749204	29302	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	7055	0.013749	0	0,6947,0,106	LOW	SILENT	SYNONYMOUS_CODING	N	gaT/gaC	D343	N	0.013749	0.934178	1	1	T>C
ERR5749205	241	PASS	C	T	6918	0.859352	0	0,0,3434,3456	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749205	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	3943	0.002283	0	3933,1,9,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749205	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	3943	0.003297	0	3921,1,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749205	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	3945	0.001774	20	3934,4,6,1	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749205	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	12040	0.002326	46	8059,3944,28,0	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749205	913	PASS	C	T	8091	0.913608	0	0,11,0,8067	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749205	1813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	7779	0.002314	0	0,7755,0,20	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcA	A336	nsp2	0.001022	0.152738	4	2	T>A
ERR5749205	1846	PASS	A	G	7783	0.941925	0	0,2,0,7772	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaA/aaG	K347	nsp2	0.001438	0.945471	2	2	A>G
ERR5749205	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	25537	0.00141	1955	12740,11961,21,747	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749205	3037	PASS	C	T	6738	0.828733	15	0,5,3366,3322	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749205	3267	PASS	C	T	7510	0.968442	0	1,0,7501,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749205	5074	PASS	T	C	3947	0.967824	0	7,0,3937,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaT/gaC	D785	nsp3	0.000986	0.967824	2	2	T>C
ERR5749205	5077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	3947	0.003547	0	3921,0,14,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtT/gtC	V786	nsp3	0.001393	0.168205	1	1	T>C
ERR5749205	5388	PASS	C	A	2372	0.949831	2147483647	0,0,2370,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749205	5986	PASS	C	T	4653	0.978294	2147483647	0,0,4649,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749205	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4638	0.003234	0	2,4564,0,19	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749205	6954	PASS	T	C	7680	0.819271	0	0,3,0,7634	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749205	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	12833	0.002104	78	6401,6405,27,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749205	10193	PASS	G	A	6915	0.859291	0	2,0,6905,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E47K	3Cpro	0.000774	0.869819	2	2	G>A
ERR5749205	10195	PASS	A	T	6915	0.967173	0	7,0,6907,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gaA/gaT	E47D	3Cpro	0.951998	0.969772	1	1	A>T
ERR5749205	11287	PASS	GTCTGGTTTT	G	7851	0.997835	0	0,17,0,7834	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749205	12741	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13864	0.002092	1	6812,7019,16,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T19I	nsp9	0.000486	0.962552	2	2	C>T
ERR5749205	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	5836	0.004626	1402	5686,61,5,84	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749205	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	11327	0.001413	0	5680,5640,8,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749205	14408	PASS	C	T	11327	0.852565	2	1,2,5656,5600	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749205	14676	PASS	C	T	4778	0.757849	2147483647	0,0,4767,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749205	15279	PASS	C	T	7952	0.895372	2147483647	0,0,7940,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749205	16176	PASS	T	C	7452	0.980005	0	0,0,3550,3900	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749205	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	7868	0.001906	0	7850,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749205	18086	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4429	0.007902	0	4381,0,47,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T16I	ExoN	0.001699	0.075758	1	1	C>T
ERR5749205	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	9551	8.38E-4	0	0,9543,0,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749205	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11862	0.002782	0	11819,0,37,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749205	21255	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	21903	9.59E-4	2	11315,10563,14,10	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcG/gcA	A199	MethTr	0.000341	0.917425	4	2	G>A
ERR5749205	21764	PASS	ATACATG	A	4752	0.994529	0	26,0,4726,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749205	21990	PASS	TTTA	T	4758	0.995376	14	1,21,6,4730	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749205	22858	PASS	C	T	11002	0.973187	6	0,3,5391,5594	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749205	23063	PASS	A	T	5387	0.861147	0	0,0,3,5359	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749205	23271	PASS	C	A	8062	0.923468	2147483647	0,0,8055,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749205	23403	PASS	A	G	8066	0.976816	0	0,2,0,8058	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749205	23604	PASS	C	A	5999	0.945991	0	3,0,5995,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749205	23709	PASS	C	T	5994	0.928095	0	0,3,1,5978	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749205	24506	PASS	T	G	6343	0.971938	0	3,0,6340,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749205	24914	PASS	G	C	14306	0.962673	3	1,0,7124,7167	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749205	26461	PASS	C	T	4004	0.838412	0	0,346,0,3643	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	Ctt/Ttt	L73F	E	0.001401	0.928597	1	1	C>T
ERR5749205	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	4953	0.001211	0	0,4947,0,6	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749205	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	4953	0.002221	0	0,4941,0,11	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749205	27972	PASS	C	T	4259	0.90162	0	0,0,4215,27	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749205	28048	PASS	G	T	4228	0.911069	0	0,3,0,4222	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749205	28111	PASS	A	G	12194	0.976874	2	2,2,7952,4228	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749205	28270	PASS	TA	T	15222	0.995073	139	70,5,7870,7277	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749205	28280	PASS	G	C	15200	0.932171	0	2,1,7889,7273	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749205	28281	PASS	A	T	15200	0.916842	5	9,4,7891,7269	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749205	28282	PASS	T	A	15200	0.903355	0	10,8,7879,7275	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749205	28881	PASS	G	A	6890	0.777794	6	3,0,3420,3388	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749205	28882	PASS	G	A	6890	0.822932	0	1,1,3453,3388	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749205	28883	PASS	G	C	6890	0.941364	0	0,0,3454,3428	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749205	28977	PASS	C	T	3504	0.865868	0	0,1,0,3490	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749205	28979	PASS	G	T	3504	0.964327	2147483647	0,0,0,3500	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Ggt/Tgt	G236C	N	0.964327	0.964327	1	1	G>T
ERR5749205	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	26146	9.94E-4	0	13123,12981,17,15	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749206	241	PASS	C	T	356	0.856742	0	0,0,178,177	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749206	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	963	0.004154	0	962,0,4,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749206	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	963	0.008307	0	955,0,8,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749206	745	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6574	0.004107	0	6545,0,28,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N160	leader	0.001671	0.915927	1	1	C>T
ERR5749206	841	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13120	0.00122	0	6553,6543,8,8	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G12	nsp2	0.000771	0.932538	2	1	C>T
ERR5749206	913	PASS	C	T	6571	0.909907	0	0,21,0,6546	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749206	1813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	5665	0.004766	0	0,5631,0,30	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcA	A336	nsp2	0.001022	0.152738	4	2	T>A
ERR5749206	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	18053	0.001828	1416	9015,8417,20,558	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749206	3037	PASS	C	T	2340	0.808547	9	0,3,1172,1157	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749206	3267	PASS	C	T	5820	0.97543	2147483647	0,0,5818,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749206	3609	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	3136	0.003189	0	3116,0,12,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cTt/cCt	L297P	nsp3	0.003189	0.071429	1	1	T>C
ERR5749206	5002	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	3810	0.003675	0	3793,1,16,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ctC/ctA	L761	nsp3	0.001115	0.976835	3	2	C>A
ERR5749206	5388	PASS	C	A	773	0.958603	2147483647	0,0,773,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749206	5497	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	771	0.007782	0	0,765,0,6	HIGH	NONE	FRAME_SHIFT	ORF1ab	aga/	R928	nsp3	0.000964	0.897745	3	2	CA>C
ERR5749206	5640	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	5866	0.002387	0	5850,0,14,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cAa/cTa	Q974L	nsp3	0.002387	0.921164	1	1	A>T
ERR5749206	5986	PASS	C	T	3141	0.975167	2147483647	0,0,3139,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749206	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2922	0.004449	0	0,2879,0,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749206	6954	PASS	T	C	6630	0.819005	0	0,1,0,6595	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749206	7926	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	8158	0.001226	0	0,8148,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1737	nsp3	0.000531	0.97019	5	2	CA>C
ERR5749206	10323	PASS	A	G	6676	0.959856	2147483647	0,0,0,6671	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749206	11287	PASS	GTCTGGTTTT	G	34	1.0	2147483647	0,0,0,34	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749206	12109	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	10110	0.002176	0	0,10066,0,23	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttT/ttC	F6	nsp8	0.002176	0.963972	1	1	T>C
ERR5749206	12781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	2028	0.004438	0	2017,1,10,0	HIGH	NONSENSE	STOP_GAINED	ORF1ab	taC/taA	Y32*	nsp9	0.001869	0.974683	2	2	C>A
ERR5749206	14408	PASS	C	T	523	0.843212	0	0,0,258,256	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749206	14676	PASS	C	T	3645	0.79369	2147483647	0,0,3630,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749206	15096	PASS	T	C	3288	0.958942	0	0,5,0,3282	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaT/aaC	N552	RdRp	0.941667	0.970182	1	1	T>C
ERR5749206	15279	PASS	C	T	4604	0.888792	0	1,0,4599,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749206	16176	PASS	T	C	4929	0.980726	0	0,0,706,4220	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749206	16293	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	707	0.008487	0	701,0,6,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C19	helicase	0.001538	0.968351	1	1	C>T
ERR5749206	16792	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14445	0.001731	50	5486,8932,0,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgt/Tgt	R186C	helicase	0.000335	0.072562	5	2	C>T
ERR5749206	17766	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3543	0.004516	0	3526,0,17,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V510	helicase	0.000768	0.920632	2	2	C>T
ERR5749206	20987	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19196	0.002605	2	9549,9511,30,34	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T110I	MethTr	0.000276	0.056129	4	2	C>T
ERR5749206	20987	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTT	C	19195	0.006356	0	9544,9530,61,61	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L111	MethTr	0.000276	0.056129	4	2	CTT>C
ERR5749206	21764	PASS	ATACATG	A	4350	0.997241	0	12,0,4338,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749206	21854	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	8681	0.002649	1	4319,4305,14,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tct/Cct	S98P	S	0.00132	0.05283	1	1	T>C
ERR5749206	21990	PASS	TTTA	T	4350	0.994483	0	0,24,1,4325	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749206	23012	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	7973	0.001756	0	4112,3839,9,7	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gaa/Caa	E484Q	S	0.001756	0.909912	2	1	G>C
ERR5749206	23063	PASS	A	T	4141	0.873702	0	0,1,0,4125	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749206	23170	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	12130	7.42E-4	41	7980,4141,0,9	HIGH	NONE	FRAME_SHIFT	S	aaa/	K537	S	0.000408	0.975449	3	2	CA>C
ERR5749206	23271	PASS	C	A	7980	0.927694	2147483647	0,0,7979,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749206	23403	PASS	A	G	7979	0.97155	0	0,1,0,7971	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749206	23525	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4432	0.002933	0	4418,0,13,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Cat/Tat	H655Y	S	0.001101	0.97751	2	2	C>T
ERR5749206	23604	PASS	C	A	4431	0.939291	0	5,0,4421,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749206	23709	PASS	C	T	4423	0.946643	0	0,1,0,4420	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749206	24166	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	4205	0.002854	0	4191,0,14,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gaA/gaT	E868D	S	0.002854	0.054348	2	2	A>T
ERR5749206	24320	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	4201	0.00238	0	0,4191,0,10	HIGH	NONE	FRAME_SHIFT	S	aaa/	K921	S	0.000763	0.138365	4	2	CA>C
ERR5749206	24506	PASS	T	G	5975	0.974561	0	4,0,5970,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749206	24914	PASS	G	C	17026	0.956361	0	0,0,8477,8538	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749206	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	12910	0.002634	34	10313,2557,39,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749206	25624	PASS	C	T	11218	0.432341	20	426,5857,398,4533	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Cac/Tac	H78Y	orf3a	0.00089	0.983312	1	1	C>T
ERR5749206	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	824	0.008495	0	817,0,7,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749206	26091	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAATA	C	8897	0.001236	0	8888,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF3a	aataaa/	NK234	orf3a	0.000569	0.128212	4	2	CAATA>C
ERR5749206	26690	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	3434	0.002912	0	3411,10,11,0	LOW	SILENT	SYNONYMOUS_CODING	M	ctG/ctC	L56	M	0.002912	0.753489	2	1	G>C
ERR5749206	27312	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	8166	0.005756	0	8119,0,47,0	HIGH	NONE	FRAME_SHIFT	ORF6	aat/aaAt	N39K?	orf6	0.000911	0.088458	4	2	T>TA
ERR5749206	27972	PASS	C	T	1379	0.900653	77	3,4,1363,4	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749206	28048	PASS	G	T	1372	0.919096	0	0,2,0,1369	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749206	28095	PASS	A	T	1375	0.955636	31	1,0,0,1374	HIGH	NONSENSE	STOP_GAINED	ORF8	Aaa/Taa	K68*	orf8	0.002672	0.967672	2	2	A>T
ERR5749206	28111	PASS	A	G	13233	0.981259	7	1,1,11854,1373	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749206	28270	PASS	TA	T	22952	0.994118	327	134,4,11668,11149	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749206	28280	PASS	G	C	22910	0.93684	9	4,0,11697,11139	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749206	28281	PASS	A	T	22910	0.915277	14	10,2,11697,11136	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749206	28282	PASS	T	A	22911	0.916547	7	13,6,11706,11145	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749206	28603	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17001	0.001118	0	8486,8420,10,10	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F110	N	0.000427	0.883357	2	2	C>T
ERR5749206	28881	PASS	G	A	2060	0.799029	0	1,0,1027,1010	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749206	28882	PASS	G	A	2060	0.826699	0	0,0,1035,1008	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749206	28883	PASS	G	C	2060	0.951942	0	0,0,1037,1023	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749206	28977	PASS	C	T	1048	0.937023	2147483647	0,0,0,1047	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749206	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	18986	0.002054	0	9527,9405,24,22	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749207	239	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTC	T	25611	6.25E-4	0	12779,12814,8,8	.	.	.	.	.	.	.	0.000495	0.25	4	1	TTC>T
ERR5749207	241	PASS	C	T	25610	0.85779	4	3,6,12765,12713	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749207	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	9244	9.74E-4	0	9231,3,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749207	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	9236	0.002274	0	8501,3,720,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749207	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26841	9.31E-4	0	0,26788,0,32	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749207	913	PASS	C	T	26842	0.916102	0	0,10,0,26804	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749207	1813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	16848	0.001128	0	0,16800,0,25	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcA	A336	nsp2	0.001022	0.152738	4	2	T>A
ERR5749207	3037	PASS	C	T	13872	0.814446	39	0,13,6940,6827	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749207	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	7022	0.002706	514	3,6994,19,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749207	3177	PASS	C	T	32275	0.926104	0	5,1,25260,6979	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P153L	nsp3	0.000773	0.96008	3	2	C>T
ERR5749207	3267	PASS	C	T	25270	0.968461	0	9,0,25252,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749207	5388	PASS	C	A	4346	0.957432	2147483647	0,0,4345,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749207	5986	PASS	C	T	9073	0.974981	2147483647	0,0,9066,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749207	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9196	0.002066	0	0,9112,0,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749207	6954	PASS	T	C	23654	0.821679	0	0,1,0,23533	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749207	7528	PASS	C	T	19243	0.915917	0	0,11,16,19173	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V1603	nsp3	0.002527	0.916131	1	1	C>T
ERR5749207	8113	PASS	A	T	32130	0.939838	0	31,0,32060,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcA/gcT	A1798	nsp3	0.939838	0.939838	1	1	A>T
ERR5749207	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	32266	7.75E-4	93	13571,18670,25,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749207	10386	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	38291	7.83E-4	0	22202,16044,20,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T111I	3Cpro	0.000642	0.160456	4	2	C>T
ERR5749207	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	15160	0.002309	0	15099,0,54,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749207	11287	PASS	GTCTGGTTTT	G	15155	0.998944	0	0,16,0,15139	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749207	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	37376	8.83E-4	11	26363,10940,20,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749207	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	17536	0.001083	0	17491,0,20,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749207	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	38689	0.00137	0	19320,19261,29,29	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749207	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	8951	0.004245	2413	8750,60,5,134	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749207	14408	PASS	C	T	17438	0.8388	0	1,1,8704,8633	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749207	14676	PASS	C	T	16597	0.742303	0	11,0,16520,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749207	15279	PASS	C	T	25953	0.890225	0	2,0,25909,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749207	15810	PASS	C	T	15065	0.052439	0	2,14216,0,838	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N790	RdRp	0.052439	0.052439	1	1	C>T
ERR5749207	16176	PASS	T	C	21083	0.980506	5	2,1,7391,13682	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749207	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	31975	3.75E-4	0	0,31963,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749207	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24513	0.002978	0	24419,0,76,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749207	21622	PASS	C	T	19586	0.928112	0	0,18,0,19520	LOW	SILENT	SYNONYMOUS_CODING	S	acC/acT	T20	S	0.000846	0.946634	3	2	C>T
ERR5749207	21764	PASS	ATACATG	A	10128	0.997235	0	28,0,10100,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749207	21990	PASS	TTTA	T	10130	0.998124	0	0,19,2,10109	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749207	22227	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	21292	5.64E-4	0	0,21280,0,12	HIGH	NONE	FRAME_SHIFT	S	tta/	L223	S	0.000419	0.824305	2	2	CT>C
ERR5749207	22450	PASS	C	T	7402	0.795596	0	1,0,7291,36	LOW	SILENT	SYNONYMOUS_CODING	S	ctC/ctT	L296	S	0.00215	0.803846	1	1	C>T
ERR5749207	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	18251	0.001479	0	0,18217,0,29	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749207	23063	PASS	A	T	11635	0.86893	2147483647	0,0,0,11579	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749207	23271	PASS	C	A	29148	0.920475	0	3,0,29112,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749207	23403	PASS	A	G	29132	0.969484	0	0,5,0,29106	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749207	23604	PASS	C	A	12327	0.946216	0	7,0,12315,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749207	23709	PASS	C	T	12308	0.942476	0	0,3,0,12283	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749207	24506	PASS	T	G	21547	0.974196	0	8,0,21537,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749207	24914	PASS	G	C	32511	0.958845	0	0,0,16208,16282	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749207	25207	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9388	0.004687	0	0,9249,0,53	LOW	SILENT	SYNONYMOUS_CODING	S	taC/taT	Y1215	S	0.004687	0.815232	1	1	C>T
ERR5749207	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	25275	0.001108	59	15816,9414,36,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749207	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	18225	0.001811	426	18145,7,18,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749207	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	18201	5.49E-4	0	18191,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749207	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	18337	0.0012	940	18061,109,79,64	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749207	26209	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	37819	9.78E-4	0	6,37731,0,66	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gtg/Ttg	V273L	orf3a	0.000792	0.234679	3	1	G>T
ERR5749207	27972	PASS	C	T	7073	0.898346	40	2,2,7009,25	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749207	28048	PASS	G	T	7042	0.917921	0	0,5,0,7036	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749207	28111	PASS	A	G	35261	0.979439	1	7,2,28192,7046	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749207	28270	PASS	TA	T	54739	0.995616	591	241,7,27868,26631	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749207	28280	PASS	G	C	54630	0.93791	28	16,2,27912,26613	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749207	28281	PASS	A	T	54630	0.914552	81	39,3,27889,26601	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749207	28282	PASS	T	A	54638	0.914272	1	27,23,27840,26620	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749207	28881	PASS	G	A	17432	0.729922	12	4,0,8515,8640	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749207	28882	PASS	G	A	17432	0.830312	6	5,1,8649,8625	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749207	28883	PASS	G	C	17432	0.945445	3	1,0,8669,8751	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749207	28977	PASS	C	T	8759	0.934696	0	0,1,1,8746	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749207	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	58025	0.00162	0	29120,28755,62,61	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749208	199	PASS	G	T	10083	0.766141	0	70,0,9984,2	.	.	.	.	.	.	.	0.615385	0.766141	1	1	G>T
ERR5749208	241	PASS	C	T	20091	0.857946	3	2,5,9937,10063	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749208	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	10329	0.00213	0	10305,2,22,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749208	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	10329	0.001065	0	10258,2,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749208	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	10329	0.001355	0	10258,2,14,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749208	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	10329	0.003776	0	10258,2,39,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749208	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10330	0.002614	0	9411,5,796,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749208	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	10330	0.001742	0	10307,5,18,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749208	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	10333	0.001548	0	10305,9,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749208	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	33960	5.89E-4	3	23608,10326,16,4	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749208	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	33961	0.001943	12	23555,10320,53,13	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749208	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23617	0.001482	0	0,23553,0,38	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749208	913	PASS	C	T	23618	0.920527	0	0,16,0,23574	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749208	2453	PASS	C	T	15912	0.737179	0	0,11,3,15697	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L550F	nsp2	0.00429	0.842201	2	2	C>T
ERR5749208	3037	PASS	C	T	21487	0.818216	52	1,21,10738,10583	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749208	3267	PASS	C	T	22556	0.970961	0	2,0,22536,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749208	3575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	13082	6.88E-4	0	13073,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/ttTa	L287F?	nsp3	0.000594	0.059126	3	1	G>GT
ERR5749208	3602	PASS	C	T	13082	0.971946	0	7,0,13064,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cac/Tac	H295Y	nsp3	0.004454	0.97247	1	1	C>T
ERR5749208	4832	PASS	C	T	33229	0.727166	64	4,35,16335,16458	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L705	nsp3	0.000542	0.727166	3	2	C>T
ERR5749208	5388	PASS	C	A	6935	0.956309	0	1,0,6932,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749208	5986	PASS	C	T	13962	0.973858	0	1,0,13950,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749208	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13625	0.001835	0	5,13465,0,33	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749208	6954	PASS	T	C	24400	0.835656	0	0,3,0,24292	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749208	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	36205	0.002044	251	16515,19615,74,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749208	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20209	0.001633	0	20139,6,35,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749208	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	20194	0.001238	0	20139,0,45,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749208	11095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20190	9.91E-4	0	20123,0,25,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A41	nsp6	0.000515	0.887707	7	2	C>T
ERR5749208	11287	PASS	GTCTGGTTTT	G	20194	0.996781	24	1,65,0,20129	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749208	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	40587	8.13E-4	3	26172,14352,25,10	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749208	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	12773	7.05E-4	0	12765,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749208	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30232	0.001786	0	15089,15046,29,30	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749208	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	14222	0.0045	2147483647	13860,125,7,220	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749208	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	27632	0.001267	1	13846,13768,19,16	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749208	14408	PASS	C	T	27632	0.843768	2	5,7,13779,13643	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749208	14676	PASS	C	T	14104	0.761061	0	13,0,14037,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749208	15279	PASS	C	T	23418	0.900675	2147483647	0,0,23387,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749208	15720	PASS	C	T	17584	0.917823	0	0,6,1,17538	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D760	RdRp	0.001002	0.917823	1	1	C>T
ERR5749208	16176	PASS	T	C	20283	0.980969	3	1,0,9495,10777	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749208	17961	PASS	A	G	13975	0.973166	0	0,1,6,13951	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atA/atG	I575M	helicase	0.973166	0.973166	1	1	A>G
ERR5749208	19320	PASS	C	T	19722	0.957053	0	1,0,19707,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H427	ExoN	0.004154	0.957053	2	2	C>T
ERR5749208	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34731	0.00239	0	34627,0,88,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749208	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34882	8.31E-4	0	34804,0,30,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749208	21764	PASS	ATACATG	A	13830	0.9953	23	64,1,13765,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749208	21990	PASS	TTTA	T	13832	0.997325	0	0,37,3,13792	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749208	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	17232	0.001393	0	0,17198,0,27	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749208	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	31745	9.14E-4	1	14476,17210,13,18	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749208	23063	PASS	A	T	14498	0.871155	0	0,1,0,14435	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749208	23271	PASS	C	A	23714	0.898035	0	3,0,23680,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749208	23403	PASS	A	G	23707	0.969714	0	0,5,0,23682	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749208	23604	PASS	C	A	16904	0.94309	0	9,0,16891,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749208	23709	PASS	C	T	16896	0.941761	0	0,7,4,16870	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749208	24506	PASS	T	G	18545	0.974818	0	8,0,18533,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749208	24914	PASS	G	C	35646	0.957134	3	1,0,17742,17883	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749208	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	30329	0.001319	592	30214,21,19,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749208	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	30280	4.95E-4	0	30265,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749208	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	58084	4.13E-4	0	8,58043,0,24	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749208	26395	PASS	C	A	24877	0.745829	190	180,43,12538,12017	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	Ctt/Att	L51I	E	0.000707	0.745829	2	1	C>A
ERR5749208	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	13372	8.23E-4	0	1,13354,0,11	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749208	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	13373	0.002243	0	1,13336,0,30	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749208	27972	PASS	C	T	10703	0.905727	17	2,1,10599,68	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749208	28048	PASS	G	T	10637	0.919808	0	0,9,0,10619	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749208	28111	PASS	A	G	31427	0.979763	2	2,2,20756,10648	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749208	28270	PASS	TA	T	40349	0.99482	505	210,7,20495,19645	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749208	28280	PASS	G	C	40266	0.940223	11	12,4,20542,19631	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749208	28281	PASS	A	T	40266	0.918889	14	20,8,20547,19623	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749208	28282	PASS	T	A	40266	0.904982	2	15,11,20469,19643	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749208	28396	PASS	G	A	20819	0.946059	402	15,1,28,20758	LOW	SILENT	SYNONYMOUS_CODING	N	cgG/cgA	R41	N	0.000496	0.946059	5	2	G>A
ERR5749208	28881	PASS	G	A	22471	0.71016	48	16,0,10924,11053	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749208	28882	PASS	G	A	22469	0.818016	12	11,3,11205,11020	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749208	28883	PASS	G	C	22467	0.939333	0	0,0,11235,11206	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749208	28977	PASS	C	T	11454	0.927536	0	0,5,0,11430	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749208	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	64527	0.001348	0	32395,32013,48,47	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749208	29640	PASS	C	T	22247	0.951634	8	0,4,10332,11893	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF10	gCa/gTa	A28V	orf10	0.002681	0.955281	2	2	C>T
ERR5749208	29779	PASS	G	T	10348	0.955644	0	0,1,0,10342	.	.	.	.	.	.	.	0.001489	0.975228	1	1	G>T
ERR5749209	241	PASS	C	T	11189	0.856198	1	2,4,5459,5668	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749209	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	12427	0.002575	0	12394,3,32,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749209	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	12428	9.66E-4	0	12350,4,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749209	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	12428	0.001448	0	12350,4,18,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749209	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	12428	0.003379	0	12350,4,42,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749209	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12422	0.00161	0	11453,9,837,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749209	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	12422	0.00161	0	12392,9,20,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749209	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	12423	8.05E-4	0	12397,11,10,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749209	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	40571	0.001011	5	28087,12435,32,9	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749209	913	PASS	C	T	28110	0.918463	0	0,19,0,28053	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749209	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	76439	0.001805	2147483647	38163,35796,57,2237	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749209	3037	PASS	C	T	21543	0.81827	42	0,14,10760,10625	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749209	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10867	0.002024	576	8,10832,22,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749209	3267	PASS	C	T	26159	0.969112	0	3,0,26141,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749209	5388	PASS	C	A	5566	0.957959	0	1,0,5565,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749209	5986	PASS	C	T	12219	0.975448	0	4,0,12211,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749209	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12633	0.001979	0	7,12473,0,35	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749209	6954	PASS	T	C	22120	0.826899	0	0,6,5,22000	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749209	7564	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	18783	5.86E-4	0	0,18772,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/	Y1617	nsp3	0.000586	0.056194	4	2	CT>C
ERR5749209	8084	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	31526	6.03E-4	0	31514,0,19,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1790	nsp3	0.000543	0.923413	4	2	GA>G
ERR5749209	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	38929	0.001567	195	18569,20299,61,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749209	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	26534	0.001319	0	26466,0,59,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749209	11199	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	52853	6.43E-4	0	26231,26376,17,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCc/gTc	A76V	nsp6	0.000309	0.056758	3	2	C>T
ERR5749209	11287	PASS	GTCTGGTTTT	G	26521	0.996908	0	0,82,0,26439	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749209	11507	PASS	G	A	28422	0.909683	3	2,0,14221,14113	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Att	V179I	nsp6	0.007744	0.914418	2	2	G>A
ERR5749209	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	22731	0.001144	0	22678,0,26,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749209	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	15569	6.42E-4	0	15560,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749209	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	40868	0.00137	0	20397,20347,32,32	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749209	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	18659	0.003055	2147483647	18256,152,12,228	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749209	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	36360	0.001953	0	18216,18100,36,35	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749209	14408	PASS	C	T	36360	0.850468	14	1,7,18135,17937	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749209	14676	PASS	C	T	16665	0.828203	0	4,0,16629,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749209	15279	PASS	C	T	26898	0.890587	0	5,0,26849,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749209	16176	PASS	T	C	23449	0.982302	0	0,0,10200,13236	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749209	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	28739	9.74E-4	0	28711,0,28,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749209	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	31197	0.00343	0	31061,0,114,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749209	20091	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	31141	6.42E-4	0	3,31118,0,20	HIGH	NONE	FRAME_SHIFT	ORF1ab	caa/Acaa	Q159T?	endoR	0.000368	0.051583	1	1	C>CA
ERR5749209	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	35063	0.001055	0	17152,17484,21,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749209	21764	PASS	ATACATG	A	14060	0.992745	0	102,0,13958,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749209	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	14059	7.82E-4	0	14048,0,11,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749209	21990	PASS	TTTA	T	14065	0.997583	0	0,34,2,14029	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749209	23063	PASS	A	T	16184	0.865855	0	0,2,0,16114	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749209	23271	PASS	C	A	29586	0.920097	0	3,0,29552,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749209	23403	PASS	A	G	29579	0.969708	0	0,3,1,29552	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749209	23604	PASS	C	A	17352	0.939085	0	22,0,17321,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749209	23709	PASS	C	T	17346	0.942235	0	0,5,6,17308	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749209	24237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14549	0.001443	0	14515,1,24,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gTt	A892V	S	0.001242	0.889739	1	1	C>T
ERR5749209	24506	PASS	T	G	22336	0.973003	0	5,0,22323,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749209	24914	PASS	G	C	44619	0.961496	0	0,0,22232,22352	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749209	26333	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13172	0.002961	0	13113,3,42,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	aCa/aTa	T30I	E	0.00158	0.943221	1	1	C>T
ERR5749209	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	15191	7.24E-4	0	0,15171,0,11	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749209	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	15194	0.00283	0	0,15149,0,43	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749209	27972	PASS	C	T	14055	0.907364	0	1,0,13921,91	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749209	28048	PASS	G	T	13970	0.925841	0	0,16,0,13950	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749209	28111	PASS	A	G	34468	0.978821	4	4,6,20464,13985	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749209	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	20451	9.29E-4	0	20436,4,19,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749209	28270	PASS	TA	T	39754	0.995271	426	193,10,20198,19368	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749209	28280	PASS	G	C	39683	0.939647	18	12,2,20230,19355	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749209	28281	PASS	A	T	39683	0.916186	4	20,14,20229,19340	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749209	28282	PASS	T	A	39686	0.909187	4	19,13,20179,19360	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749209	28292	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	40697	9.34E-4	0	20283,20376,19,19	HIGH	NONE	FRAME_SHIFT	N	aat/	N8	N	0.000304	0.055324	4	2	CA>C
ERR5749209	28881	PASS	G	A	27509	0.779745	18	12,2,13648,13496	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749209	28882	PASS	G	A	27508	0.831504	6	5,1,13746,13509	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749209	28883	PASS	G	C	27508	0.946416	3	0,1,13771,13711	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749209	28977	PASS	C	T	13991	0.932671	0	0,2,1,13965	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749209	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	71646	0.001145	0	35996,35531,52,50	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749210	241	PASS	C	T	19745	0.869486	0	0,0,9820,9858	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749210	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	11568	0.001383	0	11551,2,16,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749210	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	11568	9.51E-4	0	11521,2,11,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749210	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	11568	0.002507	0	11521,2,29,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749210	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	11563	0.00173	0	10793,2,693,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749210	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	11563	0.001124	0	11548,2,13,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749210	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	29311	8.87E-4	18	17698,11581,22,4	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749210	913	PASS	C	T	17718	0.918106	0	0,11,0,17684	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749210	1510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	17904	0.00296	0	0,17715,0,54	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G235	nsp2	0.002159	0.937304	1	1	T>C
ERR5749210	2972	PASS	G	A	8966	0.964198	0	2,0,8960,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gct/Act	A85T	nsp3	0.964198	0.964198	1	1	G>A
ERR5749210	3037	PASS	C	T	17816	0.825662	45	0,15,8904,8754	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749210	3267	PASS	C	T	16816	0.969969	0	1,0,16806,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749210	3575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	9788	0.001226	0	9776,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/ttTa	L287F?	nsp3	0.000594	0.059126	3	1	G>GT
ERR5749210	5388	PASS	C	A	5427	0.957251	2147483647	0,0,5424,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749210	5986	PASS	C	T	11592	0.974724	2147483647	0,0,11585,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749210	6310	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18594	0.003281	0	18486,3,64,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	agC/agT	S1197	nsp3	0.00099	0.94715	2	2	C>T
ERR5749210	6954	PASS	T	C	19609	0.827783	0	0,2,2,19495	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749210	8327	PASS	C	T	10477	0.90398	156	5,5,10454,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Ttt	L1870F	nsp3	0.001407	0.90398	1	1	C>T
ERR5749210	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	26742	4.11E-4	34	12900,13831,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749210	10252	PASS	C	T	14788	0.943062	0	1,0,14729,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F66	3Cpro	0.000645	0.943062	2	2	C>T
ERR5749210	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	13574	0.0014	0	13541,0,27,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749210	11287	PASS	GTCTGGTTTT	G	13569	0.998084	0	0,26,0,13543	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749210	12970	PASS	C	T	11482	0.856906	0	0,4,1,11438	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N95	nsp9	0.8352	0.861883	1	1	C>T
ERR5749210	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	8001	8.75E-4	0	7993,1,7,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749210	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25530	0.001097	0	12747,12722,16,16	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749210	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10095	0.003863	2744	9850,78,6,156	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749210	14408	PASS	C	T	19607	0.85444	3	2,4,9786,9677	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749210	14676	PASS	C	T	10505	0.828939	0	3,0,10470,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749210	15279	PASS	C	T	17569	0.896124	2147483647	0,0,17546,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749210	16176	PASS	T	C	15743	0.982786	0	1,0,7921,7816	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749210	18339	PASS	T	A	24515	0.971609	205	6,6,24495,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcA	A100	ExoN	0.971609	0.971609	1	1	T>A
ERR5749210	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	20831	5.76E-4	0	20819,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749210	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26393	0.001591	0	26329,0,45,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749210	20148	PASS	C	T	26383	0.969223	0	0,7,0,26356	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F176	endoR	0.000513	0.969223	2	2	C>T
ERR5749210	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22700	9.69E-4	0	22645,0,23,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749210	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	17345	9.22E-4	0	0,17329,0,16	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TA>T
ERR5749210	21595	PASS	C	T	14624	0.918559	0	0,4,0,14599	LOW	SILENT	SYNONYMOUS_CODING	S	gtC/gtT	V11	S	0.001296	0.918559	3	2	C>T
ERR5749210	21764	PASS	ATACATG	A	11374	0.997714	0	26,0,11348,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749210	21990	PASS	TTTA	T	11378	0.99833	0	0,19,4,11355	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749210	23063	PASS	A	T	10009	0.865621	0	0,5,0,9949	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749210	23271	PASS	C	A	17814	0.918267	0	5,0,17790,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749210	23403	PASS	A	G	17812	0.970638	0	0,2,0,17800	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749210	23604	PASS	C	A	13451	0.939038	0	12,0,13431,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749210	23683	PASS	C	T	13424	0.467521	0	1,5482,1,7876	LOW	SILENT	SYNONYMOUS_CODING	S	taC/taT	Y707	S	0.000704	0.467521	2	2	C>T
ERR5749210	23709	PASS	C	T	13446	0.945858	0	0,7,1,13431	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749210	24320	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	10162	0.001574	0	0,10146,0,16	HIGH	NONE	FRAME_SHIFT	S	aaa/	K921	S	0.000763	0.138365	4	2	CA>C
ERR5749210	24506	PASS	T	G	13765	0.972248	0	1,0,13763,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749210	24914	PASS	G	C	28478	0.962638	0	1,2,14178,14275	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749210	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	20705	0.001497	17	15096,5569,31,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749210	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	22821	7.45E-4	0	22804,0,17,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749210	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	9291	0.001076	0	0,9281,0,10	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749210	27972	PASS	C	T	9493	0.900137	0	0,0,9425,45	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749210	28048	PASS	G	T	9456	0.920685	0	0,15,0,9435	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749210	28111	PASS	A	G	26984	0.979136	0	4,2,17506,9461	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749210	28270	PASS	TA	T	34064	0.995186	369	160,7,17284,16616	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749210	28280	PASS	G	C	34005	0.938156	30	21,4,17321,16602	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749210	28281	PASS	A	T	34005	0.919776	15	19,7,17323,16602	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749210	28282	PASS	T	A	34007	0.91046	10	19,9,17272,16615	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749210	28881	PASS	G	A	14505	0.780558	5	6,2,7185,7121	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749210	28882	PASS	G	A	14505	0.827784	15	6,0,7271,7094	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749210	28883	PASS	G	C	14505	0.945674	0	0,0,7286,7211	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749210	28977	PASS	C	T	7377	0.927206	0	0,1,0,7363	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749210	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	42811	0.001705	1	21479,21221,48,43	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749210	29445	PASS	C	T	7558	0.853797	0	1,0,7531,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aCt/aTt	T391I	N	0.000907	0.853797	2	2	C>T
ERR5749211	241	PASS	C	T	2564	0.845944	0	0,0,1270,1271	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749211	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGT	A	2077	0.005296	0	2045,0,11,0	MODERATE	NONE	CODON_DELETION	ORF1ab	ggtcatgtt/	GHV82	leader	0.000686	0.081932	3	1	ATGGTCATGT>A
ERR5749211	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	2077	0.011074	0	2045,0,23,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749211	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	2077	0.004333	0	2051,0,9,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749211	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	2077	0.007222	0	2051,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749211	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	2075	0.00241	0	2071,0,5,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749211	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	8261	0.002542	23	6122,2079,21,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749211	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	8261	0.004721	35	6122,2079,38,1	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749211	714	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	6181	0.001941	0	6165,0,12,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGc/gCc	G150A	leader	0.001941	0.984148	2	1	G>C
ERR5749211	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6177	0.003885	0	0,6143,0,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749211	913	PASS	C	T	6177	0.912093	0	0,2,0,6164	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749211	1230	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AGT	A	5426	0.00129	0	0,5419,0,7	HIGH	NONE	FRAME_SHIFT	ORF1ab	tgtgat/	CD143	nsp2	0.00129	0.969658	2	2	AGT>A
ERR5749211	1426	PASS	C	T	6914	0.892537	0	2,0,6841,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y207	nsp2	0.002931	0.892537	1	1	C>T
ERR5749211	1846	PASS	A	G	7292	0.938151	2147483647	0,0,0,7283	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaA/aaG	K347	nsp2	0.001438	0.945471	2	2	A>G
ERR5749211	2084	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11837	0.001943	0	5903,5900,13,13	HIGH	NONSENSE	STOP_GAINED	ORF1ab	Cag/Tag	Q427*	nsp2	0.001943	0.253112	1	1	C>T
ERR5749211	2160	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	5935	0.003033	0	0,5910,0,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gAa/gTa	E452V	nsp2	0.000572	0.089776	3	2	A>T
ERR5749211	2403	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAAAGGGATTGTACAGAAAGTGTGTT	C	3232	0.006807	0	9,3210,0,22	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagggattgtacagaaagtgtgttaaa/	KGLYRKCVK534	nsp2	0.000951	0.061776	2	1	CAAAGGGATTGTACAGAAAGTGTGTT>C
ERR5749211	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	19610	0.001224	1564	9765,9109,24,624	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749211	3037	PASS	C	T	3766	0.821827	12	0,4,1876,1840	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749211	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	1908	0.005765	240	3,1892,11,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749211	3267	PASS	C	T	7047	0.972045	0	1,0,7041,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749211	3335	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	13995	0.002429	2	6992,6904,21,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Caa	E206Q	nsp3	0.001289	0.891976	4	3	G>C
ERR5749211	3340	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	14034	0.002423	0	7009,6896,20,20	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtG/gtA	V207	nsp3	0.000712	0.845579	3	2	G>A
ERR5749211	3429	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7043	0.001846	0	0,7023,0,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T237I	nsp3	0.001846	0.813462	1	1	C>T
ERR5749211	3483	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	9293	0.00269	27	2246,7012,1,32	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGa/gTa	G255V	nsp3	0.001819	0.962114	2	1	G>T
ERR5749211	3602	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2245	0.004454	0	2233,0,11,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cac/Tac	H295Y	nsp3	0.004454	0.97247	1	1	C>T
ERR5749211	3671	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAA	G	4485	0.003344	0	2235,2236,7,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N319	nsp3	0.000351	0.0625	6	2	GAA>G
ERR5749211	3877	PASS	T	C	2333	0.960137	2147483647	0,0,2325,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcC	A386	nsp3	0.000588	0.960227	2	1	T>C
ERR5749211	4317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	3993	0.006261	0	0,3958,0,32	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aGt/aCt	S533T	nsp3	0.001619	0.118421	2	1	G>C
ERR5749211	4338	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10293	0.003303	0	6268,3968,27,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S540F	nsp3	0.000366	0.051643	2	2	C>T
ERR5749211	4578	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTAACGATC	T	6260	0.002556	0	0,6244,0,16	HIGH	NONE	FRAME_SHIFT	ORF1ab	aacgatctaaat/	NDLN621	nsp3	0.000519	0.082979	2	2	TTAACGATC>T
ERR5749211	5388	PASS	C	A	806	0.960298	2147483647	0,0,805,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749211	5822	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5789	0.002764	0	0,5756,0,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Ttt	L1035F	nsp3	0.002438	0.069663	1	1	C>T
ERR5749211	5986	PASS	C	T	3063	0.974861	2147483647	0,0,3063,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749211	6573	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3265	0.0049	0	3248,0,17,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S1285F	nsp3	0.001862	0.957014	1	1	C>T
ERR5749211	6670	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	3259	0.005523	0	3232,0,18,0	HIGH	NONSENSE	STOP_GAINED	ORF1ab	tgG/tgA	W1317*	nsp3	0.005523	0.921348	2	2	G>A
ERR5749211	6954	PASS	T	C	7842	0.834608	0	0,2,0,7812	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749211	7528	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6036	0.003479	0	1,6005,0,24	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V1603	nsp3	0.002527	0.916131	1	1	C>T
ERR5749211	7658	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	11794	0.001526	56	5745,6027,0,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Att/Ttt	I1647F	nsp3	0.001526	0.055791	1	1	A>T
ERR5749211	7926	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5747	0.005916	0	0,5710,0,37	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCa/gTa	A1736V	nsp3	0.000531	0.97019	5	2	C>T
ERR5749211	8964	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	5748	0.004349	0	5723,0,25,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K138	nsp4	0.000553	0.981649	4	2	CA>C
ERR5749211	9198	PASS	C	T	5748	0.93476	2147483647	0,0,0,5738	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T215I	nsp4	0.000543	0.93476	4	2	C>T
ERR5749211	9962	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2145	0.004196	0	2134,0,9,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cat/Tat	H470Y	nsp4	0.003186	0.114523	1	1	C>T
ERR5749211	10138	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	10060	6.96E-4	47	7915,2138,0,7	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggt/	G29	3Cpro	0.000458	0.983567	3	3	CG>C
ERR5749211	10193	PASS	G	A	7914	0.855067	0	3,0,7899,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E47K	3Cpro	0.000774	0.869819	2	2	G>A
ERR5749211	10195	PASS	A	T	7914	0.956912	0	4,0,7906,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gaA/gaT	E47D	3Cpro	0.951998	0.969772	1	1	A>T
ERR5749211	10252	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7912	0.001643	0	7894,0,14,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F66	3Cpro	0.000645	0.943062	2	2	C>T
ERR5749211	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	41	0.097561	0	37,0,4,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CT
ERR5749211	11287	PASS	GTCTGGTTTT	G	41	0.97561	0	0,1,0,40	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749211	12357	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7197	0.006392	0	0,7148,0,47	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T89I	nsp8	0.000909	0.956941	3	2	C>T
ERR5749211	13274	PASS	C	T	8125	0.943631	0	0,1,0,8118	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cca/Tca	P84S	nsp10	0.94207	0.943631	1	1	C>T
ERR5749211	13356	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16414	0.002559	132	8233,8125,45,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T111I	nsp10	0.000806	0.091518	1	1	C>T
ERR5749211	13458	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	8285	0.00338	0	8257,0,28,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcg/	S6	nsp11	0.001017	0.058608	4	2	CG>C
ERR5749211	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16542	0.001149	0	8264,8236,10,10	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749211	14120	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15309	0.002743	0	7623,7622,25,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCa/cTa	P227L	RdRp	0.00121	0.786944	2	2	C>T
ERR5749211	14408	PASS	C	T	4404	0.835604	0	0,0,2202,2164	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749211	14676	PASS	C	T	4387	0.801459	0	1,0,4372,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749211	15279	PASS	C	T	4454	0.886394	0	1,0,4447,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749211	15720	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8104	0.002962	0	0,8072,0,27	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D760	RdRp	0.001002	0.917823	1	1	C>T
ERR5749211	16176	PASS	T	C	6511	0.980034	0	0,0,1483,5024	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749211	16559	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12260	0.002936	0	12204,0,42,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCa/gTa	A108V	helicase	0.000644	0.051993	3	2	C>T
ERR5749211	16575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12259	0.004731	0	12182,0,69,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D113	helicase	0.001088	0.827968	1	1	C>T
ERR5749211	16792	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	19602	6.12E-4	51	7332,12258,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cgt/	R186	helicase	0.000335	0.072562	5	2	CG>C
ERR5749211	16794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	19602	0.002653	27	7309,12232,32,23	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	cgT/cgC	R186	helicase	0.000354	0.077626	2	2	T>C
ERR5749211	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAA	G	7344	0.003268	0	7313,0,24,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GAA>G
ERR5749211	17678	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5210	0.002303	0	0,5193,0,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aTg	T481M	helicase	0.001162	0.968704	2	1	C>T
ERR5749211	17762	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTG	C	5289	0.002836	0	5274,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtc/	V510	helicase	0.000697	0.912542	2	2	CTG>C
ERR5749211	18576	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	9993	0.005404	0	0,9939,0,54	HIGH	NONE	FRAME_SHIFT	ORF1ab	agagtc/	RV180	ExoN	0.005404	0.876866	2	2	CAG>C
ERR5749211	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	16429	9.74E-4	0	16413,0,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749211	18744	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16428	0.002922	0	16355,0,50,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y235	ExoN	0.000912	0.953624	2	2	C>T
ERR5749211	18756	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	16426	0.002374	0	16371,0,51,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccG/ccT	P239	ExoN	0.000392	0.942688	3	2	G>T
ERR5749211	18788	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	32788	0.002074	20	16317,16317,82,51	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aAa	T250K	ExoN	0.000792	0.51652	2	1	C>A
ERR5749211	18800	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	32794	0.001067	0	16383,16310,21,19	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cAa/cGa	Q254R	ExoN	0.000701	0.072445	1	1	A>G
ERR5749211	18877	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16426	0.002557	0	0,16368,0,46	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L280	ExoN	0.000848	0.953596	2	2	C>T
ERR5749211	19164	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	9063	0.003089	0	0,9035,0,28	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K376	ExoN	0.000358	0.075732	4	2	CA>C
ERR5749211	19269	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13915	0.003593	0	4826,9031,18,36	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N410	ExoN	0.000773	0.954777	2	2	C>T
ERR5749211	20148	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	2894	0.004838	0	0,2880,0,14	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N177	endoR	0.000513	0.969223	2	2	CA>C
ERR5749211	20951	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	10600	0.001415	0	10584,1,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gat/	D99	MethTr	0.000431	0.138667	3	3	CAG>C
ERR5749211	21123	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	18633	0.002093	80	8033,10561,1,38	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F156	MethTr	0.000257	0.90982	5	2	GT>G
ERR5749211	21375	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	8035	0.002365	0	1,8014,0,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L239F	MethTr	0.002365	0.858793	2	2	G>T
ERR5749211	21707	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11619	0.001721	54	5255,6337,19,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Cat/Tat	H49Y	S	0.001048	0.072032	1	1	C>T
ERR5749211	21732	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	5277	0.005117	0	5250,0,27,0	HIGH	NONE	FRAME_SHIFT	S	ttc/ttTc	F58F?	S	0.000576	0.076745	4	2	C>CT
ERR5749211	21732	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5277	0.00398	0	5249,0,22,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cTt	P57L	S	0.000576	0.076745	4	2	C>T
ERR5749211	21764	PASS	ATACATG	A	5277	0.991472	0	45,0,5232,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749211	21889	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	5301	0.003018	0	33,5196,0,26	LOW	SILENT	SYNONYMOUS_CODING	S	acT/acC	T109	S	0.00091	0.065772	2	2	T>C
ERR5749211	21990	PASS	TTTA	T	5279	0.996401	0	0,19,2,5258	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749211	22030	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	12350	0.001781	0	12321,2,27,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gaG/gaT	E156D	S	0.000562	0.115047	2	2	G>T
ERR5749211	22289	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTTA	G	12348	6.48E-4	0	0,12340,0,8	HIGH	NONE	FRAME_SHIFT	S	gctttacat/	ALH243	S	0.000446	0.915917	3	2	GCTTTA>G
ERR5749211	22290	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12348	0.001863	0	0,12244,0,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gTt	A243V	S	0.000389	0.578006	2	2	C>T
ERR5749211	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	11586	0.001467	0	0,11565,0,17	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749211	22858	PASS	C	T	16319	0.959434	2	0,3,4674,11522	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749211	23063	PASS	A	T	4722	0.844346	0	0,2,0,4692	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749211	23191	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8757	0.002512	0	8731,2,24,0	LOW	SILENT	SYNONYMOUS_CODING	S	ttC/ttT	F543	S	0.000538	0.973337	2	2	C>T
ERR5749211	23249	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8753	0.005712	0	8674,0,50,0	HIGH	NONSENSE	STOP_GAINED	S	Caa/Taa	Q563*	S	0.001376	0.082558	1	1	C>T
ERR5749211	23271	PASS	C	A	8752	0.916248	0	1,0,8740,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749211	23403	PASS	A	G	8747	0.97199	0	0,2,0,8742	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749211	23604	PASS	C	A	4417	0.933439	0	7,0,4408,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749211	23634	PASS	C	T	4416	0.931159	2147483647	0,0,4411,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tTc	S691F	S	0.00071	0.931159	2	2	C>T
ERR5749211	23709	PASS	C	T	4414	0.932034	0	0,2,0,4410	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749211	23758	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4417	0.003622	0	0,4399,0,16	LOW	SILENT	SYNONYMOUS_CODING	S	acC/acT	T732	S	0.001489	0.964055	1	1	C>T
ERR5749211	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	6961	0.001724	22	2544,4405,0,12	HIGH	NONE	FRAME_SHIFT	S	ttg/	L753	S	0.000334	0.080808	2	2	CT>C
ERR5749211	24127	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	6714	0.001638	20	4159,2544,11,0	HIGH	NONE	FRAME_SHIFT	S	aac/	N856	S	0.000324	0.111888	4	1	TA>T
ERR5749211	24506	PASS	T	G	7385	0.974949	0	6,0,7378,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749211	24899	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	20230	0.001977	1	10105,10086,19,21	HIGH	NONE	FRAME_SHIFT	S	atc/	I1114	S	0.000315	0.09021	5	3	CA>C
ERR5749211	24914	PASS	G	C	20178	0.957528	0	0,1,10060,10105	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749211	25019	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GATAA	G	12819	0.001482	16	2679,10121,0,19	HIGH	NONE	FRAME_SHIFT	S	aaatat/	KY1154	S	0.00048	0.981297	3	2	GATAA>G
ERR5749211	25553	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12236	0.002615	0	0,12191,0,38	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	gCt/gTt	A54V	orf3a	0.001165	0.868131	3	2	C>T
ERR5749211	25587	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	12241	0.001961	0	0,12216,0,24	HIGH	NONE	FRAME_SHIFT	ORF3a	aag/	K67	orf3a	0.000598	0.813206	6	2	CAA>C
ERR5749211	25624	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14004	0.001714	11	1762,12217,0,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Cac/Tac	H78Y	orf3a	0.00089	0.983312	1	1	C>T
ERR5749211	25626	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14004	0.001999	3	1759,12209,2,29	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	caC/caT	H78	orf3a	0.000403	0.915633	3	2	C>T
ERR5749211	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	1792	0.009487	326	1756,13,0,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749211	26044	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12743	0.002276	0	12700,0,31,0	HIGH	NONSENSE	STOP_GAINED	ORF3a	Caa/Taa	Q218*	orf3a	0.000469	0.102679	3	3	C>T
ERR5749211	26208	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12742	0.001727	0	6,12704,0,26	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	agC/agT	S272	orf3a	0.000315	0.922222	2	2	C>T
ERR5749211	26208	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	12742	0.00157	0	6,12716,0,20	HIGH	NONE	FRAME_SHIFT	ORF3a	gtg/	V273	orf3a	0.000315	0.922222	2	2	CG>C
ERR5749211	26256	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18382	0.003971	114	5637,12661,0,73	LOW	SILENT	SYNONYMOUS_CODING	E	ttC/ttT	F4	E	0.000748	0.969561	2	2	C>T
ERR5749211	26257	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	18382	5.44E-4	51	5629,12743,10,0	HIGH	NONE	FRAME_SHIFT	E	tcg/	S6	E	0.000247	0.948926	4	2	GT>G
ERR5749211	26333	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5639	0.00266	0	5613,0,16,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	aCa/aTa	T30I	E	0.00158	0.943221	1	1	C>T
ERR5749211	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	5158	0.001551	0	0,5150,0,8	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749211	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	5158	0.001745	0	0,5149,0,9	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749211	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	5158	0.004653	0	0,5134,0,24	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749211	26958	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19432	0.001595	0	19398,0,32,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Cgt/Tgt	R146C	M	0.00096	0.122326	1	1	C>T
ERR5749211	27078	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19424	0.001544	0	0,19381,0,32	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Cgt/Tgt	R186C	M	0.000415	0.05783	2	2	C>T
ERR5749211	27297	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11323	0.002473	0	11271,0,29,0	LOW	SILENT	SYNONYMOUS_CODING	ORF6	atC/atT	I32	orf6	0.000978	0.91266	1	1	C>T
ERR5749211	27312	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAA	T	11320	0.001678	0	11300,0,19,0	HIGH	NONE	FRAME_SHIFT	ORF6	aat/	N39	orf6	0.000911	0.088458	4	2	TAA>T
ERR5749211	27371	PASS	C	T	11344	0.066731	2	45,10382,2,892	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF6	cCa/cTa	P57L	orf6	0.00148	0.066731	2	2	C>T
ERR5749211	27382	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GATT	G	11352	0.001409	0	47,11289,0,16	HIGH	NONE	STOP_LOST+CODON_CHANGE_PLUS_CODON_DELETION+SPLICE_SITE_REGION	ORF6	gattaa/gaa	D*61E	orf6	0.001236	0.927964	2	2	GATT>G
ERR5749211	27737	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13594	0.001618	0	20,13528,0,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	aCa/aTa	T115I	orf7a	0.001474	0.817082	2	2	C>T
ERR5749211	27741	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13595	0.002869	0	20,13505,0,41	LOW	SILENT	SYNONYMOUS_CODING	ORF7a	ctC/ctT	L116	orf7a	0.000363	0.954278	3	2	C>T
ERR5749211	27972	PASS	C	T	1973	0.904207	0	0,0,1956,15	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749211	28048	PASS	G	T	1960	0.903061	0	0,2,0,1952	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749211	28111	PASS	A	G	20261	0.980702	0	4,0,18291,1960	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749211	28147	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18303	0.002841	0	18235,1,55,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	cCt/cTt	P85L	orf8	0.000438	0.981624	4	2	C>T
ERR5749211	28227	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18297	0.002569	0	18232,0,49,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	Cat/Tat	H112Y	orf8	0.000906	0.951206	2	2	C>T
ERR5749211	28239	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTGTT	G	18295	0.002186	0	18256,0,40,0	HIGH	NONE	FRAME_SHIFT	ORF8	gtttta/	VL117	orf8	0.000417	0.984998	9	2	GTTGTT>G
ERR5749211	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	18272	0.00394	0	18209,2,72,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749211	28270	PASS	TA	T	35421	0.994805	420	184,8,18042,17195	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749211	28280	PASS	G	C	35354	0.937914	35	16,1,18081,17184	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749211	28281	PASS	A	T	35354	0.914239	42	36,8,18078,17172	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749211	28282	PASS	T	A	35357	0.907996	47	44,11,18033,17190	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749211	28321	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	18284	9.3E-4	0	0,18267,0,17	HIGH	NONE	FRAME_SHIFT	N	ttt/	F17	N	0.00045	0.947809	3	2	GT>G
ERR5749211	28434	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	32870	8.82E-4	31	14562,18271,4,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aCc/aTc	T54I	N	0.000815	0.871795	4	2	C>T
ERR5749211	28512	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14569	0.001235	0	14548,0,18,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	cCa/cTa	P80L	N	0.000621	0.172671	3	2	C>T
ERR5749211	28603	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29071	0.0043	0	14456,14366,69,69	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F110	N	0.000427	0.883357	2	2	C>T
ERR5749211	28651	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14560	0.001168	0	0,14525,0,19	LOW	SILENT	SYNONYMOUS_CODING	N	aaC/aaT	N126	N	0.000502	0.918117	3	2	C>T
ERR5749211	28881	PASS	G	A	5514	0.76333	3	2,0,2723,2707	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749211	28882	PASS	G	A	5514	0.828437	3	2,0,2751,2691	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749211	28883	PASS	G	C	5514	0.938702	0	0,0,2761,2743	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749211	28977	PASS	C	T	2815	0.930373	0	0,1,0,2804	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749211	29095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14691	0.001225	0	14658,1,19,0	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F274	N	0.000792	0.961279	2	2	C>T
ERR5749211	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	29141	0.001201	0	14654,14438,22,22	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749211	29675	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	5829	0.001029	0	2916,2908,3,3	.	.	.	.	.	.	.	0.000624	0.883495	2	1	CA>C
ERR5749211	29774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2922	0.003422	0	0,2907,0,11	.	.	.	.	.	.	.	0.002525	0.973955	1	1	C>T
ERR5749212	241	PASS	C	T	18014	0.863551	6	0,3,8925,9022	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749212	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	9667	0.002379	0	9648,0,23,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749212	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	9667	9.31E-4	0	9598,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749212	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	9667	0.001552	0	9598,0,15,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749212	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	9667	0.004034	0	9598,0,39,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749212	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	9662	0.001345	0	8783,4,756,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749212	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	9662	0.001759	0	9641,4,17,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749212	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	9662	0.001035	0	9647,4,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749212	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	9663	0.001345	0	9634,5,13,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749212	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATGGTTG	T	9663	8.28E-4	0	9634,5,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	atggttgag/	MVE85	leader	0.000587	0.476744	4	1	TATGGTTG>T
ERR5749212	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	33262	4.21E-4	10	23559,9684,13,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749212	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	33263	0.001774	10	23524,9672,48,11	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749212	913	PASS	C	T	23536	0.913324	0	0,12,0,23474	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749212	1510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	22700	0.002775	0	0,22400,0,68	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G235	nsp2	0.002159	0.937304	1	1	T>C
ERR5749212	3037	PASS	C	T	17868	0.816208	46	3,24,8938,8785	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749212	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	9020	0.002106	499	3,8995,18,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749212	3267	PASS	C	T	21456	0.970078	0	1,0,21444,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749212	5388	PASS	C	A	5556	0.955364	2147483647	0,0,5553,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749212	5986	PASS	C	T	12467	0.975696	2147483647	0,0,12458,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749212	6954	PASS	T	C	23425	0.819424	0	0,4,0,23272	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749212	7926	PASS	C	T	19725	0.97019	0	0,4,0,19713	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCa/gTa	A1736V	nsp3	0.000531	0.97019	5	2	C>T
ERR5749212	10533	PASS	G	T	17553	0.913405	0	14,0,17257,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tGt/tTt	C160F	3Cpro	0.000835	0.917216	4	2	G>T
ERR5749212	10533	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	17553	0.003133	0	17484,1,55,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tac/tTac	Y161L?	3Cpro	0.000835	0.917216	4	2	G>GT
ERR5749212	10789	PASS	C	T	16333	0.95255	0	4,0,16316,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D245	3Cpro	0.001434	0.956641	1	1	C>T
ERR5749212	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19367	0.001291	0	19300,10,30,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749212	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	19352	0.00217	0	19280,0,63,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749212	11287	PASS	GTCTGGTTTT	G	19338	0.997363	0	0,50,0,19287	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749212	12970	PASS	C	T	17709	0.855667	0	0,2,0,17658	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N95	nsp9	0.8352	0.861883	1	1	C>T
ERR5749212	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	31471	0.001366	1	15709,15664,23,25	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749212	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	11399	0.005088	3157	11119,91,6,180	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749212	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	22160	9.93E-4	0	11106,11046,11,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749212	14408	PASS	C	T	22160	0.848782	2	1,2,11056,10944	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749212	14676	PASS	C	T	13943	0.763537	0	5,0,13894,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749212	14913	PASS	C	T	18841	0.980627	141	3,4,18800,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N491	RdRp	0.011397	0.981624	1	1	C>T
ERR5749212	15279	PASS	C	T	24062	0.887956	0	4,0,24034,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749212	16176	PASS	T	C	19027	0.980922	1	1,3,8160,10855	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749212	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	21422	5.13E-4	0	21411,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749212	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28757	0.002052	0	28668,0,59,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749212	20445	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	30210	7.28E-4	0	34,30154,0,22	HIGH	NONE	FRAME_SHIFT	ORF1ab	aac/aaAc	N277K?	endoR	0.000518	0.059736	4	2	T>TA
ERR5749212	21764	PASS	ATACATG	A	12688	0.997241	0	35,0,12653,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749212	21974	PASS	G	T	12696	0.926591	132	5,10,3,12674	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gat/Tat	D138Y	S	0.001167	0.928915	2	2	G>T
ERR5749212	21990	PASS	TTTA	T	12696	0.998188	0	0,23,8,12665	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749212	23063	PASS	A	T	10473	0.866227	0	0,0,1,10430	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749212	23271	PASS	C	A	22884	0.921561	0	3,0,22856,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749212	23403	PASS	A	G	22877	0.967872	0	0,9,0,22853	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749212	23604	PASS	C	A	14226	0.938985	0	3,0,14211,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749212	23709	PASS	C	T	14205	0.943893	0	0,4,0,14181	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749212	24127	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TTTG	31237	4.48E-4	24	11037,20200,0,14	MODERATE	NONE	CODON_INSERTION	S	aac/TTGaac	N856LN	S	0.000324	0.111888	4	1	T>TTTG
ERR5749212	24506	PASS	T	G	19038	0.974052	0	6,0,19028,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749212	24914	PASS	G	C	28159	0.95742	0	0,0,14029,14106	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749212	25138	PASS	T	C	6852	0.895359	2147483647	0,0,6842,0	LOW	SILENT	SYNONYMOUS_CODING	S	aaT/aaC	N1192	S	0.001865	0.901453	2	2	T>C
ERR5749212	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	23098	0.001818	78	16181,6855,52,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749212	25481	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	32753	7.94E-4	0	16250,16334,15,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cGc/cAc	R30H	orf3a	0.000794	0.899776	2	1	G>A
ERR5749212	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	28129	6.04E-4	0	28112,0,17,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749212	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	28331	0.001165	1278	27965,185,65,81	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749212	25855	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	28110	0.011242	0	3,27735,0,366	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gac/Tac	D155Y	orf3a	0.001326	0.969697	1	1	G>T
ERR5749212	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	52005	2.88E-4	0	2,51985,0,15	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749212	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	10522	0.003041	0	0,10487,0,32	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749212	27915	PASS	G	A	10731	0.95909	0	2,0,10717,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	Gga/Aga	G8R	orf8	0.949134	0.95909	1	1	G>A
ERR5749212	27972	PASS	C	T	10744	0.901154	44	1,2,10671,36	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749212	28048	PASS	G	T	10718	0.911271	0	0,16,1,10691	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749212	28111	PASS	A	G	30181	0.97684	0	2,1,19446,10723	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749212	28270	PASS	TA	T	37713	0.994776	460	198,8,19158,18358	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749212	28280	PASS	G	C	37631	0.938508	21	15,3,19200,18337	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749212	28281	PASS	A	T	37631	0.919003	36	26,5,19185,18333	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749212	28282	PASS	T	A	37633	0.913294	24	24,7,19130,18354	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749212	28881	PASS	G	A	19330	0.710502	90	48,2,10795,7971	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749212	28882	PASS	G	A	19328	0.773955	105	52,1,11071,7945	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749212	28883	PASS	G	C	19328	0.922755	0	4,2,11244,8057	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749212	28977	PASS	C	T	8268	0.924891	0	0,2,12,8244	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749212	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	43586	8.26E-4	0	22661,20853,28,26	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749213	241	PASS	C	T	12179	0.862797	6	0,2,6070,6066	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749213	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	13631	9.54E-4	0	13618,2,13,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749213	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	13630	6.6E-4	0	13582,2,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749213	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	13630	6.6E-4	0	13582,2,9,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749213	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	13630	0.002128	0	13582,2,29,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749213	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	13626	0.002202	0	12591,4,948,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749213	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	30376	3.62E-4	0	16723,13640,6,5	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749213	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	30376	8.56E-4	2	16713,13634,16,10	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749213	815	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16729	0.001196	0	16689,9,24,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgc/Tgc	R4C	nsp2	0.001196	0.125156	1	1	C>T
ERR5749213	913	PASS	C	T	16722	0.916457	0	0,8,0,16696	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749213	1510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	17853	0.003417	0	0,17582,0,69	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G235	nsp2	0.002159	0.937304	1	1	T>C
ERR5749213	3037	PASS	C	T	20369	0.79567	64	1,25,10163,9985	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749213	3267	PASS	C	T	15462	0.971349	0	6,0,15447,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749213	4255	PASS	G	A	33057	0.827298	46	34,7,16422,16377	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccG/ccA	P512	nsp3	0.001102	0.871853	2	1	G>A
ERR5749213	5388	PASS	C	A	7845	0.959082	2147483647	0,0,7842,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749213	5986	PASS	C	T	13181	0.976178	0	2,0,13168,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749213	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12588	0.00135	0	3,12441,0,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749213	6954	PASS	T	C	17865	0.81864	0	0,7,0,17763	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749213	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	29625	9.79E-4	70	16522,13073,29,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749213	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13894	0.001943	0	13842,3,29,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749213	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	13884	0.001585	0	13844,0,35,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749213	11287	PASS	GTCTGGTTTT	G	13888	0.99784	0	0,30,0,13858	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749213	11507	PASS	G	A	29560	0.899222	1	4,2,14775,14675	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Att	V179I	nsp6	0.007744	0.914418	2	2	G>A
ERR5749213	13115	PASS	C	T	10161	0.078929	0	9261,0,898,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L31	nsp10	0.001806	0.922167	1	1	C>T
ERR5749213	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26076	0.002109	0	13019,12977,30,29	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749213	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	13236	0.005138	2147483647	12902,96,8,227	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749213	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	25694	0.001129	1	12883,12798,16,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749213	14408	PASS	C	T	25694	0.838445	3	2,4,12822,12669	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749213	14676	PASS	C	T	10847	0.752466	0	2,0,10809,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749213	15279	PASS	C	T	18570	0.880775	0	3,0,18539,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749213	16176	PASS	T	C	19188	0.981812	2	2,0,10770,8407	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749213	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	23375	5.99E-4	0	23361,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749213	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28688	0.001778	0	28618,0,53,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749213	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	16187	6.8E-4	0	0,16175,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TA>T
ERR5749213	21255	PASS	G	T	28447	0.917425	1603	75,73,28244,14	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcG/gcT	A199	MethTr	0.000341	0.917425	4	2	G>T
ERR5749213	21764	PASS	ATACATG	A	13090	0.996944	0	40,0,13050,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749213	21990	PASS	TTTA	T	13095	0.997709	0	0,30,4,13061	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749213	23063	PASS	A	T	12255	0.85459	0	0,2,0,12197	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749213	23271	PASS	C	A	16764	0.924183	2147483647	0,0,16757,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749213	23403	PASS	A	G	16761	0.96999	0	0,7,0,16740	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749213	23604	PASS	C	A	15892	0.966209	0	2,0,15880,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749213	23709	PASS	C	T	15875	0.937827	0	0,6,2,15849	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749213	24506	PASS	T	G	14621	0.974899	0	3,0,14614,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749213	24914	PASS	G	C	34170	0.956892	0	0,0,17003,17138	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749213	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	24210	0.002272	75	16978,7158,66,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749213	25553	PASS	C	T	17252	0.868131	0	0,12,0,17177	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	gCt/gTt	A54V	orf3a	0.001165	0.868131	3	2	C>T
ERR5749213	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	19252	0.001402	357	19155,30,12,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749213	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	19341	9.31E-4	0	19323,0,18,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749213	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	19475	0.001643	1106	19207,107,70,71	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749213	26319	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	9777	0.001432	0	9719,12,17,0	LOW	SILENT	SYNONYMOUS_CODING	E	gtA/gtG	V25	E	0.001432	0.971582	2	1	A>G
ERR5749213	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	12167	9.04E-4	0	2,12148,0,11	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749213	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	12167	9.04E-4	0	2,12154,0,11	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749213	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	12167	0.001808	0	2,12142,0,22	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749213	27972	PASS	C	T	10796	0.913672	22	1,1,10727,31	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749213	28048	PASS	G	T	10763	0.92307	0	0,10,0,10748	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749213	28111	PASS	A	G	26849	0.976647	7	3,6,16070,10764	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749213	28270	PASS	TA	T	31032	0.994844	350	155,7,15838,15034	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749213	28280	PASS	G	C	30965	0.937704	16	9,1,15865,15028	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749213	28281	PASS	A	T	30965	0.920878	30	19,3,15868,15011	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749213	28282	PASS	T	A	30965	0.911578	13	18,7,15838,15030	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749213	28881	PASS	G	A	13359	0.772513	18	7,0,6628,6561	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749213	28882	PASS	G	A	13359	0.827757	9	4,0,6693,6528	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749213	28883	PASS	G	C	13360	0.941018	3	0,1,6704,6644	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749213	28977	PASS	C	T	6804	0.919753	0	0,2,0,6779	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749213	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	49987	0.00152	1	25105,24767,48,44	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749214	241	PASS	C	T	7528	0.852683	0	1,1,3748,3747	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749214	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	13838	0.002023	0	12826,0,983,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749214	913	PASS	C	T	17410	0.917117	0	0,7,0,17378	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749214	3037	PASS	C	T	17972	0.811373	45	0,15,8975,8862	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749214	3267	PASS	C	T	18282	0.968275	0	1,0,18263,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749214	4276	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20249	0.003605	0	8,20139,0,91	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y519	nsp3	0.00102	0.812261	1	1	C>T
ERR5749214	5388	PASS	C	A	5317	0.960128	2147483647	0,0,5314,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749214	5986	PASS	C	T	11596	0.970852	2147483647	0,0,11591,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749214	6582	PASS	C	T	11391	0.968396	2147483647	0,0,11378,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T1288I	nsp3	0.001257	0.973714	2	2	C>T
ERR5749214	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11357	0.002025	0	3,11231,0,32	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749214	6954	PASS	T	C	20116	0.821287	0	0,2,0,20023	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749214	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	23966	8.35E-4	30	16452,7494,20,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749214	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	21825	0.002566	0	21744,0,74,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749214	11287	PASS	GTCTGGTTTT	G	21817	0.998304	0	0,36,0,21780	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749214	11507	PASS	G	A	26959	0.906562	6	5,1,13486,13365	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Att	V179I	nsp6	0.007744	0.914418	2	2	G>A
ERR5749214	13208	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAT	A	29516	4.07E-4	0	14758,14747,6,6	HIGH	NONE	FRAME_SHIFT	ORF1ab	atg/	M63	nsp10	0.000407	0.953357	4	2	AAT>A
ERR5749214	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	32500	0.001477	2	16223,16179,26,30	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749214	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	6395	0.00516	1880	6227,53,3,108	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749214	14408	PASS	C	T	12403	0.851246	0	3,3,6190,6138	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749214	14676	PASS	C	T	12428	0.777679	0	4,0,12384,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749214	15237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19273	0.003736	0	19169,22,73,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H599	RdRp	0.001014	0.955128	2	2	C>T
ERR5749214	15279	PASS	C	T	19246	0.884028	0	2,0,19206,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749214	16176	PASS	T	C	20363	0.98129	0	0,0,9331,11019	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749214	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	27204	9.93E-4	0	27177,0,27,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749214	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23469	0.001704	0	23406,0,43,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749214	20578	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	28059	0.001746	0	27976,0,80,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtg/Ttg	V320L	endoR	0.00085	0.958277	3	1	G>T
ERR5749214	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30716	8.14E-4	1	15022,15325,14,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749214	21762	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12809	0.002108	0	12760,0,34,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gTt	A67V	S	0.001297	0.875707	2	2	C>T
ERR5749214	21764	PASS	ATACATG	A	12809	0.996877	0	40,0,12769,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749214	21990	PASS	TTTA	T	12815	0.997503	0	0,32,3,12780	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749214	21991	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTA	T	12818	7.8E-4	0	6,12800,0,10	HIGH	NONE	FRAME_SHIFT	S	tat/	Y144	S	0.00078	0.991378	2	1	TTA>T
ERR5749214	23063	PASS	A	T	14568	0.856123	0	0,4,0,14485	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749214	23271	PASS	C	A	20349	0.920438	0	1,0,20313,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749214	23403	PASS	A	G	20350	0.969484	0	0,1,0,20331	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749214	23604	PASS	C	A	15564	0.951748	0	8,0,15550,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749214	23709	PASS	C	T	15544	0.931292	0	0,12,0,15499	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749214	24506	PASS	T	G	17244	0.974078	0	13,0,17224,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749214	24914	PASS	G	C	41403	0.9601	3	0,2,20623,20748	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749214	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	27779	8.64E-4	22	19223,8527,25,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749214	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	12487	0.002883	358	12399,25,19,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749214	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	12531	7.98E-4	0	12521,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749214	27078	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34521	0.032328	0	3,33284,0,1206	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Cgt/Tgt	R186C	M	0.000415	0.05783	2	2	C>T
ERR5749214	27312	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	20368	0.002062	0	20326,0,42,0	HIGH	NONE	FRAME_SHIFT	ORF6	aat/aaAt	N39K?	orf6	0.000911	0.088458	4	2	T>TA
ERR5749214	27972	PASS	C	T	8395	0.901012	0	0,0,8341,29	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749214	28010	PASS	T	C	8359	0.934801	0	0,2,0,8347	LOW	SILENT	SYNONYMOUS_CODING	ORF8	atT/atC	I39	orf8	0.933761	0.934801	1	1	T>C
ERR5749214	28048	PASS	G	T	8375	0.906746	0	0,15,0,8357	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749214	28111	PASS	A	G	30040	0.979261	1	4,2,21644,8378	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749214	28270	PASS	TA	T	41851	0.995197	456	201,9,21350,20300	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749214	28280	PASS	G	C	41763	0.940593	16	15,4,21380,20293	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749214	28281	PASS	A	T	41763	0.914566	60	31,3,21371,20292	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749214	28282	PASS	T	A	41764	0.909132	19	29,12,21315,20295	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749214	28881	PASS	G	A	11358	0.770382	9	6,1,5608,5585	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749214	28882	PASS	G	A	11358	0.836415	2	6,3,5675,5578	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749214	28883	PASS	G	C	11358	0.942508	3	0,1,5689,5654	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749214	28960	PASS	G	T	5795	0.921139	0	0,7,0,5777	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	caG/caT	Q229H	N	0.00273	0.921139	2	2	G>T
ERR5749214	28977	PASS	C	T	5796	0.933402	0	0,4,0,5780	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749214	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	38084	0.002127	536	32254,5710,9,79	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749214	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	64102	0.001076	2	32196,31801,46,40	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749214	29284	PASS	C	T	32282	0.931014	2147483647	0,0,0,32253	LOW	SILENT	SYNONYMOUS_CODING	N	atC/atT	I337	N	0.000393	0.931014	3	2	C>T
ERR5749215	241	PASS	C	T	3093	0.860653	0	0,0,1539,1542	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749215	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	4072	0.00221	0	3774,0,291,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749215	815	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11745	0.005023	0	11674,0,67,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgc/Tgc	R4C	nsp2	0.001196	0.125156	1	1	C>T
ERR5749215	913	PASS	C	T	11750	0.91183	0	0,6,0,11726	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749215	2672	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	18503	0.001351	0	18461,0,34,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gca/Tca	A623S	nsp2	0.001351	0.18509	3	1	G>T
ERR5749215	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	36782	0.001658	2804	18350,17173,42,1119	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749215	2855	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTCGG	C	22120	4.97E-4	6	3608,18501,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctcggt/	LG46	nsp3	0.000497	0.926613	2	2	CTCGG>C
ERR5749215	3037	PASS	C	T	7161	0.820835	15	0,5,3576,3539	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749215	3267	PASS	C	T	11326	0.96848	2147483647	0,0,11318,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749215	4255	PASS	G	A	16949	0.826715	16	11,2,8418,8404	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccG/ccA	P512	nsp3	0.001102	0.871853	2	1	G>A
ERR5749215	4832	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTAG	C	14751	5.42E-4	0	7380,7364,4,4	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ctaggt/cgt	LG705R	nsp3	0.000542	0.727166	3	2	CTAG>C
ERR5749215	5388	PASS	C	A	2034	0.951327	2147483647	0,0,2032,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749215	5986	PASS	C	T	5358	0.973124	2147483647	0,0,5351,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749215	6954	PASS	T	C	10697	0.832944	2147483647	0,0,0,10639	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749215	7740	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATAG	A	10787	8.34E-4	0	10778,0,9,0	MODERATE	NONE	CODON_DELETION	ORF1ab	agt/	S1675	nsp3	0.000834	0.078818	3	2	ATAG>A
ERR5749215	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	10642	0.001785	21	7991,2632,19,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749215	11104	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	15540	0.001223	0	15465,0,19,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccT/ccC	P44	nsp6	0.000866	0.675414	2	1	T>C
ERR5749215	11287	PASS	GTCTGGTTTT	G	15538	0.999099	0	0,13,0,15524	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749215	11464	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	5641	0.001064	0	5635,0,6,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tgg/	W165	nsp6	0.001064	0.906658	2	2	GT>G
ERR5749215	11507	PASS	G	A	11213	0.904397	0	1,1,5618,5557	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Att	V179I	nsp6	0.007744	0.914418	2	2	G>A
ERR5749215	13458	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13335	0.004199	0	13270,0,58,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCg/tTg	S6L	nsp11	0.001017	0.058608	4	2	C>T
ERR5749215	13459	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	13334	0.00165	0	13313,0,22,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L8	nsp11	0.000691	0.060726	5	2	GT>G
ERR5749215	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26635	0.001464	0	13292,13267,22,22	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749215	14408	PASS	C	T	4641	0.846585	0	0,0,2316,2297	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749215	14676	PASS	C	T	9548	0.793046	0	1,0,9509,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749215	15279	PASS	C	T	10880	0.880699	2147483647	0,0,10867,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749215	16176	PASS	T	C	11190	0.981859	2	1,1,3316,7868	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749215	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	11014	8.17E-4	0	11005,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749215	18658	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	17258	6.95E-4	0	17242,4,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tgt/	C207	ExoN	0.000507	0.115741	3	2	TG>T
ERR5749215	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	17254	6.95E-4	0	17242,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749215	19483	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	7946	0.002014	0	0,7917,0,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gct/Tct	A482S	ExoN	0.001112	0.089844	3	1	G>T
ERR5749215	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8711	0.005166	0	8662,0,46,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749215	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	17348	0.001268	2	8640,8688,9,13	HIGH	NONE	FRAME_SHIFT	S	ctt/Tctt	L5S?	S	0.000394	0.091869	4	1	G>GT
ERR5749215	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17321	0.001155	0	8481,8657,13,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749215	21764	PASS	ATACATG	A	6719	0.998214	0	12,0,6707,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749215	21990	PASS	TTTA	T	6722	0.998066	0	0,13,4,6705	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749215	23063	PASS	A	T	7468	0.867434	0	0,1,0,7431	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749215	23271	PASS	C	A	15980	0.916834	0	1,0,15958,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749215	23403	PASS	A	G	15974	0.966007	0	0,8,0,15958	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749215	23604	PASS	C	A	7105	0.935679	0	4,0,7096,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749215	23709	PASS	C	T	7098	0.942519	0	0,6,0,7084	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749215	24506	PASS	T	G	11492	0.972416	0	3,0,11488,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749215	24914	PASS	G	C	25417	0.959633	0	0,1,12664,12739	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749215	25587	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	11554	9.52E-4	0	0,11543,0,11	HIGH	NONE	FRAME_SHIFT	ORF3a	aag/aaAg	K67K?	orf3a	0.000598	0.813206	6	2	C>CA
ERR5749215	25710	PASS	C	T	5232	0.768731	0	1,0,5216,0	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	ctC/ctT	L106	orf3a	0.002127	0.789778	2	2	C>T
ERR5749215	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	15995	0.001	0	0,15979,0,16	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749215	26645	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	6184	9.7E-4	0	6178,0,6,0	HIGH	NONE	FRAME_SHIFT	M	agg/	R42	M	0.00097	0.828654	2	2	CAG>C
ERR5749215	27145	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	25205	4.76E-4	0	1,25192,0,12	HIGH	NONE	FRAME_SHIFT	M	gac/	D209	M	0.000476	0.863895	2	2	CAG>C
ERR5749215	27641	PASS	C	T	12974	0.906891	0	4,0,12937,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	tCa/tTa	S83L	orf7a	0.000983	0.911213	2	2	C>T
ERR5749215	27972	PASS	C	T	3310	0.902115	0	0,0,3275,22	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749215	28048	PASS	G	T	3293	0.920134	0	0,1,0,3290	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749215	28111	PASS	A	G	19157	0.979485	5	1,1,15856,3290	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749215	28270	PASS	TA	T	30846	0.995105	277	130,8,15659,15036	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749215	28270	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAA	T	30846	6.81E-4	53	130,8,11,10	.	.	.	.	.	.	.	0.000322	1	2	1	TAA>T
ERR5749215	28280	PASS	G	C	30790	0.942968	0	5,4,15695,15040	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749215	28281	PASS	A	T	30790	0.919292	18	12,2,15698,15040	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749215	28282	PASS	T	A	30791	0.909616	6	11,5,15660,15046	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749215	28881	PASS	G	A	6315	0.714014	6	2,0,3069,3118	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749215	28882	PASS	G	A	6315	0.817261	9	4,0,3148,3107	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749215	28883	PASS	G	C	6315	0.942518	0	0,0,3158,3152	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749215	28977	PASS	C	T	3208	0.93298	0	0,2,0,3203	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749215	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	34848	0.001406	0	17487,17292,31,30	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749215	29284	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	17530	6.27E-4	0	0,17519,0,11	HIGH	NONE	FRAME_SHIFT	N	aaa/	K338	N	0.000393	0.931014	3	2	CA>C
ERR5749215	29686	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	5744	0.001045	0	2870,2868,3,3	.	.	.	.	.	.	.	0.001045	0.802514	2	1	CAG>C
ERR5749216	239	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTC	T	985	0.004061	0	490,491,2,2	.	.	.	.	.	.	.	0.000495	0.25	4	1	TTC>T
ERR5749216	241	PASS	C	T	985	0.86599	0	0,0,487,489	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749216	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	1952	0.004098	0	1920,24,8,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749216	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	1952	0.008197	0	1912,24,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749216	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9158	0.017908	24	7075,1882,153,21	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L140	leader	0.000316	0.135802	3	2	C>T
ERR5749216	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	9158	0.002293	2	7211,1923,18,3	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749216	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7222	0.002215	0	0,7198,0,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749216	913	PASS	C	T	7223	0.919978	0	0,3,0,7208	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749216	1735	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	5424	0.002028	0	5413,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtg/	V311	nsp2	0.002028	0.062222	1	1	TG>T
ERR5749216	2062	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7701	0.003116	0	7643,18,29,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A419	nsp2	0.001265	0.822961	2	1	C>T
ERR5749216	2232	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10121	0.002865	27	2432,7647,1,33	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A476V	nsp2	0.000499	0.381237	2	2	C>T
ERR5749216	2453	PASS	C	T	2432	0.734786	2147483647	0,0,0,2399	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L550F	nsp2	0.00429	0.842201	2	2	C>T
ERR5749216	2494	PASS	G	T	2433	0.950678	0	0,2,0,2427	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gaG/gaT	E563D	nsp2	0.002624	0.951457	2	2	G>T
ERR5749216	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	20519	0.00156	1563	10236,9597,21,614	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749216	2805	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	10317	0.001648	0	0,10284,0,19	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gAa/gGa	E29G	nsp3	0.001648	0.173333	2	1	A>G
ERR5749216	3037	PASS	C	T	2448	0.812092	9	0,3,1222,1202	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749216	3267	PASS	C	T	6762	0.968353	2147483647	0,0,6758,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749216	3429	PASS	C	T	6760	0.813462	0	0,360,0,6376	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T237I	nsp3	0.001846	0.813462	1	1	C>T
ERR5749216	3802	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	3809	0.0021	19	2100,1701,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N363	nsp3	0.000554	0.064198	4	2	TA>T
ERR5749216	4136	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	6178	0.001942	21	4057,2108,13,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Ttt	V473F	nsp3	0.00075	0.974623	4	2	G>T
ERR5749216	4317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	4069	0.004178	0	0,4048,0,19	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aGt/aCt	S533T	nsp3	0.001619	0.118421	2	1	G>C
ERR5749216	4331	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9657	0.001967	0	5574,4048,12,8	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L538	nsp3	0.000987	0.928955	1	1	C>T
ERR5749216	4764	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	3448	0.00203	0	3441,0,7,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F683	nsp3	0.000673	0.93404	4	2	AT>A
ERR5749216	5178	PASS	C	T	4910	0.874949	0	0,6,0,4858	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T820I	nsp3	0.00175	0.88249	2	1	C>T
ERR5749216	5388	PASS	C	A	790	0.946835	2147483647	0,0,789,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749216	5986	PASS	C	T	2324	0.978485	2147483647	0,0,2324,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749216	6196	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2324	0.021945	0	0,2264,0,54	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P1159	nsp3	0.004402	0.945644	1	1	C>T
ERR5749216	6310	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8420	0.002138	0	8392,0,18,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	agC/agT	S1197	nsp3	0.00099	0.94715	2	2	C>T
ERR5749216	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	2183	0.008704	0	0,2162,0,19	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L1328S?	nsp3	0.000731	0.14377	4	2	C>CT
ERR5749216	6954	PASS	T	C	6924	0.823801	0	0,1,0,6882	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749216	7926	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	4619	0.001948	0	0,4610,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1737	nsp3	0.000531	0.97019	5	2	CAA>C
ERR5749216	7945	PASS	C	T	4621	0.922311	65	2,1,0,4615	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y1742	nsp3	0.001244	0.950558	2	2	C>T
ERR5749216	8512	PASS	A	G	1904	0.805147	2147483647	0,0,0,1899	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caA/caG	Q1931	nsp3	0.8	0.822278	1	1	A>G
ERR5749216	8692	PASS	C	T	1956	0.975971	2147483647	0,0,1949,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y46	nsp4	0.967679	0.97884	1	1	C>T
ERR5749216	9202	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	4276	0.002572	0	0,4265,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	gat/	D217	nsp4	0.002572	0.155556	1	1	TG>T
ERR5749216	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	5099	0.00353	10	4307,774,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749216	9661	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8340	0.003717	0	4291,4009,17,16	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F369	nsp4	0.000584	0.920378	2	2	C>T
ERR5749216	10228	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5684	0.004398	0	5646,0,27,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ctC/ctT	L58	3Cpro	0.000533	0.961998	2	2	C>T
ERR5749216	10642	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	8107	0.002467	0	0,8078,0,22	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acG/acC	T196	3Cpro	0.001264	0.951979	3	1	G>C
ERR5749216	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	10363	0.002316	16	8679,1652,24,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749216	11750	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17035	0.020194	3	8439,8089,250,221	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L260F	nsp6	0.001019	0.70989	2	1	C>T
ERR5749216	12269	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	4817	0.00436	0	4796,0,21,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aag/	K61	nsp8	0.000434	0.213333	2	1	GA>G
ERR5749216	12343	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	4812	0.003533	0	0,4780,0,18	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T84	nsp8	0.003533	0.064234	1	1	T>C
ERR5749216	12781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2608	0.004218	0	2591,6,11,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y32	nsp9	0.001869	0.974683	2	2	C>T
ERR5749216	12884	PASS	A	G	2601	0.055748	0	2444,1,150,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Aca/Gca	T67A	nsp9	0.001655	0.08541	1	1	A>G
ERR5749216	13059	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTG	C	8530	0.001172	14	5918,2602,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gta/	V13	nsp10	0.000448	0.855104	3	2	CTG>C
ERR5749216	13459	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	7086	0.002399	0	7069,0,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/ttTa	L8F?	nsp11	0.000691	0.060726	5	2	G>GT
ERR5749216	13459	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTT	G	7086	0.00127	0	7077,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L8	nsp11	0.000691	0.060726	5	2	GTT>G
ERR5749216	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14148	0.001272	0	7064,7047,10,11	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749216	14087	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	5823	0.002233	0	5802,0,19,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tGg/tTg	W216L	RdRp	0.001684	0.130841	2	1	G>T
ERR5749216	14408	PASS	C	T	2629	0.827691	0	0,0,1313,1297	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749216	14676	PASS	C	T	5264	0.81193	0	1,0,5254,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749216	15279	PASS	C	T	5559	0.895305	2147483647	0,0,5556,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749216	16176	PASS	T	C	6429	0.982268	0	0,0,1083,5345	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749216	16508	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	10432	0.001821	0	10407,0,24,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGt/gTt	G91V	helicase	0.000561	0.074909	2	2	G>T
ERR5749216	16559	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	10431	0.001726	0	10397,0,31,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCa/gAa	A108E	helicase	0.000644	0.051993	3	2	C>A
ERR5749216	16792	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16144	0.00192	16	5704,10400,5,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgt/Tgt	R186C	helicase	0.000335	0.072562	5	2	C>T
ERR5749216	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	5711	0.003152	0	5691,0,19,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E201K	helicase	0.000535	0.100775	3	2	G>A
ERR5749216	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	5711	0.001401	0	5703,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749216	17081	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GACC	G	5711	0.001926	0	0,5700,0,11	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ccacct/cct	PP283P	helicase	0.001926	0.120301	3	2	GACC>G
ERR5749216	17749	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	4612	0.003469	0	4587,0,16,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gct/Act	A505T	helicase	0.001521	0.987943	4	2	G>A
ERR5749216	17762	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4612	0.002602	0	4598,0,13,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A509V	helicase	0.000697	0.912542	2	2	C>T
ERR5749216	18658	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	11289	0.002303	0	11256,2,27,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tgt/Cgt	C207R	ExoN	0.000507	0.115741	3	2	T>C
ERR5749216	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	11287	0.001418	0	11271,0,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749216	18747	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11284	0.001684	0	11257,0,23,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V236	ExoN	0.000375	0.982946	4	2	C>T
ERR5749216	19320	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3370	0.004154	0	3354,0,15,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H427	ExoN	0.004154	0.957053	2	2	C>T
ERR5749216	19343	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTTTTG	C	3369	0.002078	0	3362,0,7,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tttgtt/	FV436	ExoN	0.000519	0.192257	7	2	CTTTTG>C
ERR5749216	20718	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	2345	0.010661	0	0,2311,0,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atA	M20I	MethTr	0.000898	0.920213	3	1	G>A
ERR5749216	20844	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12834	0.004208	47	10417,2346,58,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P62	MethTr	0.000293	0.905571	5	2	C>T
ERR5749216	20930	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	10484	0.001526	0	10468,0,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggt/	G92	MethTr	0.000902	0.95585	2	2	CG>C
ERR5749216	20987	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	20902	0.00134	0	10451,10424,14,14	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L111	MethTr	0.000276	0.056129	4	2	CT>C
ERR5749216	21034	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10476	0.002482	0	0,10420,0,29	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L126F	MethTr	0.001871	0.915185	1	1	C>T
ERR5749216	21101	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	10484	0.001908	0	0,10455,0,28	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGt/gTt	G148V	MethTr	0.001498	0.083467	2	2	G>T
ERR5749216	21764	PASS	ATACATG	A	3553	0.99803	0	7,0,3546,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749216	21812	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3553	0.003659	0	3538,0,13,0	LOW	SILENT	SYNONYMOUS_CODING	S	Cta/Tta	L84	S	0.001506	0.06449	1	1	C>T
ERR5749216	21990	PASS	TTTA	T	3557	0.99494	0	0,18,4,3535	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749216	22771	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	9731	0.001644	0	0,9695,0,17	LOW	SILENT	SYNONYMOUS_CODING	S	agA/agG	R403	S	0.000511	0.112051	3	3	A>G
ERR5749216	23063	PASS	A	T	4009	0.852332	0	0,1,0,3973	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749216	23271	PASS	C	A	10437	0.91281	0	1,0,10422,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749216	23403	PASS	A	G	10428	0.968642	0	0,2,0,10419	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749216	23604	PASS	C	A	3695	0.945602	0	4,0,3691,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749216	23709	PASS	C	T	3694	0.942339	0	0,1,0,3691	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749216	23780	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	3696	0.002706	0	0,3686,0,10	HIGH	NONE	FRAME_SHIFT	S	atg/	M740	S	0.002014	0.967596	3	2	AT>A
ERR5749216	24010	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATTTATTGAAGATCTAC	A	2786	0.002154	0	46,2736,0,6	HIGH	NONE	FRAME_SHIFT	S	attgaagatctacttttc/	IEDLLF818	S	0.000455	0.926398	4	2	ATTTATTGAAGATCTAC>A
ERR5749216	24506	PASS	T	G	6926	0.9743	0	4,0,6919,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749216	24616	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6909	0.002895	0	1,6880,0,25	LOW	SILENT	SYNONYMOUS_CODING	S	atC/atT	I1018	S	0.001268	0.127917	3	2	C>T
ERR5749216	24914	PASS	G	C	8850	0.965085	0	0,0,21,8818	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749216	25572	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	8625	0.002087	0	0,8605,0,18	HIGH	NONE	FRAME_SHIFT	ORF3a	aaaatc/	KI61	orf3a	0.000543	0.959687	4	2	CAA>C
ERR5749216	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	1376	0.006541	108	1356,7,3,6	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749216	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTAATCCAGTA	T	8218	0.001095	0	0,8209,0,9	MODERATE	NONE	CODON_DELETION	ORF3a	gttaatccagta/	VNPV256	orf3a	0.000249	0.122153	5	2	TGTTAATCCAGTA>T
ERR5749216	26158	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	8218	0.001704	0	0,8204,0,14	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF3a	gttaat/gat	VN256D	orf3a	0.000297	0.905181	6	2	GTTA>G
ERR5749216	26270	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	13405	5.97E-4	33	5168,8229,8,0	HIGH	NONE	FRAME_SHIFT	E	aca/	T9	E	0.000586	0.930791	3	2	CA>C
ERR5749216	26526	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	5178	0.002704	0	2,5160,0,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Gca/Aca	A2T	M	0.001224	0.951192	3	1	G>A
ERR5749216	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	3396	0.010012	0	0,3362,0,34	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749216	26895	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18965	0.002426	0	18910,2,48,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Cat/Tat	H125Y	M	0.000874	0.97046	1	1	C>T
ERR5749216	27209	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	7652	0.00196	0	7628,0,15,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF6	cAt/cGt	H3R	orf6	0.00088	0.957103	3	2	A>G
ERR5749216	27240	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAT	G	7652	0.001176	0	7643,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF6	atatta/	IL14	orf6	0.000521	0.117458	2	2	GAT>G
ERR5749216	27312	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	7649	0.001046	0	7641,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF6	aat/aaAt	N39K?	orf6	0.000911	0.088458	4	2	T>TA
ERR5749216	27389	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7660	0.004439	0	18,7601,0,37	.	.	.	.	.	.	.	0.001157	0.899553	2	1	C>T
ERR5749216	27476	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	18267	5.47E-4	21	10605,7652,10,0	HIGH	NONE	FRAME_SHIFT	ORF7a	aca/	T28	orf7a	0.000547	0.22827	4	2	CA>C
ERR5749216	27745	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AG	A	10623	9.41E-4	0	0,10613,0,10	HIGH	NONE	FRAME_SHIFT	ORF7a	aga/	R118	orf7a	0.000941	0.082742	2	2	AG>A
ERR5749216	27972	PASS	C	T	1447	0.906012	0	0,0,1430,14	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749216	28048	PASS	G	T	1434	0.920502	0	0,3,0,1430	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749216	28111	PASS	A	G	16076	0.978664	0	1,0,14635,1432	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749216	28200	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TC	T	14640	7.51E-4	0	14629,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF8	tcg/	S103	orf8	0.000751	0.981434	2	2	TC>T
ERR5749216	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14634	0.007448	0	14492,0,112,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749216	28270	PASS	TA	T	28376	0.995806	280	121,5,14474,13783	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749216	28280	PASS	G	C	28328	0.937729	19	10,1,14501,13769	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749216	28281	PASS	A	T	28328	0.921738	53	19,0,14496,13779	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749216	28282	PASS	T	A	28330	0.914155	12	16,6,14463,13784	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749216	28287	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	29141	9.61E-4	45	14481,14578,59,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gGa/gTa	G5V	N	0.000961	0.079824	2	1	G>T
ERR5749216	28292	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	29149	0.002058	0	14510,14579,30,30	HIGH	NONE	FRAME_SHIFT	N	aat/	N8	N	0.000304	0.055324	4	2	CA>C
ERR5749216	28321	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	14636	5.47E-4	0	0,14628,0,8	HIGH	NONE	FRAME_SHIFT	N	ggt/Tggt	G18W?	N	0.00045	0.947809	3	2	G>GT
ERR5749216	28516	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	8867	0.001579	0	8844,0,18,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D81E	N	0.001273	0.990661	2	2	T>A
ERR5749216	28881	PASS	G	A	4514	0.767169	0	1,0,2240,2214	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749216	28882	PASS	G	A	4514	0.821444	0	1,0,2264,2213	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749216	28883	PASS	G	C	4514	0.946389	0	0,0,2268,2244	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749216	28977	PASS	C	T	2297	0.93818	2147483647	0,0,0,2294	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749216	29077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9374	0.00192	0	9339,0,18,0	LOW	SILENT	SYNONYMOUS_CODING	N	taC/taT	Y268	N	0.000408	0.88565	3	2	C>T
ERR5749217	241	PASS	C	T	3983	0.85639	0	1,2,1980,1990	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749217	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	5664	0.007945	0	5615,5,45,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749217	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	5664	0.001766	0	5579,5,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749217	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	5664	0.002295	0	5579,5,13,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749217	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	5664	0.009887	0	5579,5,56,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749217	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	5667	0.003	1	5030,16,453,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749217	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	5667	0.003176	0	5633,16,18,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749217	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	5665	0.002118	0	5620,16,12,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttatg/gtg	VM84V	leader	0.000554	0.991848	4	1	GTTA>G
ERR5749217	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	5665	0.003001	0	5620,16,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749217	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	5672	0.001939	0	5627,23,11,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749217	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	15938	0.001443	10	10254,5659,19,4	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749217	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	15938	7.53E-4	22	10211,5644,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749217	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	15938	0.003953	5	10211,5644,45,18	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749217	913	PASS	C	T	10278	0.918175	0	0,8,0,10259	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749217	3037	PASS	C	T	8053	0.809139	39	0,13,4018,3962	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749217	3095	PASS	T	C	4056	0.950444	2147483647	0,0,0,4053	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tca/Cca	S126P	nsp3	0.937591	0.970297	1	1	T>C
ERR5749217	3177	PASS	C	T	15892	0.901774	4	5,0,11820,4045	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P153L	nsp3	0.000773	0.96008	3	2	C>T
ERR5749217	3267	PASS	C	T	11834	0.969917	0	2,0,11828,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749217	5388	PASS	C	A	2809	0.952296	2147483647	0,0,2809,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749217	5986	PASS	C	T	6327	0.970128	0	1,0,6321,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749217	6359	PASS	G	A	27255	0.085782	0	12347,12323,1280,1276	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gac/Aac	D1214N	nsp3	0.001065	0.085782	2	1	G>A
ERR5749217	6954	PASS	T	C	11715	0.830303	0	0,2,0,11656	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749217	9251	PASS	G	A	4199	0.893784	2147483647	0,0,4190,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Att	V233I	nsp4	0.893784	0.893784	1	1	G>A
ERR5749217	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	12855	0.003034	0	12794,0,48,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749217	11287	PASS	GTCTGGTTTT	G	12850	0.993152	0	0,88,0,12762	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749217	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16725	0.001136	0	8348,8330,11,10	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749217	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	2615	0.005354	530	2552,30,1,31	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749217	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	5076	0.002561	0	2544,2525,7,6	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749217	14408	PASS	C	T	5076	0.835697	0	0,0,2530,2503	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749217	14676	PASS	C	T	7666	0.796113	0	4,0,7645,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749217	15279	PASS	C	T	10733	0.876828	2147483647	0,0,10717,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749217	15396	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	10725	7.46E-4	0	7,10709,0,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	tataga/	YR653	RdRp	0.000524	0.116667	1	1	CTA>C
ERR5749217	15960	PASS	C	T	6242	0.811919	0	1,0,6227,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A840	RdRp	0.001581	0.81574	1	1	C>T
ERR5749217	16176	PASS	T	C	10280	0.983366	8	2,0,4033,6242	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749217	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12178	0.001724	0	12146,0,22,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749217	21188	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	15093	0.001259	0	15022,3,20,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAt/aGt	N177S	MethTr	0.001259	0.977881	1	1	A>G
ERR5749217	21764	PASS	ATACATG	A	6576	0.99635	0	24,0,6552,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749217	21990	PASS	TTTA	T	6580	0.996657	0	0,22,2,6556	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749217	22280	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ACTTTACTTG	A	12263	9.79E-4	0	4,12247,0,12	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	cttgctttacat/cat	LALH242H	S	0.00046	0.997799	1	1	ACTTTACTTG>A
ERR5749217	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	9539	0.001782	0	0,9519,0,17	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749217	23063	PASS	A	T	7735	0.864383	0	0,1,1,7696	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749217	23271	PASS	C	A	13006	0.916731	0	2,0,12985,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749217	23277	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13006	0.003537	0	12930,2,58,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCt/aTt	T572I	S	0.001007	0.74768	1	1	C>T
ERR5749217	23403	PASS	A	G	12998	0.97138	0	0,2,0,12990	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749217	23604	PASS	C	A	8219	0.93223	0	6,0,8205,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749217	23709	PASS	C	T	8214	0.946798	0	0,3,9,8191	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749217	24010	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATTTATTGAAGATCTAC	A	7755	9.03E-4	0	54,7700,0,7	HIGH	NONE	FRAME_SHIFT	S	attgaagatctacttttc/	IEDLLF818	S	0.000455	0.926398	4	2	ATTTATTGAAGATCTAC>A
ERR5749217	24432	PASS	A	T	15902	0.937303	13	6,0,9276,6615	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cAa/cTa	Q957L	S	0.935743	0.949489	1	1	A>T
ERR5749217	24506	PASS	T	G	9282	0.970804	0	6,0,9275,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749217	24914	PASS	G	C	22110	0.957757	0	0,0,11027,11070	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749217	25495	PASS	A	G	20926	0.907388	0	2,2,10399,10502	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Ata/Gta	I35V	orf3a	0.000735	0.911134	2	1	A>G
ERR5749217	26013	PASS	C	T	21403	0.972994	0	2,0,21393,0	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	ttC/ttT	F207	orf3a	0.000839	0.974528	1	1	C>T
ERR5749217	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	21373	7.02E-4	0	0,21355,0,15	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749217	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	6570	0.003196	0	0,6544,0,21	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749217	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	6570	0.001218	0	0,6562,0,8	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749217	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	6573	0.008672	0	0,6511,0,57	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749217	27972	PASS	C	T	4611	0.896118	19	1,1,4569,25	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749217	28048	PASS	G	T	4591	0.92115	0	0,2,0,4583	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749217	28111	PASS	A	G	17449	0.979254	17	0,3,12850,4591	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749217	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	12829	0.001013	0	12818,1,13,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749217	28270	PASS	TA	T	24885	0.994937	330	131,3,12658,12101	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749217	28280	PASS	G	C	24837	0.938157	9	8,2,12689,12084	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749217	28281	PASS	A	T	24837	0.907235	11	18,8,12679,12080	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749217	28282	PASS	T	A	24840	0.902778	5	14,8,12647,12095	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749217	28406	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTACCCAATA	T	12867	0.00101	0	11,12840,0,13	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	N	ttacccaataat/tat	LPNN45Y	N	0.00043	0.921074	3	2	TTACCCAATA>T
ERR5749217	28407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TACCCAATA	T	12867	0.001166	0	11,12841,0,15	HIGH	NONE	FRAME_SHIFT	N	cccaataat/	PNN46	N	0.000382	0.179673	1	1	TACCCAATA>T
ERR5749217	28881	PASS	G	A	8272	0.722921	30	10,0,4026,4080	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749217	28882	PASS	G	A	8267	0.83041	3	2,0,4110,4069	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749217	28883	PASS	G	C	8267	0.940244	0	0,0,4120,4135	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749217	28977	PASS	C	T	4214	0.931182	2147483647	0,0,0,4203	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749217	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	22233	0.001619	147	17991,4175,8,30	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749217	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	35774	0.001286	0	17961,17750,26,26	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749218	241	PASS	C	T	6858	0.864684	0	0,0,3414,3421	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749218	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	10087	0.002776	39	10054,4,26,2	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749218	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	10088	0.001487	19	10018,6,14,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749218	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	10088	0.001784	0	10018,6,18,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749218	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	10088	0.002676	0	10018,6,27,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749218	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	10088	0.001586	0	10063,9,16,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749218	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	27146	0.002063	14	17002,10077,43,13	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749218	913	PASS	C	T	17046	0.915229	0	0,14,0,17003	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749218	967	PASS	T	C	29172	0.976279	1	3,3,12109,17044	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caT/caC	H54	nsp2	0.973649	0.978486	1	1	T>C
ERR5749218	2166	PASS	A	G	19197	0.940616	0	0,7,0,19149	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K454R	nsp2	0.932132	0.94762	1	1	A>G
ERR5749218	3037	PASS	C	T	15724	0.820656	45	0,15,7858,7734	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749218	3267	PASS	C	T	17493	0.970331	0	1,0,17481,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749218	4255	PASS	G	A	32523	0.801925	23	25,8,16168,16048	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccG/ccA	P512	nsp3	0.001102	0.871853	2	1	G>A
ERR5749218	5388	PASS	C	A	5226	0.962304	2147483647	0,0,5223,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749218	5986	PASS	C	T	10676	0.976208	0	2,0,10668,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749218	6196	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10677	0.004402	0	0,10616,0,52	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P1159	nsp3	0.004402	0.945644	1	1	C>T
ERR5749218	6320	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	19935	0.001756	26	19883,0,47,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Ttt	V1201F	nsp3	0.001197	0.080147	2	2	G>T
ERR5749218	6954	PASS	T	C	18347	0.818063	0	0,4,0,18263	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749218	7067	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	34734	9.21E-4	73	16276,18408,41,7	HIGH	NONSENSE	STOP_GAINED	ORF1ab	Gaa/Taa	E1450*	nsp3	0.000274	0.059217	5	3	G>T
ERR5749218	7945	PASS	C	T	17690	0.916902	303	9,3,0,17654	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y1742	nsp3	0.001244	0.950558	2	2	C>T
ERR5749218	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	21911	4.56E-4	20	13496,8404,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749218	11287	PASS	GTCTGGTTTT	G	16949	0.998053	0	0,33,0,16916	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749218	11507	PASS	G	A	24343	0.908516	9	4,0,12173,12089	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Att	V179I	nsp6	0.007744	0.914418	2	2	G>A
ERR5749218	12125	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	14682	0.001703	0	4,14601,0,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y12H	nsp8	0.000847	0.113436	1	1	T>C
ERR5749218	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24020	0.001166	0	11995,11963,16,17	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749218	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	6204	0.005158	1528	6038,64,6,92	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749218	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	12027	0.001746	0	6028,5989,11,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749218	14408	PASS	C	T	12027	0.845182	9	0,3,6006,5920	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749218	14676	PASS	C	T	11032	0.769489	0	3,0,10990,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749218	15099	PASS	A	G	15707	0.907239	0	0,2,9,15677	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	agA/agG	R553	RdRp	0.871069	0.907239	1	1	A>G
ERR5749218	15279	PASS	C	T	16920	0.970449	0	5,0,16905,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749218	16176	PASS	T	C	16147	0.980925	6	2,0,7719,8420	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749218	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	21455	6.53E-4	0	21441,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749218	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	21456	4.66E-4	0	0,21446,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749218	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23887	0.001549	0	23823,0,39,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749218	20987	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	36846	3.26E-4	0	18422,18414,6,6	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L111	MethTr	0.000276	0.056129	4	2	CT>C
ERR5749218	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29275	7.86E-4	0	14346,14600,12,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749218	21764	PASS	ATACATG	A	10543	0.99668	0	35,0,10508,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749218	21990	PASS	TTTA	T	10546	0.998293	0	0,18,3,10525	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749218	23063	PASS	A	T	11900	0.856134	0	0,5,0,11837	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749218	23271	PASS	C	A	18333	0.914362	0	4,0,18310,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749218	23403	PASS	A	G	18319	0.972542	0	0,2,0,18304	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749218	23418	PASS	A	T	18330	0.91844	0	0,2,0,18302	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAa/gTa	E619V	S	0.01172	0.91844	1	1	A>T
ERR5749218	23604	PASS	C	A	13130	0.940823	0	11,0,13115,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749218	23709	PASS	C	T	13116	0.935194	0	0,1,4,13090	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749218	23758	PASS	C	T	13131	0.964055	0	0,1,0,13127	LOW	SILENT	SYNONYMOUS_CODING	S	acC/acT	T732	S	0.001489	0.964055	1	1	C>T
ERR5749218	24382	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10830	0.002493	0	1,10796,0,30	LOW	SILENT	SYNONYMOUS_CODING	S	tcC/tcT	S940	S	0.002118	0.920404	2	1	C>T
ERR5749218	24506	PASS	T	G	13521	0.977886	0	6,0,13510,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749218	24914	PASS	G	C	32900	0.96079	0	0,1,16397,16487	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749218	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	21165	0.001465	31	15102,6023,35,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749218	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	15183	7.24E-4	0	15172,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749218	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	15284	0.001505	741	15037,82,91,53	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749218	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	39546	4.05E-4	0	1,39528,0,16	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749218	26416	PASS	G	T	18595	0.913418	0	17,19,9143,9395	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	Gtt/Ttt	V58F	E	0.000457	0.913418	2	2	G>T
ERR5749218	26681	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11012	0.011987	9	10779,91,135,3	LOW	SILENT	SYNONYMOUS_CODING	M	ttC/ttT	F53	M	0.001297	0.074505	1	1	C>T
ERR5749218	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	10917	0.003023	0	1,10881,0,33	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749218	27532	PASS	C	T	16660	0.982473	290	3,9,16636,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Cat/Tat	H47Y	orf7a	0.001165	0.982473	2	1	C>T
ERR5749218	27972	PASS	C	T	8783	0.907663	0	1,0,8726,32	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749218	28048	PASS	G	T	8761	0.919073	0	0,12,0,8745	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749218	28111	PASS	A	G	25551	0.979492	12	1,4,16780,8760	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749218	28239	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTGTT	G	16780	5.36E-4	0	16770,1,9,0	HIGH	NONE	FRAME_SHIFT	ORF8	gtttta/	VL117	orf8	0.000417	0.984998	9	2	GTTGTT>G
ERR5749218	28270	PASS	TA	T	32483	0.995074	393	162,5,16565,15758	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749218	28280	PASS	G	C	32398	0.937465	9	11,4,16584,15738	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749218	28281	PASS	A	T	32398	0.915519	46	23,2,16579,15744	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749218	28282	PASS	T	A	32400	0.913735	8	20,11,16545,15753	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749218	28881	PASS	G	A	12376	0.772544	6	3,0,6123,6101	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749218	28882	PASS	G	A	12376	0.839932	0	1,0,6194,6077	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749218	28883	PASS	G	C	12376	0.941904	0	2,2,6201,6161	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749218	28977	PASS	C	T	6302	0.928118	0	0,3,1,6284	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749218	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	50894	0.001081	0	25564,25238,34,32	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749218	29679	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14419	0.001595	0	7190,7124,13,13	.	.	.	.	.	.	.	0.000443	0.838763	2	1	C>T
ERR5749219	241	PASS	C	T	102	0.901961	0	0,0,51,51	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749219	323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	51	0.078431	0	0,47,0,4	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/ttTa	L21F?	leader	0.039216	0.118012	2	1	G>GT
ERR5749219	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATGG	T	176	0.022727	0	172,0,4,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	atggtt/	MV85	leader	0.000587	0.476744	4	1	TATGG>T
ERR5749219	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	3504	0.028253	0	3405,0,99,0	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749219	913	PASS	C	T	3503	0.914645	0	0,6,0,3489	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749219	3037	PASS	C	T	502	0.808765	0	0,0,253,247	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749219	3095	PASS	T	C	254	0.96063	2147483647	0,0,0,254	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tca/Cca	S126P	nsp3	0.937591	0.970297	1	1	T>C
ERR5749219	3177	PASS	C	T	2960	0.918919	0	0,0,2705,253	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P153L	nsp3	0.000773	0.96008	3	2	C>T
ERR5749219	3267	PASS	C	T	2706	0.970806	0	1,0,2702,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749219	4551	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3435	0.017176	0	0,3368,0,64	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T611I	nsp3	0.001721	0.897919	3	2	C>T
ERR5749219	4578	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTAACGATC	T	3438	0.016289	0	0,3382,0,56	HIGH	NONE	FRAME_SHIFT	ORF1ab	aacgatctaaat/	NDLN621	nsp3	0.000519	0.082979	2	2	TTAACGATC>T
ERR5749219	5388	PASS	C	A	133	0.924812	2147483647	0,0,133,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749219	5986	PASS	C	T	600	0.976667	2147483647	0,0,600,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749219	6383	PASS	G	C	3054	0.05632	0	1427,1433,91,92	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gcc/Ccc	A1222P	nsp3	0.000859	0.05632	3	1	G>C
ERR5749219	6516	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	2183	0.027027	91	655,1469,0,59	HIGH	NONE	FRAME_SHIFT	ORF1ab	att/	I1268	nsp3	0.000479	0.186047	4	2	TA>T
ERR5749219	6578	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	655	0.035115	0	631,0,24,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Ttt	L1287F	nsp3	0.035115	0.944039	1	1	C>T
ERR5749219	6954	PASS	T	C	1988	0.784205	0	0,69,0,1909	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749219	9561	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	942	0.009554	0	933,0,9,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCa/tTa	S336L	nsp4	0.00171	0.161742	2	2	C>T
ERR5749219	10595	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	3546	0.027637	0	0,3435,0,110	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F181L	3Cpro	0.000964	0.076408	1	1	T>C
ERR5749219	11074	PASS	C	CT	6432	0.055815	0	6070,0,359,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CT
ERR5749219	11074	PASS	CT	C	6432	0.050373	0	6108,0,324,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000965	0.945355	5	2	CT>C
ERR5749219	11287	PASS	GTCTGGTTTT	G	6432	0.998445	0	0,10,0,6422	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749219	13290	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	3190	0.029154	0	0,3076,0,109	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTt/tCt	F89S	nsp10	0.029154	0.107576	2	1	T>C
ERR5749219	13554	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1636	0.034841	0	0,1571,0,61	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y38	RdRp	0.000637	0.920199	2	2	C>T
ERR5749219	14120	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4379	0.013473	0	2150,2148,37,37	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCa/cTa	P227L	RdRp	0.00121	0.786944	2	2	C>T
ERR5749219	14408	PASS	C	T	88	0.818182	0	0,0,44,44	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749219	14676	PASS	C	T	2104	0.829848	0	1,0,2098,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749219	15279	PASS	C	T	963	0.88785	2147483647	0,0,963,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749219	15960	PASS	C	T	2185	0.778032	2147483647	0,0,2174,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A840	RdRp	0.001581	0.81574	1	1	C>T
ERR5749219	16117	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	2187	0.020119	0	0,2138,0,49	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gat/Tat	D893Y	RdRp	0.001841	0.244898	3	1	G>T
ERR5749219	16176	PASS	T	C	2284	0.981611	0	0,0,97,2186	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749219	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	9132	0.001424	0	9119,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749219	19188	PASS	AT	A	5618	0.06319	0	0,5263,0,355	HIGH	NONE	FRAME_SHIFT	ORF1ab	tgg/	W385	ExoN	0.000427	0.06319	2	1	AT>A
ERR5749219	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	831	0.016847	0	816,0,15,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749219	21101	PASS	G	GT	5545	0.060595	0	0,5209,0,336	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttc/ttTc	F150F?	MethTr	0.001498	0.083467	2	2	G>GT
ERR5749219	21764	PASS	ATACATG	A	1372	0.999271	0	1,0,1371,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749219	21990	PASS	TTTA	T	1373	0.998543	0	0,2,1,1370	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749219	22690	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	5236	0.02139	13	5020,1,126,1	LOW	SILENT	SYNONYMOUS_CODING	S	acT/acC	T376	S	0.000815	0.051311	2	1	T>C
ERR5749219	23042	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	845	0.030769	0	0,815,0,29	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Cca	S494P	S	0.030769	0.900602	1	1	T>C
ERR5749219	23063	PASS	A	T	846	0.884161	0	0,1,0,843	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749219	23271	PASS	C	A	5922	0.922661	2147483647	0,0,5915,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749219	23403	PASS	A	G	5919	0.972799	2147483647	0,0,0,5914	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749219	23604	PASS	C	A	1108	0.951264	0	1,0,1104,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749219	23709	PASS	C	T	1105	0.947511	0	0,1,0,1104	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749219	24432	PASS	A	T	3128	0.949489	0	0,0,1938,1189	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cAa/cTa	Q957L	S	0.935743	0.949489	1	1	A>T
ERR5749219	24506	PASS	T	G	1938	0.9742	2147483647	0,0,1938,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749219	24914	PASS	G	C	11502	0.961137	3	1,0,5728,5766	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749219	25276	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	931	0.042965	0	0,888,0,43	LOW	SILENT	SYNONYMOUS_CODING	S	acC/acA	T1238	S	0.005906	0.9348	2	2	C>A
ERR5749219	25495	PASS	A	G	12773	0.907539	5	5,2,6350,6406	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Ata/Gta	I35V	orf3a	0.000735	0.911134	2	1	A>G
ERR5749219	25572	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	6430	0.016796	0	0,6322,0,108	HIGH	NONE	FRAME_SHIFT	ORF3a	atc/aAtc	I62N?	orf3a	0.000543	0.959687	4	2	C>CA
ERR5749219	26013	PASS	C	T	1827	0.950739	0	1,0,1826,0	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	ttC/ttT	F207	orf3a	0.000839	0.974528	1	1	C>T
ERR5749219	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	1826	0.005476	0	0,1816,0,10	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749219	26822	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	957	0.015674	0	0,940,0,17	LOW	SILENT	SYNONYMOUS_CODING	M	ttC/ttT	F100	M	0.001495	0.855211	1	1	C>T
ERR5749219	27384	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	3126	0.005118	0	0,3095,0,22	LOW	SILENT	SYNONYMOUS_CODING	ORF6	gaT/gaC	D61	orf6	0.00154	0.931035	3	3	T>C
ERR5749219	27389	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3126	0.026871	0	0,3030,0,91	.	.	.	.	.	.	.	0.001157	0.899553	2	1	C>T
ERR5749219	27972	PASS	C	T	261	0.923372	0	0,0,259,2	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749219	28048	PASS	G	T	259	0.915058	2147483647	0,0,0,259	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749219	28111	PASS	A	G	9945	0.981398	0	2,0,9680,259	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749219	28270	PASS	TA	T	18793	0.991167	414	164,4,9479,9148	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749219	28273	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	AT	18763	0.004317	235	9552,9153,81,0	HIGH	NONE	FRAME_SHIFT+START_LOST	N	atg/Tatg	M1Y?	N	0.000399	0.842333	4	1	A>AT
ERR5749219	28280	PASS	G	C	18761	0.936144	18	7,0,9497,9140	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749219	28281	PASS	A	T	18761	0.913384	21	19,5,9496,9141	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749219	28282	PASS	T	A	18762	0.913442	11	14,5,9550,9146	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749219	28881	PASS	G	A	635	0.784252	0	0,0,314,314	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749219	28882	PASS	G	A	635	0.801575	0	0,0,319,307	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749219	28883	PASS	G	C	635	0.924409	0	0,0,319,316	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749219	28977	PASS	C	T	323	0.93808	2147483647	0,0,0,323	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749219	29640	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1368	0.016813	37	426,917,0,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF10	gCa/gTa	A28V	orf10	0.002681	0.955281	2	2	C>T
ERR5749220	241	PASS	C	T	17904	0.834171	6	0,3,8862,8938	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749220	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	10295	0.002137	0	10271,0,22,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749220	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	10294	7.77E-4	0	10261,0,8,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749220	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	10294	0.001846	0	10261,0,19,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749220	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10286	0.002139	0	9507,0,707,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749220	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	10286	0.001069	0	10275,0,11,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749220	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	10286	0.001167	0	10273,0,12,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749220	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	32305	4.02E-4	11	21983,10307,12,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749220	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	32303	9.6E-4	7	21971,10295,25,6	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749220	913	PASS	C	T	21986	0.910261	0	0,7,0,21952	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749220	3037	PASS	C	T	14105	0.812123	29	2,15,7036,6932	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749220	3267	PASS	C	T	18080	0.969414	0	1,0,18069,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749220	5388	PASS	C	A	3889	0.950116	2147483647	0,0,3886,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749220	5986	PASS	C	T	7931	0.977052	2147483647	0,0,7926,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749220	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	8320	0.006971	0	1,8260,0,58	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L1328S?	nsp3	0.000731	0.14377	4	2	C>CT
ERR5749220	6894	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	23024	0.001173	0	22954,1,63,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tGt/tTt	C1392F	nsp3	0.00096	0.897867	3	2	G>T
ERR5749220	6954	PASS	T	C	23009	0.808336	0	0,6,1,22864	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749220	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	27115	6.27E-4	84	8587,18511,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749220	11082	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	14341	6.28E-4	0	14336,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000427	0.179468	2	1	TG>T
ERR5749220	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	14341	0.001674	0	14293,0,37,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749220	11287	PASS	GTCTGGTTTT	G	14337	0.997559	0	0,35,0,14302	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749220	11782	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	19563	0.001073	0	12,19334,0,208	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K270N	nsp6	0.001073	0.917917	2	2	A>C
ERR5749220	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30357	0.001515	0	15157,15113,25,25	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749220	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	8872	0.004396	2022	8709,52,3,107	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749220	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	17337	0.001038	0	8698,8632,9,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749220	14408	PASS	C	T	17337	0.844725	4	1,3,8664,8556	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749220	14676	PASS	C	T	13063	0.674118	0	3,0,12992,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749220	15279	PASS	C	T	22455	0.913605	0	1,0,22428,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749220	16176	PASS	T	C	16014	0.977582	0	0,0,5778,10228	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749220	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	10954	0.001461	0	10938,0,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749220	18687	PASS	C	T	16466	0.981963	0	3,0,16438,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C216	ExoN	0.000374	0.981963	3	2	C>T
ERR5749220	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17773	0.002138	0	17725,0,40,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749220	21462	PASS	T	C	15092	0.959051	0	1,0,15069,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaT/aaC	N268	MethTr	0.00078	0.959051	2	2	T>C
ERR5749220	21764	PASS	ATACATG	A	9315	0.996457	0	32,0,9282,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749220	21990	PASS	TTTA	T	9318	0.997639	0	0,22,3,9293	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749220	22264	PASS	C	T	20184	0.963387	108	3,3,0,20171	LOW	SILENT	SYNONYMOUS_CODING	S	aaC/aaT	N234	S	0.001131	0.963496	2	2	C>T
ERR5749220	23063	PASS	A	T	6726	0.859352	0	0,3,0,6692	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749220	23271	PASS	C	A	21302	0.916674	0	4,0,21283,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749220	23403	PASS	A	G	21298	0.970608	0	0,2,0,21275	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749220	23604	PASS	C	A	9721	0.940027	0	9,0,9710,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749220	23709	PASS	C	T	9718	0.938876	0	0,3,1,9704	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749220	24506	PASS	T	G	16964	0.975595	0	6,0,16957,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749220	24914	PASS	G	C	18385	0.959804	0	1,1,9157,9210	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749220	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	18976	0.001159	52	10754,8179,30,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749220	25413	PASS	C	T	10932	0.967892	0	3,0,10917,0	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	atC/atT	I7	orf3a	0.00145	0.968329	2	1	C>T
ERR5749220	25572	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10927	0.029102	0	0,10534,0,382	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	tcC/tcT	S60	orf3a	0.000543	0.959687	4	2	C>T
ERR5749220	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	26968	0.00115	1254	26626,155,77,80	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749220	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	5675	0.001762	0	1,5664,0,10	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749220	27494	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28541	8.41E-4	5	17814,10687,13,12	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	cCt/cTt	P34L	orf7a	0.000672	0.961447	2	2	C>T
ERR5749220	27972	PASS	C	T	5433	0.901528	39	1,2,5375,32	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749220	28048	PASS	G	T	5404	0.914878	0	0,8,0,5394	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749220	28095	PASS	A	T	5411	0.95657	186	6,1,0,5393	HIGH	NONSENSE	STOP_GAINED	ORF8	Aaa/Taa	K68*	orf8	0.002672	0.967672	2	2	A>T
ERR5749220	28111	PASS	A	G	19831	0.976451	5	2,2,14415,5401	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749220	28147	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14430	0.001663	0	14388,3,24,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	cCt/cTt	P85L	orf8	0.000438	0.981624	4	2	C>T
ERR5749220	28270	PASS	TA	T	27876	0.995157	303	137,7,14229,13512	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749220	28280	PASS	G	C	27817	0.931445	7	10,4,14248,13496	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749220	28281	PASS	A	T	27817	0.911637	14	10,2,14255,13499	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749220	28282	PASS	T	A	27821	0.909565	0	13,11,14223,13508	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749220	28881	PASS	G	A	11633	0.743488	9	4,0,5717,5718	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749220	28882	PASS	G	A	11632	0.818604	6	5,1,5812,5690	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749220	28883	PASS	G	C	11632	0.940767	3	2,0,5826,5795	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749220	28977	PASS	C	T	5942	0.932346	0	0,2,0,5929	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749220	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	26268	9.14E-4	0	13198,13027,17,15	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749221	241	PASS	C	T	13008	0.871079	0	2,2,6462,6501	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749221	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	10780	0.003432	0	10731,14,37,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749221	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	10780	0.00167	0	10603,12,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749221	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	10780	0.003247	0	10603,12,35,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749221	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	10780	0.010019	33	10603,12,105,3	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749221	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10778	0.001763	2	9832,17,674,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749221	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	10778	0.003433	0	10721,20,37,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749221	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	10776	0.001206	0	10743,20,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749221	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	10776	0.00167	0	10730,21,18,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749221	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	30765	6.5E-4	24	19972,10771,19,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749221	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	30764	0.00234	6	19921,10747,52,20	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749221	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTTG	A	30764	4.23E-4	13	19921,10747,12,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcatttgac/	KSFD141	leader	0.000303	0.999303	4	1	AAAGTCATTTG>A
ERR5749221	913	PASS	C	T	19977	0.913851	0	0,7,0,19945	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749221	1682	PASS	A	G	16304	0.088077	0	14820,0,1481,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Atc/Gtc	I293V	nsp2	0.088077	0.088077	1	1	A>G
ERR5749221	1698	PASS	C	T	16304	0.978778	0	3,0,16297,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCa/gTa	A298V	nsp2	0.978778	0.978778	1	1	C>T
ERR5749221	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	137	0.029197	9	66,64,1,6	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749221	3037	PASS	C	T	13406	0.809936	45	0,15,6675,6612	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749221	3095	PASS	T	C	6760	0.942899	0	0,2,0,6750	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tca/Cca	S126P	nsp3	0.937591	0.970297	1	1	T>C
ERR5749221	3177	PASS	C	T	25849	0.896514	10	6,6,19060,6746	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P153L	nsp3	0.000773	0.96008	3	2	C>T
ERR5749221	3267	PASS	C	T	19082	0.96929	0	1,0,19067,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749221	5388	PASS	C	A	5250	0.961714	0	1,0,5247,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749221	5986	PASS	C	T	9780	0.976074	0	2,0,9775,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749221	6954	PASS	T	C	18851	0.817675	0	0,3,3,18738	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749221	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	26531	0.001508	113	13725,12766,40,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749221	10138	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22349	9.84E-4	1	15803,6515,15,8	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N28	3Cpro	0.000458	0.983567	3	3	C>T
ERR5749221	11082	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	19602	6.63E-4	0	19597,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000427	0.179468	2	1	TG>T
ERR5749221	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	19602	0.004234	0	19469,0,108,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749221	11287	PASS	GTCTGGTTTT	G	19602	0.99597	0	0,79,2,19521	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749221	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	11386	7.9E-4	0	11376,1,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749221	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28357	0.001552	0	14158,14125,25,25	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749221	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	13477	0.003933	2147483647	13168,117,1,188	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749221	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	26215	0.002212	1	13123,13045,31,27	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749221	14408	PASS	C	T	26215	0.843677	6	0,2,13061,12932	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749221	14676	PASS	C	T	12330	0.76764	0	7,0,12282,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749221	15279	PASS	C	T	20367	0.887318	0	3,0,20336,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749221	15960	PASS	C	T	9644	0.81574	2147483647	0,0,9610,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A840	RdRp	0.001581	0.81574	1	1	C>T
ERR5749221	16176	PASS	T	C	17984	0.979371	2	0,2,8327,9645	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749221	17999	PASS	C	T	21253	0.974498	0	3,3,10250,10991	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T588I	helicase	0.001094	0.974498	2	1	C>T
ERR5749221	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	22341	5.37E-4	0	22329,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749221	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24472	0.002738	0	24389,0,67,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749221	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29491	0.001085	0	14446,14712,18,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749221	21707	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24905	0.001767	5	10037,14814,14,30	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Cat/Tat	H49Y	S	0.001048	0.072032	1	1	C>T
ERR5749221	21764	PASS	ATACATG	A	10056	0.995525	0	44,0,10011,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749221	21990	PASS	TTTA	T	10063	0.998112	0	0,19,7,10037	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749221	22323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26928	0.001188	6	7390,19491,12,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCt/tTt	S254F	S	0.000812	0.978946	3	2	C>T
ERR5749221	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25936	8.87E-4	9	11892,14000,7,17	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749221	23063	PASS	A	T	11882	0.877041	0	0,2,1,11840	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749221	23271	PASS	C	A	21113	0.925733	0	2,0,21094,4	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749221	23403	PASS	A	G	21114	0.966989	0	0,0,2,21088	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749221	23604	PASS	C	A	12974	0.945275	0	9,0,12952,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749221	23709	PASS	C	T	12968	0.941009	0	0,1,2,12954	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749221	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	27905	5.02E-4	5	14919,12972,10,4	HIGH	NONE	FRAME_SHIFT	S	ttg/	L753	S	0.000334	0.080808	2	2	CT>C
ERR5749221	24010	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATTTATTGAAGATCTAC	A	15052	7.97E-4	0	154,14888,0,12	HIGH	NONE	FRAME_SHIFT	S	attgaagatctacttttc/	IEDLLF818	S	0.000455	0.926398	4	2	ATTTATTGAAGATCTAC>A
ERR5749221	24432	PASS	A	T	26914	0.942483	18	9,0,16054,10839	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cAa/cTa	Q957L	S	0.935743	0.949489	1	1	A>T
ERR5749221	24506	PASS	T	G	16065	0.973358	0	6,0,16057,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749221	24914	PASS	G	C	32525	0.959139	0	0,0,16197,16302	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749221	25495	PASS	A	G	30136	0.903371	2	2,1,14975,15119	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Ata/Gta	I35V	orf3a	0.000735	0.911134	2	1	A>G
ERR5749221	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	16835	8.91E-4	0	16819,1,15,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749221	25916	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16839	0.002257	0	10,16784,0,39	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aCa/aTa	T175I	orf3a	0.001191	0.964713	2	2	C>T
ERR5749221	26013	PASS	C	T	38566	0.940932	0	6,0,38522,0	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	ttC/ttT	F207	orf3a	0.000839	0.974528	1	1	C>T
ERR5749221	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	10290	0.002041	0	3,10255,0,21	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749221	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	10291	0.002818	0	2,10255,0,29	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749221	27972	PASS	C	T	8418	0.905322	22	0,1,8352,43	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749221	28048	PASS	G	T	8383	0.925683	0	0,9,0,8365	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749221	28111	PASS	A	G	27947	0.978101	0	7,3,19543,8384	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749221	28270	PASS	TA	T	37942	0.995467	468	179,3,19305,18465	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749221	28280	PASS	G	C	37879	0.937987	8	9,3,19360,18446	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749221	28281	PASS	A	T	37879	0.918451	17	17,5,19347,18451	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749221	28282	PASS	T	A	37882	0.91228	1	13,10,19305,18465	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749221	28406	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTACCCAATA	T	19571	5.11E-4	0	12,19547,0,10	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	N	ttacccaataat/tat	LPNN45Y	N	0.00043	0.921074	3	2	TTACCCAATA>T
ERR5749221	28407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TACCCAATA	T	19571	6.64E-4	0	12,19546,0,13	HIGH	NONE	FRAME_SHIFT	N	cccaataat/	PNN46	N	0.000382	0.179673	1	1	TACCCAATA>T
ERR5749221	28881	PASS	G	A	16524	0.77802	11	9,2,8186,8141	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749221	28882	PASS	G	A	16524	0.837388	18	7,0,8262,8110	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749221	28883	PASS	G	C	16524	0.943355	0	1,0,8280,8220	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749221	28977	PASS	C	T	8405	0.93135	0	0,8,2,8376	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749221	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	35557	0.00135	161	27133,8345,12,42	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749221	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	53902	0.001095	0	27081,26735,34,33	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749222	241	PASS	C	T	13823	0.866454	0	0,1,6885,6889	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749222	292	PASS	C	T	6943	0.950886	0	0,5,0,6934	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N9	leader	0.939339	0.96124	1	1	C>T
ERR5749222	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	10403	0.002307	0	10378,0,24,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749222	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	10403	0.002115	0	10332,0,22,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749222	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	10403	0.00471	0	10332,0,49,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749222	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10398	0.001923	0	9543,4,735,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749222	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	10398	0.002981	0	10363,4,31,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749222	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	10396	0.001731	0	10368,5,18,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttatg/gtg	VM84V	leader	0.000554	0.991848	4	1	GTTA>G
ERR5749222	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	31059	0.005151	36	20502,10385,128,32	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749222	913	PASS	C	T	20629	0.911193	0	0,12,0,20601	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749222	3037	PASS	C	T	14349	0.813855	39	0,13,7178,7060	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749222	3267	PASS	C	T	20059	0.970537	0	4,0,20046,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749222	4234	PASS	C	T	33318	0.714088	11	2,9,16119,16504	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D505	nsp3	0.00099	0.714088	3	3	C>T
ERR5749222	4285	PASS	G	A	16729	0.899038	0	0,2,0,16675	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaG/gaA	E522	nsp3	0.000939	0.899038	2	2	G>A
ERR5749222	5388	PASS	C	A	4923	0.958156	2147483647	0,0,4923,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749222	5986	PASS	C	T	8855	0.976398	2147483647	0,0,8849,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749222	6954	PASS	T	C	18575	0.796178	0	0,6,4,18431	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749222	7070	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	32483	0.001077	129	13805,18632,35,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggc/Cgc	G1451R	nsp3	0.000698	0.101434	3	1	G>C
ERR5749222	8562	PASS	TTAA	T	9169	0.998037	0	0,18,0,9151	MODERATE	NONE	CODON_DELETION	ORF1ab	aat/	N5	nsp4	0.996172	0.998037	1	1	TTAA>T
ERR5749222	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	26260	0.001257	88	13980,12247,33,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749222	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	20840	0.001296	0	20790,0,37,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749222	11287	PASS	GTCTGGTTTT	G	20838	0.994865	22	1,107,0,20731	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749222	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	32257	9.61E-4	5	21144,11050,17,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749222	12125	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	15473	0.001228	0	6,15419,0,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y12H	nsp8	0.000847	0.113436	1	1	T>C
ERR5749222	12880	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16073	0.019287	18	15700,6,356,2	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I65	nsp9	0.004753	0.894516	2	2	C>T
ERR5749222	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29062	0.001583	0	14503,14467,25,26	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749222	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	14403	0.002708	2438	14151,108,5,131	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749222	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	28209	8.15E-4	0	14129,14071,12,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749222	14408	PASS	C	T	28209	0.855649	9	1,5,14071,13931	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749222	14676	PASS	C	T	12884	0.753105	0	3,0,12828,2	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749222	15279	PASS	C	T	20404	0.891443	0	3,0,20369,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749222	16176	PASS	T	C	18320	0.980131	2	2,1,7879,10428	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749222	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	17851	0.0014	0	17825,0,25,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749222	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	22162	4.96E-4	0	1,22150,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749222	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21404	0.002616	0	21319,0,57,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749222	21764	PASS	ATACATG	A	10007	0.994304	0	57,0,9950,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749222	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	10007	7.99E-4	0	9999,0,8,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749222	21990	PASS	TTTA	T	10010	0.996204	0	0,38,4,9968	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749222	23063	PASS	A	T	12054	0.864692	0	0,3,0,12002	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749222	23271	PASS	C	A	22556	0.923125	0	3,0,22530,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749222	23403	PASS	A	G	22537	0.964991	0	0,0,1,22521	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749222	23604	PASS	C	A	12705	0.945533	0	7,0,12677,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749222	23709	PASS	C	T	12687	0.941278	0	0,3,1,12666	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749222	24506	PASS	T	G	16608	0.973868	0	6,0,16593,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749222	24914	PASS	G	C	33853	0.959176	0	0,0,16874,16955	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749222	25626	PASS	C	T	32878	0.766622	1	4,2,16820,15961	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	caC/caT	H78	orf3a	0.000403	0.915633	3	2	C>T
ERR5749222	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	10633	8.46E-4	0	1,10622,0,9	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749222	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	10632	0.002351	0	0,10603,0,25	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749222	27494	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	36582	0.001039	0	19219,17299,22,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	cCt/cTt	P34L	orf7a	0.000672	0.961447	2	2	C>T
ERR5749222	27577	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAATTTGCTTTTGCTTGTCCTGACGGCGTAAAACACGTCTATCAGTT	C	19257	6.23E-4	0	19243,2,12,0	HIGH	NONE	FRAME_SHIFT	ORF7a	caatttgcttttgcttgtcctgacggcgtaaaacacgtctatcagtta/	QFAFACPDGVKHVYQL62	orf7a	0.000614	0.952205	4	2	CAATTTGCTTTTGCTTGTCCTGACGGCGTAAAACACGTCTATCAGTT>C
ERR5749222	27900	PASS	T	C	7991	0.130897	0	6864,1,1122,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	Ttt/Ctt	F3L	orf8	0.130897	0.130897	1	1	T>C
ERR5749222	27925	PASS	C	T	7985	0.084533	0	7250,1,729,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aCa/aTa	T11I	orf8	0.002789	0.084533	2	1	C>T
ERR5749222	27972	PASS	C	T	8019	0.910837	17	2,1,7950,42	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749222	28048	PASS	G	T	7983	0.923963	0	0,10,0,7968	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749222	28111	PASS	A	G	30046	0.979398	4	6,0,22036,7989	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749222	28237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTGT	G	22047	5.9E-4	0	22034,0,13,0	MODERATE	NONE	CODON_DELETION	ORF8	gtt/	V117	orf8	0.000442	0.966707	4	2	GTGT>G
ERR5749222	28249	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	22036	4.54E-4	0	22030,1,10,0	HIGH	NONE	FRAME_SHIFT	ORF8	ttc/	F120	orf8	0.000443	0.063605	3	2	AT>A
ERR5749222	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22033	0.021559	11	21462,2,498,1	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749222	28270	PASS	TA	T	42806	0.994884	564	218,4,21744,20843	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749222	28280	PASS	G	C	42732	0.936301	8	12,5,21797,20819	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749222	28281	PASS	A	T	42732	0.920973	32	38,12,21777,20821	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749222	28282	PASS	T	A	42734	0.91543	23	32,12,21749,20835	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749222	28651	PASS	C	T	16719	0.918117	0	0,10,2,16675	LOW	SILENT	SYNONYMOUS_CODING	N	aaC/aaT	N126	N	0.000502	0.918117	3	2	C>T
ERR5749222	28881	PASS	G	A	16502	0.7753	9	4,0,8189,8084	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749222	28882	PASS	G	A	16502	0.832142	7	7,2,8257,8097	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749222	28883	PASS	G	C	16502	0.94134	0	0,0,8277,8213	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749222	28977	PASS	C	T	8395	0.927099	0	0,1,0,8374	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749222	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	34653	0.001587	297	26235,8335,3,55	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749222	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	52099	0.00119	0	26154,25833,37,37	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749223	241	PASS	C	T	1057	0.859981	0	0,0,523,529	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749223	367	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	2347	0.002556	4	1809,532,6,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtg/	V35	leader	0.002556	0.909053	2	2	CG>C
ERR5749223	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	1814	0.007718	0	1800,0,14,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749223	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	1814	0.041345	0	1739,0,75,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749223	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTTG	A	8473	0.002596	0	6639,1812,18,4	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcatttgac/	KSFD141	leader	0.000303	0.999303	4	1	AAAGTCATTTG>A
ERR5749223	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	6654	0.00511	0	0,6620,0,34	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L35	nsp2	0.000551	0.081967	3	2	CT>C
ERR5749223	913	PASS	C	T	6654	0.903216	0	0,2,0,6645	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749223	1267	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	10483	0.001812	34	5938,4525,19,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggA	G154	nsp2	0.001789	0.9811	2	1	C>A
ERR5749223	1599	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	10508	0.001427	43	4551,5939,0,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGt/gTt	G265V	nsp2	0.001427	0.96468	2	1	G>T
ERR5749223	2144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	6078	0.004278	0	0,6037,0,40	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtc/Ttc	V447F	nsp2	0.004278	0.752119	2	1	G>T
ERR5749223	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	14729	0.00129	1453	7360,6818,7,512	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749223	3037	PASS	C	T	2733	0.822905	6	0,2,1369,1347	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749223	3095	PASS	T	C	1378	0.937591	2147483647	0,0,0,1376	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tca/Cca	S126P	nsp3	0.937591	0.970297	1	1	T>C
ERR5749223	3177	PASS	C	T	7843	0.904246	0	2,0,6458,1374	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P153L	nsp3	0.000773	0.96008	3	2	C>T
ERR5749223	3230	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	6465	0.008043	0	6409,0,54,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggt/Tgt	G171C	nsp3	0.001231	0.979167	2	1	G>T
ERR5749223	3267	PASS	C	T	6465	0.970456	2147483647	0,0,6461,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749223	5074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	3867	0.004396	0	3842,0,17,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaT/gaC	D785	nsp3	0.000986	0.967824	2	2	T>C
ERR5749223	5206	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	3865	0.002587	0	0,3854,0,11	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atT	M829I	nsp3	0.001901	0.0725	2	1	G>T
ERR5749223	5388	PASS	C	A	750	0.962667	2147483647	0,0,750,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749223	5986	PASS	C	T	2810	0.975801	2147483647	0,0,2810,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749223	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	3177	0.008499	0	0,3150,0,27	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L1328S?	nsp3	0.000731	0.14377	4	2	C>CT
ERR5749223	6954	PASS	T	C	5308	0.826677	0	0,1,0,5280	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749223	7528	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4629	0.002808	0	14,4598,0,15	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V1603	nsp3	0.002527	0.916131	1	1	C>T
ERR5749223	7740	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	5119	0.006642	0	5084,0,35,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gAt/gGt	D1674G	nsp3	0.000834	0.078818	3	2	A>G
ERR5749223	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	5119	0.003516	5	4499,602,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749223	9928	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	1916	0.006785	0	1899,0,16,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atT	M458I	nsp4	0.006785	0.950518	1	1	G>T
ERR5749223	11287	PASS	GTCTGGTTTT	G	25	0.96	0	0,1,0,24	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749223	11417	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	1831	0.004369	0	1823,0,8,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Ttt	V149F	nsp6	0.00274	0.951155	2	2	G>T
ERR5749223	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10503	0.00219	0	5240,5225,12,12	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749223	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	2634	0.005695	794	2557,27,1,47	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749223	14408	PASS	C	T	5078	0.84935	3	0,1,2546,2508	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749223	14676	PASS	C	T	4219	0.824366	2147483647	0,0,4208,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749223	14805	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4221	0.002843	0	0,4203,0,15	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y455	RdRp	0.001051	0.904964	2	2	C>T
ERR5749223	15279	PASS	C	T	3688	0.889371	2147483647	0,0,3683,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749223	15708	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	8220	0.001946	0	0,8193,0,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atT	M756I	RdRp	0.001488	0.095967	1	1	G>T
ERR5749223	15797	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	8246	0.001455	0	2,8199,0,12	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cTt/cCt	L786P	RdRp	0.001418	0.07734	2	1	T>C
ERR5749223	15839	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	8248	0.002182	0	3,8220,0,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tGg/tTg	W800L	RdRp	0.001405	0.074516	2	1	G>T
ERR5749223	15960	PASS	C	T	4650	0.789462	0	1,0,4621,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A840	RdRp	0.001581	0.81574	1	1	C>T
ERR5749223	16176	PASS	T	C	5688	0.977848	0	0,0,1034,4652	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749223	17122	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	10848	0.002028	41	3919,6899,0,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gct/Cct	A296P	helicase	0.000476	0.056834	3	2	G>C
ERR5749223	17795	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTG	C	3687	0.007052	0	3661,0,26,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gta/	V521	helicase	0.00111	0.966723	2	2	CTG>C
ERR5749223	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17438	0.001663	0	17398,0,29,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C216	ExoN	0.000374	0.981963	3	2	C>T
ERR5749223	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	17438	0.00109	0	17419,0,19,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749223	19329	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	5114	0.00352	0	5092,0,19,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcC	A430	ExoN	0.001217	0.228916	1	1	T>C
ERR5749223	21255	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCA	G	14608	0.002054	84	7573,7006,30,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	tcatct/tct	SS201S	MethTr	0.000341	0.917425	4	2	GTCA>G
ERR5749223	21334	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	7601	0.001842	0	0,7576,0,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gca/Tca	A226S	MethTr	0.000897	0.077475	3	1	G>T
ERR5749223	21764	PASS	ATACATG	A	4457	0.995288	0	21,0,4436,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749223	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	4457	0.004263	0	4438,0,19,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749223	21809	PASS	G	A	4457	0.889163	2147483647	0,0,4452,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gtc/Atc	V83I	S	0.00315	0.889163	2	1	G>A
ERR5749223	21812	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4457	0.004263	0	4430,0,20,0	LOW	SILENT	SYNONYMOUS_CODING	S	Cta/Tta	L84	S	0.001506	0.06449	1	1	C>T
ERR5749223	21817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	4457	0.004487	0	4437,0,20,0	HIGH	NONE	FRAME_SHIFT	S	ttt/	F86	S	0.000689	0.961354	3	2	AT>A
ERR5749223	21990	PASS	TTTA	T	4457	0.997083	0	0,13,1,4443	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749223	22344	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	3623	0.003588	0	3600,2,20,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gGt/gTt	G261V	S	0.003588	0.103064	2	1	G>T
ERR5749223	22620	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	12763	0.002272	42	9106,3618,31,0	HIGH	NONSENSE	STOP_GAINED	S	tGg/tAg	W353*	S	0.002272	0.059178	2	2	G>A
ERR5749223	23063	PASS	A	T	4387	0.842717	2147483647	0,0,0,4372	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749223	23271	PASS	C	A	10122	0.920569	0	1,0,10114,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749223	23403	PASS	A	G	10118	0.96353	0	0,5,0,10107	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749223	23604	PASS	C	A	3735	0.937082	0	5,0,3729,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749223	23709	PASS	C	T	3732	0.932744	0	0,2,0,3725	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749223	24432	PASS	A	T	8708	0.940744	2	2,0,5223,3478	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cAa/cTa	Q957L	S	0.935743	0.949489	1	1	A>T
ERR5749223	24506	PASS	T	G	5226	0.974168	0	2,0,5224,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749223	24914	PASS	G	C	28383	0.960258	0	1,2,14149,14217	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749223	25495	PASS	A	G	24341	0.89076	0	0,0,12109,12198	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Ata/Gta	I35V	orf3a	0.000735	0.911134	2	1	A>G
ERR5749223	25573	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	12252	0.001796	0	0,12214,0,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Aaa/Gaa	K61E	orf3a	0.001796	0.954465	3	2	A>G
ERR5749223	25660	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	700	0.007143	0	666,29,5,0	HIGH	NONE	FRAME_SHIFT	ORF3a	tac/	Y91	orf3a	0.000716	0.91928	2	2	GT>G
ERR5749223	26013	PASS	C	T	7996	0.962481	2147483647	0,0,7991,0	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	ttC/ttT	F207	orf3a	0.000839	0.974528	1	1	C>T
ERR5749223	26395	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9745	0.003284	0	4901,4578,21,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	Ctt/Ttt	L51F	E	0.000707	0.745829	2	1	C>T
ERR5749223	26710	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTTG	C	3871	0.002842	0	3860,0,11,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtttt/ttt	CF64F	M	0.000649	0.102857	1	1	CTTG>C
ERR5749223	26907	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14325	0.002653	0	14285,0,38,0	LOW	SILENT	SYNONYMOUS_CODING	M	Ctg/Ttg	L129	M	0.000817	0.976032	1	1	C>T
ERR5749223	27461	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	9000	0.003667	0	3,8958,0,39	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	tGt/tTt	C23F	orf7a	0.002221	0.974441	1	1	G>T
ERR5749223	27506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	16256	0.001538	91	7231,8986,26,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	gGa/gCa	G38A	orf7a	0.000715	0.985435	4	2	G>C
ERR5749223	27534	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	7265	0.002615	0	7239,0,19,0	LOW	SILENT	SYNONYMOUS_CODING	ORF7a	caT/caC	H47	orf7a	0.002615	0.933333	2	2	T>C
ERR5749223	27972	PASS	C	T	1251	0.928857	0	0,0,1240,10	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749223	28048	PASS	G	T	1241	0.921837	0	0,2,0,1239	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749223	28111	PASS	A	G	17407	0.978572	0	3,0,16156,1239	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749223	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	G	16152	0.001981	0	16071,4,34,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	ttC/ttG	F120L	orf8	0.000422	0.995511	4	3	C>G
ERR5749223	28270	PASS	TA	T	31294	0.99543	333	144,6,15964,15187	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749223	28280	PASS	G	C	31236	0.935363	9	6,1,16004,15179	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749223	28281	PASS	A	T	31236	0.904437	25	19,4,15980,15169	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749223	28282	PASS	T	A	31239	0.91533	1	12,9,15963,15181	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749223	28302	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	32132	0.003703	2	15926,16042,72,81	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	cGa/cTa	R10L	N	0.001527	0.953728	4	2	G>T
ERR5749223	28394	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CGG	C	16168	0.001546	0	2,16141,0,25	HIGH	NONE	FRAME_SHIFT	N	cgg/	R41	N	0.001221	0.917026	3	2	CGG>C
ERR5749223	28434	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCG	C	25497	0.001255	61	9334,16131,0,32	HIGH	NONE	FRAME_SHIFT	N	gct/	A55	N	0.000815	0.871795	4	2	CCG>C
ERR5749223	28881	PASS	G	A	2193	0.769722	0	0,0,1091,1070	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749223	28882	PASS	G	A	2193	0.825809	0	1,1,1098,1067	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749223	28883	PASS	G	C	2193	0.944368	0	0,0,1103,1089	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749223	28884	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	2197	0.004552	0	1097,1089,5,5	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gGa/gCa	G204A	N	0.004552	0.935815	1	1	G>C
ERR5749223	28960	PASS	G	A	1110	0.813514	2147483647	0,0,0,1098	LOW	SILENT	SYNONYMOUS_CODING	N	caG/caA	Q229	N	0.00273	0.921139	2	2	G>A
ERR5749223	28977	PASS	C	T	1110	0.943243	2147483647	0,0,0,1107	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749223	29091	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	7966	0.002762	0	7944,0,22,0	HIGH	NONE	FRAME_SHIFT	N	ttc/	F274	N	0.000452	0.073908	3	1	CT>C
ERR5749223	29096	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	7966	0.004394	0	7924,0,35,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Ggc/Cgc	G275R	N	0.003164	0.051234	2	1	G>C
ERR5749223	29421	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	1999	0.004502	0	1990,0,9,0	HIGH	NONE	FRAME_SHIFT	N	ccg/	P383	N	0.002705	0.052892	2	2	CG>C
ERR5749223	29640	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	3357	0.002681	18	1358,1990,0,9	HIGH	NONE	FRAME_SHIFT	ORF10	gca/	A28	orf10	0.002681	0.955281	2	2	CA>C
ERR5749223	29733	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	1355	0.00369	0	0,1350,0,5	.	.	.	.	.	.	.	0.001821	0.915943	2	1	CG>C
ERR5749224	239	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTC	T	18202	5.49E-4	0	9063,9130,5,5	.	.	.	.	.	.	.	0.000495	0.25	4	1	TTC>T
ERR5749224	241	PASS	C	T	18200	0.844396	12	0,5,9028,9072	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749224	412	PASS	C	T	11500	0.976	0	4,0,11494,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G49	leader	0.968277	0.983986	1	1	C>T
ERR5749224	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	11485	6.97E-4	0	11462,0,8,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749224	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	11485	7.84E-4	0	11462,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749224	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	11481	0.001916	0	10739,0,710,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749224	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	31079	4.18E-4	8	19568,11495,11,2	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749224	913	PASS	C	T	19562	0.881658	0	0,13,0,19499	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749224	3037	PASS	C	T	14938	0.797028	36	0,12,7474,7296	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749224	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	7555	0.002515	455	4,7523,18,5	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749224	3267	PASS	C	T	17751	0.969861	0	1,0,17742,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749224	3961	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	23985	4.17E-4	0	23981,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K415	nsp3	0.000417	0.869983	2	2	CA>C
ERR5749224	5388	PASS	C	A	4940	0.960526	2147483647	0,0,4940,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749224	5986	PASS	C	T	9305	0.970231	0	0,0,9294,3	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749224	6185	PASS	C	T	9294	0.910265	0	0,5,0,9279	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cac/Tac	H1156Y	nsp3	0.910265	0.954999	1	1	C>T
ERR5749224	6954	PASS	T	C	20603	0.786439	0	0,5,1,20454	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749224	8151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	47002	7.02E-4	1162	23028,23458,466,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gTc/gGc	V1811G	nsp3	0.00055	0.34	2	1	T>G
ERR5749224	9286	PASS	C	T	16031	0.95097	0	3,0,16017,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N244	nsp4	0.949239	0.971567	1	1	C>T
ERR5749224	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	27750	8.29E-4	86	11697,16030,23,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749224	11287	PASS	GTCTGGTTTT	G	15363	0.998438	0	0,24,0,15339	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749224	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	29277	0.001093	8	19488,9725,19,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749224	12741	PASS	C	T	26547	0.960184	9	0,3,14081,12453	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T19I	nsp9	0.000486	0.962552	2	2	C>T
ERR5749224	13115	PASS	C	T	7272	0.922167	2147483647	0,0,7265,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L31	nsp10	0.001806	0.922167	1	1	C>T
ERR5749224	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	31103	0.00119	1	15547,15474,20,23	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749224	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10942	0.007677	2147483647	10603,61,5,266	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749224	14408	PASS	C	T	21063	0.826093	6	1,4,10553,10324	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749224	14676	PASS	C	T	11912	0.791639	0	5,0,11875,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749224	15279	PASS	C	T	20733	0.89196	0	5,0,20691,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749224	16176	PASS	T	C	16953	0.973928	0	0,0,7497,9447	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749224	17615	PASS	A	G	10639	0.88044	2147483647	0,0,0,10583	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749224	18504	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	25907	8.11E-4	0	1,25381,0,462	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K155N	ExoN	0.000518	0.094148	4	3	A>C
ERR5749224	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21981	0.003139	0	21899,0,72,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749224	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28385	8.81E-4	0	13937,14126,15,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749224	21764	PASS	ATACATG	A	9530	0.996118	0	38,0,9493,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749224	21990	PASS	TTTA	T	9532	0.993391	0	0,63,2,9467	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749224	22432	PASS	C	T	5791	0.721637	2147483647	0,0,5704,0	LOW	SILENT	SYNONYMOUS_CODING	S	gaC/gaT	D290	S	0.002959	0.755028	1	1	C>T
ERR5749224	23063	PASS	A	T	8280	0.833092	0	0,3,1,8225	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749224	23271	PASS	C	A	19862	0.935656	2147483647	0,0,19841,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749224	23403	PASS	A	G	19850	0.961008	2147483647	0,0,0,19817	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749224	23604	PASS	C	A	11704	0.937201	0	6,0,11695,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749224	23709	PASS	C	T	11694	0.913289	0	0,7,4,11655	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749224	24237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8704	0.001608	0	8681,0,14,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gTt	A892V	S	0.001242	0.889739	1	1	C>T
ERR5749224	24506	PASS	T	G	15995	0.974242	0	10,0,15983,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749224	24914	PASS	G	C	26960	0.953487	0	0,1,13442,13498	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749224	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	24941	0.001083	428	24866,10,12,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749224	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	25151	0.002107	1788	24674,152,168,128	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749224	25854	PASS	C	T	24867	0.924961	0	0,5,0,24806	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	taC/taT	Y154	orf3a	0.000876	0.939185	1	1	C>T
ERR5749224	27065	PASS	G	A	27646	0.693084	0	0,10,4,27146	LOW	SILENT	SYNONYMOUS_CODING	M	ttG/ttA	L181	M	0.001008	0.897124	3	2	G>A
ERR5749224	27972	PASS	C	T	7795	0.894291	0	0,0,7738,25	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749224	28048	PASS	G	T	7763	0.887157	0	0,14,0,7742	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749224	28111	PASS	A	G	24501	0.975756	5	8,1,16708,7773	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749224	28198	PASS	G	T	16720	0.936842	0	6,0,16677,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tGt/tTt	C102F	orf8	0.000718	0.94386	4	2	G>T
ERR5749224	28270	PASS	TA	T	32118	0.993897	428	189,8,16466,15456	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749224	28271	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AA	A	32112	0.001246	114	16603,15465,40,0	.	.	.	.	.	.	.	0.000482	0.924941	3	2	AA>A
ERR5749224	28280	PASS	G	C	32050	0.927457	16	15,4,16522,15437	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749224	28281	PASS	A	T	32050	0.903027	25	23,6,16522,15438	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749224	28282	PASS	T	A	32054	0.90073	15	25,10,16467,15452	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749224	28321	PASS	G	T	16702	0.928811	0	0,9,4,16646	LOW	SILENT	SYNONYMOUS_CODING	N	acG/acT	T16	N	0.00045	0.947809	3	2	G>T
ERR5749224	28881	PASS	G	A	13200	0.772424	18	7,0,6552,6457	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749224	28882	PASS	G	A	13200	0.831515	6	5,1,6644,6440	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749224	28883	PASS	G	C	13200	0.931364	6	1,4,6658,6523	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749224	28977	PASS	C	T	6770	0.902807	0	0,3,2,6747	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749224	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	23244	0.001033	86	16465,6724,4,23	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749224	29642	PASS	C	T	13593	0.91297	2	0,2,6094,7471	HIGH	NONSENSE	STOP_GAINED	ORF10	Caa/Taa	Q29*	orf10	0.001806	0.941176	2	2	C>T
ERR5749225	241	PASS	C	T	256	0.90625	0	0,0,128,126	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749225	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	4315	0.002317	0	3978,0,337,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749225	673	PASS	C	T	8138	0.602236	2147483647	2554,325,1252,4004	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y136	leader	0.000454	0.602236	3	2	C>T
ERR5749225	913	PASS	C	T	3807	0.912267	0	0,1,0,3802	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749225	3037	PASS	C	T	1854	0.820928	9	0,3,925,907	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749225	3177	PASS	C	T	5904	0.924797	0	2,0,4970,925	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P153L	nsp3	0.000773	0.96008	3	2	C>T
ERR5749225	3267	PASS	C	T	4975	0.972864	2147483647	0,0,4974,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749225	4307	PASS	A	G	3924	0.193935	0	0,3125,0,790	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Aag/Gag	K530E	nsp3	0.193935	0.193935	1	1	A>G
ERR5749225	5388	PASS	C	A	665	0.96391	2147483647	0,0,665,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749225	5986	PASS	C	T	2910	0.976632	0	1,0,2909,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749225	6954	PASS	T	C	3948	0.805978	2147483647	0,0,0,3922	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749225	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	3961	0.011108	5	3756,161,44,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749225	10387	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	11684	0.004707	171	5316,6303,55,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T111	3Cpro	0.00094	0.973895	1	1	T>C
ERR5749225	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	10250	0.008878	0	9763,0,91,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749225	11287	PASS	GTCTGGTTTT	G	10242	0.998926	0	0,11,0,10231	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749225	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	4078	0.004659	937	3979,37,4,55	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749225	14408	PASS	C	T	7935	0.849527	0	0,0,3967,3929	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749225	14676	PASS	C	T	3446	0.741439	0	1,0,3430,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749225	15279	PASS	C	T	2030	0.896059	2147483647	0,0,2029,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749225	15839	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	8042	0.004725	0	3,7995,0,38	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tGg/tCg	W800S	RdRp	0.001405	0.074516	2	1	G>C
ERR5749225	16176	PASS	T	C	3918	0.980347	0	0,0,422,3494	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749225	16792	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CGTG	C	10829	0.004156	96	4261,6523,0,45	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	cgtgta/cta	RV186L	helicase	0.000335	0.072562	5	2	CGTG>C
ERR5749225	17122	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	6112	0.002454	23	1851,4244,0,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gct/Tct	A296S	helicase	0.000476	0.056834	3	2	G>T
ERR5749225	18658	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	20395	0.008188	0	20223,5,167,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tgt/	C207	ExoN	0.000507	0.115741	3	2	TG>T
ERR5749225	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	20390	8.34E-4	0	20373,0,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749225	18747	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20388	0.006965	0	20209,0,165,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V236	ExoN	0.000375	0.982946	4	2	C>T
ERR5749225	18747	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	20388	0.005395	0	20278,0,110,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tataat/	YN237	ExoN	0.000375	0.982946	4	2	CTA>C
ERR5749225	19955	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2619	0.0084	0	2596,0,22,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T112I	endoR	0.0084	0.934633	1	1	C>T
ERR5749225	21764	PASS	ATACATG	A	4329	0.998383	0	7,0,4322,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749225	21990	PASS	TTTA	T	4330	0.979446	0	0,89,0,4241	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749225	21991	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTA	T	4332	0.012235	0	2,4246,0,53	HIGH	NONE	FRAME_SHIFT	S	tat/	Y144	S	0.00078	0.991378	2	1	TTA>T
ERR5749225	21991	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTAT	T	4332	0.007156	0	2,4246,0,31	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.00078	0.991378	2	1	TTAT>T
ERR5749225	22792	PASS	C	T	6764	0.866203	0	0,6,0,6746	LOW	SILENT	SYNONYMOUS_CODING	S	atC/atT	I410	S	0.000722	0.949572	3	3	C>T
ERR5749225	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	6765	0.001774	0	0,6750,0,12	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749225	23063	PASS	A	T	3833	0.863553	2147483647	0,0,0,3820	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749225	23271	PASS	C	A	6774	0.926336	2147483647	0,0,6764,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749225	23403	PASS	A	G	6769	0.965578	0	0,1,0,6764	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749225	23575	PASS	C	T	3644	0.894896	2147483647	0,0,3641,0	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C671	S	0.001569	0.894896	2	2	C>T
ERR5749225	23604	PASS	C	A	3644	0.941822	0	2,0,3640,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749225	23709	PASS	C	T	3642	0.939319	2147483647	0,0,0,3637	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749225	23802	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	3645	0.002195	0	0,3637,0,8	HIGH	NONE	FRAME_SHIFT	S	act/	T747	S	0.001717	0.977181	3	2	CT>C
ERR5749225	24127	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	4328	0.006007	19	3445,857,15,11	HIGH	NONE	FRAME_SHIFT	S	aac/	N856	S	0.000324	0.111888	4	1	TA>T
ERR5749225	24506	PASS	T	G	3553	0.979454	0	1,0,3552,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749225	24914	PASS	G	C	33498	0.956774	0	0,0,16695,16784	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749225	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	415	0.031325	151	390,12,1,12	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749225	26209	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	5549	0.010092	0	2,5472,0,74	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gtg/Ttg	V273L	orf3a	0.000792	0.234679	3	1	G>T
ERR5749225	26257	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	9746	0.003283	66	4195,5511,2,37	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	Gtt/Ttt	V5F	E	0.000247	0.948926	4	2	G>T
ERR5749225	26564	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	7512	0.003994	106	3283,4191,30,0	LOW	SILENT	SYNONYMOUS_CODING	M	aaA/aaG	K14	M	0.003994	0.071529	1	1	A>G
ERR5749225	27476	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	15109	0.002184	76	6345,8731,0,33	HIGH	NONE	FRAME_SHIFT	ORF7a	acagta/	TV28	orf7a	0.000547	0.22827	4	2	CAG>C
ERR5749225	27493	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15142	0.001189	39	6377,8745,0,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Cct/Tct	P34S	orf7a	0.000794	0.971493	2	1	C>T
ERR5749225	27807	PASS	C	T	6378	0.96143	0	0,1,0,6371	LOW	SILENT	SYNONYMOUS_CODING	ORF7b	Cta/Tta	L18	orf7b	0.000505	0.965257	2	2	C>T
ERR5749225	28111	PASS	A	G	12994	0.979375	0	3,0,12990,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749225	28198	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	12994	0.003309	0	12945,0,45,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tGt/tAt	C102Y	orf8	0.000718	0.94386	4	2	G>A
ERR5749225	28250	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TCTG	12977	0.025198	0	12652,0,327,0	MODERATE	NONE	CODON_INSERTION	ORF8	ttc/CTGttc	F120LF	orf8	0.000494	0.993968	5	3	T>TCTG
ERR5749225	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	12971	0.02521	0	12647,0,327,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749225	28270	PASS	TA	T	25202	0.995596	204	106,9,12839,12252	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749225	28280	PASS	G	C	25163	0.938958	0	3,2,12876,12237	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749225	28281	PASS	A	T	25163	0.921472	16	13,3,12862,12246	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749225	28282	PASS	T	A	25163	0.91106	2	6,3,12831,12256	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749225	28292	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	25858	6.19E-4	0	12893,12949,8,8	HIGH	NONE	FRAME_SHIFT	N	aat/	N8	N	0.000304	0.055324	4	2	CA>C
ERR5749225	28370	PASS	A	T	12990	0.939723	0	0,4,0,12954	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Agt/Tgt	S33C	N	0.935248	0.946374	1	1	A>T
ERR5749225	28795	PASS	A	G	764	0.979058	2147483647	0,0,764,0	LOW	SILENT	SYNONYMOUS_CODING	N	gaA/gaG	E174	N	0.97356	0.979058	1	1	A>G
ERR5749225	28881	PASS	G	A	1498	0.723632	3	1,0,730,742	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749225	28882	PASS	G	A	1498	0.81976	0	0,0,746,741	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749225	28883	PASS	G	C	1498	0.951268	0	1,0,748,748	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749225	28977	PASS	C	T	764	0.935864	0	0,1,0,763	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749225	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	25584	0.002228	0	12834,12667,38,35	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749226	241	PASS	C	T	54	0.851852	0	0,0,27,27	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749226	680	PASS	G	T	516	0.166667	59	357,66,93,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gat/Tat	D139Y	leader	0.000661	0.166667	3	2	G>T
ERR5749226	892	PASS	T	C	450	0.082222	0	0,411,0,37	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G29	nsp2	0.000495	0.082222	2	2	T>C
ERR5749226	913	PASS	C	T	450	0.891111	2147483647	0,0,0,448	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749226	1651	PASS	TA	T	577	0.076256	0	533,0,44,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	att/	I283	nsp2	0.076256	0.076256	1	1	TA>T
ERR5749226	3037	PASS	C	T	201	0.810945	0	0,0,101,100	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749226	3095	PASS	T	C	101	0.970297	2147483647	0,0,0,101	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tca/Cca	S126P	nsp3	0.937591	0.970297	1	1	T>C
ERR5749226	3177	PASS	C	T	501	0.96008	0	0,0,399,101	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P153L	nsp3	0.000773	0.96008	3	2	C>T
ERR5749226	3267	PASS	C	T	400	0.97	2147483647	0,0,399,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749226	3282	PASS	T	C	400	0.1575	0	335,0,65,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gTt/gCt	V188A	nsp3	0.1575	0.1575	1	1	T>C
ERR5749226	4835	PASS	G	A	382	0.052356	0	178,177,13,12	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggt/Agt	G706S	nsp3	0.001394	0.052356	2	1	G>A
ERR5749226	5388	PASS	C	A	77	0.883117	2147483647	0,0,77,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749226	5822	PASS	C	T	445	0.069663	0	0,408,0,36	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Ttt	L1035F	nsp3	0.002438	0.069663	1	1	C>T
ERR5749226	5986	PASS	C	T	275	0.985455	2147483647	0,0,275,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749226	6954	PASS	T	C	398	0.80402	2147483647	0,0,0,396	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749226	7798	PASS	G	T	717	0.185495	0	562,0,155,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaG/aaT	K1693N	nsp3	0.001127	0.936026	1	1	G>T
ERR5749226	10201	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	650	0.018462	0	637,0,12,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atA	M49I	3Cpro	0.018462	0.126654	2	1	G>A
ERR5749226	11241	PASS	G	A	2090	0.08134	0	0,1900,0,187	HIGH	NONSENSE	STOP_GAINED	ORF1ab	tGg/tAg	W90*	nsp6	0.08134	0.08134	1	1	G>A
ERR5749226	11287	PASS	GTCTGGTTTT	G	2091	0.998565	0	0,3,0,2088	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749226	14408	PASS	C	T	84	0.821429	0	0,0,42,42	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749226	14676	PASS	C	T	313	0.741214	2147483647	0,0,312,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749226	15279	PASS	C	T	341	0.868035	2147483647	0,0,341,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749226	15797	PASS	T	C	1293	0.07734	0	0,1187,0,103	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cTt/cCt	L786P	RdRp	0.001418	0.07734	2	1	T>C
ERR5749226	15960	PASS	C	T	470	0.731915	2147483647	0,0,465,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A840	RdRp	0.001581	0.81574	1	1	C>T
ERR5749226	16176	PASS	T	C	558	0.97491	0	0,0,88,470	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749226	19034	PASS	T	C	903	0.060908	0	847,0,56,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTt/aCt	I332T	ExoN	0.000384	0.060908	2	2	T>C
ERR5749226	21101	PASS	G	GT	1246	0.083467	0	0,1142,0,104	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttc/ttTc	F150F?	MethTr	0.001498	0.083467	2	2	G>GT
ERR5749226	21764	PASS	ATACATG	A	446	0.997758	0	1,0,445,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749226	21990	PASS	TTTA	T	447	1.0	0	0,0,1,446	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749226	22113	PASS	G	T	955	0.050262	0	896,0,58,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gGt/gTt	G184V	S	0.00046	0.050262	2	2	G>T
ERR5749226	23063	PASS	A	T	393	0.816794	2147483647	0,0,0,389	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749226	23271	PASS	C	A	750	0.937333	2147483647	0,0,750,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749226	23277	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	750	0.037333	0	706,0,44,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCt/aTt	T572I	S	0.001007	0.74768	1	1	C>T
ERR5749226	23403	PASS	A	G	750	0.965333	2147483647	0,0,0,749	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749226	23604	PASS	C	A	307	0.947883	2147483647	0,0,307,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749226	23709	PASS	C	T	307	0.944625	2147483647	0,0,0,306	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749226	23855	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	120	0.033333	0	116,0,4,0	HIGH	NONE	FRAME_SHIFT	S	cgt/	R765	S	0.000815	0.181818	2	2	CG>C
ERR5749226	24320	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	332	0.009036	0	0,329,0,3	HIGH	NONE	FRAME_SHIFT	S	aaa/	K921	S	0.000763	0.138365	4	2	CA>C
ERR5749226	24432	PASS	A	T	854	0.940281	0	0,0,522,332	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cAa/cTa	Q957L	S	0.935743	0.949489	1	1	A>T
ERR5749226	24506	PASS	T	G	522	0.97318	2147483647	0,0,522,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749226	24914	PASS	G	C	3936	0.949949	0	0,0,1960,1975	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749226	25495	PASS	A	G	5262	0.899848	0	0,0,2614,2643	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Ata/Gta	I35V	orf3a	0.000735	0.911134	2	1	A>G
ERR5749226	26013	PASS	C	T	596	0.958054	2147483647	0,0,596,0	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	ttC/ttT	F207	orf3a	0.000839	0.974528	1	1	C>T
ERR5749226	27972	PASS	C	T	59	0.966102	2147483647	0,0,59,0	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749226	28048	PASS	G	T	59	0.932203	2147483647	0,0,0,59	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749226	28111	PASS	A	G	2206	0.982321	0	0,0,2147,59	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749226	28270	PASS	TA	T	4110	0.994891	30	17,2,2126,1963	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749226	28280	PASS	G	C	4103	0.94175	0	1,1,2131,1963	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749226	28281	PASS	A	T	4103	0.898367	0	1,0,2129,1964	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749226	28282	PASS	T	A	4103	0.902754	0	3,2,2120,1964	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749226	28881	PASS	G	A	77	0.805195	0	0,0,39,38	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749226	28882	PASS	G	A	77	0.883117	0	0,0,39,38	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749226	28883	PASS	G	C	77	0.935065	0	0,0,39,38	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749226	28977	PASS	C	T	39	0.897436	2147483647	0,0,0,39	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749227	241	PASS	C	T	27721	0.857978	2	5,7,13791,13771	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749227	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	16520	0.001513	0	16499,2,25,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749227	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	16518	0.001695	0	16472,2,28,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749227	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	16493	0.001758	0	15305,2,1095,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749227	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	16493	6.06E-4	0	16481,2,10,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749227	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	48578	9.47E-4	2	32006,16518,28,18	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749227	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	32022	0.001031	0	2,31948,0,38	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749227	913	PASS	C	T	32023	0.901227	0	0,13,2,31945	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749227	1510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	33397	0.003533	0	0,32908,0,132	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G235	nsp2	0.002159	0.937304	1	1	T>C
ERR5749227	2702	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	58479	8.04E-4	2147483647	58037,38,95,195	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F633V	nsp2	0.000632	0.333333	1	1	T>G
ERR5749227	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	115883	0.001467	2147483647	57904,53933,100,3645	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749227	3037	PASS	C	T	31073	0.806327	97	0,32,15532,15286	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749227	3267	PASS	C	T	31619	0.971821	0	6,0,31595,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749227	5388	PASS	C	A	10177	0.957158	0	2,0,10170,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749227	5986	PASS	C	T	19161	0.975575	0	1,0,19154,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749227	6295	PASS	A	G	32827	0.968532	0	2,0,32799,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atA/atG	I1192M	nsp3	0.001427	0.968532	1	1	A>G
ERR5749227	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18452	0.001463	0	2,18178,0,40	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749227	6954	PASS	T	C	37850	0.811731	0	0,3,1,37626	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749227	9391	PASS	C	T	52720	0.805102	18	0,6,26373,26059	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D279	nsp4	0.00048	0.805102	2	2	C>T
ERR5749227	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	48114	6.65E-4	111	21491,26591,32,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749227	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26632	0.001239	0	26556,2,37,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749227	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	26615	0.001315	0	26539,0,68,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749227	11264	PASS	T	C	26612	0.956786	0	0,2,1,26603	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Ttg/Ctg	L98	nsp6	0.001454	0.956786	1	1	T>C
ERR5749227	11287	PASS	GTCTGGTTTT	G	26613	0.997633	0	0,63,1,26549	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749227	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	53311	7.5E-4	0	33311,19920,26,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749227	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	61362	9.94E-4	0	30656,30563,33,34	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749227	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	17223	0.007432	2147483647	16742,118,8,348	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749227	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	33328	6.9E-4	3	16728,16602,14,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749227	14408	PASS	C	T	33328	0.833263	7	2,6,16646,16402	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749227	14676	PASS	C	T	21361	0.759328	0	10,0,21271,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749227	14925	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28441	0.006927	0	28232,8,197,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V495	RdRp	0.002531	0.98996	1	1	C>T
ERR5749227	15279	PASS	C	T	36355	0.884473	0	7,0,36295,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749227	16176	PASS	T	C	30766	0.979263	3	1,0,13351,17405	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749227	16575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34594	0.006042	0	34310,0,246,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D113	helicase	0.001088	0.827968	1	1	C>T
ERR5749227	18086	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17065	0.001699	0	17028,1,32,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T16I	ExoN	0.001699	0.075758	1	1	C>T
ERR5749227	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	36970	8.39E-4	0	1,36899,0,37	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCc/gTc	A371V	ExoN	0.00034	0.247423	2	2	C>T
ERR5749227	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	40505	0.002247	0	40376,0,96,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749227	20930	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	32215	0.00118	0	32138,22,39,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aTg	T91M	MethTr	0.000902	0.95585	2	2	C>T
ERR5749227	21255	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	78969	6.2E-4	1	40872,38033,29,24	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcG/gcA	A199	MethTr	0.000341	0.917425	4	2	G>A
ERR5749227	21762	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTATACA	C	18903	0.002063	0	18864,0,39,0	MODERATE	NONE	CODON_DELETION	S	atacat/	IH68	S	0.001297	0.875707	2	2	CTATACA>C
ERR5749227	21764	PASS	ATACATG	A	18903	0.996403	0	68,0,18835,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749227	21990	PASS	TTTA	T	18910	0.997567	0	0,46,6,18858	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749227	23063	PASS	A	T	16616	0.85213	0	0,3,0,16526	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749227	23271	PASS	C	A	31591	0.92463	0	1,0,31559,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749227	23403	PASS	A	G	31586	0.964636	0	0,2,2,31563	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749227	23604	PASS	C	A	21867	0.961083	0	11,0,21852,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749227	23709	PASS	C	T	21844	0.933529	0	0,9,1,21802	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749227	24506	PASS	T	G	27177	0.975604	0	8,0,27163,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749227	24914	PASS	G	C	44542	0.957007	0	1,1,22189,22318	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749227	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	38475	0.001923	146	23942,14423,92,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749227	25523	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	24558	0.003543	1	274,24149,0,125	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	gGa/gTa	G44V	orf3a	0.000994	0.895931	1	1	G>T
ERR5749227	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	38972	0.001026	562	38846,22,19,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749227	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	38924	9.25E-4	0	38888,0,36,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749227	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	39201	0.001173	2307	38593,221,184,156	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749227	26013	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	75376	0.001114	0	75252,0,87,0	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	ttC/ttT	F207	orf3a	0.000839	0.974528	1	1	C>T
ERR5749227	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	16654	0.001081	0	1,16635,0,18	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749227	27972	PASS	C	T	16157	0.91465	62	2,3,16056,60	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749227	28048	PASS	G	T	16104	0.918716	0	0,31,0,16069	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749227	28111	PASS	A	G	43532	0.97372	0	4,2,27400,16107	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749227	28270	PASS	TA	T	52982	0.994923	649	273,9,27058,25655	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749227	28280	PASS	G	C	52865	0.938731	14	12,3,27095,25634	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749227	28281	PASS	A	T	52865	0.925489	36	42,13,27100,25608	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749227	28282	PASS	T	A	52869	0.906902	11	34,19,27030,25642	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749227	28881	PASS	G	A	26095	0.762177	27	10,0,12957,12771	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749227	28882	PASS	G	A	26095	0.817973	21	8,0,13095,12734	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749227	28883	PASS	G	C	26095	0.941023	18	0,6,13115,12945	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749227	28977	PASS	C	T	13345	0.916448	0	0,6,12,13291	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749227	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	46255	6.92E-4	129	32895,13278,3,30	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749227	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	65318	8.88E-4	0	32819,32403,37,37	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749228	241	PASS	C	T	19560	0.859714	11	2,8,9747,9709	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749228	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	11784	0.001782	0	11749,6,21,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749228	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	11769	0.001614	0	10965,7,747,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749228	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	33067	0.001119	1	21241,11785,25,12	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749228	913	PASS	C	T	21250	0.899624	0	0,10,0,21196	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749228	1510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	20590	0.003837	0	0,20245,0,92	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G235	nsp2	0.002159	0.937304	1	1	T>C
ERR5749228	2453	PASS	C	T	17159	0.753599	0	0,28,1,16927	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L550F	nsp2	0.00429	0.842201	2	2	C>T
ERR5749228	3037	PASS	C	T	22856	0.806528	53	1,21,11431,11240	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749228	3267	PASS	C	T	21965	0.971364	0	5,0,21946,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749228	5388	PASS	C	A	7366	0.961037	0	2,0,7360,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749228	5892	PASS	C	T	18004	0.891524	0	0,11,0,17965	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCc/aTc	T1058I	nsp3	0.012179	0.912046	1	1	C>T
ERR5749228	5986	PASS	C	T	121	0.991736	2147483647	0,0,121,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749228	6525	PASS	C	T	38420	0.968636	7	0,5,14560,23839	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T1269I	nsp3	0.000813	0.968636	1	1	C>T
ERR5749228	6954	PASS	T	C	23826	0.793587	0	0,3,2,23657	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749228	8151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	52089	6.53E-4	1326	25496,26033,517,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gTc/gGc	V1811G	nsp3	0.00055	0.34	2	1	T>G
ERR5749228	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	33044	4.24E-4	36	18106,14924,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749228	9733	PASS	C	T	18108	0.936382	0	0,2,2,18085	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F393	nsp4	0.001381	0.936382	2	2	C>T
ERR5749228	9733	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	18108	0.001381	0	2,18081,0,25	HIGH	NONE	FRAME_SHIFT+STOP_GAINED	ORF1ab	agt/Tagt	S395*?	nsp4	0.001381	0.936382	2	2	C>CT
ERR5749228	10323	PASS	A	G	19012	0.94493	0	0,5,0,18976	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749228	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	18100	0.001105	0	18049,0,42,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749228	11287	PASS	GTCTGGTTTT	G	18089	0.997236	0	0,50,0,18039	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749228	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	39494	7.85E-4	6	23661,15785,15,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749228	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28092	0.00121	0	14026,13988,18,19	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749228	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	11360	0.006162	2147483647	11076,77,7,196	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749228	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	22027	4.54E-4	0	11068,10963,5,5	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749228	14408	PASS	C	T	22027	0.827348	7	2,6,11003,10817	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749228	14676	PASS	C	T	12998	0.793891	0	6,0,12953,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749228	15279	PASS	C	T	21666	0.893381	0	1,0,21637,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749228	16176	PASS	T	C	19950	0.976842	0	2,1,10070,9871	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749228	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	21811	0.001559	0	21777,0,34,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749228	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	25102	9.56E-4	0	25078,0,24,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749228	18744	PASS	C	T	25099	0.953624	0	2,0,25036,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y235	ExoN	0.000912	0.953624	2	2	C>T
ERR5749228	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34200	0.002164	0	34102,0,83,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749228	21762	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTATACA	C	14978	0.00207	0	14947,0,31,0	MODERATE	NONE	CODON_DELETION	S	atacat/	IH68	S	0.001297	0.875707	2	2	CTATACA>C
ERR5749228	21764	PASS	ATACATG	A	14978	0.996128	0	57,0,14920,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749228	21990	PASS	TTTA	T	14986	0.997398	0	0,39,8,14939	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749228	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30059	0.001098	16	13975,16035,9,25	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749228	23063	PASS	A	T	13968	0.850802	0	0,4,1,13871	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749228	23271	PASS	C	A	21665	0.918901	0	5,0,21641,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749228	23403	PASS	A	G	21655	0.956777	0	0,2,0,21634	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749228	23604	PASS	C	A	17770	0.942938	0	10,0,17753,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749228	23709	PASS	C	T	17759	0.931471	0	0,7,2,17720	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749228	24506	PASS	T	G	17130	0.977116	0	11,0,17116,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749228	24914	PASS	G	C	38457	0.957147	0	0,1,19140,19289	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749228	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	26848	0.001974	58	19688,7087,63,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749228	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	25411	0.001495	471	25323,14,19,19	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749228	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	25378	6.3E-4	0	25362,0,16,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749228	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	25631	0.002302	2639	25144,139,139,172	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749228	26072	PASS	A	G	60423	0.951608	0	11,0,60343,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cAt/cGt	H227R	orf3a	0.951608	0.953498	1	1	A>G
ERR5749228	26748	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	12609	0.001269	0	8,12243,0,350	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Atc/Ctc	I76L	M	0.001056	0.926238	2	1	A>C
ERR5749228	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	12629	0.001109	0	0,12615,0,14	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749228	27145	PASS	C	T	27993	0.863895	188	6,11,1,27939	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	aCa/aTa	T208I	M	0.000476	0.863895	2	2	C>T
ERR5749228	27461	PASS	G	T	17496	0.969593	32	1,10,0,17480	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	tGt/tTt	C23F	orf7a	0.002221	0.974441	1	1	G>T
ERR5749228	27972	PASS	C	T	12669	0.907096	43	1,2,12581,49	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749228	28048	PASS	G	T	12625	0.908356	0	0,13,0,12604	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749228	28111	PASS	A	G	33929	0.975272	2	1,2,21284,12635	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749228	28270	PASS	TA	T	40861	0.995203	370	189,14,21013,19652	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749228	28280	PASS	G	C	40774	0.934591	8	6,1,21053,19641	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749228	28281	PASS	A	T	40774	0.916491	0	12,12,21046,19627	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749228	28282	PASS	T	A	40776	0.906882	0	14,12,21009,19652	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749228	28881	PASS	G	A	18797	0.760068	18	7,0,9329,9182	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749228	28882	PASS	G	A	18796	0.814854	4	4,1,9427,9160	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749228	28883	PASS	G	C	18796	0.93621	0	2,1,9439,9330	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749228	28977	PASS	C	T	9599	0.908532	0	0,2,0,9579	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749228	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	59749	0.001071	0	30056,29593,42,39	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749228	29511	PASS	G	T	19877	0.828395	681	1,227,10070,9576	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGt/aTt	S413I	N	0.800125	0.828395	1	1	G>T
ERR5749228	29743	PASS	C	T	10056	0.859785	0	0,6,0,10013	.	.	.	.	.	.	.	0.001027	0.859785	2	1	C>T
ERR5749229	241	PASS	C	T	1378	0.886067	0	0,0,688,687	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749229	379	PASS	C	T	2959	0.944238	0	0,0,2265,693	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V38	leader	0.847169	0.944238	2	1	C>T
ERR5749229	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	13144	0.001141	0	0,13129,0,15	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTg	L35F?	nsp2	0.000551	0.081967	3	2	C>CT
ERR5749229	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13144	0.001446	0	0,13110,0,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749229	913	PASS	C	T	13144	0.923539	0	0,9,0,13125	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749229	2062	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	15016	0.001265	0	14910,22,43,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcA	A419	nsp2	0.001265	0.822961	2	1	C>A
ERR5749229	2062	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15016	0.001931	0	14910,22,37,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A419	nsp2	0.001265	0.822961	2	1	C>T
ERR5749229	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	34608	0.0013	2604	17265,16231,26,987	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749229	2775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	17379	0.003107	0	0,17278,0,56	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K19R	nsp3	0.000437	0.951613	3	2	A>G
ERR5749229	2815	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	17385	0.001668	0	0,17356,0,29	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K33	nsp3	0.001668	0.067104	2	2	TA>T
ERR5749229	3037	PASS	C	T	5717	0.820535	6	0,2,2855,2824	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749229	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	2893	0.004148	308	2,2878,12,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749229	3267	PASS	C	T	13301	0.972859	2147483647	0,0,13295,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749229	3575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	4760	0.002731	0	4747,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/ttTa	L287F?	nsp3	0.000594	0.059126	3	1	G>GT
ERR5749229	3671	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	9475	0.002216	0	4717,4679,12,12	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E318K	nsp3	0.000351	0.0625	6	2	G>A
ERR5749229	3802	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAA	T	8382	9.54E-4	19	3622,4749,0,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N363	nsp3	0.000554	0.064198	4	2	TAA>T
ERR5749229	5388	PASS	C	A	1189	0.954584	2147483647	0,0,1188,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749229	5986	PASS	C	T	4839	0.977268	2147483647	0,0,4837,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749229	6320	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	14485	0.003314	0	14437,0,48,0	HIGH	NONE	FRAME_SHIFT+STOP_GAINED	ORF1ab	gaa/Tgaa	E1202*?	nsp3	0.001197	0.080147	2	2	G>GT
ERR5749229	6843	PASS	C	T	15503	0.922467	0	2,0,10978,4503	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S1375F	nsp3	0.000753	0.922467	2	1	C>T
ERR5749229	6954	PASS	T	C	10966	0.818165	0	0,1,0,10913	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749229	7564	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	8975	0.001226	0	0,8964,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/	Y1617	nsp3	0.000586	0.056194	4	2	CT>C
ERR5749229	7771	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	11918	0.001343	0	11891,0,18,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caT/caC	H1684	nsp3	0.001343	1	2	2	T>C
ERR5749229	8084	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	11531	0.001301	0	11518,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1790	nsp3	0.000543	0.923413	4	2	GA>G
ERR5749229	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	7080	0.001271	6	5623,1448,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749229	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16282	0.002334	0	16217,0,41,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749229	11287	PASS	GTCTGGTTTT	G	16275	0.999386	0	0,10,0,16265	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749229	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18253	0.001096	0	9120,9099,10,10	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749229	13554	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	9131	9.86E-4	0	0,9122,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N39	RdRp	0.000637	0.920199	2	2	CA>C
ERR5749229	14408	PASS	C	T	1016	0.86811	0	0,0,507,504	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749229	14676	PASS	C	T	7999	0.804101	0	4,0,7971,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749229	15279	PASS	C	T	7665	0.895499	2147483647	0,0,7656,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749229	15411	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	7658	0.00222	0	0,7578,0,20	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaT/aaC	N657	RdRp	0.00222	0.952192	2	2	T>C
ERR5749229	15620	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	10424	0.001535	0	10386,0,17,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cTt/cCt	L727P	RdRp	0.001388	0.088584	1	1	T>C
ERR5749229	16176	PASS	T	C	9060	0.982781	4	0,10,1344,7704	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749229	17615	PASS	A	G	7036	0.918135	2147483647	0,0,0,7024	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749229	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	16058	0.001059	0	16033,0,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749229	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	20141	0.002284	0	0,20095,0,46	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749229	19328	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	8216	8.52E-4	0	8209,0,7,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F431	ExoN	0.000459	0.937906	4	2	CT>C
ERR5749229	19343	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	8216	0.002191	0	8198,0,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F436	ExoN	0.000519	0.192257	7	2	CT>C
ERR5749229	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6833	0.002488	0	6813,0,18,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749229	21004	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	34710	7.49E-4	0	17324,17290,13,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gca/Aca	A116T	MethTr	0.000749	0.857814	3	1	G>A
ERR5749229	21094	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	17408	0.001264	0	2,17371,0,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Aaa/Gaa	K146E	MethTr	0.000554	0.211111	5	2	A>G
ERR5749229	21123	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTT	G	31254	8.0E-4	63	13845,17383,0,25	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F156	MethTr	0.000257	0.90982	5	2	GTT>G
ERR5749229	21234	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	13838	6.5E-4	0	13830,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/Tgtt	V194C?	MethTr	0.000472	0.857572	5	2	C>CT
ERR5749229	21764	PASS	ATACATG	A	6419	0.998598	0	9,0,6410,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749229	21817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	6417	0.002182	0	6404,0,14,0	HIGH	NONE	FRAME_SHIFT	S	ttt/	F86	S	0.000689	0.961354	3	2	AT>A
ERR5749229	21867	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	12798	6.25E-4	0	6396,6395,4,4	HIGH	NONE	FRAME_SHIFT	S	aga/	R102	S	0.000625	0.861881	2	2	GA>G
ERR5749229	21990	PASS	TTTA	T	6421	0.998754	0	0,8,2,6411	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749229	21991	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTA	T	6425	9.34E-4	0	6,6413,0,6	HIGH	NONE	FRAME_SHIFT	S	tat/	Y144	S	0.00078	0.991378	2	1	TTA>T
ERR5749229	22030	PASS	G	T	12986	0.115047	0	11433,2,1551,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gaG/gaT	E156D	S	0.000562	0.115047	2	2	G>T
ERR5749229	23063	PASS	A	T	6241	0.871655	2147483647	0,0,0,6217	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749229	23271	PASS	C	A	16412	0.926944	0	1,0,16402,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749229	23287	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	16412	0.001462	0	16382,0,27,0	LOW	SILENT	SYNONYMOUS_CODING	S	gcT/gcC	A575	S	0.001462	0.947477	1	1	T>C
ERR5749229	23403	PASS	A	G	16405	0.982749	0	0,6,0,16391	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749229	23604	PASS	C	A	6416	0.951372	0	4,0,6408,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749229	23709	PASS	C	T	6406	0.945832	0	0,3,0,6391	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749229	23712	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATT	A	6407	0.001249	0	0,6399,0,8	HIGH	NONE	FRAME_SHIFT	S	ttt/	F718	S	0.000679	0.958955	3	2	ATT>A
ERR5749229	24506	PASS	T	G	8963	0.975455	0	5,0,8958,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749229	24899	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	G	23368	0.001027	0	11672,11614,13,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Caa/Gaa	Q1113E	S	0.000315	0.09021	5	3	C>G
ERR5749229	24899	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	23366	4.28E-4	0	11689,11669,5,5	HIGH	NONE	FRAME_SHIFT	S	atc/	I1114	S	0.000315	0.09021	5	3	CA>C
ERR5749229	24914	PASS	G	C	23298	0.962486	3	1,0,11603,11668	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749229	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	17196	0.001338	34	13046,4120,30,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749229	25391	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTA	T	13121	0.001143	0	13106,0,15,0	HIGH	NONE	FRAME_SHIFT+START_LOST	ORF3a	atg/	M1	orf3a	0.000585	0.191026	1	1	TTA>T
ERR5749229	25571	PASS	C	T	13114	0.92039	0	0,3,0,13091	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	tCc/tTc	S60F	orf3a	0.001558	0.922217	1	1	C>T
ERR5749229	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	2118	0.006138	168	2092,9,4,9	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749229	26044	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	G	14553	0.00158	0	14520,0,23,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Caa/Gaa	Q218E	orf3a	0.000469	0.102679	3	3	C>G
ERR5749229	27972	PASS	C	T	2363	0.903512	0	0,0,2346,11	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749229	28048	PASS	G	T	2351	0.920459	0	0,3,0,2348	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749229	28111	PASS	A	G	21757	0.978857	0	2,0,19396,2355	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749229	28270	PASS	TA	T	37625	0.995827	359	157,7,19175,18293	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749229	28280	PASS	G	C	37552	0.939098	11	9,2,19204,18271	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749229	28281	PASS	A	T	37552	0.917528	62	37,5,19174,18279	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749229	28282	PASS	T	A	37555	0.910212	2	15,11,19151,18285	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749229	28881	PASS	G	A	5303	0.777484	0	1,0,2638,2618	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749229	28882	PASS	G	A	5303	0.845371	0	1,1,2661,2604	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749229	28883	PASS	G	C	5303	0.95116	0	0,0,2662,2638	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749229	28977	PASS	C	T	2691	0.920476	2147483647	0,0,0,2686	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749229	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	32749	0.001221	0	16428,16261,24,22	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749229	29445	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTG	C	4279	0.001402	0	4273,0,6,0	HIGH	NONE	FRAME_SHIFT	N	gtg/	V392	N	0.000907	0.853797	2	2	CTG>C
ERR5749230	241	PASS	C	T	1978	0.873104	0	0,1,983,993	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749230	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	3765	0.001594	0	3759,0,6,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749230	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	3765	0.00239	0	3750,0,9,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749230	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	3765	0.001594	0	3750,0,6,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749230	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	22688	0.002204	5	18873,3765,45,5	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749230	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18908	0.001111	0	0,18866,0,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749230	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	18908	6.35E-4	0	0,18896,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L35	nsp2	0.000551	0.081967	3	2	CT>C
ERR5749230	913	PASS	C	T	18910	0.9055	0	0,5,0,18876	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749230	2160	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAG	A	19575	7.15E-4	0	0,19561,0,14	HIGH	NONE	FRAME_SHIFT	ORF1ab	gagaag/	EK453	nsp2	0.000572	0.089776	3	2	AAG>A
ERR5749230	2185	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	19578	9.7E-4	0	3,19556,0,19	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F461	nsp2	0.000441	0.963529	4	3	GT>G
ERR5749230	3037	PASS	C	T	9073	0.81197	18	0,6,4525,4481	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749230	3267	PASS	C	T	19846	0.970422	2147483647	0,0,19830,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749230	4237	PASS	T	C	23081	0.909493	4	1,3,11565,11456	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaT/aaC	N506	nsp3	0.000302	0.918634	2	2	T>C
ERR5749230	4255	PASS	G	A	23121	0.811167	54	19,0,11501,11458	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccG/ccA	P512	nsp3	0.001102	0.871853	2	1	G>A
ERR5749230	5100	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	9009	0.001443	0	8997,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tca/	S794	nsp3	0.001443	0.071429	2	2	CA>C
ERR5749230	5388	PASS	C	A	2541	0.95671	2147483647	0,0,2537,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749230	5575	PASS	C	T	2545	0.961493	65	2,0,0,2540	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y952	nsp3	0.01018	0.961493	1	1	C>T
ERR5749230	5986	PASS	C	T	8829	0.974742	2147483647	0,0,8823,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749230	6383	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	43094	8.59E-4	1	21430,21491,21,19	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gcc/Acc	A1222T	nsp3	0.000859	0.05632	3	1	G>A
ERR5749230	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7710	0.00415	0	0,7593,0,42	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749230	6954	PASS	T	C	14623	0.806674	0	0,2,0,14523	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749230	7798	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	17741	0.001127	0	17645,0,91,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaG/aaT	K1693N	nsp3	0.001127	0.936026	1	1	G>T
ERR5749230	9060	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATTG	A	13684	7.31E-4	0	13675,0,10,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	tgttat/tat	CY170Y	nsp4	0.000621	0.433333	5	2	ATTG>A
ERR5749230	10683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	14893	0.001813	0	5,14855,0,33	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A210D	3Cpro	0.001813	0.252205	2	1	C>A
ERR5749230	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	21881	0.004113	0	21210,0,90,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749230	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	21869	0.003155	0	21776,0,87,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749230	11199	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	43580	7.57E-4	0	21631,21747,17,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCc/gTc	A76V	nsp6	0.000309	0.056758	3	2	C>T
ERR5749230	11287	PASS	GTCTGGTTTT	G	21874	0.997988	0	0,44,0,21830	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749230	11355	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAAG	C	27739	5.77E-4	14	5851,21872,0,16	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	agaact/act	RT129T	nsp6	0.000455	0.982262	3	2	CAAG>C
ERR5749230	11507	PASS	G	A	11601	0.907077	0	0,0,5819,5753	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Att	V179I	nsp6	0.007744	0.914418	2	2	G>A
ERR5749230	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	27776	0.001152	4	21884,5838,23,9	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749230	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	13606	7.35E-4	0	13597,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749230	13164	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13606	0.001249	0	13556,0,18,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T47I	nsp10	0.001249	0.952318	1	1	C>T
ERR5749230	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23615	0.001143	0	11793,11770,14,14	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749230	14168	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	15096	0.00212	0	0,15064,0,32	HIGH	NONE	FRAME_SHIFT	ORF1ab	atatta/	IL244	RdRp	0.000479	0.314961	1	1	CTA>C
ERR5749230	14408	PASS	C	T	1607	0.835719	0	0,1,796,795	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749230	14676	PASS	C	T	10577	0.802023	0	6,0,10535,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749230	15279	PASS	C	T	11334	0.908152	0	3,0,11318,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749230	15289	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TGG	11334	0.001147	0	11321,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gat/gGGat	D618G?	RdRp	0.000698	0.157576	2	1	T>TGG
ERR5749230	15420	PASS	T	G	11323	0.91663	0	0,19,0,11294	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcG	A660	RdRp	0.908883	0.934773	1	1	T>G
ERR5749230	15542	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	16950	5.9E-4	0	16939,1,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gcc/	A702	RdRp	0.00059	0.073325	3	2	CG>C
ERR5749230	15983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	9735	0.001335	0	9722,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T850	RdRp	0.000701	0.338235	2	1	TA>T
ERR5749230	16176	PASS	T	C	11966	0.979024	0	0,1,2225,9736	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749230	16508	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	23673	8.87E-4	0	23652,0,21,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L92	helicase	0.000561	0.074909	2	2	GT>G
ERR5749230	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	15813	0.001265	0	15793,0,20,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749230	17502	PASS	C	T	12337	0.984113	0	4,0,12326,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F422	helicase	0.000611	0.9865	2	2	C>T
ERR5749230	17747	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTG	C	10421	0.001056	0	10407,3,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctgct/	PA504	helicase	0.000839	0.968462	2	2	CTG>C
ERR5749230	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	23020	0.001086	0	22995,0,25,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749230	18897	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	23023	9.56E-4	0	4,22990,0,27	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttT/ttC	F286	ExoN	0.00046	0.060685	3	3	T>C
ERR5749230	19011	PASS	C	T	27065	0.970922	0	2,0,27049,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D324	ExoN	0.000408	0.975746	4	2	C>T
ERR5749230	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	27036	7.4E-4	0	0,27016,0,20	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749230	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9572	0.00188	0	9548,0,19,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749230	20844	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	40417	3.71E-4	35	23121,17281,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tataat/	YN63	MethTr	0.000293	0.905571	5	2	CTA>C
ERR5749230	20857	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	40417	8.66E-4	6	23092,17258,39,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Ttt	V67F	MethTr	0.000531	0.099366	2	2	G>T
ERR5749230	20930	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23134	0.001254	0	23088,0,30,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aTg	T91M	MethTr	0.000902	0.95585	2	2	C>T
ERR5749230	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	23131	0.001427	0	0,23098,0,33	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TA>T
ERR5749230	21077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	23136	0.00147	0	5,23097,0,34	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K141	MethTr	0.000492	0.955529	4	2	CA>C
ERR5749230	21733	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	11027	0.001814	0	10973,12,22,0	LOW	SILENT	SYNONYMOUS_CODING	S	ccT/ccC	P57	S	0.001662	0.065814	2	1	T>C
ERR5749230	21762	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTATACA	C	11015	0.00236	0	10989,0,26,0	MODERATE	NONE	CODON_DELETION	S	atacat/	IH68	S	0.001297	0.875707	2	2	CTATACA>C
ERR5749230	21764	PASS	ATACATG	A	11015	0.99655	0	38,0,10977,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749230	21854	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	21978	0.00132	2	10962,10936,16,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tct/Cct	S98P	S	0.00132	0.05283	1	1	T>C
ERR5749230	21990	PASS	TTTA	T	11020	0.995191	0	0,53,5,10962	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749230	22113	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	19581	4.6E-4	0	19577,0,9,0	HIGH	NONE	FRAME_SHIFT	S	ggt/	G184	S	0.00046	0.050262	2	2	GT>G
ERR5749230	23063	PASS	A	T	10209	0.871878	0	0,3,0,10160	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749230	23271	PASS	C	A	22998	0.92008	0	4,0,22968,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749230	23403	PASS	A	G	22979	0.964315	0	0,3,0,22960	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749230	23522	PASS	G	A	11372	0.959726	107	1,3,11362,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gaa/Aaa	E654K	S	0.00053	0.959726	5	2	G>A
ERR5749230	23604	PASS	C	A	11366	0.937885	0	7,0,11353,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749230	23709	PASS	C	T	11350	0.937533	0	0,2,3,11327	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749230	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18334	0.001091	25	6947,11352,15,6	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L752F	S	0.000334	0.080808	2	2	C>T
ERR5749230	24127	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TTTTTG	16083	6.84E-4	40	9127,6956,0,11	HIGH	NONE	FRAME_SHIFT+STOP_GAINED	S	aac/TTTTGaac	N856F*?	S	0.000324	0.111888	4	1	T>TTTTTG
ERR5749230	24506	PASS	T	G	12893	0.97487	0	4,0,12886,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749230	24914	PASS	G	C	32473	0.95969	0	0,0,16168,16281	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749230	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	25415	0.001849	27	20017,5335,54,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749230	25422	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGGAACTGTAACTTTGAAGCAAGGTGAAATC	T	20189	5.45E-4	0	20178,0,11,0	MODERATE	NONE	CODON_DELETION	ORF3a	ggaactgtaactttgaagcaaggtgaaatc/	GTVTLKQGEI11	orf3a	0.000545	0.213989	6	1	TGGAACTGTAACTTTGAAGCAAGGTGAAATC>T
ERR5749230	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	3513	0.005693	298	3467,20,4,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749230	26509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	10243	0.001172	0	0,10231,0,12	.	.	.	.	.	.	.	0.000852	0.946613	3	1	CT>C
ERR5749230	27294	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAT	C	18443	6.51E-4	0	18432,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF6	atc/	I32	orf6	0.000651	0.875122	2	2	CAT>C
ERR5749230	27765	PASS	C	T	16226	0.964317	2147483647	0,0,0,16216	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7b	Ctt/Ttt	L4F	orf7b	0.00109	0.970449	1	1	C>T
ERR5749230	27972	PASS	C	T	4645	0.905705	17	1,1,4592,37	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749230	28048	PASS	G	T	4608	0.926866	0	0,6,0,4600	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749230	28111	PASS	A	G	28285	0.978893	0	3,0,23659,4610	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749230	28198	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	23671	7.18E-4	0	23654,0,17,0	HIGH	NONE	FRAME_SHIFT	ORF8	tcg/	S103	orf8	0.000718	0.94386	4	2	GT>G
ERR5749230	28239	PASS	GTTGTT	G	23605	0.983478	0	398,0,23215,0	HIGH	NONE	FRAME_SHIFT	ORF8	gtttta/	VL117	orf8	0.000417	0.984998	9	2	GTTGTT>G
ERR5749230	28249	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	ATC	23281	0.001203	0	23252,0,28,0	HIGH	NONE	FRAME_SHIFT	ORF8	ttc/CTttc	F120L?	orf8	0.000443	0.063605	3	2	A>ATC
ERR5749230	28250	PASS	T	TCTG	23281	0.992741	0	148,0,23112,0	MODERATE	NONE	CODON_INSERTION	ORF8	ttc/CTGttc	F120LF	orf8	0.000494	0.993968	5	3	T>TCTG
ERR5749230	28250	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TATG	23281	7.73E-4	0	148,0,18,0	MODERATE	NONE	CODON_INSERTION	ORF8	ttc/ATGttc	F120MF	orf8	0.000494	0.993968	5	3	T>TATG
ERR5749230	28253	PASS	CA	C	23281	0.993557	0	150,0,23131,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749230	28254	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	ATC	23281	6.44E-4	0	23266,0,15,0	HIGH	NONE	FRAME_SHIFT+STOP_LOST+SPLICE_SITE_REGION	ORF8	taa/tCTaa	*122S?	orf8	0.000541	0.914398	3	2	A>ATC
ERR5749230	28270	PASS	TA	T	45060	0.995917	286	166,18,23115,21761	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749230	28271	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AA	A	45060	0.00142	163	23217,21778,63,1	.	.	.	.	.	.	.	0.000482	0.924941	3	2	AA>A
ERR5749230	28273	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	AT	45061	3.99E-4	37	23257,21779,17,1	HIGH	NONE	FRAME_SHIFT+START_LOST	N	atg/Tatg	M1Y?	N	0.000399	0.842333	4	1	A>AT
ERR5749230	28280	PASS	G	C	45061	0.941834	23	14,2,23193,21736	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749230	28281	PASS	A	T	45061	0.931227	35	19,2,23185,21740	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749230	28282	PASS	T	A	45064	0.914122	25	60,29,23149,21743	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749230	28881	PASS	G	A	8237	0.772733	1	4,2,4080,4043	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749230	28882	PASS	G	A	8237	0.828821	3	2,0,4124,4047	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749230	28883	PASS	G	C	8237	0.945854	0	0,0,4131,4101	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749230	28977	PASS	C	T	4189	0.934113	2147483647	0,0,0,4185	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749230	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	31639	0.003761	986	27421,4060,8,125	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749230	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTC	T	31639	6.01E-4	166	27449,4171,0,19	HIGH	NONE	FRAME_SHIFT	N	tct/	S255	N	0.000601	0.054952	4	2	TTC>T
ERR5749230	29172	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	27435	6.2E-4	0	27416,2,17,0	HIGH	NONE	FRAME_SHIFT	N	tgg/	W301	N	0.00062	0.92843	2	2	AT>A
ERR5749230	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	54540	0.00132	0	27377,27066,42,40	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749231	241	PASS	C	T	8099	0.86097	0	1,2,4019,4035	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749231	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	8508	0.001646	0	8484,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749231	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	8496	0.001295	0	7953,0,502,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749231	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	8494	0.001413	0	8477,0,12,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749231	657	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8530	0.001641	0	8,8496,0,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A131V	leader	0.001202	0.365979	3	1	C>T
ERR5749231	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	33849	4.43E-4	8	25311,8521,14,1	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749231	913	PASS	C	T	25311	0.892221	0	0,20,0,25251	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749231	1813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	19512	0.001281	0	0,19455,0,30	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcA	A336	nsp2	0.001022	0.152738	4	2	T>A
ERR5749231	2189	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	26466	4.91E-4	0	2,26451,0,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/	L462	nsp2	0.000491	0.960061	3	2	CT>C
ERR5749231	3037	PASS	C	T	14899	0.798778	31	2,16,7453,7295	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749231	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	7544	0.003049	593	9,7505,23,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749231	3267	PASS	C	T	26403	0.969814	0	5,0,26376,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749231	3671	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	18546	0.001024	0	9247,9161,10,10	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E318K	nsp3	0.000351	0.0625	6	2	G>A
ERR5749231	3671	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GA	18543	5.93E-4	1	9270,9259,5,6	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/aaAt	N319K?	nsp3	0.000351	0.0625	6	2	G>GA
ERR5749231	3802	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	29903	0.001003	15	20575,9298,15,15	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N363	nsp3	0.000554	0.064198	4	2	TA>T
ERR5749231	3961	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	20522	5.36E-4	0	20510,3,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K415	nsp3	0.000417	0.869983	2	2	CA>C
ERR5749231	5388	PASS	C	A	4628	0.964347	2147483647	0,0,4623,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749231	5986	PASS	C	T	11071	0.975702	0	1,0,11063,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749231	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10356	0.001545	0	0,10195,0,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749231	6706	PASS	C	T	10362	0.883999	64	2,5,0,10322	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N1329	nsp3	0.000687	0.883999	2	2	C>T
ERR5749231	7070	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	36527	0.003696	581	11737,24610,132,4	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggc/Agc	G1451S	nsp3	0.000698	0.101434	3	1	G>A
ERR5749231	8950	PASS	C	T	39304	0.970257	5	1,7,14879,24380	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I132	nsp4	0.002808	0.982604	1	1	C>T
ERR5749231	9402	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	22979	0.001306	0	11484,11461,15,15	HIGH	NONE	FRAME_SHIFT	ORF1ab	ata/	I284	nsp4	0.000453	0.058824	2	2	CTA>C
ERR5749231	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	25264	4.75E-4	31	13732,11520,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749231	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	26357	0.001897	0	25655,4,50,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749231	11082	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	26338	4.56E-4	0	26340,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000427	0.179468	2	1	TG>T
ERR5749231	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	26338	0.001747	0	26259,0,66,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749231	11287	PASS	GTCTGGTTTT	G	26341	0.996659	0	0,85,0,26253	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749231	11442	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	11599	6.9E-4	0	11591,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L158	nsp6	0.00069	0.064428	2	2	CT>C
ERR5749231	13329	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	13310	6.76E-4	0	11,13290,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	tgt/	C103	nsp10	0.000676	0.882106	2	2	CT>C
ERR5749231	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34320	0.001311	0	17145,17095,23,24	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749231	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	4364	0.006416	1214	4229,58,2,75	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749231	14408	PASS	C	T	8420	0.843112	4	1,3,4200,4154	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749231	14676	PASS	C	T	14931	0.802023	0	8,0,14879,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749231	15279	PASS	C	T	22713	0.89856	0	3,0,22666,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749231	16176	PASS	T	C	19007	0.974851	2	0,2,6545,12446	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749231	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	23590	0.001187	0	23562,0,28,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749231	19328	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	16068	6.22E-4	0	16055,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F431	ExoN	0.000459	0.937906	4	2	CT>C
ERR5749231	19524	PASS	C	T	16068	0.953697	0	0,3,0,16045	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ctC/ctT	L495	ExoN	0.000745	0.953697	2	2	C>T
ERR5749231	20507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	60387	6.29E-4	11	23038,37311,9,29	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L297	endoR	0.000629	0.062609	1	1	AT>A
ERR5749231	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23043	9.98E-4	0	22990,2,25,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749231	20987	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	56704	0.001358	0	28357,28275,38,39	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L111	MethTr	0.000276	0.056129	4	2	CT>C
ERR5749231	21123	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	57087	6.13E-4	11	28611,28441,12,23	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F156	MethTr	0.000257	0.90982	5	2	GT>G
ERR5749231	21234	PASS	C	T	28604	0.73668	0	15,0,28349,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A192	MethTr	0.000472	0.857572	5	2	C>T
ERR5749231	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	36085	0.025495	2830	18025,17032,0,920	HIGH	NONE	FRAME_SHIFT	S	ctt/Tctt	L5S?	S	0.000394	0.091869	4	1	G>GT
ERR5749231	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GTT	36085	0.002577	290	18025,17032,0,93	HIGH	NONE	FRAME_SHIFT	S	ctt/TTctt	L5F?	S	0.000394	0.091869	4	1	G>GTT
ERR5749231	21575	PASS	C	T	34784	0.864478	2	3,6,16458,17879	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749231	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	34766	0.004142	409	16694,17917,0,144	HIGH	NONE	FRAME_SHIFT	S	gtt/Tgtt	V6C?	S	0.000619	0.877942	3	2	C>CT
ERR5749231	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	34766	7.77E-4	76	16694,17917,0,27	HIGH	NONE	FRAME_SHIFT	S	gtt/TTgtt	V6L?	S	0.000619	0.877942	3	2	C>CTT
ERR5749231	21658	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18169	0.00721	0	0,18012,0,138	LOW	SILENT	SYNONYMOUS_CODING	S	ttC/ttT	F32	S	0.001649	0.937508	2	2	C>T
ERR5749231	21764	PASS	ATACATG	A	11752	0.996767	0	36,0,11714,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749231	21990	PASS	TTTA	T	11760	0.997449	0	0,30,7,11723	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749231	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	20273	0.001282	0	0,20239,0,26	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749231	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	33878	9.45E-4	0	13580,20247,14,19	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749231	23063	PASS	A	T	13569	0.863881	0	0,2,0,13498	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749231	23271	PASS	C	A	27679	0.925431	0	4,0,27652,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749231	23403	PASS	A	G	27667	0.960025	2147483647	0,0,0,27643	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749231	23604	PASS	C	A	14451	0.944156	0	7,0,14436,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749231	23709	PASS	C	T	14424	0.931295	0	0,11,0,14384	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749231	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	32364	4.02E-4	1	17905,14446,8,5	HIGH	NONE	FRAME_SHIFT	S	ttg/	L753	S	0.000334	0.080808	2	2	CT>C
ERR5749231	23817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	32364	9.27E-4	26	17875,14437,27,6	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTt/cCt	L752P	S	0.000646	0.066832	1	1	T>C
ERR5749231	24506	PASS	T	G	20241	0.974507	0	6,0,20229,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749231	24914	PASS	G	T	36913	0.815458	21	61,95,18301,18365	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Tac	D1118Y	S	0.815458	1	2	1	G>T
ERR5749231	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	25876	0.002783	103	18301,7481,81,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749231	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	18144	0.001819	485	18067,13,15,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749231	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	18111	6.63E-4	0	18098,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749231	25844	PASS	C	T	18064	0.911703	0	0,10,1,18020	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aCt/aTt	T151I	orf3a	0.001226	0.938776	1	1	C>T
ERR5749231	26509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	12619	9.51E-4	0	0,12605,0,12	.	.	.	.	.	.	.	0.000852	0.946613	3	1	CT>C
ERR5749231	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	12031	0.001081	0	0,12016,0,13	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749231	27552	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	26663	5.63E-4	0	26646,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF7a	ttt/	F54	orf7a	0.000563	0.985801	6	1	AT>A
ERR5749231	27577	PASS	C	T	26593	0.952205	0	2,0,26505,0	HIGH	NONSENSE	STOP_GAINED	ORF7a	Caa/Taa	Q62*	orf7a	0.000614	0.952205	4	2	C>T
ERR5749231	27972	PASS	C	T	10124	0.89678	0	0,0,10032,64	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749231	28048	PASS	G	T	10073	0.912836	0	0,19,0,10037	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749231	28057	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10078	0.001687	0	0,10056,0,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	gCa/gTa	A55V	orf8	0.001401	0.051498	1	1	C>T
ERR5749231	28111	PASS	A	G	34173	0.976677	8	2,3,24087,10075	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749231	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24065	9.56E-4	0	23957,3,26,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749231	28270	PASS	TA	T	46430	0.99412	593	268,13,23708,22449	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749231	28280	PASS	G	C	46319	0.92977	37	22,3,23770,22416	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749231	28281	PASS	A	T	46319	0.88223	55	42,8,23745,22439	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749231	28282	PASS	T	A	46323	0.92643	13	33,17,23753,22449	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749231	28877	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	25017	9.59E-4	0	12549,12372,22,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Agt/Tgt	S202C	N	0.000959	0.88894	1	1	A>T
ERR5749231	28878	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	25011	0.001	0	12592,12358,14,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGt/aCt	S202T	N	0.001	0.909986	3	2	G>C
ERR5749231	28881	PASS	G	A	24907	0.786325	4	4,1,12415,12210	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749231	28882	PASS	G	A	24906	0.828836	0	3,2,12487,12161	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749231	28883	PASS	G	C	24907	0.94098	6	0,2,12493,12380	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749231	28916	PASS	G	A	12621	0.878219	0	0,4,0,12539	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Ggt/Agt	G215S	N	0.878219	0.878219	1	1	G>A
ERR5749231	28977	PASS	C	T	12649	0.92537	0	0,2,2,12621	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749231	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	63162	9.82E-4	0	31738,31317,39,37	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749231	29524	PASS	T	C	23206	0.932604	0	1,3,8505,14655	LOW	SILENT	SYNONYMOUS_CODING	N	acT/acC	T417	N	0.001002	0.932604	2	1	T>C
ERR5749232	241	PASS	C	T	16564	0.863439	9	1,6,8249,8258	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749232	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	15866	0.00145	0	15842,4,23,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749232	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	15867	0.00126	0	15765,5,20,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749232	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	15867	0.004223	0	15765,5,67,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749232	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	15856	0.001514	0	14626,9,1076,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749232	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	15856	6.94E-4	0	15836,9,11,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749232	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	15854	6.94E-4	0	15831,9,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749232	600	PASS	G	A	15860	0.779004	0	0,2985,0,12857	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGc/gAc	G112D	leader	0.779004	0.779004	1	1	G>A
ERR5749232	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	40410	0.001114	0	24498,15859,28,17	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749232	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24524	0.00106	0	0,24477,0,29	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749232	913	PASS	C	T	24524	0.917754	0	0,13,0,24470	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749232	1510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	23309	0.003346	0	0,23020,0,85	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G235	nsp2	0.002159	0.937304	1	1	T>C
ERR5749232	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	80426	0.001293	2147483647	40128,37743,77,2283	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749232	3037	PASS	C	T	25734	0.825367	50	1,20,12859,12675	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749232	3267	PASS	C	T	22728	0.971841	0	1,0,22711,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749232	4255	PASS	G	A	47403	0.816446	46	30,5,23549,23454	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccG/ccA	P512	nsp3	0.001102	0.871853	2	1	G>A
ERR5749232	5388	PASS	C	A	8539	0.959012	2147483647	0,0,8537,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749232	5986	PASS	C	T	16061	0.973165	0	2,0,16047,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749232	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15547	0.001093	0	4,15310,0,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749232	6954	PASS	T	C	25273	0.817631	0	0,9,1,25124	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749232	7564	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	17913	6.7E-4	0	0,17900,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/	Y1617	nsp3	0.000586	0.056194	4	2	CT>C
ERR5749232	8602	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	15906	0.001383	0	7,15860,0,25	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtG/gtA	V16	nsp4	0.000932	0.056	3	2	G>A
ERR5749232	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	39251	5.1E-4	54	20754,18476,20,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749232	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	22563	0.002748	0	21923,6,62,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749232	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22563	0.001418	0	22496,6,36,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749232	11287	PASS	GTCTGGTTTT	G	22546	0.996186	19	1,84,2,22458	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749232	11507	PASS	G	A	37524	0.908112	9	4,0,18769,18643	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Att	V179I	nsp6	0.007744	0.914418	2	2	G>A
ERR5749232	12459	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	50309	0.001113	2	23555,26684,24,33	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T123I	nsp8	0.000658	0.986093	1	1	C>T
ERR5749232	12513	PASS	C	T	23579	0.983587	0	4,0,23561,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aTg	T141M	nsp8	0.000794	0.984064	2	2	C>T
ERR5749232	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34823	0.001321	0	17389,17335,27,27	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749232	14120	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34702	0.00121	0	17305,17290,27,28	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCa/cTa	P227L	RdRp	0.00121	0.786944	2	2	C>T
ERR5749232	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	13904	0.003884	2147483647	13519,163,7,207	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749232	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	26932	0.001003	0	13504,13421,14,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749232	14408	PASS	C	T	26932	0.846205	1	3,4,13433,13282	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749232	14676	PASS	C	T	14930	0.794374	0	6,0,14871,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749232	15279	PASS	C	T	25326	0.883242	0	3,0,25287,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749232	16176	PASS	T	C	24883	0.978861	3	0,1,12677,12192	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749232	17750	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	15238	0.001509	0	15203,2,32,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A505D	helicase	0.001509	0.881487	2	1	C>A
ERR5749232	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	30552	0.001244	0	30514,0,38,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749232	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	37452	0.001922	0	37350,5,75,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749232	21764	PASS	ATACATG	A	16277	0.997973	0	33,0,16244,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749232	21990	PASS	TTTA	T	16283	0.996131	0	0,63,5,16215	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749232	22484	PASS	G	T	12213	0.742078	12	1,6,94,11982	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gta/Tta	V308L	S	0.003485	0.765485	2	1	G>T
ERR5749232	23063	PASS	A	T	16935	0.866785	0	0,3,1,16854	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749232	23271	PASS	C	A	25423	0.918814	0	4,0,25391,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749232	23403	PASS	A	G	25419	0.965892	0	0,7,0,25388	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749232	23604	PASS	C	A	20224	0.941703	0	13,0,20198,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749232	23709	PASS	C	T	20207	0.942644	0	0,1,3,20167	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749232	24506	PASS	T	G	19711	0.975344	0	7,0,19697,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749232	24914	PASS	G	C	46205	0.957342	0	0,0,22996,23168	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749232	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	31299	0.002045	120	21736,9480,78,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749232	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	25210	0.001349	329	25128,8,22,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749232	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	25188	7.54E-4	0	25169,0,19,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749232	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	25423	0.001573	1645	24997,176,101,111	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749232	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	63667	3.46E-4	0	1,63643,0,22	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749232	26730	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	31026	4.19E-4	0	15489,15550,6,7	HIGH	NONE	FRAME_SHIFT	M	tac/	Y71	M	0.000371	0.919543	3	2	GT>G
ERR5749232	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	15607	0.001089	0	1,15581,0,17	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749232	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	15607	5.77E-4	0	1,15596,0,9	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749232	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	15608	0.001602	0	1,15576,0,25	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749232	26936	PASS	C	T	35216	0.941078	0	7,0,35171,4	LOW	SILENT	SYNONYMOUS_CODING	M	ctC/ctT	L138	M	0.001308	0.968147	2	1	C>T
ERR5749232	27972	PASS	C	T	14150	0.900353	54	3,3,14016,78	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749232	28048	PASS	G	T	14083	0.923241	0	0,14,0,14056	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749232	28111	PASS	A	G	35131	0.978054	2	5,5,21020,14085	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749232	28270	PASS	TA	T	40716	0.995088	446	197,9,20746,19770	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749232	28280	PASS	G	C	40645	0.937581	24	12,1,20792,19751	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749232	28281	PASS	A	T	40645	0.918268	26	27,8,20784,19752	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749232	28282	PASS	T	A	40648	0.907818	12	28,14,20739,19769	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749232	28881	PASS	G	A	19921	0.751267	27	13,1,9832,9763	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749232	28882	PASS	G	A	19918	0.828798	15	6,0,9976,9743	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749232	28883	PASS	G	C	19921	0.943125	6	1,4,9986,9896	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749232	28977	PASS	C	T	10166	0.920913	0	0,1,0,10137	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749232	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	44186	0.001064	166	33975,10107,11,41	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749232	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	67517	0.001022	0	33900,33490,43,43	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749232	29386	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	10480	0.00105	0	10468,1,11,0	HIGH	NONE	FRAME_SHIFT	N	aag/aaAg	K373K?	N	0.000887	0.899197	4	2	C>CA
ERR5749233	241	PASS	C	T	12227	0.859001	0	0,1,6073,6092	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749233	412	PASS	C	T	8240	0.981068	2147483647	0,0,8239,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G49	leader	0.968277	0.983986	1	1	C>T
ERR5749233	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	8235	0.003764	0	8196,8,31,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749233	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	8239	0.001699	0	8103,12,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749233	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	8239	0.003398	0	8103,12,28,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749233	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	8239	0.009467	0	8103,12,78,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749233	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	8234	0.002065	2	7455,15,555,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749233	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	8234	0.003522	0	8190,15,29,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749233	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	8237	0.002185	32	8191,15,16,2	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttatg/gtg	VM84V	leader	0.000554	0.991848	4	1	GTTA>G
ERR5749233	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	8236	0.001214	0	8200,19,10,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749233	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	31725	7.25E-4	28	23459,8233,23,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749233	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	31725	4.1E-4	0	23364,8218,10,3	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749233	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	31725	0.003593	37	23364,8218,101,13	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749233	751	PASS	C	T	23489	0.943591	0	5,0,23471,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N162	leader	0.000662	0.943591	2	2	C>T
ERR5749233	913	PASS	C	T	23479	0.91026	0	0,14,0,23430	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749233	1813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	16042	0.001184	0	0,16011,0,23	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcA	A336	nsp2	0.001022	0.152738	4	2	T>A
ERR5749233	3037	PASS	C	T	14750	0.800407	33	0,11,7381,7246	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749233	3267	PASS	C	T	23624	0.969946	2147483647	0,0,23604,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749233	3802	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	30460	6.89E-4	3	21521,8918,13,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N363	nsp3	0.000554	0.064198	4	2	TA>T
ERR5749233	5388	PASS	C	A	3660	0.960383	2147483647	0,0,3658,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749233	5986	PASS	C	T	9508	0.97318	0	2,0,9495,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749233	6185	PASS	C	T	9511	0.954999	105	3,0,1,9504	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cac/Tac	H1156Y	nsp3	0.910265	0.954999	1	1	C>T
ERR5749233	6954	PASS	T	C	22162	0.824519	0	0,9,3,22041	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749233	9286	PASS	C	T	13772	0.954908	0	3,0,13758,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N244	nsp4	0.949239	0.971567	1	1	C>T
ERR5749233	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	26597	5.64E-4	47	12809,13770,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749233	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	23285	0.001632	0	23198,0,57,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749233	11199	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	46351	8.41E-4	0	23013,23144,20,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCc/gTc	A76V	nsp6	0.000309	0.056758	3	2	C>T
ERR5749233	11287	PASS	GTCTGGTTTT	G	23278	0.994759	22	1,120,0,23156	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749233	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	34469	0.001364	22	24742,9651,42,5	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749233	12269	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	26447	4.54E-4	0	26434,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aag/	K61	nsp8	0.000434	0.213333	2	1	GA>G
ERR5749233	12741	PASS	C	T	31110	0.962552	0	0,0,15533,15559	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T19I	nsp9	0.000486	0.962552	2	2	C>T
ERR5749233	13115	PASS	C	T	11241	0.918068	0	1,0,11221,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L31	nsp10	0.001806	0.922167	1	1	C>T
ERR5749233	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	40300	9.93E-4	1	20130,20058,23,25	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749233	14407	PASS	C	T	22317	0.799973	17	1,8,11248,10846	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cct/Tct	P323S	RdRp	0.000388	0.799973	2	2	C>T
ERR5749233	14408	PASS	C	T	22317	0.828427	9	1,5,11252,10816	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749233	14676	PASS	C	T	13995	0.766488	0	6,0,13953,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749233	15279	PASS	C	T	21873	0.905409	0	2,0,21848,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749233	16176	PASS	T	C	18436	0.979714	0	0,0,6627,11800	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749233	17615	PASS	A	G	13168	0.931728	0	0,0,2,13138	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749233	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	19591	8.68E-4	0	19574,0,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749233	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21431	0.002706	0	21356,1,59,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749233	20091	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	21386	4.68E-4	0	4,21372,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	caa/Acaa	Q159T?	endoR	0.000368	0.051583	1	1	C>CA
ERR5749233	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	31975	9.7E-4	2	15640,15951,17,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749233	21764	PASS	ATACATG	A	10568	0.99612	0	41,0,10527,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749233	21990	PASS	TTTA	T	10581	0.997826	0	0,23,12,10546	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749233	22432	PASS	C	T	7987	0.699261	0	1,0,7871,1	LOW	SILENT	SYNONYMOUS_CODING	S	gaC/gaT	D290	S	0.002959	0.755028	1	1	C>T
ERR5749233	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29763	0.001142	0	11987,17698,14,22	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749233	23063	PASS	A	T	11997	0.862049	0	0,4,2,11932	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749233	23271	PASS	C	A	26297	0.91885	0	4,0,26263,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749233	23403	PASS	A	G	26291	0.9725	0	0,9,0,26267	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749233	23604	PASS	C	A	12766	0.946734	0	10,0,12750,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749233	23709	PASS	C	T	12746	0.920995	0	0,7,3,12704	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749233	24127	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TTTG	26739	5.98E-4	30	10103,16636,0,16	MODERATE	NONE	CODON_INSERTION	S	aac/TTGaac	N856LN	S	0.000324	0.111888	4	1	T>TTTG
ERR5749233	24506	PASS	T	G	18529	0.972691	0	9,0,18518,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749233	24914	PASS	G	C	33103	0.957859	3	1,0,16494,16585	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749233	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	19461	6.17E-4	0	19449,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749233	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	19634	0.001324	1036	19252,148,125,80	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749233	25854	PASS	C	T	19436	0.939185	0	0,1,3,19403	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	taC/taT	Y154	orf3a	0.000876	0.939185	1	1	C>T
ERR5749233	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	38288	5.75E-4	0	4,38259,0,22	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749233	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	10767	0.002322	0	3,10725,0,25	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749233	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	10767	0.001115	0	3,10750,0,12	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749233	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	10767	0.007337	0	2,10676,0,79	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749233	27065	PASS	G	A	31135	0.763803	0	0,4,15,30752	LOW	SILENT	SYNONYMOUS_CODING	M	ttG/ttA	L181	M	0.001008	0.897124	3	2	G>A
ERR5749233	27972	PASS	C	T	9292	0.914981	0	0,0,9192,77	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749233	28048	PASS	G	T	9232	0.919086	0	0,11,0,9217	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749233	28111	PASS	A	G	32909	0.977939	9	3,4,23659,9232	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749233	28198	PASS	G	T	23668	0.935271	0	8,0,23607,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tGt/tTt	C102F	orf8	0.000718	0.94386	4	2	G>T
ERR5749233	28270	PASS	TA	T	45937	0.993469	715	298,10,23281,22356	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749233	28271	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AA	A	45933	0.001459	194	23501,22368,67,0	.	.	.	.	.	.	.	0.000482	0.924941	3	2	AA>A
ERR5749233	28280	PASS	G	C	45844	0.933535	41	15,0,23408,22338	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749233	28281	PASS	A	T	45844	0.911373	32	26,6,23397,22341	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749233	28282	PASS	T	A	45846	0.909523	5	23,15,23345,22351	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749233	28321	PASS	G	T	23667	0.941691	0	0,10,20,23576	LOW	SILENT	SYNONYMOUS_CODING	N	acG/acT	T16	N	0.00045	0.947809	3	2	G>T
ERR5749233	28406	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTACCCAATA	T	23687	5.07E-4	0	16,23656,0,12	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	N	ttacccaataat/tat	LPNN45Y	N	0.00043	0.921074	3	2	TTACCCAATA>T
ERR5749233	28407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TACCCAATA	T	23687	6.75E-4	0	16,23655,0,16	HIGH	NONE	FRAME_SHIFT	N	cccaataat/	PNN46	N	0.000382	0.179673	1	1	TACCCAATA>T
ERR5749233	28881	PASS	G	A	19959	0.769778	4	4,1,9911,9797	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749233	28882	PASS	G	A	19959	0.835012	24	9,0,9992,9767	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749233	28883	PASS	G	C	19959	0.940478	0	3,2,10015,9919	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749233	28977	PASS	C	T	10185	0.910947	0	0,6,1,10146	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749233	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	53998	7.96E-4	0	27139,26788,24,25	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749233	29642	PASS	C	T	17404	0.934555	3	3,2,7039,10321	HIGH	NONSENSE	STOP_GAINED	ORF10	Caa/Taa	Q29*	orf10	0.001806	0.941176	2	2	C>T
ERR5749234	239	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTCG	T	5646	0.001417	0	2813,2823,4,4	.	.	.	.	.	.	.	0.000495	0.25	4	1	TTCG>T
ERR5749234	241	PASS	C	T	5645	0.869265	0	0,0,2807,2814	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749234	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	9708	0.007417	0	9605,30,72,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749234	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	9712	0.001133	0	9571,36,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749234	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	9712	0.001442	0	9571,36,14,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749234	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	9712	0.007311	0	9571,36,71,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749234	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	9715	0.001853	9	8841,42,616,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749234	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	9715	0.003088	0	9643,42,30,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749234	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	9717	0.002984	0	9632,44,29,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749234	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATGGTTG	T	9717	9.26E-4	13	9632,44,8,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	atggttgag/	MVE85	leader	0.000587	0.476744	4	1	TATGGTTG>T
ERR5749234	673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTTA	21958	0.001366	106	12265,9663,0,30	MODERATE	NONE	CODON_INSERTION	ORF1ab	ggc/TTAggc	G137LG	leader	0.000454	0.602236	3	2	C>CTTA
ERR5749234	673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	21958	4.55E-4	21	12264,9684,1,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggc/	G137	leader	0.000454	0.602236	3	2	CG>C
ERR5749234	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	21928	0.001368	15	12237,9656,23,7	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749234	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	21928	4.56E-4	15	12203,9640,2,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749234	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	21928	0.003147	43	12203,9640,55,14	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749234	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12258	0.001387	0	0,12230,0,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749234	913	PASS	C	T	12259	0.906028	0	0,8,0,12230	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749234	2185	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	11932	6.7E-4	0	5,11919,0,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L462S?	nsp2	0.000441	0.963529	4	3	G>GT
ERR5749234	3037	PASS	C	T	13726	0.826825	21	4,16,6853,6760	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749234	3267	PASS	C	T	13508	0.971276	0	2,0,13499,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749234	4529	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTTTAC	T	9636	9.34E-4	0	4,9622,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	tacttt/	YF605	nsp3	0.000527	0.402778	3	1	TTTTAC>T
ERR5749234	4832	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26922	0.002303	0	13413,13370,41,41	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L705	nsp3	0.000542	0.727166	3	2	C>T
ERR5749234	5388	PASS	C	A	4617	0.959281	2147483647	0,0,4614,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749234	5497	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	4613	0.001517	0	0,4606,0,7	HIGH	NONE	FRAME_SHIFT	ORF1ab	aga/	R928	nsp3	0.000964	0.897745	3	2	CA>C
ERR5749234	5986	PASS	C	T	9446	0.977133	0	1,0,9442,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749234	6954	PASS	T	C	15270	0.802227	0	0,12,1,15155	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749234	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	17200	6.98E-4	10	13127,4061,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749234	10252	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	15511	6.45E-4	0	15501,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L67	3Cpro	0.000645	0.943062	2	2	CT>C
ERR5749234	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	18240	0.00307	0	18147,0,67,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749234	11287	PASS	GTCTGGTTTT	G	18244	0.996054	0	0,72,0,18172	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749234	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	16291	0.00135	0	16240,0,24,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749234	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24254	0.001402	0	12114,12078,18,19	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749234	14098	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTGATTTCATACAAACCACGCCA	G	12407	8.06E-4	0	12299,97,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtgatttcatacaaaccacgccaggt/	GDFIQTTPG220	RdRp	0.000806	0.065317	4	2	GGTGATTTCATACAAACCACGCCA>G
ERR5749234	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	5278	0.005305	1255	5129,69,1,75	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749234	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	10191	0.004906	1	5097,5047,27,23	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749234	14408	PASS	C	T	10191	0.851438	3	0,1,5081,4976	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749234	14676	PASS	C	T	8541	0.766538	0	3,0,8502,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749234	15279	PASS	C	T	13590	0.933701	0	2,0,13570,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749234	16176	PASS	T	C	14751	0.978374	0	0,0,7115,7631	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749234	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	23645	5.5E-4	0	23632,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749234	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15764	0.001522	0	15717,0,26,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749234	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16099	0.001429	0	16055,0,24,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749234	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23190	0.001251	2	11348,11556,15,19	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749234	21764	PASS	ATACATG	A	10183	0.997447	0	26,0,10157,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749234	21990	PASS	TTTA	T	10185	0.996465	0	0,36,3,10146	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749234	22290	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	16320	5.51E-4	0	0,16311,0,9	HIGH	NONE	FRAME_SHIFT	S	tta/	L244	S	0.000389	0.578006	2	2	CT>C
ERR5749234	22712	PASS	C	T	24814	0.842266	6	3,7,12370,12296	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Cct/Tct	P384S	S	0.001254	0.842266	2	2	C>T
ERR5749234	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	12507	0.001599	0	0,12475,0,20	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749234	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24560	9.36E-4	1	12018,12484,13,11	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749234	23063	PASS	A	T	12027	0.867881	0	0,2,0,11969	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749234	23271	PASS	C	A	13384	0.918335	0	2,0,13353,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749234	23403	PASS	A	G	13374	0.961941	0	0,2,2,13354	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749234	23604	PASS	C	A	12237	0.954809	0	4,0,12225,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749234	23709	PASS	C	T	12227	0.943322	0	0,2,3,12206	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749234	24506	PASS	T	G	13635	0.977998	0	4,0,13630,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749234	24914	PASS	G	C	33087	0.955874	0	0,0,16480,16583	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749234	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	21152	0.001324	22	16046,5063,35,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749234	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	9658	0.003003	363	9585,26,11,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749234	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	9621	9.35E-4	0	9612,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749234	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	33749	7.41E-4	0	0,33712,0,25	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749234	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTAATCCAGTA	T	33749	3.56E-4	0	0,33712,0,12	MODERATE	NONE	CODON_DELETION	ORF3a	gttaatccagta/	VNPV256	orf3a	0.000249	0.122153	5	2	TGTTAATCCAGTA>T
ERR5749234	26159	PASS	T	C	33753	0.053032	0	0,31489,0,2101	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	gTt/gCt	V256A	orf3a	0.000311	0.053032	2	2	T>C
ERR5749234	26509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	8215	8.52E-4	0	4,8204,0,7	.	.	.	.	.	.	.	0.000852	0.946613	3	1	CT>C
ERR5749234	26730	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	21396	7.48E-4	0	10674,10721,8,8	HIGH	NONE	FRAME_SHIFT	M	tac/	Y71	M	0.000371	0.919543	3	2	GT>G
ERR5749234	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	10776	0.001206	0	2,10760,0,13	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749234	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	10774	0.004177	0	0,10724,0,45	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749234	27741	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	16813	6.54E-4	0	9,16792,0,11	HIGH	NONE	FRAME_SHIFT	ORF7a	aga/	R118	orf7a	0.000363	0.954278	3	2	CA>C
ERR5749234	27816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	23642	5.08E-4	1	6819,16809,4,8	HIGH	NONE	FRAME_SHIFT	ORF7b	tta/	L22	orf7b	0.000423	0.053007	1	1	GT>G
ERR5749234	27972	PASS	C	T	6841	0.924426	21	1,1,6791,26	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749234	28048	PASS	G	T	6815	0.913866	0	0,10,0,6803	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749234	28111	PASS	A	G	23875	0.979267	3	1,1,17042,6821	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749234	28239	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTGT	G	17045	0.001232	0	17012,2,21,0	HIGH	NONE	FRAME_SHIFT	ORF8	gtttta/	VL117	orf8	0.000417	0.984998	9	2	GTTGT>G
ERR5749234	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17036	0.001878	0	16942,4,34,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749234	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	17032	7.63E-4	0	17019,4,13,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749234	28270	PASS	TA	T	33010	0.994547	379	176,10,16812,16018	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749234	28280	PASS	G	C	32937	0.934481	5	10,5,16856,16001	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749234	28281	PASS	A	T	32937	0.912044	31	17,2,16844,16010	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749234	28282	PASS	T	A	32939	0.903701	0	10,9,16810,16017	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749234	28881	PASS	G	A	8444	0.718854	21	7,0,4124,4149	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749234	28882	PASS	G	A	8443	0.812744	3	2,0,4220,4122	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749234	28883	PASS	G	C	8444	0.939602	2	1,2,4233,4203	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749234	28977	PASS	C	T	4317	0.933287	2147483647	0,0,0,4308	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749234	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	50476	0.00103	0	25366,25027,33,31	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749234	29421	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7504	0.003332	0	7473,0,25,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	cCg/cTg	P383L	N	0.002705	0.052892	2	2	C>T
ERR5749235	241	PASS	C	T	13874	0.860819	0	0,1,6895,6924	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749235	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	10597	7.55E-4	0	10591,0,8,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749235	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	10597	0.00217	0	10568,0,23,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749235	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10589	0.002644	0	9847,2,689,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749235	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	27350	0.00106	16	16711,10608,24,5	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749235	823	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16722	0.001435	0	16674,5,28,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V6	nsp2	0.001213	0.901722	1	1	C>T
ERR5749235	913	PASS	C	T	16725	0.912167	0	0,16,0,16686	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749235	1684	PASS	C	T	16528	0.973136	0	1,0,16517,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I293	nsp2	0.000638	0.973136	2	2	C>T
ERR5749235	3037	PASS	C	T	11338	0.822544	21	0,7,5671,5593	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749235	3267	PASS	C	T	14508	0.970706	0	3,0,14498,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749235	3832	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	18512	0.001026	0	18491,2,19,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L373	nsp3	0.000689	0.327273	4	2	CT>C
ERR5749235	4255	PASS	G	A	29353	0.768882	51	18,0,14591,14450	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccG/ccA	P512	nsp3	0.001102	0.871853	2	1	G>A
ERR5749235	5388	PASS	C	A	3427	0.9644	2147483647	0,0,3427,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749235	5986	PASS	C	T	3012	0.972444	0	1,0,3009,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749235	6762	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16955	0.001474	2	10004,6904,13,12	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T1348I	nsp3	0.001474	0.966761	2	1	C>T
ERR5749235	6954	PASS	T	C	9986	0.834969	0	0,2,0,9935	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749235	8084	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	18189	7.15E-4	0	18178,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1790	nsp3	0.000543	0.923413	4	2	GA>G
ERR5749235	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	16536	0.002177	0	16478,0,51,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749235	11104	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	16535	0.001331	0	16451,0,22,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccT/ccC	P44	nsp6	0.000866	0.675414	2	1	T>C
ERR5749235	11287	PASS	GTCTGGTTTT	G	16523	0.997034	0	0,49,0,16474	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749235	11442	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	9586	8.35E-4	0	9578,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L158	nsp6	0.00069	0.064428	2	2	CT>C
ERR5749235	11507	PASS	G	A	19081	0.909386	0	2,1,9544,9487	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Att	V179I	nsp6	0.007744	0.914418	2	2	G>A
ERR5749235	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	22693	0.00119	6	13064,9578,19,8	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749235	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	15353	0.001759	0	15303,0,29,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749235	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22313	0.001479	0	11136,11106,18,18	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749235	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12855	0.003423	2599	12610,97,4,141	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749235	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	25124	5.57E-4	0	12594,12530,7,7	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749235	14408	PASS	C	T	25124	0.844651	2	16,19,12525,12386	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749235	14676	PASS	C	T	9254	0.828074	0	2,0,9237,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749235	15279	PASS	C	T	18254	0.884025	0	6,0,18218,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749235	16176	PASS	T	C	16147	0.98012	0	0,1,7436,8704	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749235	16794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	31453	9.86E-4	3	16419,14989,20,14	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	cgT/cgC	R186	helicase	0.000354	0.077626	2	2	T>C
ERR5749235	17058	PASS	G	A	16442	0.976037	2147483647	0,0,0,16431	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atA	M274I	helicase	0.00262	0.976037	2	1	G>A
ERR5749235	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	19234	0.001144	0	19212,0,22,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749235	19160	PASS	C	T	13380	0.871076	0	0,6,0,13348	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S374F	ExoN	0.001215	0.871076	1	1	C>T
ERR5749235	19175	PASS	A	G	13388	0.961309	0	0,2,0,13377	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gAt/gGt	D379G	ExoN	0.961309	0.961309	1	1	A>G
ERR5749235	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13652	0.001978	0	6681,6805,14,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749235	21764	PASS	ATACATG	A	6621	0.997432	0	17,0,6604,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749235	21990	PASS	TTTA	T	6624	0.996226	0	0,25,3,6596	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749235	23063	PASS	A	T	7195	0.871716	0	0,1,0,7159	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749235	23271	PASS	C	A	19343	0.916042	0	1,0,19314,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749235	23403	PASS	A	G	19341	0.976733	0	0,3,0,19325	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749235	23604	PASS	C	A	8498	0.939044	0	3,0,8489,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749235	23709	PASS	C	T	8483	0.936461	0	0,3,0,8469	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749235	24445	PASS	G	A	13855	0.983905	0	1,0,13851,0	LOW	SILENT	SYNONYMOUS_CODING	S	acG/acA	T961	S	0.007263	0.983905	2	1	G>A
ERR5749235	24506	PASS	T	G	13852	0.972639	0	3,0,13847,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749235	24914	PASS	G	C	31664	0.959639	0	0,1,15777,15858	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749235	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	16681	0.001918	376	16592,12,17,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749235	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	16766	0.001551	800	16514,98,74,55	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749235	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	10434	0.00115	0	0,10420,0,12	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749235	27741	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	14018	7.13E-4	0	1,14007,0,10	HIGH	NONE	FRAME_SHIFT	ORF7a	aga/	R118	orf7a	0.000363	0.954278	3	2	CA>C
ERR5749235	27972	PASS	C	T	6052	0.915069	77	3,4,6003,27	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749235	28001	PASS	G	T	11919	0.830607	17	22,42,5881,5962	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ccG/ccT	P36	orf8	0.00085	0.830607	2	1	G>T
ERR5749235	28048	PASS	G	T	6024	0.931773	0	0,1,0,6019	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749235	28111	PASS	A	G	20600	0.980291	0	2,1,14562,6029	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749235	28270	PASS	TA	T	28290	0.995334	289	131,7,14375,13783	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749235	28280	PASS	G	C	28237	0.941601	7	7,2,14404,13772	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749235	28281	PASS	A	T	28237	0.919538	16	13,3,14398,13778	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749235	28282	PASS	T	A	28237	0.916103	21	17,4,14369,13781	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749235	28732	PASS	C	T	25986	0.966905	0	2,5,8565,17395	LOW	SILENT	SYNONYMOUS_CODING	N	aaC/aaT	N153	N	0.000892	0.966905	2	2	C>T
ERR5749235	28881	PASS	G	A	16803	0.749747	24	8,0,8228,8273	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749235	28882	PASS	G	A	16803	0.838957	11	9,2,8396,8263	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749235	28883	PASS	G	C	16803	0.944355	0	0,0,8421,8368	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749235	28977	PASS	C	T	8568	0.928688	0	0,4,0,8548	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749235	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	54287	0.001124	0	27240,26949,38,36	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749236	239	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTC	T	12372	0.001293	0	6164,6193,8,8	.	.	.	.	.	.	.	0.000495	0.25	4	1	TTC>T
ERR5749236	241	PASS	C	T	12374	0.850897	9	1,5,6145,6137	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749236	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	12281	0.002199	0	12249,6,27,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749236	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	12280	6.51E-4	0	12178,5,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749236	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	12280	0.001059	0	12178,5,13,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749236	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	12280	0.005945	14	12178,5,72,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749236	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	12272	0.002445	65	12236,3,27,3	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749236	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	12270	0.001059	0	12244,5,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749236	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	12269	0.00106	0	12239,6,13,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749236	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	33734	7.41E-4	46	21416,12293,25,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749236	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	33734	0.001838	63	21373,12284,57,5	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749236	745	PASS	C	T	21443	0.43063	0	11415,1,10014,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N160	leader	0.001671	0.915927	1	1	C>T
ERR5749236	841	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	42800	7.71E-4	0	21384,21327,18,17	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G12	nsp2	0.000771	0.932538	2	1	C>T
ERR5749236	843	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTG	C	42798	3.04E-4	0	21412,21375,7,6	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctgat/	PD13	nsp2	0.000301	0.050923	4	2	CTG>C
ERR5749236	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21434	0.001166	0	0,21389,0,29	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749236	913	PASS	C	T	21436	0.913697	0	0,8,0,21399	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749236	967	PASS	T	C	35221	0.975384	0	3,4,13771,21427	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caT/caC	H54	nsp2	0.973649	0.978486	1	1	T>C
ERR5749236	2166	PASS	A	G	27607	0.938349	0	0,3,0,27552	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K454R	nsp2	0.932132	0.94762	1	1	A>G
ERR5749236	3037	PASS	C	T	17375	0.810705	44	1,18,8677,8534	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749236	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	8783	0.002277	544	5,8756,20,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749236	3267	PASS	C	T	21034	0.972711	2147483647	0,0,21023,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749236	4255	PASS	G	A	37352	0.860382	61	31,3,18563,18577	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccG/ccA	P512	nsp3	0.001102	0.871853	2	1	G>A
ERR5749236	5388	PASS	C	A	5522	0.958348	2147483647	0,0,5519,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749236	5986	PASS	C	T	11141	0.973701	0	1,0,11132,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749236	6954	PASS	T	C	22055	0.814736	0	0,2,1,21915	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749236	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	27521	9.81E-4	69	15192,12302,27,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749236	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22301	0.00139	0	22232,3,33,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749236	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	22291	0.001122	0	22240,0,41,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749236	11287	PASS	GTCTGGTTTT	G	22298	0.997354	0	0,59,1,22238	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749236	11507	PASS	G	A	25961	0.889488	15	6,0,13006,12839	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Att	V179I	nsp6	0.007744	0.914418	2	2	G>A
ERR5749236	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	35713	7.56E-4	3	22602,13059,16,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749236	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34452	0.001509	0	17202,17145,29,31	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749236	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10092	0.004756	2404	9862,84,4,135	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749236	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	19648	0.00168	0	9845,9779,17,16	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749236	14408	PASS	C	T	19648	0.831993	0	4,4,9802,9663	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749236	14599	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14000	0.002929	0	13950,3,42,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L387	RdRp	0.000639	0.922766	3	2	C>T
ERR5749236	14676	PASS	C	T	13993	0.746659	0	5,0,13928,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749236	15279	PASS	C	T	22823	0.954958	0	4,0,22809,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749236	16176	PASS	T	C	21199	0.981131	0	1,1,8974,12206	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749236	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	23360	8.13E-4	0	23341,0,19,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749236	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25237	0.001823	0	25166,0,52,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749236	21764	PASS	ATACATG	A	11722	0.996673	0	39,0,11683,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749236	21990	PASS	TTTA	T	11731	0.996931	0	0,36,9,11686	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749236	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29839	0.001039	1	13187,16599,15,16	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749236	23063	PASS	A	T	13187	0.86244	0	0,6,0,13112	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749236	23271	PASS	C	A	24051	0.923246	0	2,0,24021,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749236	23403	PASS	A	G	24047	0.963197	0	0,2,0,24022	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749236	23604	PASS	C	A	14417	0.947284	0	14,0,14389,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749236	23709	PASS	C	T	14393	0.936914	0	0,5,3,14359	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749236	23758	PASS	C	T	14420	0.953329	2147483647	0,0,0,14411	LOW	SILENT	SYNONYMOUS_CODING	S	acC/acT	T732	S	0.001489	0.964055	1	1	C>T
ERR5749236	24506	PASS	T	G	19792	0.975546	0	7,0,19781,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749236	24914	PASS	G	C	36998	0.957106	0	0,0,18441,18530	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749236	25553	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16854	0.015011	0	0,16548,0,299	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	gCt/gTt	A54V	orf3a	0.001165	0.868131	3	2	C>T
ERR5749236	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	16947	0.001416	694	16665,98,113,53	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749236	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	42247	4.02E-4	0	1,42226,0,17	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749236	26416	PASS	G	T	25252	0.903928	1	30,27,12421,12737	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	Gtt/Ttt	V58F	E	0.000457	0.913418	2	2	G>T
ERR5749236	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	12215	0.004585	0	0,12151,0,56	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749236	27532	PASS	C	T	21197	0.979101	240	4,7,21175,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Cat/Tat	H47Y	orf7a	0.001165	0.982473	2	1	C>T
ERR5749236	27972	PASS	C	T	9034	0.90093	33	3,2,8939,62	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749236	28048	PASS	G	T	8978	0.925485	0	0,13,0,8965	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749236	28111	PASS	A	G	30537	0.979173	12	7,8,21529,8984	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749236	28270	PASS	TA	T	41579	0.995166	372	191,15,21273,20105	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749236	28280	PASS	G	C	41507	0.934613	21	11,1,21333,20090	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749236	28281	PASS	A	T	41507	0.913701	11	18,8,21309,20088	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749236	28282	PASS	T	A	41511	0.900243	4	22,14,21266,20106	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749236	28881	PASS	G	A	17066	0.758174	9	6,1,8440,8377	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749236	28882	PASS	G	A	17065	0.825022	18	7,0,8544,8361	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749236	28883	PASS	G	C	17065	0.944858	0	2,2,8558,8485	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749236	28977	PASS	C	T	8690	0.932911	0	0,2,0,8676	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749236	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	56909	0.001054	0	28575,28231,38,36	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749236	29781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	7668	0.002347	0	0,7647,0,21	.	.	.	.	.	.	.	0.00173	0.972321	2	1	G>T
ERR5749237	222	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6393	0.008603	0	3158,3158,32,32	.	.	.	.	.	.	.	0.002134	0.864859	1	1	C>T
ERR5749237	239	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTC	T	6384	0.001253	0	3182,3194,4,4	.	.	.	.	.	.	.	0.000495	0.25	4	1	TTC>T
ERR5749237	241	PASS	C	T	6383	0.86041	0	0,0,3174,3167	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749237	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	9234	0.001624	0	8702,0,510,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749237	635	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9259	0.00216	0	0,9235,0,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgt/Tgt	R124C	leader	0.00148	0.880435	1	1	C>T
ERR5749237	657	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9260	0.001836	0	0,9243,0,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A131V	leader	0.001202	0.365979	3	1	C>T
ERR5749237	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22866	0.001006	12	13585,9249,19,5	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L140	leader	0.000316	0.135802	3	2	C>T
ERR5749237	913	PASS	C	T	13595	0.916808	0	0,9,0,13568	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749237	1191	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11727	0.001535	0	0,11698,0,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCa/cTa	P129L	nsp2	0.000749	0.916048	3	2	C>T
ERR5749237	2232	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24618	0.001056	5	8857,15716,8,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A476V	nsp2	0.000499	0.381237	2	2	C>T
ERR5749237	3037	PASS	C	T	12581	0.815039	24	1,11,6284,6197	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749237	3267	PASS	C	T	14458	0.967077	2147483647	0,0,14453,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749237	3961	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	11930	6.71E-4	0	11924,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K415	nsp3	0.000417	0.869983	2	2	CA>C
ERR5749237	4280	PASS	G	A	14054	0.888075	0	0,1,0,14001	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gta/Ata	V521I	nsp3	0.002822	0.896067	2	1	G>A
ERR5749237	5388	PASS	C	A	3789	0.964634	2147483647	0,0,3787,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749237	5497	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	3787	0.001584	0	0,3780,0,6	HIGH	NONE	FRAME_SHIFT	ORF1ab	aga/	R928	nsp3	0.000964	0.897745	3	2	CA>C
ERR5749237	5986	PASS	C	T	8642	0.976741	0	1,0,8632,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749237	6954	PASS	T	C	16136	0.825979	0	0,8,0,16049	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749237	7423	PASS	C	T	12746	0.966342	0	3,0,12713,3	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1568	nsp3	0.000941	0.970543	2	2	C>T
ERR5749237	8084	PASS	G	A	17862	0.923413	0	9,0,17837,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E1789K	nsp3	0.000543	0.923413	4	2	G>A
ERR5749237	8084	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GA	17862	0.020994	0	17483,0,375,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctc/Actc	L1791T?	nsp3	0.000543	0.923413	4	2	G>GA
ERR5749237	8964	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	12390	0.001211	0	12373,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K138	nsp4	0.000553	0.981649	4	2	CA>C
ERR5749237	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	16930	0.001654	43	11512,5390,28,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749237	10323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	14116	0.001346	0	0,14055,0,19	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749237	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	19175	0.002973	0	19100,0,71,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749237	11104	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	19172	0.001148	0	19079,0,24,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccT/ccC	P44	nsp6	0.000866	0.675414	2	1	T>C
ERR5749237	11152	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19159	0.001357	0	19095,0,26,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V60	nsp6	0.000678	0.974465	2	2	C>T
ERR5749237	11287	PASS	GTCTGGTTTT	G	19178	0.998279	0	0,33,0,19145	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749237	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25103	0.001394	0	12535,12498,19,19	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749237	13554	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	12555	6.37E-4	0	0,12547,0,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N39	RdRp	0.000637	0.920199	2	2	CA>C
ERR5749237	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	5319	0.003948	1579	5163,62,0,93	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749237	14408	PASS	C	T	10268	0.839014	0	1,1,5121,5075	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749237	14676	PASS	C	T	10000	0.8048	0	2,0,9971,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749237	15279	PASS	C	T	15382	0.956313	0	1,0,15370,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749237	15371	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30686	9.12E-4	1	15311,15280,19,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aTg	T644M	RdRp	0.00056	0.786959	4	2	C>T
ERR5749237	16176	PASS	T	C	14867	0.982108	7	2,0,5974,8887	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749237	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAA	G	15956	9.4E-4	0	15915,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GAA>G
ERR5749237	17615	PASS	A	G	12138	0.909705	0	0,1,0,12104	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749237	18501	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	21430	5.13E-4	0	0,21419,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K155	ExoN	0.000336	0.857143	4	2	CA>C
ERR5749237	18658	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	20745	6.75E-4	0	20724,7,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tgt/	C207	ExoN	0.000507	0.115741	3	2	TG>T
ERR5749237	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	20738	0.001157	0	20714,0,24,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749237	18800	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	41396	7.01E-4	0	20678,20601,17,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cAa/cGa	Q254R	ExoN	0.000701	0.072445	1	1	A>G
ERR5749237	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	19440	6.69E-4	0	0,19427,0,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749237	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15208	0.001315	0	15178,0,21,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749237	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24409	0.003441	0	11931,12136,47,48	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749237	21764	PASS	ATACATG	A	10003	0.997101	0	29,0,9974,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749237	21990	PASS	TTTA	T	10007	0.996802	0	0,32,3,9972	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749237	22227	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	18266	4.93E-4	0	0,18257,0,9	HIGH	NONE	FRAME_SHIFT	S	tta/	L223	S	0.000419	0.824305	2	2	CT>C
ERR5749237	22290	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	18273	5.47E-4	0	2,18261,0,10	HIGH	NONE	FRAME_SHIFT	S	tta/	L244	S	0.000389	0.578006	2	2	CT>C
ERR5749237	23063	PASS	A	T	10957	0.864379	0	0,3,0,10905	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749237	23271	PASS	C	A	17044	0.920793	0	4,0,17021,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749237	23403	PASS	A	G	17035	0.966187	0	0,4,0,17018	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749237	23604	PASS	C	A	11680	0.943579	0	11,0,11662,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749237	23709	PASS	C	T	11658	0.932321	0	0,6,1,11633	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749237	24506	PASS	T	G	14039	0.971864	0	4,0,14032,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749237	24914	PASS	G	C	32181	0.956745	0	0,0,16035,16117	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749237	25782	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9200	0.001739	0	9152,0,17,0	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	tgC/tgT	C130	orf3a	0.000916	0.955348	1	1	C>T
ERR5749237	26333	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9491	0.00158	0	9469,0,15,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	aCa/aTa	T30I	E	0.00158	0.943221	1	1	C>T
ERR5749237	26730	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	20321	4.92E-4	0	10142,10179,5,5	HIGH	NONE	FRAME_SHIFT	M	tac/	Y71	M	0.000371	0.919543	3	2	GT>G
ERR5749237	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	10217	8.81E-4	0	0,10208,0,9	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749237	26895	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28909	0.001072	0	28866,0,31,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Cat/Tat	H125Y	M	0.000874	0.97046	1	1	C>T
ERR5749237	27078	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28897	0.001038	0	4,28847,0,32	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Cgt/Tgt	R186C	M	0.000415	0.05783	2	2	C>T
ERR5749237	27567	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTTTAGCACTCAATTTGCT	C	17376	5.18E-4	0	17362,0,9,0	MODERATE	NONE	CODON_DELETION	ORF7a	agcactcaatttgctttt/	STQFAF60	orf7a	0.000449	0.998291	4	1	CTTTAGCACTCAATTTGCT>C
ERR5749237	27972	PASS	C	T	6334	0.903536	0	0,0,6292,30	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749237	28048	PASS	G	T	6312	0.91936	0	0,5,0,6303	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749237	28111	PASS	A	G	25129	0.979068	2	3,0,18801,6316	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749237	28250	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TCTG	18799	6.92E-4	0	18784,5,13,0	MODERATE	NONE	CODON_INSERTION	ORF8	ttc/CTGttc	F120LF	orf8	0.000494	0.993968	5	3	T>TCTG
ERR5749237	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18794	0.002607	0	18689,6,55,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749237	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	18786	9.05E-4	0	18771,6,17,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749237	28270	PASS	TA	T	36401	0.995192	407	167,5,18571,17655	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749237	28280	PASS	G	C	36336	0.935051	26	15,2,18594,17624	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749237	28281	PASS	A	T	36336	0.911245	40	23,3,18587,17636	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749237	28282	PASS	T	A	36336	0.90431	30	27,7,18537,17654	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749237	28881	PASS	G	A	10787	0.783721	9	6,1,5350,5306	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749237	28882	PASS	G	A	10787	0.826458	6	3,0,5394,5286	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749237	28883	PASS	G	C	10787	0.945768	0	5,4,5399,5371	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749237	28977	PASS	C	T	5497	0.924686	0	0,1,0,5487	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749237	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	29465	0.002036	475	23937,5429,0,65	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749237	29095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23966	0.001627	0	23900,1,40,0	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F274	N	0.000792	0.961279	2	2	C>T
ERR5749237	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	47553	0.001262	0	23884,23571,38,36	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749237	29769	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6503	0.001999	0	0,6479,0,13	.	.	.	.	.	.	.	0.001999	0.945205	1	1	C>T
ERR5749238	241	PASS	C	T	15283	0.853301	3	0,2,7596,7613	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749238	292	PASS	C	T	7682	0.939339	2147483647	0,0,0,7671	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N9	leader	0.939339	0.96124	1	1	C>T
ERR5749238	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	12189	0.00722	0	12099,1,88,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749238	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	12189	0.003692	0	12119,0,45,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749238	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	12189	0.001641	27	12119,0,19,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749238	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12178	0.00271	0	10997,0,1000,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749238	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	12178	0.001971	0	12153,1,24,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749238	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	12179	7.39E-4	0	12157,6,9,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749238	635	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12208	0.043742	0	0,11588,0,613	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgt/Tgt	R124C	leader	0.00148	0.880435	1	1	C>T
ERR5749238	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	27499	0.002073	0	15252,12185,31,26	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749238	913	PASS	C	T	15284	0.907616	0	0,7,0,15256	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749238	1027	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	13184	0.00182	120	13125,15,18,6	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccT/ccC	P74	nsp2	0.001454	0.276316	1	1	T>C
ERR5749238	3037	PASS	C	T	17174	0.808955	30	1,13,8577,8455	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749238	3267	PASS	C	T	14807	0.968191	0	2,0,14799,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749238	4234	PASS	C	T	32599	0.692199	28	3,18,15726,16107	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D505	nsp3	0.00099	0.714088	3	3	C>T
ERR5749238	4285	PASS	G	A	16401	0.872935	0	0,2,4,16319	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaG/gaA	E522	nsp3	0.000939	0.899038	2	2	G>A
ERR5749238	5388	PASS	C	A	4774	0.952241	2147483647	0,0,4771,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749238	5986	PASS	C	T	9957	0.973185	2147483647	0,0,9951,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749238	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	10116	0.00435	0	1,10071,0,44	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L1328S?	nsp3	0.000731	0.14377	4	2	C>CT
ERR5749238	6954	PASS	T	C	14866	0.822414	0	0,3,2,14768	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749238	7423	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11208	0.002587	0	11171,0,29,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1568	nsp3	0.000941	0.970543	2	2	C>T
ERR5749238	7564	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	11202	8.93E-4	0	0,11189,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/	Y1617	nsp3	0.000586	0.056194	4	2	CT>C
ERR5749238	8562	PASS	TTAA	T	10189	0.996172	0	0,39,0,10150	MODERATE	NONE	CODON_DELETION	ORF1ab	aat/	N5	nsp4	0.996172	0.998037	1	1	TTAA>T
ERR5749238	8964	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	13940	8.61E-4	0	13924,3,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K138	nsp4	0.000553	0.981649	4	2	CA>C
ERR5749238	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	27570	9.43E-4	67	15010,12534,26,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749238	10323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	16014	0.001936	0	0,15948,0,34	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749238	11287	PASS	GTCTGGTTTT	G	14178	0.997038	0	0,42,0,14136	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749238	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	28749	0.001322	7	15606,13085,17,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749238	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20476	0.00127	0	10218,10204,15,15	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749238	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	14844	0.005389	2147483647	14440,107,11,280	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749238	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	28730	4.18E-4	0	14420,14323,6,6	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749238	14408	PASS	C	T	28730	0.828019	7	2,6,14342,14152	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749238	14676	PASS	C	T	9214	0.799653	0	4,0,9185,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749238	15279	PASS	C	T	15420	0.879313	0	1,0,15392,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749238	16176	PASS	T	C	16680	0.980755	0	0,0,9368,7308	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749238	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	17287	0.001157	0	17257,0,20,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749238	18504	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	20940	0.001003	0	1,20599,0,300	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K155N	ExoN	0.000518	0.094148	4	3	A>C
ERR5749238	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	22298	8.07E-4	0	22280,0,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749238	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25428	0.002281	0	25336,0,63,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749238	21597	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11961	0.009865	0	2,11800,0,132	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCt/tTt	S12F	S	0.00218	0.901607	2	1	C>T
ERR5749238	21764	PASS	ATACATG	A	10542	0.994972	0	53,0,10489,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749238	21990	PASS	TTTA	T	10547	0.997535	0	0,26,4,10517	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749238	23063	PASS	A	T	12158	0.85269	0	0,4,0,12080	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749238	23271	PASS	C	A	15684	0.903532	0	0,0,15659,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749238	23403	PASS	A	G	15678	0.962623	0	0,3,1,15659	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749238	23604	PASS	C	A	13830	0.933695	0	13,0,13806,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749238	23709	PASS	C	T	13816	0.935654	0	0,2,3,13787	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749238	24506	PASS	T	G	12467	0.971846	0	6,0,12460,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749238	24914	PASS	G	C	34768	0.956598	0	0,1,17318,17429	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749238	25587	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	15739	7.62E-4	0	0,15727,0,12	HIGH	NONE	FRAME_SHIFT	ORF3a	aag/	K67	orf3a	0.000598	0.813206	6	2	CA>C
ERR5749238	25626	PASS	C	T	32065	0.769749	2	1,2,16267,15721	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	caC/caT	H78	orf3a	0.000403	0.915633	3	2	C>T
ERR5749238	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	16367	0.001833	445	16288,18,12,19	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749238	25710	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTATCTT	C	16329	0.002143	0	16294,0,35,0	MODERATE	NONE	CODON_DELETION	ORF3a	ctttat/	LY108	orf3a	0.002127	0.789778	2	2	CTATCTT>C
ERR5749238	25844	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16317	0.001226	0	9,16265,0,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aCt/aTt	T151I	orf3a	0.001226	0.938776	1	1	C>T
ERR5749238	26681	PASS	C	T	11610	0.074505	1	10653,64,884,6	LOW	SILENT	SYNONYMOUS_CODING	M	ttC/ttT	F53	M	0.001297	0.074505	1	1	C>T
ERR5749238	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	11534	0.002168	0	1,11506,0,25	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749238	27684	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTCTCCAATTTT	C	14888	6.05E-4	0	42,14837,0,9	HIGH	NONE	FRAME_SHIFT	ORF7a	ccaatttttctt/	PIFL99	orf7a	0.000478	0.90411	2	2	CTCTCCAATTTT>C
ERR5749238	27972	PASS	C	T	9356	0.89301	37	2,2,9255,52	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749238	28048	PASS	G	T	9305	0.913702	0	0,14,0,9281	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749238	28111	PASS	A	G	24891	0.978546	3	3,4,15574,9304	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749238	28270	PASS	TA	T	29938	0.995056	334	146,6,15350,14440	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749238	28280	PASS	G	C	29891	0.935432	12	11,3,15392,14430	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749238	28281	PASS	A	T	29891	0.904654	21	19,5,15392,14419	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749238	28282	PASS	T	A	29934	0.904624	11	25,12,15340,14475	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749238	28651	PASS	C	T	15336	0.901082	0	0,1,0,15298	LOW	SILENT	SYNONYMOUS_CODING	N	aaC/aaT	N126	N	0.000502	0.918117	3	2	C>T
ERR5749238	28881	PASS	G	A	13941	0.755613	6	3,0,6874,6862	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749238	28882	PASS	G	A	13939	0.820647	6	5,1,6959,6842	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749238	28883	PASS	G	C	13939	0.937226	0	1,1,6975,6950	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749238	28977	PASS	C	T	7113	0.922114	0	0,3,0,7094	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749238	29095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26099	0.001763	0	26030,2,49,0	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F274	N	0.000792	0.961279	2	2	C>T
ERR5749238	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	51790	0.00141	0	26010,25667,45,43	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749239	210	PASS	G	T	1100	0.718182	0	24,0,1063,13	.	.	.	.	.	.	.	0.001452	1	2	1	G>T
ERR5749239	241	PASS	C	T	2172	0.872007	0	0,0,1084,1080	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749239	685	PASS	AAAGTCATTT	A	15793	0.999303	0	8,3,11818,3964	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749239	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11826	0.001438	0	0,11797,0,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749239	1191	PASS	C	T	10088	0.912173	0	0,6,0,10060	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCa/cTa	P129L	nsp2	0.000749	0.916048	3	2	C>T
ERR5749239	1267	PASS	C	T	18360	0.9811	0	1,2,8256,10091	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G154	nsp2	0.001789	0.9811	2	1	C>T
ERR5749239	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	35038	0.001027	2424	17480,16486,29,940	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749239	3037	PASS	C	T	9309	0.818455	21	0,7,4656,4588	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749239	3575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	6983	0.001432	0	6973,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/ttTa	L287F?	nsp3	0.000594	0.059126	3	1	G>GT
ERR5749239	4423	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	9601	8.33E-4	0	9590,3,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K569	nsp3	0.00063	0.953796	2	2	CA>C
ERR5749239	5184	PASS	C	T	6020	0.894684	0	0,2,0,6000	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P822L	nsp3	0.004643	0.894684	2	2	C>T
ERR5749239	6337	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	11704	6.84E-4	0	11696,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F1207	nsp3	0.000579	0.91624	3	2	GT>G
ERR5749239	6539	PASS	C	T	6938	0.979821	0	2,0,6934,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cac/Tac	H1274Y	nsp3	0.001998	0.979821	1	1	C>T
ERR5749239	8653	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTC	G	6776	0.001328	0	6767,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tct/	S34	nsp4	0.001328	0.132353	2	2	GTC>G
ERR5749239	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	10457	0.00153	12	8425,2016,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749239	9891	PASS	C	T	3620	0.958011	0	1,0,3618,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A446V	nsp4	0.002963	0.958011	1	1	C>T
ERR5749239	10252	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	12292	7.32E-4	0	12283,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L67	3Cpro	0.000645	0.943062	2	2	CT>C
ERR5749239	11418	PASS	T	C	5729	0.985512	2147483647	0,0,5727,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gTt/gCt	V149A	nsp6	0.985512	0.985512	1	1	T>C
ERR5749239	12946	PASS	T	C	5657	0.880148	2147483647	0,0,0,5643	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taT/taC	Y87	nsp9	0.880148	0.880148	1	1	T>C
ERR5749239	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	10116	0.002175	0	10094,0,22,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749239	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16428	0.001217	0	8206,8185,10,10	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749239	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	4185	0.00454	936	4105,28,0,49	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749239	14408	PASS	C	T	8176	0.846624	6	0,2,4087,4029	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749239	15141	PASS	C	T	10474	0.952167	0	0,5,0,10461	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acC/acT	T567	RdRp	0.002591	0.952167	1	1	C>T
ERR5749239	15451	PASS	G	A	9289	0.980299	2147483647	0,0,0,9282	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggt/Agt	G671S	RdRp	0.069405	0.980299	1	1	G>A
ERR5749239	16466	PASS	C	T	17983	0.96252	3	2,1,14657,3306	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCa/cTa	P77L	helicase	0.002134	0.96252	2	1	C>T
ERR5749239	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	19091	6.81E-4	0	19078,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749239	19164	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16788	0.001132	0	0,16762,0,21	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D375	ExoN	0.000358	0.075732	4	2	C>T
ERR5749239	19188	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	16798	6.55E-4	0	0,16787,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	tgg/	W385	ExoN	0.000427	0.06319	2	1	AT>A
ERR5749239	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11821	0.003638	0	11772,0,46,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749239	20262	PASS	A	G	17881	0.963481	0	2,0,17863,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttA/ttG	L214	endoR	0.000483	0.963481	2	2	A>G
ERR5749239	20320	PASS	C	T	17863	0.916979	2147483647	0,0,17835,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cat/Tat	H234Y	endoR	0.000651	0.916979	2	2	C>T
ERR5749239	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23155	0.001252	0	23089,0,30,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749239	21123	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	31534	3.81E-4	39	16689,14833,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F156	MethTr	0.000257	0.90982	5	2	GT>G
ERR5749239	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	18584	5.92E-4	0	9271,9302,5,6	HIGH	NONE	FRAME_SHIFT	S	ctt/Tctt	L5S?	S	0.000394	0.091869	4	1	G>GT
ERR5749239	21618	PASS	C	G	9322	0.955482	0	0,2,0,9306	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aGa	T19R	S	0.001611	0.955482	3	2	C>G
ERR5749239	21854	PASS	T	C	265	0.05283	0	125,124,8,7	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tct/Cct	S98P	S	0.00132	0.05283	1	1	T>C
ERR5749239	21864	PASS	T	C	265	0.071698	0	122,122,10,10	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aTa/aCa	I101T	S	0.071698	0.071698	1	1	T>C
ERR5749239	21987	PASS	G	A	167	0.922156	50	7,0,27,133	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gGt/gAt	G142D	S	0.000998	0.922156	5	2	G>A
ERR5749239	22028	PASS	GAGTTCA	G	34	1.0	2147483647	0,0,34,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	gagttcaga/gga	EFR156G	S	0.000645	1	2	1	GAGTTCA>G
ERR5749239	22917	PASS	T	G	8908	0.970925	0	2,0,8906,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTg/cGg	L452R	S	0.005552	0.975153	2	1	T>G
ERR5749239	22995	PASS	C	A	8869	0.67268	0	96,0,8771,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aAa	T478K	S	0.000881	0.67268	2	2	C>A
ERR5749239	23403	PASS	A	G	15194	0.96288	0	0,2,0,15178	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749239	23604	PASS	C	G	9420	0.94862	2147483647	0,0,9414,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cGt	P681R	S	0.003105	0.969595	3	1	C>G
ERR5749239	23817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	15294	0.001242	38	5873,9397,0,19	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTt/cCt	L752P	S	0.000646	0.066832	1	1	T>C
ERR5749239	24320	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	7802	0.001666	0	0,7786,0,13	HIGH	NONE	FRAME_SHIFT	S	aaa/	K921	S	0.000763	0.138365	4	2	CA>C
ERR5749239	24410	PASS	G	A	7813	0.846282	2147483647	0,0,0,7791	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gat/Aat	D950N	S	0.001947	0.846282	2	1	G>A
ERR5749239	24745	PASS	C	T	22882	0.95538	9	1,3,15415,7450	LOW	SILENT	SYNONYMOUS_CODING	S	gtC/gtT	V1061	S	0.00048	0.961619	3	2	C>T
ERR5749239	25469	PASS	C	T	13769	0.956206	0	1,0,13755,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	tCa/tTa	S26L	orf3a	0.001214	0.959377	2	2	C>T
ERR5749239	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	3434	0.003494	164	3393,20,4,9	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749239	26767	PASS	T	C	7562	0.958741	0	0,2,0,7556	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	aTc/aCc	I82T	M	0.954318	0.968313	2	1	T>C
ERR5749239	27638	PASS	T	C	10854	0.96066	2147483647	0,0,10830,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	gTt/gCt	V82A	orf7a	0.001695	0.96066	1	1	T>C
ERR5749239	27739	PASS	C	T	10872	0.957506	0	0,2,11,10855	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Ctc/Ttc	L116F	orf7a	0.001001	0.957506	1	1	C>T
ERR5749239	27752	PASS	C	T	10873	0.943806	0	0,6,11,10844	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	aCa/aTa	T120I	orf7a	0.000582	0.943806	2	2	C>T
ERR5749239	28247	PASS	AGATTTC	A	16434	0.998357	0	51,0,16407,0	MODERATE	NONE	CODON_DELETION	ORF8	gatttc/	DF119	orf8	0.000374	0.998357	3	1	AGATTTC>A
ERR5749239	28270	PASS	TA	T	32669	0.985277	526	81,400,16347,15841	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749239	28271	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AA	A	32670	0.001867	116	16423,16186,5,56	.	.	.	.	.	.	.	0.000482	0.924941	3	2	AA>A
ERR5749239	28273	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AA	A	32719	0.004065	364	16425,16159,2,131	HIGH	NONE	FRAME_SHIFT+START_LOST	N	atg/	M1	N	0.000399	0.842333	4	1	AA>A
ERR5749239	28461	PASS	A	G	13005	0.980008	221	5,7,12991,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAc/gGc	D63G	N	0.980008	0.980008	1	1	A>G
ERR5749239	28881	PASS	G	T	4393	0.81038	14	16,30,2185,2158	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aTg	R203M	N	0.000709	0.947368	4	2	G>T
ERR5749239	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	45506	0.001033	0	22844,22580,29,29	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749239	29402	PASS	G	T	4111	0.94235	0	2,0,4105,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Tat	D377Y	N	0.002634	0.94235	1	1	G>T
ERR5749239	29427	PASS	G	A	4111	0.949404	0	3,0,4104,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGa/aAa	R385K	N	0.949404	0.949404	1	1	G>A
ERR5749239	29675	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	8128	0.00123	0	4062,4056,5,5	.	.	.	.	.	.	.	0.000624	0.883495	2	1	CA>C
ERR5749239	29739	PASS	C	T	4075	0.072147	0	0,3688,0,382	.	.	.	.	.	.	.	0.001961	0.706433	1	1	C>T
ERR5749239	29742	PASS	G	T	4075	0.931288	0	0,1,0,4074	.	.	.	.	.	.	.	0.847293	0.931288	2	1	G>T
ERR5749240	241	PASS	C	T	24	0.833333	0	0,0,12,12	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749240	445	PASS	T	C	54	1.0	2147483647	0,0,54,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtT/gtC	V60	leader	1	1	1	1	T>C
ERR5749240	709	PASS	G	C	401	0.127182	0	349,0,52,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gaG/gaC	E148D	leader	0.127182	0.127182	1	1	G>C
ERR5749240	901	PASS	A	G	385	0.981818	2147483647	0,0,0,385	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcA/tcG	S32	nsp2	0.981818	0.981818	1	1	A>G
ERR5749240	929	PASS	A	G	385	0.987013	2147483647	0,0,0,384	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Att/Gtt	I42V	nsp2	0.000823	0.987013	3	2	A>G
ERR5749240	932	PASS	GAC	G	385	0.184416	0	0,314,0,71	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T44	nsp2	0.00048	0.184416	2	2	GAC>G
ERR5749240	1614	PASS	TTC	T	327	0.055046	8	270,39,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/	L271	nsp2	0.011131	0.055046	2	2	TTC>T
ERR5749240	1912	PASS	C	T	409	0.08802	57	121,251,0,37	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S369	nsp2	0.000681	0.08802	2	1	C>T
ERR5749240	2084	PASS	C	T	241	0.253112	0	88,88,32,33	HIGH	NONSENSE	STOP_GAINED	ORF1ab	Cag/Tag	Q427*	nsp2	0.001943	0.253112	1	1	C>T
ERR5749240	2672	PASS	G	C	778	0.18509	0	630,0,147,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gca/Cca	A623P	nsp2	0.001351	0.18509	3	1	G>C
ERR5749240	3037	PASS	C	T	38	0.921053	0	0,0,19,19	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749240	3253	PASS	CA	C	673	0.07578	0	622,0,51,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N179	nsp3	0.000764	0.07578	1	1	CA>C
ERR5749240	3365	PASS	C	T	1282	0.053042	0	574,634,36,38	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Ttt	L216F	nsp3	0.0014	0.053042	1	1	C>T
ERR5749240	4338	PASS	C	T	213	0.051643	4	177,19,17,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S540F	nsp3	0.000366	0.051643	2	2	C>T
ERR5749240	4861	PASS	TAA	T	95	0.115789	0	0,84,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaaagt/	KS715	nsp3	0.000632	0.115789	2	1	TAA>T
ERR5749240	5069	PASS	G	C	400	0.2075	0	317,0,83,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gct/Cct	A784P	nsp3	0.2075	0.2075	1	1	G>C
ERR5749240	5206	PASS	G	C	400	0.0725	0	0,369,0,31	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atC	M829I	nsp3	0.001901	0.0725	2	1	G>C
ERR5749240	6205	PASS	GA	G	529	0.134216	46	387,71,71,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1163	nsp3	0.000463	0.134216	1	1	GA>G
ERR5749240	6286	PASS	C	T	458	0.949782	2147483647	0,0,458,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acC/acT	T1189	nsp3	0.000549	0.949782	2	2	C>T
ERR5749240	6741	PASS	G	T	49	0.204082	0	0,39,0,10	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cGg/cTg	R1341L	nsp3	0.001093	0.204082	3	2	G>T
ERR5749240	6869	PASS	A	T	373	0.168901	0	304,0,69,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Act/Tct	T1384S	nsp3	0.000929	0.168901	2	2	A>T
ERR5749240	7491	PASS	G	C	199	0.100503	0	177,0,21,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tGt/tCt	C1591S	nsp3	0.100503	0.100503	1	1	G>C
ERR5749240	7674	PASS	C	T	421	0.109264	0	373,1,47,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCg/gTg	A1652V	nsp3	0.000682	0.109264	3	2	C>T
ERR5749240	7691	PASS	C	T	421	0.095012	0	376,1,44,0	HIGH	NONSENSE	STOP_GAINED	ORF1ab	Cag/Tag	Q1658*	nsp3	0.003784	0.095012	1	1	C>T
ERR5749240	8015	PASS	GC	G	181	0.392265	0	110,0,71,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gcg/	A1766	nsp3	0.00385	0.392265	3	2	GC>G
ERR5749240	8739	PASS	C	T	114	0.201754	0	89,0,25,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T62I	nsp4	0.201754	0.201754	1	1	C>T
ERR5749240	8772	PASS	C	T	114	0.166667	0	92,0,22,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T73I	nsp4	0.001457	0.166667	1	1	C>T
ERR5749240	9203	PASS	G	T	365	0.931507	0	0,0,2,363	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gat/Tat	D217Y	nsp4	0.931507	0.964515	2	1	G>T
ERR5749240	9541	PASS	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	245	0.061224	6	198,32,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749240	9552	PASS	CAG	C	245	0.073469	8	195,32,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ccagtt/	PV333	nsp4	0.073469	0.073469	1	1	CAG>C
ERR5749240	10369	PASS	C	T	533	0.120075	0	0,465,0,67	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	cgC/cgT	R105	3Cpro	0.001225	0.120075	1	1	C>T
ERR5749240	10470	PASS	C	T	554	0.104693	0	496,0,58,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCa/tTa	S139L	3Cpro	0.001439	0.104693	1	1	C>T
ERR5749240	10683	PASS	C	T	567	0.252205	0	0,419,0,148	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A210V	3Cpro	0.001813	0.252205	2	1	C>T
ERR5749240	10702	PASS	C	T	560	0.098214	0	6,497,0,57	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D216	3Cpro	0.000396	0.098214	2	2	C>T
ERR5749240	11135	PASS	T	C	1673	0.169157	0	1367,0,302,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F55L	nsp6	0.001762	0.169157	2	2	T>C
ERR5749240	11287	PASS	GTCTGGTTTT	G	1676	0.168258	0	1,1393,0,282	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749240	11654	PASS	T	C	254	0.129921	57	144,74,36,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749240	12459	PASS	C	T	402	0.064677	122	258,118,0,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T123I	nsp8	0.000658	0.986093	1	1	C>T
ERR5749240	13554	PASS	C	T	517	0.083172	0	0,468,0,47	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y38	RdRp	0.000637	0.920199	2	2	C>T
ERR5749240	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	86	0.05814	0	40,40,3,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cct/Tct	P323S	RdRp	0.000388	0.799973	2	2	C>T
ERR5749240	14408	PASS	C	T	86	0.895349	0	0,0,43,43	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749240	15237	PASS	C	T	156	0.955128	0	5,0,151,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H599	RdRp	0.001014	0.955128	2	2	C>T
ERR5749240	15542	PASS	C	T	791	0.073325	0	728,0,63,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aTg	T701M	RdRp	0.00059	0.073325	3	2	C>T
ERR5749240	15774	PASS	C	T	776	0.078608	0	0,714,0,62	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	agC/agT	S778	RdRp	0.006387	0.078608	2	2	C>T
ERR5749240	16439	PASS	T	A	276	0.054348	0	0,261,0,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTg/aAg	M68K	helicase	0.016667	0.054348	1	1	T>A
ERR5749240	16524	PASS	ATG	A	1039	0.115496	0	919,0,120,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/	V98	helicase	0.00047	0.926983	2	2	ATG>A
ERR5749240	16792	PASS	CGT	C	1323	0.072562	102	283,944,0,96	HIGH	NONE	FRAME_SHIFT	ORF1ab	gta/	V187	helicase	0.000335	0.072562	5	2	CGT>C
ERR5749240	17602	PASS	GT	G	217	0.156682	104	211,183,0,34	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/	Y457	helicase	0.001035	0.156682	1	1	GT>G
ERR5749240	17630	PASS	A	C	217	0.179724	0	0,178,0,39	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAa/aCa	K465T	helicase	0.179724	0.179724	1	1	A>C
ERR5749240	17810	PASS	T	A	268	0.093284	0	238,0,30,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTt/aAt	I525N	helicase	0.093284	0.093284	1	1	T>A
ERR5749240	17999	PASS	C	T	393	0.063613	43	125,242,0,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T588I	helicase	0.001094	0.974498	2	1	C>T
ERR5749240	18029	PASS	C	T	393	0.063613	41	125,243,0,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCa/gTa	A598V	helicase	0.001444	0.063613	1	1	C>T
ERR5749240	18642	PASS	A	G	2198	0.078253	0	2024,0,174,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atA/atG	I201M	ExoN	0.000464	0.078253	3	2	A>G
ERR5749240	20179	PASS	C	T	59	0.20339	0	0,46,0,13	HIGH	NONSENSE	STOP_GAINED	ORF1ab	Caa/Taa	Q187*	endoR	0.001915	0.20339	1	1	C>T
ERR5749240	20719	PASS	CTA	C	110	0.209091	0	0,87,0,23	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctatta/	LL21	MethTr	0.000341	0.209091	2	2	CTA>C
ERR5749240	21134	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	1161	0.014643	48	569,575,17,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cAa/cGa	Q159R	MethTr	0.001194	0.689661	1	1	A>G
ERR5749240	21255	PASS	G	C	646	0.739938	439	69,59,513,2	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcG/gcC	A199	MethTr	0.000341	0.917425	4	2	G>C
ERR5749240	21748	PASS	T	A	318	0.943396	2147483647	0,0,318,0	LOW	SILENT	SYNONYMOUS_CODING	S	gtT/gtA	V62	S	0.943396	0.943396	1	1	T>A
ERR5749240	21811	PASS	C	T	318	0.179245	0	258,0,59,0	LOW	SILENT	SYNONYMOUS_CODING	S	gtC/gtT	V83	S	0.001327	0.179245	1	1	C>T
ERR5749240	22227	PASS	C	T	683	0.824305	2147483647	0,0,0,682	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gTt	A222V	S	0.000419	0.824305	2	2	C>T
ERR5749240	22384	PASS	T	C	446	0.118834	0	392,0,54,0	LOW	SILENT	SYNONYMOUS_CODING	S	acT/acC	T274	S	0.001609	0.118834	1	1	T>C
ERR5749240	22444	PASS	C	T	444	0.182432	0	353,0,87,0	LOW	SILENT	SYNONYMOUS_CODING	S	gaC/gaT	D294	S	0.004885	0.182432	1	1	C>T
ERR5749240	22454	PASS	GA	G	882	0.11678	1	390,389,54,49	HIGH	NONE	FRAME_SHIFT	S	aca/	T299	S	0.001722	0.11678	2	2	GA>G
ERR5749240	22759	PASS	AT	A	1510	0.12649	0	0,1319,0,191	HIGH	NONE	FRAME_SHIFT	S	ttt/	F400	S	0.000578	0.12649	2	2	AT>A
ERR5749240	23086	PASS	C	T	205	0.131707	0	0,172,0,33	LOW	SILENT	SYNONYMOUS_CODING	S	taC/taT	Y508	S	0.00176	0.131707	2	2	C>T
ERR5749240	23249	PASS	C	T	860	0.082558	0	775,0,81,0	HIGH	NONSENSE	STOP_GAINED	S	Caa/Taa	Q563*	S	0.001376	0.082558	1	1	C>T
ERR5749240	23403	PASS	A	G	860	0.974419	2147483647	0,0,0,860	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749240	23460	PASS	G	C	1252	0.052716	0	1,1183,0,67	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tGg/tCg	W633S	S	0.001089	0.052716	2	2	G>C
ERR5749240	23625	PASS	CTA	C	136	0.117647	0	120,0,16,0	HIGH	NONE	FRAME_SHIFT	S	gctagt/	AS688	S	0.002362	0.901054	2	2	CTA>C
ERR5749240	23816	PASS	CT	C	198	0.080808	24	62,120,0,16	HIGH	NONE	FRAME_SHIFT	S	ttg/	L753	S	0.000334	0.080808	2	2	CT>C
ERR5749240	24127	PASS	TAACGGCCTTACTG	T	143	0.111888	41	65,62,16,0	HIGH	NONE	FRAME_SHIFT	S	aacggccttactgtt/	NGLTV856	S	0.000324	0.111888	4	1	TAACGGCCTTACTG>T
ERR5749240	24512	PASS	C	T	440	0.154545	0	370,0,70,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L984F	S	0.001476	0.154545	1	1	C>T
ERR5749240	25422	PASS	TGGAACTGTA	T	1687	0.213989	0	1326,0,361,0	MODERATE	NONE	CODON_DELETION	ORF3a	ggaactgta/	GTV11	orf3a	0.000545	0.213989	6	1	TGGAACTGTA>T
ERR5749240	25572	PASS	CA	C	1683	0.128936	0	0,1466,0,217	HIGH	NONE	FRAME_SHIFT	ORF3a	atc/	I62	orf3a	0.000543	0.959687	4	2	CA>C
ERR5749240	26280	PASS	A	T	432	0.06713	55	147,255,0,30	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	ttA/ttT	L12F	E	0.000789	0.06713	2	2	A>T
ERR5749240	26710	PASS	CTTG	C	175	0.102857	0	157,0,18,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtttt/ttt	CF64F	M	0.000649	0.102857	1	1	CTTG>C
ERR5749240	26801	PASS	C	G	176	0.954545	2147483647	0,0,0,176	LOW	SILENT	SYNONYMOUS_CODING	M	ctC/ctG	L93	M	0.002753	0.954545	3	1	C>G
ERR5749240	26803	PASS	G	C	176	0.090909	0	0,159,0,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	aGc/aCc	S94T	M	0.010562	0.090909	1	1	G>C
ERR5749240	27340	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAT	A	8	0.25	0	3,3,1,1	HIGH	NONE	FRAME_SHIFT	ORF6	aataaa/	NK47	orf6	0.000451	0.25	2	2	AAT>A
ERR5749240	27509	PASS	C	T	928	0.067888	0	858,4,65,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	aCa/aTa	T39I	orf7a	0.000843	0.067888	1	1	C>T
ERR5749240	27513	PASS	C	T	925	0.911351	0	67,0,858,0	LOW	SILENT	SYNONYMOUS_CODING	ORF7a	taC/taT	Y40	orf7a	0.001863	0.982462	2	2	C>T
ERR5749240	27577	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	923	0.03792	0	869,0,53,0	HIGH	NONSENSE	STOP_GAINED	ORF7a	Caa/Taa	Q62*	orf7a	0.000614	0.952205	4	2	C>T
ERR5749240	27816	PASS	GT	G	981	0.053007	11	57,872,0,52	HIGH	NONE	FRAME_SHIFT	ORF7b	tta/	L22	orf7b	0.000423	0.053007	1	1	GT>G
ERR5749240	28287	PASS	G	T	9972	0.079824	2	4519,4533,469,449	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gGa/gTa	G5V	N	0.000961	0.079824	2	1	G>T
ERR5749240	28310	PASS	C	A	6264	0.906928	1	1,10,1268,4984	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Ccc/Acc	P13T	N	0.00095	0.92832	2	1	C>A
ERR5749240	28341	PASS	C	T	6268	0.05919	362	1266,4584,3,406	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCa/tTa	S23L	N	0.02923	0.05919	1	1	C>T
ERR5749240	28512	PASS	CAG	C	805	0.172671	0	666,0,139,0	HIGH	NONE	FRAME_SHIFT	N	gat/	D81	N	0.000621	0.172671	3	2	CAG>C
ERR5749240	29095	PASS	C	T	93	0.344086	0	60,0,33,0	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F274	N	0.000792	0.961279	2	2	C>T
ERR5749240	29645	PASS	G	T	203	0.901478	5	1,0,51,151	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF10	Gta/Tta	V30L	orf10	0.901478	0.901478	1	1	G>T
ERR5749240	29708	PASS	C	T	53	0.150943	0	0,43,0,10	.	.	.	.	.	.	.	0.003269	0.150943	1	1	C>T
ERR5749241	239	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTC	T	14966	8.69E-4	1	7450,7504,7,6	.	.	.	.	.	.	.	0.000495	0.25	4	1	TTC>T
ERR5749241	241	PASS	C	T	14964	0.859129	0	1,2,7422,7460	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749241	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	13953	0.003798	0	13899,0,53,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749241	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	13953	0.001075	0	13830,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749241	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	13953	0.001505	0	13830,0,21,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749241	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	13953	0.00602	0	13830,0,84,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749241	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	13960	0.002436	2	12681,13,1061,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749241	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	13960	8.6E-4	0	13935,13,12,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749241	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	13964	6.45E-4	0	13926,20,9,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749241	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	37825	0.0023	3	23780,13938,51,36	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749241	913	PASS	C	T	23837	0.905861	0	0,15,0,23785	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749241	2062	PASS	C	T	28762	0.822961	0	10,0,28620,18	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A419	nsp2	0.001265	0.822961	2	1	C>T
ERR5749241	3037	PASS	C	T	19745	0.81332	61	1,24,9865,9698	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749241	3096	PASS	C	T	9930	0.927492	0	0,4,0,9911	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCa/tTa	S126L	nsp3	0.001801	0.932094	1	1	C>T
ERR5749241	3177	PASS	C	T	33075	0.902706	2	9,2,23095,9905	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P153L	nsp3	0.000773	0.96008	3	2	C>T
ERR5749241	3267	PASS	C	T	23135	0.971299	0	6,0,23113,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749241	3575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	12856	0.001089	0	12842,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/ttTa	L287F?	nsp3	0.000594	0.059126	3	1	G>GT
ERR5749241	3671	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GA	25587	6.25E-4	0	12796,12788,8,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/aaAt	N319K?	nsp3	0.000351	0.0625	6	2	G>GA
ERR5749241	5388	PASS	C	A	6635	0.960965	2147483647	0,0,6633,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749241	5784	PASS	C	T	42299	0.091752	0	18724,19189,2145,2180	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T1022I	nsp3	0.001294	0.919357	2	1	C>T
ERR5749241	5986	PASS	C	T	13566	0.975748	2147483647	0,0,13557,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749241	6954	PASS	T	C	25070	0.822537	0	0,7,0,24944	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749241	7528	PASS	C	T	17781	0.909285	0	0,7,43,17685	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V1603	nsp3	0.002527	0.916131	1	1	C>T
ERR5749241	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	34524	8.98E-4	88	17715,16777,31,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749241	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	22452	0.00245	0	21772,1,55,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749241	11082	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	22444	4.9E-4	0	22439,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000427	0.179468	2	1	TG>T
ERR5749241	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	22444	0.001827	0	22359,0,62,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749241	11287	PASS	GTCTGGTTTT	G	22443	0.997505	0	0,56,0,22387	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749241	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	41043	9.5E-4	2	25210,15756,27,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749241	11750	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	49413	0.003056	5	25069,24059,121,100	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L260F	nsp6	0.001019	0.70989	2	1	C>T
ERR5749241	12125	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	18138	0.001103	0	2,18062,0,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y12H	nsp8	0.000847	0.113436	1	1	T>C
ERR5749241	12756	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	38259	8.89E-4	4	17571,20631,20,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T24I	nsp9	0.000889	0.877514	1	1	C>T
ERR5749241	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34259	0.001284	0	17103,17069,25,25	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749241	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12549	0.004781	2147483647	12205,115,2,215	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749241	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	24294	0.001852	0	12179,12092,23,22	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749241	14408	PASS	C	T	24294	0.839714	15	0,5,12119,11951	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749241	14676	PASS	C	T	14911	0.801422	0	7,0,14872,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749241	15279	PASS	C	T	24655	0.892963	0	3,0,24621,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749241	15983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	11892	0.001093	0	11880,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T850	RdRp	0.000701	0.338235	2	1	TA>T
ERR5749241	16176	PASS	T	C	22370	0.981046	0	2,2,10457,11900	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749241	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	26925	5.57E-4	0	26909,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749241	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	27813	3.95E-4	0	0,27802,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749241	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	32425	0.002128	0	32334,0,73,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749241	20987	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	48909	2.86E-4	0	24468,24434,7,7	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L111	MethTr	0.000276	0.056129	4	2	CT>C
ERR5749241	21764	PASS	ATACATG	A	14103	0.995887	0	58,0,14045,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749241	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	14102	6.38E-4	0	14093,0,9,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749241	21990	PASS	TTTA	T	14107	0.998228	0	0,25,3,14079	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749241	22450	PASS	C	T	10117	0.783632	19	1,1,9933,59	LOW	SILENT	SYNONYMOUS_CODING	S	ctC/ctT	L296	S	0.00215	0.803846	1	1	C>T
ERR5749241	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	17824	0.001234	0	0,17792,0,23	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749241	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	32399	0.001173	9	14543,17790,12,26	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749241	23063	PASS	A	T	14552	0.862837	0	0,4,0,14471	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749241	23271	PASS	C	A	24563	0.92277	0	2,0,24540,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749241	23403	PASS	A	G	24563	0.97085	0	0,5,0,24542	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749241	23604	PASS	C	A	17620	0.942906	0	13,0,17595,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749241	23709	PASS	C	T	17606	0.940418	0	0,7,9,17567	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749241	24506	PASS	T	G	19543	0.972369	0	6,0,19534,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749241	24914	PASS	G	C	40494	0.957599	0	0,0,20171,20285	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749241	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	24480	0.001144	562	24386,27,6,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749241	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	24431	5.32E-4	0	24418,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749241	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	24623	0.001462	1345	24139,146,203,104	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749241	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	55110	3.27E-4	0	8,55082,0,18	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749241	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	13657	0.00227	0	1,13620,0,31	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749241	27922	PASS	T	C	11938	0.076814	0	10976,0,946,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aTc/aCc	I10T	orf8	0.076814	0.076814	1	1	T>C
ERR5749241	27972	PASS	C	T	11985	0.907718	74	4,4,11889,54	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749241	28048	PASS	G	T	11936	0.928368	0	0,17,0,11912	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749241	28111	PASS	A	G	33568	0.976704	1	4,3,21616,11933	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749241	28270	PASS	TA	T	41873	0.995033	478	209,9,21348,20317	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749241	28280	PASS	G	C	41788	0.937925	6	11,5,21379,20298	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749241	28281	PASS	A	T	41788	0.916052	6	27,17,21376,20290	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749241	28282	PASS	T	A	41791	0.910914	18	24,9,21336,20312	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749241	28881	PASS	G	A	20078	0.757097	16	11,2,9923,9839	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749241	28882	PASS	G	A	20076	0.828801	7	7,2,10039,9834	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749241	28883	PASS	G	C	20076	0.943415	1	2,3,10052,9992	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749241	28977	PASS	C	T	10229	0.927363	0	0,3,1,10198	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749241	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	59810	0.00102	0	30038,29661,39,37	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749242	239	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTC	T	11356	7.04E-4	0	5657,5691,4,4	.	.	.	.	.	.	.	0.000495	0.25	4	1	TTC>T
ERR5749242	241	PASS	C	T	11355	0.856275	3	0,2,5646,5659	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749242	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	14713	7.48E-4	0	14701,0,11,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749242	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	14715	0.001087	0	14672,2,16,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749242	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	14715	0.001223	0	14672,2,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749242	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	14705	8.84E-4	0	14690,2,13,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749242	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	14705	6.12E-4	0	14690,2,9,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttatg/gtg	VM84V	leader	0.000554	0.991848	4	1	GTTA>G
ERR5749242	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	38460	9.62E-4	22	23694,14720,31,6	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749242	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23720	0.001223	0	1,23663,0,31	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749242	913	PASS	C	T	23721	0.913073	0	0,12,1,23668	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749242	1510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	22322	0.003091	0	0,22115,0,77	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G235	nsp2	0.002159	0.937304	1	1	T>C
ERR5749242	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	76712	0.001382	2147483647	38301,35985,51,2193	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749242	3037	PASS	C	T	22014	0.821296	55	1,22,11004,10834	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749242	3267	PASS	C	T	23632	0.970421	0	4,0,23618,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749242	4237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTA	T	46398	3.02E-4	0	23224,23161,7,7	HIGH	NONE	FRAME_SHIFT	ORF1ab	ata/	I508	nsp3	0.000302	0.918634	2	2	TTA>T
ERR5749242	5170	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	12218	6.55E-4	0	0,12210,0,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T819	nsp3	0.000565	0.894036	2	2	CCA>C
ERR5749242	5388	PASS	C	A	7628	0.958049	2147483647	0,0,7623,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749242	5986	PASS	C	T	15062	0.976032	0	1,0,15047,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749242	6954	PASS	T	C	24132	0.836483	0	0,2,0,24036	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749242	7067	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	47486	0.001516	152	23182,24195,79,9	HIGH	NONSENSE	STOP_GAINED	ORF1ab	Gaa/Taa	E1450*	nsp3	0.000274	0.059217	5	3	G>T
ERR5749242	7070	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	47486	8.84E-4	113	23186,24199,41,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggc/Agc	G1451S	nsp3	0.000698	0.101434	3	1	G>A
ERR5749242	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	23114	0.001428	0	23039,0,61,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749242	11287	PASS	GTCTGGTTTT	G	23120	0.998227	0	0,41,0,23079	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749242	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	16103	5.59E-4	0	16094,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749242	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	32235	0.001303	1	16097,16047,22,24	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749242	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	8366	0.003586	1958	8140,105,0,114	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749242	14408	PASS	C	T	16219	0.847216	2	1,2,8102,8032	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749242	14676	PASS	C	T	14414	0.830581	0	11,0,14356,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749242	15240	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24045	0.001955	0	23964,29,47,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N600	RdRp	0.000934	0.931284	2	2	C>T
ERR5749242	15279	PASS	C	T	24015	0.913554	0	8,0,23974,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749242	15924	PASS	C	T	11861	0.959025	0	1,0,11852,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y828	RdRp	0.001719	0.970414	1	1	C>T
ERR5749242	16176	PASS	T	C	23038	0.982681	0	0,1,11170,11860	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749242	17124	PASS	T	C	40620	0.985672	2	8,9,16368,24221	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcC	A296	helicase	0.000471	0.985672	2	2	T>C
ERR5749242	17615	PASS	A	G	19074	0.938608	0	0,1,2,19039	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749242	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	29008	7.24E-4	0	28987,0,21,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749242	19079	PASS	A	G	28361	0.962695	0	4,0,28342,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gAa/gGa	E347G	ExoN	0.001121	0.967175	2	1	A>G
ERR5749242	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	28382	4.23E-4	0	0,28370,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749242	19854	PASS	C	T	21138	0.965654	662	21,5,0,21094	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D78	endoR	0.950322	0.965654	1	1	C>T
ERR5749242	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28217	0.001524	0	28156,0,43,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749242	20178	PASS	C	T	28222	0.867727	112	3,3,0,28200	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V186	endoR	0.000533	0.867727	2	2	C>T
ERR5749242	21621	PASS	C	T	17009	0.938209	0	0,10,0,16986	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCc/aTc	T20I	S	0.00148	0.944623	2	2	C>T
ERR5749242	21764	PASS	ATACATG	A	16044	0.997569	26	38,1,16005,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749242	21990	PASS	TTTA	T	16043	0.99813	0	0,30,1,16012	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749242	22771	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AG	A	17597	5.11E-4	0	1,17587,0,9	HIGH	NONE	FRAME_SHIFT	S	ggt/	G404	S	0.000511	0.112051	3	3	AG>A
ERR5749242	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25028	0.001079	2	7421,17569,6,21	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749242	23063	PASS	A	T	7393	0.85351	0	0,1,0,7337	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749242	23123	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	7437	0.04007	0	11,7093,0,332	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Cca/Aca	P521T	S	0.04007	0.854414	2	1	C>A
ERR5749242	23271	PASS	C	A	25707	0.915159	0	1,0,25677,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749242	23323	PASS	T	C	50894	0.951252	1	2,3,25590,25254	LOW	SILENT	SYNONYMOUS_CODING	S	atT/atC	I587	S	0.000758	0.951252	2	2	T>C
ERR5749242	23403	PASS	A	G	25694	0.972172	0	0,4,0,25675	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749242	23604	PASS	C	A	19012	0.942405	0	14,0,18988,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749242	23709	PASS	C	T	18991	0.93281	0	0,7,5,18941	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749242	24237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15295	0.001242	0	15266,0,20,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gTt	A892V	S	0.001242	0.889739	1	1	C>T
ERR5749242	24506	PASS	T	G	18843	0.975004	0	12,0,18827,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749242	24914	PASS	G	C	48640	0.960362	0	0,1,24241,24360	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749242	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	28417	0.001302	76	19698,8655,49,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749242	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	G	8672	0.001614	0	1,8655,0,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tGc	S1252C	S	0.000828	0.956514	4	2	C>G
ERR5749242	25660	PASS	G	T	21110	0.91928	1135	5,38,21040,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gtt/Ttt	V90F	orf3a	0.000716	0.91928	2	2	G>T
ERR5749242	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	21108	0.001421	487	21010,18,13,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749242	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	21070	9.02E-4	0	21051,0,19,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749242	26158	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	58793	3.57E-4	0	0,58772,0,21	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF3a	gttaat/gat	VN256D	orf3a	0.000297	0.905181	6	2	GTTA>G
ERR5749242	26270	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	71635	5.86E-4	0	12747,58827,7,37	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	aCa/aTa	T9I	E	0.000586	0.930791	3	2	C>T
ERR5749242	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	15504	0.001612	0	0,15475,0,25	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749242	27972	PASS	C	T	13377	0.901772	19	1,1,13241,79	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749242	28001	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	26551	9.42E-4	2	13233,13248,26,22	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ccG/ccT	P36	orf8	0.00085	0.830607	2	1	G>T
ERR5749242	28048	PASS	G	T	13305	0.918001	0	0,23,0,13273	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749242	28057	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13311	0.002179	0	0,13275,0,34	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	gCa/gTa	A55V	orf8	0.001401	0.051498	1	1	C>T
ERR5749242	28078	PASS	T	C	13317	0.977397	0	0,5,0,13302	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	gTg/gCg	V62A	orf8	0.974665	0.977397	1	1	T>C
ERR5749242	28111	PASS	A	G	34930	0.977956	0	8,4,21595,13315	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749242	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	21586	5.56E-4	0	21580,3,12,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749242	28270	PASS	TA	T	41960	0.995234	508	202,5,21309,20451	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749242	28280	PASS	G	C	41870	0.936398	13	13,4,21345,20420	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749242	28281	PASS	A	T	41870	0.919131	15	16,5,21339,20428	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749242	28282	PASS	T	A	41874	0.905813	11	24,12,21293,20443	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749242	28881	PASS	G	A	20903	0.756016	11	7,1,10303,10307	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749242	28882	PASS	G	A	20902	0.833557	6	3,0,10440,10272	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749242	28883	PASS	G	C	20902	0.945221	0	2,1,10449,10417	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749242	28977	PASS	C	T	10637	0.93062	0	0,0,1,10620	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749242	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	45775	0.001595	321	35098,10565,10,68	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749242	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	69808	0.001361	0	35016,34630,59,57	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749242	29721	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCACATTTTCACCGAGGCCACGCGGAGT	C	11296	0.001062	0	0,11284,0,12	.	.	.	.	.	.	.	0.001062	0.880471	2	1	CCACATTTTCACCGAGGCCACGCGGAGT>C
ERR5749242	29769	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11305	0.011499	0	0,11154,0,140	.	.	.	.	.	.	.	0.001999	0.945205	1	1	C>T
ERR5749243	241	PASS	C	T	21779	0.862574	0	1,2,10828,10872	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749243	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	12491	0.003202	0	12450,5,40,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749243	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	12497	0.00136	0	12343,11,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749243	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	12497	0.002641	0	12343,11,33,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749243	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	12497	0.006802	0	12343,11,85,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749243	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12492	0.002081	0	11454,14,780,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749243	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	12492	0.003522	13	12435,13,43,1	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749243	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	12490	0.001121	0	12458,14,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749243	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	12493	0.001761	34	12445,15,20,2	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749243	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	34334	5.24E-4	0	21811,12502,11,7	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749243	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	34334	3.79E-4	2	21754,12477,7,6	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749243	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	34334	0.00233	3	21754,12477,54,26	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749243	913	PASS	C	T	21812	0.919861	0	0,14,0,21775	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749243	2305	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTAAATAAATTTTTGGCTTTGTGTGCTGACTCTATCATTATTGGTGGAGCTAAACTTAAAGC	G	13645	7.33E-4	0	13635,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtaaataaatttttggctttgtgtgctgactctatcattattggtggagctaaacttaaagccttg/	VNKFLALCADSIIIGGAKLKAL502	nsp2	0.000443	0.070409	4	3	GCTTGTAAATAAATTTTTGGCTTTGTGTGCTGACTCTATCATTATTGGTGGAGCTAAACTTAAAGC>G
ERR5749243	3037	PASS	C	T	17342	0.814612	63	0,21,8662,8536	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749243	3267	PASS	C	T	20637	0.969763	0	1,0,20622,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749243	4094	PASS	A	G	41648	0.967802	6	6,18,16496,25097	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Act/Gct	T459A	nsp3	0.965312	0.967802	1	1	A>G
ERR5749243	4960	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	14575	0.003087	0	2,14527,0,45	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtG/gtT	V747	nsp3	0.000673	0.062723	2	2	G>T
ERR5749243	5388	PASS	C	A	5224	0.95559	0	1,0,5218,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749243	5512	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5219	0.002299	0	0,5204,0,13	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N931	nsp3	0.002299	0.987013	1	1	C>T
ERR5749243	5986	PASS	C	T	10520	0.971768	0	3,0,10507,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749243	6954	PASS	T	C	21600	0.821852	0	0,5,0,21473	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749243	7058	PASS	G	A	21682	0.910617	0	0,7,0,21625	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggt/Agt	G1447S	nsp3	0.000616	0.910617	2	2	G>A
ERR5749243	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	33045	9.68E-4	110	14897,18116,32,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749243	11020	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20692	0.00116	0	1,20657,0,24	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ctC/ctT	L16	nsp6	0.00116	1	1	1	C>T
ERR5749243	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	20863	0.001198	0	20808,0,46,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749243	11287	PASS	GTCTGGTTTT	G	20857	0.996692	0	0,68,0,20788	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749243	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	17519	0.001313	0	17472,0,23,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749243	12970	PASS	C	T	16464	0.852648	0	0,5,0,16411	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N95	nsp9	0.8352	0.861883	1	1	C>T
ERR5749243	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	11353	0.001233	0	11340,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749243	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30234	0.001224	0	15086,15066,19,19	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749243	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	14802	0.003851	2147483647	14465,116,4,210	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749243	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	28773	0.001599	0	14424,14328,24,22	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749243	14408	PASS	C	T	28773	0.845376	5	2,5,14364,14181	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749243	14676	PASS	C	T	13353	0.82356	0	5,0,13317,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749243	15279	PASS	C	T	21863	0.87966	0	2,0,21821,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749243	16176	PASS	T	C	20039	0.979789	0	1,1,9251,10776	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749243	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	22921	4.8E-4	0	22910,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749243	18744	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22917	0.032029	0	22078,1,774,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y235	ExoN	0.000912	0.953624	2	2	C>T
ERR5749243	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27642	0.001519	0	27573,3,46,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749243	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	21814	6.88E-4	0	0,21797,0,15	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TA>T
ERR5749243	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	32839	7.0E-4	0	16036,16415,15,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749243	21764	PASS	ATACATG	A	10794	0.994071	0	63,0,10730,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749243	21990	PASS	TTTA	T	10799	0.997315	0	0,29,4,10766	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749243	22427	PASS	G	A	7928	0.86163	0	3,0,7903,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gta/Ata	V289I	S	0.856544	0.86163	1	1	G>A
ERR5749243	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	15859	0.001639	0	25,15803,0,27	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749243	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28185	8.52E-4	6	12319,15809,14,11	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749243	23063	PASS	A	T	12325	0.869209	0	0,2,0,12271	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749243	23271	PASS	C	A	22729	0.920806	0	2,0,22699,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749243	23403	PASS	A	G	22716	0.967556	0	0,4,0,22703	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749243	23481	PASS	C	T	36662	0.951339	7	0,5,13896,22688	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCt/tTt	S640F	S	0.001098	0.964516	1	1	C>T
ERR5749243	23604	PASS	C	A	13917	0.944313	0	6,0,13896,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749243	23709	PASS	C	T	13907	0.945279	0	0,5,11,13870	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749243	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	31739	5.99E-4	5	17808,13911,8,11	HIGH	NONE	FRAME_SHIFT	S	ttg/	L753	S	0.000334	0.080808	2	2	CT>C
ERR5749243	24506	PASS	T	G	18450	0.973767	0	6,0,18438,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749243	24616	PASS	C	T	18426	0.127917	1	24,15104,6,3243	LOW	SILENT	SYNONYMOUS_CODING	S	atC/atT	I1018	S	0.001268	0.127917	3	2	C>T
ERR5749243	24914	PASS	G	C	35607	0.959699	0	0,0,17728,17847	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749243	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	23110	0.001255	211	23025,11,22,9	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749243	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	23247	0.001204	833	22907,157,97,61	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749243	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	44735	0.001542	0	0,44665,0,69	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749243	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	10642	9.4E-4	0	1,10620,0,10	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749243	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	G	10642	7.52E-4	0	0,10628,0,8	HIGH	NONE	FRAME_SHIFT	M	cttgtaggcttgatgtggctcagctacttcattgcttctttc/	LVGLMWLSYFIASF87	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT>G
ERR5749243	26822	PASS	C	T	10650	0.855211	0	0,2,0,10509	LOW	SILENT	SYNONYMOUS_CODING	M	ttC/ttT	F100	M	0.001495	0.855211	1	1	C>T
ERR5749243	27389	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17212	0.002382	0	63,17072,0,47	.	.	.	.	.	.	.	0.001157	0.899553	2	1	C>T
ERR5749243	27972	PASS	C	T	9441	0.903188	0	0,0,9332,66	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749243	28048	PASS	G	T	9380	0.914819	0	0,9,0,9359	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749243	28111	PASS	A	G	30508	0.980005	0	1,0,21106,9389	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749243	28239	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTGT	G	21113	4.74E-4	0	21103,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF8	gtttta/	VL117	orf8	0.000417	0.984998	9	2	GTTGT>G
ERR5749243	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	21088	5.22E-4	0	21084,2,11,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749243	28270	PASS	TA	T	40966	0.994947	534	212,5,20817,19942	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749243	28280	PASS	G	C	40877	0.939795	26	10,0,20865,19935	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749243	28281	PASS	A	T	40877	0.909876	46	28,4,20841,19928	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749243	28282	PASS	T	A	40878	0.90775	4	18,12,20805,19937	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749243	28407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TACCCAATA	T	21124	5.21E-4	0	5,21108,0,11	HIGH	NONE	FRAME_SHIFT	N	cccaataat/	PNN46	N	0.000382	0.179673	1	1	TACCCAATA>T
ERR5749243	28881	PASS	G	A	19622	0.785853	6	5,1,9738,9651	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749243	28882	PASS	G	A	19621	0.837878	3	10,6,9807,9647	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749243	28883	PASS	G	C	19621	0.943275	0	1,0,9824,9772	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749243	28977	PASS	C	T	9983	0.914154	0	0,3,0,9957	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749243	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	54956	0.001165	0	27597,27268,38,38	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749244	199	PASS	G	T	5234	0.758884	0	28,0,5196,1	.	.	.	.	.	.	.	0.615385	0.766141	1	1	G>T
ERR5749244	241	PASS	C	T	10436	0.856267	0	0,0,5194,5199	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749244	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	13673	0.001902	0	13639,3,26,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749244	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	13670	0.001097	0	13273,3,342,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749244	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	31865	6.9E-4	23	18157,13684,19,3	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749244	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18172	0.001761	0	0,18118,0,33	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749244	913	PASS	C	T	18172	0.910962	0	0,8,0,18136	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749244	2453	PASS	C	T	14117	0.796345	0	0,7,3,13972	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L550F	nsp2	0.00429	0.842201	2	2	C>T
ERR5749244	3037	PASS	C	T	18742	0.812187	44	1,18,9363,9214	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749244	3045	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18773	0.001332	0	9350,9385,16,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCa/cTa	P109L	nsp3	0.001332	0.07971	2	2	C>T
ERR5749244	3267	PASS	C	T	18667	0.968661	0	3,0,18647,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749244	3671	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	23274	9.02E-4	0	11615,11552,13,12	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E318K	nsp3	0.000351	0.0625	6	2	G>A
ERR5749244	3802	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	28947	6.56E-4	7	17237,11687,8,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N363	nsp3	0.000554	0.064198	4	2	TA>T
ERR5749244	4270	PASS	T	C	17887	0.944708	0	0,19,1,17851	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaT/aaC	N517	nsp3	0.944708	0.944708	1	1	T>C
ERR5749244	5388	PASS	C	A	5326	0.518776	2147483647	0,0,2881,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749244	5388	PASS	C	G	5326	0.446301	2147483647	0,0,2441,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gGt	A890G	nsp3	0.446301	1	2	1	C>G
ERR5749244	5986	PASS	C	T	12538	0.973999	2147483647	0,0,12529,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749244	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11961	0.001672	0	0,11824,0,28	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749244	6954	PASS	T	C	18636	0.831348	2147483647	0,0,0,18547	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749244	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	26835	4.84E-4	25	16544,10278,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749244	10323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	18161	0.001211	0	2,18085,0,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749244	11082	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	19179	6.26E-4	0	19174,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000427	0.179468	2	1	TG>T
ERR5749244	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	19179	0.002086	0	19107,0,51,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749244	11287	PASS	GTCTGGTTTT	G	19182	0.998071	0	0,37,0,19145	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749244	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	33754	8.3E-4	0	19180,14531,17,12	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749244	11935	PASS	A	G	18263	0.976236	207	16,7,18235,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caA/caG	Q31	nsp7	0.000833	0.976236	2	2	A>G
ERR5749244	12025	PASS	C	T	18240	0.948026	0	2,0,18225,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S61	nsp7	0.001295	0.948026	1	1	C>T
ERR5749244	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	20323	9.84E-4	0	20286,0,20,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749244	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26254	0.001028	0	13116,13074,14,15	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749244	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	7880	0.00533	2304	7675,70,2,132	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749244	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	15290	5.89E-4	0	7664,7626,5,4	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749244	14408	PASS	C	T	15290	0.834532	4	1,3,7630,7536	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749244	14676	PASS	C	T	11359	0.815389	0	3,0,11325,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749244	15279	PASS	C	T	20045	0.885009	0	1,0,20020,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749244	16176	PASS	T	C	19311	0.98084	6	0,2,10041,9260	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749244	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	25759	4.27E-4	0	25748,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749244	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	22311	4.48E-4	0	0,22301,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749244	19320	PASS	C	T	18913	0.951885	0	7,0,18890,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H427	ExoN	0.004154	0.957053	2	2	C>T
ERR5749244	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25194	0.002223	0	25119,0,59,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749244	20400	PASS	A	C	26232	0.882129	0	0,83,8,26138	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gaA/gaC	E260D	endoR	0.882129	0.882129	1	1	A>C
ERR5749244	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28486	7.72E-4	1	13923,14224,14,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749244	21597	PASS	C	T	14310	0.901607	0	0,2,0,14273	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCt/tTt	S12F	S	0.00218	0.901607	2	1	C>T
ERR5749244	21764	PASS	ATACATG	A	13132	0.997182	51	35,2,13095,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749244	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	13129	6.09E-4	0	13121,0,8,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749244	21990	PASS	TTTA	T	13136	0.997564	0	0,32,5,13099	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749244	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	14553	0.001924	0	0,14520,0,28	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749244	23063	PASS	A	T	15101	0.863982	2147483647	0,0,0,15025	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749244	23271	PASS	C	A	20333	0.924507	0	1,0,20308,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749244	23403	PASS	A	G	20329	0.969994	0	0,5,0,20311	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749244	23595	PASS	C	T	15912	0.86771	0	2,0,15860,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCt/aTt	T678I	S	0.003401	0.86771	1	1	C>T
ERR5749244	23604	PASS	C	A	15912	0.932881	0	17,0,15869,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749244	23709	PASS	C	T	15911	0.941676	0	0,4,2,15878	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749244	24214	PASS	T	C	13254	0.950807	0	5,0,13235,0	LOW	SILENT	SYNONYMOUS_CODING	S	tcT/tcC	S884	S	0.950807	0.950807	1	1	T>C
ERR5749244	24506	PASS	T	G	15995	0.974429	0	7,0,15983,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749244	24914	PASS	G	C	40434	0.959564	0	1,1,20145,20253	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749244	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	25708	0.002606	92	18904,6716,82,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749244	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	13984	0.001573	195	13916,17,13,9	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749244	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	13958	7.88E-4	0	13947,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749244	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	13777	5.81E-4	0	0,13768,0,8	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749244	27972	PASS	C	T	9835	0.889171	40	1,2,9734,55	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749244	28048	PASS	G	T	9779	0.905512	0	0,17,0,9758	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749244	28111	PASS	A	G	26794	0.973949	3	6,1,16991,9777	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749244	28270	PASS	TA	T	32589	0.994323	352	182,14,16778,15626	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749244	28280	PASS	G	C	32501	0.938986	5	6,2,16809,15620	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749244	28281	PASS	A	T	32501	0.912772	21	21,6,16803,15613	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749244	28282	PASS	T	A	32506	0.912232	5	19,11,16771,15629	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749244	28396	PASS	G	A	17015	0.93782	191	6,3,2,16983	LOW	SILENT	SYNONYMOUS_CODING	N	cgG/cgA	R41	N	0.000496	0.946059	5	2	G>A
ERR5749244	28406	PASS	T	C	17016	0.921074	214	7,7,1,16967	LOW	SILENT	SYNONYMOUS_CODING	N	Tta/Cta	L45	N	0.00043	0.921074	3	2	T>C
ERR5749244	28881	PASS	G	A	16681	0.773994	7	7,2,8288,8199	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749244	28882	PASS	G	A	16681	0.829926	4	4,1,8357,8178	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749244	28883	PASS	G	C	16681	0.944847	2	3,1,8361,8298	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749244	28977	PASS	C	T	8502	0.91155	0	0,2,0,8480	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749244	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	41596	0.00137	308	33047,8436,6,55	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749244	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	65726	0.001172	0	33011,32603,47,47	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749244	29779	PASS	G	T	10211	0.959455	0	0,6,0,10203	.	.	.	.	.	.	.	0.001489	0.975228	1	1	G>T
ERR5749245	241	PASS	C	T	6271	0.862861	3	0,1,3126,3112	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749245	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	10520	0.003042	0	10472,13,32,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749245	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	10524	0.0019	0	10354,18,20,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749245	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	10524	0.00152	0	10354,18,16,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749245	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	10524	0.009787	0	10354,18,103,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749245	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	10532	0.003513	0	10466,27,37,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749245	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	10531	9.5E-4	0	10470,29,10,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttatg/gtg	VM84V	leader	0.000554	0.991848	4	1	GTTA>G
ERR5749245	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	10531	0.001899	0	10470,29,20,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749245	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	10531	0.002089	0	10461,29,22,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749245	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATGGTTG	T	10531	0.001329	0	10461,29,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	atggttgag/	MVE85	leader	0.000587	0.476744	4	1	TATGGTTG>T
ERR5749245	635	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10517	0.001521	0	0,10494,0,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgt/Tgt	R124C	leader	0.00148	0.880435	1	1	C>T
ERR5749245	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	25060	7.18E-4	14	14535,10501,15,3	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749245	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	25063	0.003152	42	14479,10491,63,16	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749245	913	PASS	C	T	14547	0.908847	0	0,12,0,14506	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749245	2232	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26549	0.006102	11	12549,13809,98,82	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A476V	nsp2	0.000499	0.381237	2	2	C>T
ERR5749245	3037	PASS	C	T	16702	0.82074	41	1,17,8336,8226	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749245	3267	PASS	C	T	15908	0.970267	2147483647	0,0,15892,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749245	4551	PASS	C	T	11579	0.897919	2147483647	0,0,0,11467	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T611I	nsp3	0.001721	0.897919	3	2	C>T
ERR5749245	5388	PASS	C	A	5099	0.960188	2147483647	0,0,5094,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749245	5986	PASS	C	T	11554	0.97542	2147483647	0,0,11544,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749245	6954	PASS	T	C	17505	0.807712	0	0,6,4,17373	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749245	7070	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	31234	0.001537	153	13620,17557,50,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggc/Agc	G1451S	nsp3	0.000698	0.101434	3	1	G>A
ERR5749245	7735	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19664	0.00239	0	19600,0,50,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I1672	nsp3	0.000658	0.954659	3	2	C>T
ERR5749245	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	21021	0.001047	26	15486,5513,22,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749245	10323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	18798	0.001224	0	2,18723,0,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749245	10369	PASS	C	T	18813	0.073513	0	4,17367,0,1428	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	cgC/cgT	R105	3Cpro	0.001225	0.120075	1	1	C>T
ERR5749245	11287	PASS	GTCTGGTTTT	G	20356	0.99548	0	0,92,0,20264	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749245	12162	PASS	A	G	37246	0.969876	2	2,1,17823,19407	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cAg/cGg	Q24R	nsp8	0.000894	0.982497	1	1	A>G
ERR5749245	12754	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30546	0.003634	9	10468,19948,32,85	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C23	nsp9	0.001216	0.947969	1	1	C>T
ERR5749245	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25876	0.001739	0	12916,12871,26,26	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749245	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	6928	0.003897	1711	6767,59,2,96	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749245	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	13452	0.001933	0	6750,6683,14,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749245	14408	PASS	C	T	13452	0.846789	9	0,3,6726,6623	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749245	14599	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10720	0.001399	0	10696,1,15,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L387	RdRp	0.000639	0.922766	3	2	C>T
ERR5749245	14676	PASS	C	T	10719	0.732904	0	3,0,10677,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749245	15279	PASS	C	T	15719	0.895922	0	2,0,15700,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749245	16176	PASS	T	C	16636	0.978601	0	0,1,7978,8650	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749245	17562	PASS	G	T	31299	0.90562	3	15,20,15838,15398	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	cgG/cgT	R442	helicase	0.000543	0.90562	3	2	G>T
ERR5749245	17562	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCGT	G	31299	5.43E-4	52	15866,15416,0,17	MODERATE	NONE	CODON_DELETION	ORF1ab	cgt/	R443	helicase	0.000543	0.90562	3	2	GCGT>G
ERR5749245	17615	PASS	A	G	15851	0.898366	0	0,0,3,15804	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749245	19483	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	16191	0.001112	0	0,16156,0,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gct/Act	A482T	ExoN	0.001112	0.089844	3	1	G>A
ERR5749245	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22872	0.002142	0	22806,0,52,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749245	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27911	0.001075	3	13665,13905,18,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749245	21764	PASS	ATACATG	A	12584	0.99698	0	38,0,12546,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749245	21867	PASS	G	T	25087	0.861881	201	10,104,12462,12444	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aGa/aTa	R102I	S	0.000625	0.861881	2	2	G>T
ERR5749245	21990	PASS	TTTA	T	12592	0.997141	0	0,36,5,12551	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749245	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	15527	0.001481	0	0,15496,0,23	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749245	23063	PASS	A	T	14637	0.859056	0	0,3,1,14566	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749245	23183	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTCAACTTCAATGGTTTA	T	32495	4.0E-4	33	17821,14661,13,0	HIGH	NONE	FRAME_SHIFT	S	ttcaacttcaatggttta/	FNFNGL541	S	0.000388	0.135922	2	2	TTCAACTTCAATGGTTTA>T
ERR5749245	23271	PASS	C	A	17825	0.929369	0	2,0,17782,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749245	23309	PASS	G	C	17813	0.954191	0	0,0,17745,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gag/Cag	E583Q	S	0.003492	0.954191	2	2	G>C
ERR5749245	23403	PASS	A	G	17852	0.964542	0	0,2,29,17804	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749245	23604	PASS	C	A	14987	0.949356	0	6,0,14976,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749245	23709	PASS	C	T	14982	0.932786	0	0,2,9,14949	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749245	24127	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	24343	7.39E-4	8	12616,11715,6,12	HIGH	NONE	FRAME_SHIFT	S	aac/	N856	S	0.000324	0.111888	4	1	TA>T
ERR5749245	24506	PASS	T	G	15079	0.973871	0	1,0,15074,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749245	24914	PASS	G	C	41667	0.955864	0	1,1,20750,20887	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749245	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	10687	9.36E-4	0	10677,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749245	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	40998	0.001171	0	0,40944,0,48	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749245	26158	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	40998	5.61E-4	0	0,40967,0,23	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF3a	gttaat/gat	VN256D	orf3a	0.000297	0.905181	6	2	GTTA>G
ERR5749245	26730	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	26942	6.31E-4	0	13453,13498,8,9	HIGH	NONE	FRAME_SHIFT	M	tac/	Y71	M	0.000371	0.919543	3	2	GT>G
ERR5749245	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	13556	6.64E-4	0	0,13545,0,9	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749245	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	13556	0.001402	0	0,13537,0,19	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749245	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	13556	0.002951	0	0,13511,0,40	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749245	27567	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTTTAGCACTCAA	C	19315	6.21E-4	0	19299,2,12,0	MODERATE	NONE	CODON_DELETION	ORF7a	agcactcaattt/	STQF60	orf7a	0.000449	0.998291	4	1	CTTTAGCACTCAA>C
ERR5749245	27972	PASS	C	T	9735	0.900257	0	1,0,9658,50	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749245	28048	PASS	G	T	9693	0.915197	0	0,15,0,9674	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749245	28111	PASS	A	G	29198	0.977978	1	6,4,19487,9691	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749245	28237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTGT	G	19497	5.64E-4	0	19486,0,11,0	MODERATE	NONE	CODON_DELETION	ORF8	gtt/	V117	orf8	0.000442	0.966707	4	2	GTGT>G
ERR5749245	28270	PASS	TA	T	37599	0.995	468	190,5,19242,18169	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749245	28280	PASS	G	C	37511	0.935965	21	13,2,19281,18138	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749245	28281	PASS	A	T	37511	0.914212	2	20,15,19267,18146	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749245	28282	PASS	T	A	37515	0.909316	7	24,14,19218,18158	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749245	28881	PASS	G	A	11182	0.739403	6	5,1,5540,5484	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749245	28882	PASS	G	A	11182	0.823466	18	7,0,5599,5460	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749245	28883	PASS	G	C	11183	0.940356	0	1,1,5613,5559	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749245	28977	PASS	C	T	5705	0.916214	0	0,4,0,5690	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749245	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	64125	0.001653	0	32194,31767,70,68	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749245	29445	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTG	C	8823	9.07E-4	0	8815,0,8,0	HIGH	NONE	FRAME_SHIFT	N	gtg/	V392	N	0.000907	0.853797	2	2	CTG>C
ERR5749246	241	PASS	C	T	12006	0.869065	0	1,1,5986,5994	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749246	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	10884	0.001194	0	10873,1,13,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749246	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	10883	0.002113	0	10850,1,23,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749246	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10878	0.001195	0	10059,3,748,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749246	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	10878	8.27E-4	0	10866,3,9,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749246	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	10877	0.001103	0	10861,4,12,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749246	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	34009	0.001059	17	23080,10893,31,5	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749246	913	PASS	C	T	23097	0.916786	0	0,12,0,23052	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749246	1912	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	46019	0.002738	4	26933,18940,84,50	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S369	nsp2	0.000681	0.08802	2	1	C>T
ERR5749246	2110	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26979	0.024426	0	0,26102,0,841	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N435	nsp2	0.024426	0.811371	1	1	C>T
ERR5749246	2453	PASS	C	T	12693	0.754825	0	0,14,4,12511	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L550F	nsp2	0.00429	0.842201	2	2	C>T
ERR5749246	3037	PASS	C	T	17008	0.819732	24	0,8,8497,8379	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749246	3267	PASS	C	T	24135	0.971867	0	3,0,24119,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749246	5388	PASS	C	A	5483	0.957687	2147483647	0,0,5479,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749246	5986	PASS	C	T	2807	0.976844	2147483647	0,0,2806,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749246	6248	PASS	A	T	27337	0.983539	0	10,0,27313,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Aac/Tac	N1177Y	nsp3	0.983539	0.983539	1	1	A>T
ERR5749246	6954	PASS	T	C	24869	0.815795	0	0,1,0,24724	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749246	7564	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	18715	6.41E-4	0	0,18703,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/	Y1617	nsp3	0.000586	0.056194	4	2	CT>C
ERR5749246	7764	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19018	0.001052	0	18978,0,20,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCc/tTc	S1682F	nsp3	0.001052	0.964731	1	1	C>T
ERR5749246	8512	PASS	A	G	10543	0.809162	2147483647	0,0,0,10478	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caA/caG	Q1931	nsp3	0.8	0.822278	1	1	A>G
ERR5749246	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	28252	7.43E-4	52	15569,12662,21,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749246	10323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	17915	0.004131	0	1,17806,0,75	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749246	11020	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9278	0.001725	0	6,9250,0,16	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ctC/ctT	L16	nsp6	0.00116	1	1	1	C>T
ERR5749246	11082	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	26568	5.27E-4	0	26569,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000427	0.179468	2	1	TG>T
ERR5749246	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	26568	0.001393	0	26488,0,57,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749246	11104	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	26561	8.66E-4	0	26445,0,26,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccT/ccC	P44	nsp6	0.000866	0.675414	2	1	T>C
ERR5749246	11287	PASS	GTCTGGTTTT	G	26571	0.997629	0	0,61,0,26508	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749246	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	38381	9.38E-4	6	25612,12713,23,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749246	11750	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	50070	0.001019	5	25514,24415,40,29	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L260F	nsp6	0.001019	0.70989	2	1	C>T
ERR5749246	11782	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	25577	0.00215	0	5,25263,0,58	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaA/aaG	K270	nsp6	0.001073	0.917917	2	2	A>G
ERR5749246	11824	PASS	C	T	25618	0.906472	0	0,11,0,25556	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I284	nsp6	0.000465	0.922016	2	2	C>T
ERR5749246	12125	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	18434	0.001085	0	4,18355,0,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y12H	nsp8	0.000847	0.113436	1	1	T>C
ERR5749246	13308	PASS	A	G	13648	0.928707	164	5,2,1,13627	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K95R	nsp10	0.001976	0.928707	2	1	A>G
ERR5749246	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19141	0.001515	0	7,19068,0,35	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749246	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	8827	0.004645	2009	8590,103,7,122	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749246	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	17106	7.6E-4	0	8581,8526,7,6	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749246	14408	PASS	C	T	17106	0.859289	1	3,4,8540,8462	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749246	14676	PASS	C	T	15804	0.710516	0	8,0,15736,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749246	15279	PASS	C	T	24500	0.908694	0	2,0,24475,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749246	16176	PASS	T	C	20861	0.98164	4	1,0,8170,12685	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749246	17747	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTG	C	15172	9.23E-4	0	15155,3,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctgct/	PA504	helicase	0.000839	0.968462	2	2	CTG>C
ERR5749246	18504	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	34186	7.02E-4	0	7,33698,0,437	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K155N	ExoN	0.000518	0.094148	4	3	A>C
ERR5749246	18636	PASS	G	T	60192	0.963467	1	1,3,25888,34278	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtG/gtT	V199	ExoN	0.00055	0.963467	3	2	G>T
ERR5749246	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	25905	5.02E-4	0	25892,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749246	18981	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28718	0.001184	0	28679,0,36,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H314	ExoN	0.001184	0.929465	1	1	C>T
ERR5749246	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24861	0.002896	0	24772,0,76,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749246	20578	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	24567	0.001099	0	24510,0,52,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtg/Ttg	V320L	endoR	0.00085	0.958277	3	1	G>T
ERR5749246	20987	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	53312	3.75E-4	0	26656,26636,10,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L111	MethTr	0.000276	0.056129	4	2	CT>C
ERR5749246	21305	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	27611	8.69E-4	0	2,27542,0,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cGc/cAc	R216H	MethTr	0.000727	0.703943	1	1	G>A
ERR5749246	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	37577	0.001304	2	18363,18731,27,32	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749246	21621	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18915	0.00148	0	0,18870,0,29	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCc/aTc	T20I	S	0.00148	0.944623	2	2	C>T
ERR5749246	21736	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12530	0.001596	0	12484,16,21,0	LOW	SILENT	SYNONYMOUS_CODING	S	ttC/ttT	F58	S	0.001596	0.804427	3	2	C>T
ERR5749246	21764	PASS	ATACATG	A	12513	0.995285	0	58,0,12454,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749246	21990	PASS	TTTA	T	12520	0.997524	0	0,31,5,12484	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749246	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	33717	0.001008	8	14174,19491,20,16	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749246	23063	PASS	A	T	14168	0.857778	0	0,4,0,14102	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749246	23271	PASS	C	A	26669	0.924444	0	2,0,26648,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749246	23403	PASS	A	G	26659	0.968791	2147483647	0,0,0,26640	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749246	23604	PASS	C	A	14845	0.9387	0	13,0,14814,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749246	23709	PASS	C	T	14834	0.939598	0	0,5,3,14804	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749246	23802	PASS	C	T	14856	0.977181	245	7,1,0,14840	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCt/aTt	T747I	S	0.001717	0.977181	3	2	C>T
ERR5749246	23855	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	9810	8.15E-4	0	9802,0,8,0	HIGH	NONE	FRAME_SHIFT	S	cgt/	R765	S	0.000815	0.181818	2	2	CG>C
ERR5749246	24506	PASS	T	G	20718	0.975335	0	10,0,20702,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749246	24914	PASS	G	C	36604	0.958174	0	0,0,18238,18334	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749246	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	28167	8.88E-4	53	18684,9448,32,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749246	25391	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTA	T	18801	5.85E-4	0	18790,0,11,0	HIGH	NONE	FRAME_SHIFT+START_LOST	ORF3a	atg/	M1	orf3a	0.000585	0.191026	1	1	TTA>T
ERR5749246	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	17892	0.001509	399	17815,21,11,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749246	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	17880	6.15E-4	0	17868,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749246	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	18027	0.001331	875	17718,117,106,65	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749246	26526	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	13890	0.001224	0	3,13849,0,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Gca/Tca	A2S	M	0.001224	0.951192	3	1	G>T
ERR5749246	27476	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	44736	0.001051	9	24620,20065,21,28	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	aCa/aTa	T28I	orf7a	0.000547	0.22827	4	2	C>T
ERR5749246	27972	PASS	C	T	9477	0.901868	19	1,1,9396,49	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749246	28001	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	18829	0.001222	0	9393,9384,13,12	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ccG/ccA	P36	orf8	0.00085	0.830607	2	1	G>A
ERR5749246	28048	PASS	G	T	9429	0.916004	0	0,18,0,9409	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749246	28111	PASS	A	G	33998	0.979793	6	4,4,24543,9429	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749246	28270	PASS	TA	T	47640	0.994983	514	230,11,24239,23162	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749246	28280	PASS	G	C	47546	0.938249	26	10,0,24296,23148	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749246	28281	PASS	A	T	47546	0.91688	34	23,4,24286,23141	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749246	28282	PASS	T	A	47549	0.909903	11	28,15,24232,23161	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749246	28603	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	38230	7.06E-4	2	19081,18926,14,17	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F110	N	0.000427	0.883357	2	2	C>T
ERR5749246	28657	PASS	C	T	19157	0.862766	0	0,10,2,19073	LOW	SILENT	SYNONYMOUS_CODING	N	gaC/gaT	D128	N	0.00124	0.862766	1	1	C>T
ERR5749246	28881	PASS	G	A	20058	0.770266	12	5,0,9949,9850	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749246	28882	PASS	G	A	20057	0.83856	12	5,0,10036,9829	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749246	28883	PASS	G	C	20057	0.946104	2	1,2,10051,9976	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749246	28977	PASS	C	T	10229	0.923746	0	0,1,0,10203	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749246	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	41543	0.001131	144	31268,10176,11,39	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749246	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	62155	0.001014	0	31209,30819,44,41	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749246	29311	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	31317	4.15E-4	0	8,31292,0,13	HIGH	NONE	FRAME_SHIFT	N	aaa/	K347	N	0.000335	0.790798	3	2	CA>C
ERR5749246	29781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	8092	0.00173	0	0,8073,0,19	.	.	.	.	.	.	.	0.00173	0.972321	2	1	G>T
ERR5749247	210	PASS	G	T	1927	0.800208	5	19,1,1872,33	.	.	.	.	.	.	.	0.001452	1	2	1	G>T
ERR5749247	241	PASS	C	T	3772	0.848887	0	0,0,1877,1879	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749247	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	6026	0.001825	0	5754,0,269,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749247	553	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	6030	0.002322	0	0,5994,0,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caG/caT	Q96H	leader	0.002322	0.830163	2	2	G>T
ERR5749247	625	PASS	G	T	6044	0.298809	0	0,4052,0,1991	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaG/aaT	K120N	leader	0.004721	0.298809	2	1	G>T
ERR5749247	913	PASS	C	T	10918	0.918208	0	0,8,0,10893	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749247	1190	PASS	C	T	8754	0.883139	0	0,2,0,8728	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cca/Tca	P129S	nsp2	0.002242	0.938547	1	1	C>T
ERR5749247	1357	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	10723	0.001772	0	10644,0,20,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcC	A184	nsp2	0.000493	0.077966	3	2	T>C
ERR5749247	1461	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AG	A	21229	5.18E-4	30	10572,10646,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggt/	G220	nsp2	0.000518	0.90899	2	2	AG>A
ERR5749247	1874	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	11620	0.001635	0	1,11572,0,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gca/Tca	A357S	nsp2	0.001611	0.344371	2	1	G>T
ERR5749247	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	25660	0.001325	2173	12823,11958,18,804	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749247	2890	PASS	G	A	4354	0.982545	0	1,0,4352,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtG/gtA	V57	nsp3	0.934783	0.983505	1	1	G>A
ERR5749247	3037	PASS	C	T	8638	0.824265	12	0,4,4317,4263	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749247	3267	PASS	C	T	11240	0.971174	0	1,0,11233,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749247	4832	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTAG	C	18944	0.001003	0	9474,9454,9,10	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ctaggt/cgt	LG705R	nsp3	0.000542	0.727166	3	2	CTAG>C
ERR5749247	5206	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	7364	0.001901	0	0,7342,0,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atT	M829I	nsp3	0.001901	0.0725	2	1	G>T
ERR5749247	5388	PASS	C	A	2290	0.966812	2147483647	0,0,2288,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749247	5986	PASS	C	T	5856	0.975581	2147483647	0,0,5851,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749247	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6979	0.002293	0	0,6897,0,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749247	6954	PASS	T	C	11063	0.819308	0	0,1,0,11006	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749247	8084	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	12613	0.001903	0	12590,0,24,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1790	nsp3	0.000543	0.923413	4	2	GA>G
ERR5749247	8964	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	10414	0.001344	0	10400,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K138	nsp4	0.000553	0.981649	4	2	CA>C
ERR5749247	9130	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	10405	0.00221	0	0,10363,0,25	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtG/gtC	V192	nsp4	0.001321	0.963415	2	1	G>C
ERR5749247	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	11839	0.001689	16	9499,2320,20,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749247	11082	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	19347	9.82E-4	0	19331,0,19,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000427	0.179468	2	1	TG>T
ERR5749247	11095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTT	C	19347	0.001499	0	19312,0,29,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L43	nsp6	0.000515	0.887707	7	2	CTT>C
ERR5749247	11287	PASS	GTCTGGTTTT	G	19343	0.997208	0	0,54,0,19289	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749247	11417	PASS	G	T	5218	0.931583	0	2,0,5211,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Ttt	V149F	nsp6	0.00274	0.951155	2	2	G>T
ERR5749247	11750	PASS	C	T	25565	0.688089	46	0,14,13100,11245	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L260F	nsp6	0.001019	0.70989	2	1	C>T
ERR5749247	11750	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	G	25565	0.003286	0	0,14,49,1135	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Gtc	L260V	nsp6	0.001019	0.70989	2	1	C>G
ERR5749247	11935	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATG	A	16808	8.33E-4	0	16788,6,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtc/	V33	nsp7	0.000833	0.976236	2	2	ATG>A
ERR5749247	13164	PASS	C	T	11706	0.941398	0	1,0,11697,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T47I	nsp10	0.001249	0.952318	1	1	C>T
ERR5749247	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	4457	0.004263	1143	4354,35,3,65	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749247	14408	PASS	C	T	8660	0.843418	6	0,2,4327,4249	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749247	14676	PASS	C	T	8508	0.724612	0	13,0,8455,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749247	15279	PASS	C	T	10559	0.893645	0	1,0,10544,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749247	15872	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	8319	0.001683	0	8301,4,14,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gAa/gGa	E811G	RdRp	0.001683	0.05155	1	1	A>G
ERR5749247	16176	PASS	T	C	11970	0.978446	0	0,0,3651,8313	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749247	16575	PASS	C	T	15160	0.827968	0	26,0,15081,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D113	helicase	0.001088	0.827968	1	1	C>T
ERR5749247	16647	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	15108	0.003045	0	0,14960,0,132	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acG/acT	T137	helicase	0.000746	0.885245	2	1	G>T
ERR5749247	17762	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTG	C	8507	9.4E-4	0	8499,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtc/	V510	helicase	0.000697	0.912542	2	2	CTG>C
ERR5749247	18366	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	14631	0.001435	0	14579,0,24,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ctA/ctG	L109	ExoN	0.000756	0.984275	2	2	A>G
ERR5749247	18501	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	14583	0.001166	0	0,14566,0,17	HIGH	NONE	FRAME_SHIFT	ORF1ab	gga/Agga	G156R?	ExoN	0.000336	0.857143	4	2	C>CA
ERR5749247	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	21680	5.54E-4	0	21669,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749247	18803	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	43253	7.86E-4	23	21541,21494,76,115	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aGc/aTc	S255I	ExoN	0.000786	0.897116	2	1	G>T
ERR5749247	19329	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	8823	0.002153	0	8801,0,20,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcC	A430	ExoN	0.001217	0.228916	1	1	T>C
ERR5749247	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8329	0.003242	0	8293,0,29,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749247	20233	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18912	0.00111	0	18882,0,22,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ccc/Tcc	P205S	endoR	0.000964	0.980008	2	1	C>T
ERR5749247	20930	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16624	0.002948	0	16565,0,51,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aTg	T91M	MethTr	0.000902	0.95585	2	2	C>T
ERR5749247	20930	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	16624	9.02E-4	0	16609,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggt/	G92	MethTr	0.000902	0.95585	2	2	CG>C
ERR5749247	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	16622	0.001324	0	0,16600,0,22	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TA>T
ERR5749247	21123	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	32662	0.00101	5	16013,16588,25,35	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggG/ggT	G155	MethTr	0.000257	0.90982	5	2	G>T
ERR5749247	21516	PASS	C	T	9457	0.885376	0	11,0,9414,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N286	MethTr	0.000412	0.905456	2	2	C>T
ERR5749247	21764	PASS	ATACATG	A	9148	0.993988	0	55,0,9093,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749247	21990	PASS	TTTA	T	9152	0.996941	0	0,28,4,9120	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749247	23063	PASS	A	T	9102	0.871786	0	0,3,0,9060	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749247	23271	PASS	C	A	15644	0.916262	0	1,0,15622,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749247	23403	PASS	A	G	15639	0.972569	0	0,1,0,15633	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749247	23604	PASS	C	A	8963	0.962513	0	3,0,8952,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749247	23664	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	8941	0.00123	30	8858,8930,0,11	HIGH	NONE	FRAME_SHIFT	S	gaa/	E702	S	0.000837	0.918	2	2	CAG>C
ERR5749247	23709	PASS	C	T	8951	0.943582	0	0,3,0,8939	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749247	23817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	14239	0.001966	9	5267,8941,6,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTt/cCt	L752P	S	0.000646	0.066832	1	1	T>C
ERR5749247	24506	PASS	T	G	11528	0.973282	0	16,0,11508,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749247	24914	PASS	G	C	32341	0.961164	3	1,0,16116,16204	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749247	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	3673	0.007079	561	3628,13,0,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749247	26060	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGG	C	19992	5.5E-4	0	19981,0,11,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF3a	ggtgtt/gtt	GV224V	orf3a	0.000459	0.822477	2	2	CTGG>C
ERR5749247	26062	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	20001	0.00155	0	19941,9,38,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Ggt/Tgt	G224C	orf3a	0.001077	0.906894	1	1	G>T
ERR5749247	26151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	19964	5.01E-4	0	0,19954,0,10	HIGH	NONE	FRAME_SHIFT	ORF3a	gga/	G254	orf3a	0.000501	0.913698	4	2	CG>C
ERR5749247	26416	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	18233	0.00362	28	8967,9092,106,65	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	Gtt/Ttt	V58F	E	0.000457	0.913418	2	2	G>T
ERR5749247	26526	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	9230	0.001733	0	5,9196,0,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Gca/Tca	A2S	M	0.001224	0.951192	3	1	G>T
ERR5749247	26645	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	8492	0.001413	0	8480,0,12,0	HIGH	NONE	FRAME_SHIFT	M	agg/	R42	M	0.00097	0.828654	2	2	CAG>C
ERR5749247	26717	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	16857	0.001602	1	8417,8367,14,16	LOW	SILENT	SYNONYMOUS_CODING	M	ttT/ttC	F65	M	0.001602	0.063291	2	2	T>C
ERR5749247	27552	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	13760	7.99E-4	0	13749,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF7a	ttt/	F54	orf7a	0.000563	0.985801	6	1	AT>A
ERR5749247	27752	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	13756	5.82E-4	0	0,13748,0,8	HIGH	NONE	FRAME_SHIFT	ORF7a	gaa/	E121	orf7a	0.000582	0.943806	2	2	CAG>C
ERR5749247	27972	PASS	C	T	3389	0.894659	19	1,1,3357,19	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749247	28048	PASS	G	T	3371	0.923168	0	0,4,0,3365	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749247	28095	PASS	A	T	3374	0.959395	67	2,0,0,3369	HIGH	NONSENSE	STOP_GAINED	ORF8	Aaa/Taa	K68*	orf8	0.002672	0.967672	2	2	A>T
ERR5749247	28111	PASS	A	G	21687	0.981464	7	3,2,18307,3368	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749247	28270	PASS	TA	T	35500	0.996254	324	133,4,18105,17262	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749247	28280	PASS	G	C	35440	0.934678	11	9,2,18123,17243	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749247	28281	PASS	A	T	35440	0.916676	27	22,5,18113,17249	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749247	28282	PASS	T	A	35441	0.910838	10	15,6,18070,17261	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749247	28651	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	15883	0.001385	0	0,15861,0,22	HIGH	NONE	FRAME_SHIFT	N	aaa/	K127	N	0.000502	0.918117	3	2	CA>C
ERR5749247	28881	PASS	G	A	6337	0.766293	0	1,0,3134,3110	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749247	28882	PASS	G	A	6336	0.830019	0	1,0,3167,3112	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749247	28883	PASS	G	C	6336	0.941604	6	0,2,3166,3160	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749247	28977	PASS	C	T	3223	0.936395	0	0,1,0,3219	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749247	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	35315	0.001274	0	17733,17506,26,26	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749247	29386	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	4846	0.001444	0	4839,0,7,0	HIGH	NONE	FRAME_SHIFT	N	aag/	K373	N	0.000887	0.899197	4	2	CA>C
ERR5749247	29757	PASS	G	T	3833	0.840856	0	0,15,0,3813	.	.	.	.	.	.	.	0.840856	0.933071	1	1	G>T
ERR5749248	241	PASS	C	T	22629	0.85713	1	2,4,11259,11270	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749248	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	11661	6.86E-4	0	11655,3,8,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749248	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	11661	6.86E-4	0	11639,3,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749248	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	11645	0.002319	0	10779,3,809,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749248	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	11645	6.87E-4	0	11634,3,8,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749248	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	30064	7.98E-4	19	18359,11673,21,3	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749248	913	PASS	C	T	18361	0.891128	0	0,13,0,18313	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749248	3037	PASS	C	T	17732	0.82884	54	0,18,8863,8715	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749248	3267	PASS	C	T	17794	0.969147	0	3,0,17782,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749248	5170	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	11763	6.8E-4	0	1,11754,0,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T819	nsp3	0.000565	0.894036	2	2	CCA>C
ERR5749248	5388	PASS	C	A	5846	0.957749	2147483647	0,0,5843,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749248	5986	PASS	C	T	10797	0.9724	2147483647	0,0,10791,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749248	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	10513	0.008751	0	3,10415,0,92	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L1328S?	nsp3	0.000731	0.14377	4	2	C>CT
ERR5749248	6954	PASS	T	C	19682	0.823087	0	0,2,1,19574	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749248	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	28358	6.35E-4	55	13966,14374,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749248	11074	PASS	C	CT	16174	0.06968	0	14794,4,1127,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CT
ERR5749248	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	16174	0.011624	0	14794,4,188,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749248	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16174	0.00371	0	16074,4,72,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749248	11075	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TC	16170	8.04E-4	0	16156,4,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/tCtt	F35S?	nsp6	0.000555	0.885796	4	2	T>TC
ERR5749248	11082	PASS	TG	T	16101	0.085585	0	14792,0,1378,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000427	0.179468	2	1	TG>T
ERR5749248	11083	PASS	G	T	16101	0.873859	0	2,0,14667,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749248	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	16101	0.029129	0	15570,0,469,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/tTat	Y38L?	nsp6	0.000477	0.901695	5	2	G>GT
ERR5749248	11287	PASS	GTCTGGTTTT	G	16164	0.998268	0	0,28,0,16136	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749248	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	31263	8.64E-4	5	18754,12459,14,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749248	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29006	0.001034	0	14491,14455,15,15	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749248	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	11532	0.003555	2529	11338,51,7,131	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749248	14408	PASS	C	T	22597	0.847015	4	1,3,11290,11132	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749248	14676	PASS	C	T	11783	0.740898	0	3,0,11747,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749248	15279	PASS	C	T	19258	0.910583	0	2,0,19240,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749248	16176	PASS	T	C	18459	0.98001	0	0,1,9039,9408	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749248	16391	PASS	C	T	9042	0.731697	0	0,2,0,9012	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A52V	helicase	0.71923	0.732678	1	1	C>T
ERR5749248	17615	PASS	A	G	12948	0.893188	0	0,1,1,12897	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749248	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	21347	6.56E-4	0	21333,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749248	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25318	0.002449	0	25242,0,64,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749248	20578	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	22670	0.001103	0	22608,0,58,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtg/Ttg	V320L	endoR	0.00085	0.958277	3	1	G>T
ERR5749248	21764	PASS	ATACATG	A	10937	0.9968	0	35,0,10902,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749248	21990	PASS	TTTA	T	10942	0.998081	0	0,21,4,10917	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749248	23063	PASS	A	T	11072	0.867323	0	0,2,1,11015	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749248	23271	PASS	C	A	17795	0.927452	0	2,0,17780,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749248	23403	PASS	A	G	17787	0.965649	0	0,1,0,17777	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749248	23604	PASS	C	A	13399	0.955594	0	6,0,13385,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749248	23709	PASS	C	T	13381	0.937224	0	0,4,2,13364	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749248	24506	PASS	T	G	15877	0.973862	0	4,0,15869,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749248	24914	PASS	G	C	29914	0.960152	0	0,0,14904,14986	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749248	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	21599	0.001204	319	21515,25,14,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749248	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	21560	6.03E-4	0	21546,1,13,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749248	26730	PASS	G	C	20291	0.915332	1	3,5,10104,10139	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Gtt/Ctt	V70L	M	0.000371	0.919543	3	2	G>C
ERR5749248	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	10257	8.77E-4	0	0,10248,0,9	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749248	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	10260	0.001559	0	0,10243,0,16	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749248	27972	PASS	C	T	9038	0.911927	0	0,0,8979,36	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749248	28048	PASS	G	T	9010	0.919756	0	0,9,0,8995	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749248	28111	PASS	A	G	27573	0.981322	2	3,0,18552,9013	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749248	28270	PASS	TA	T	35916	0.995629	377	156,5,18328,17431	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749248	28280	PASS	G	C	35858	0.935747	44	16,0,18358,17408	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749248	28281	PASS	A	T	35858	0.907106	32	22,4,18337,17418	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749248	28282	PASS	T	A	35858	0.895839	17	22,8,18273,17426	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749248	28881	PASS	G	A	15208	0.735665	18	7,0,7489,7480	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749248	28882	PASS	G	A	15208	0.828577	12	5,0,7600,7440	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749248	28883	PASS	G	C	15208	0.940163	3	0,1,7620,7570	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749248	28977	PASS	C	T	7744	0.924329	0	0,1,2,7726	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749248	29109	PASS	C	A	21863	0.940585	0	13,0,21846,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	cCa/cAa	P279Q	N	0.004059	0.940585	2	2	C>A
ERR5749248	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	43423	0.001382	0	21791,21536,37,37	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749248	29451	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTCT	8050	0.019006	0	7896,1,153,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_INSERTION	N	cct/cTTCct	P396LP	N	0.007675	0.757685	2	2	C>CTCT
ERR5749248	29627	PASS	C	T	15241	0.967915	0	0,0,7187,8050	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF10	Cgt/Tgt	R24C	orf10	0.001148	0.967915	1	1	C>T
ERR5749249	241	PASS	C	T	44	0.886364	0	0,0,22,22	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749249	913	PASS	C	T	501	0.898204	2147483647	0,0,0,501	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749249	1968	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	401	0.0399	0	385,0,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ata/	I389	nsp2	0.001009	0.95	2	2	CA>C
ERR5749249	2160	PASS	A	C	401	0.089776	0	0,362,0,39	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gAa/gCa	E452A	nsp2	0.000572	0.089776	3	2	A>C
ERR5749249	2250	PASS	G	C	299	0.06689	0	279,0,20,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGa/gCa	G482A	nsp2	0.013729	0.06689	1	1	G>C
ERR5749249	2453	PASS	C	T	299	0.772575	2147483647	0,0,0,298	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L550F	nsp2	0.00429	0.842201	2	2	C>T
ERR5749249	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	2434	0.002876	209	1216,1136,1,73	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749249	3037	PASS	C	T	184	0.804348	0	0,0,92,90	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749249	3267	PASS	C	T	616	0.967532	2147483647	0,0,615,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749249	3609	PASS	T	C	224	0.071429	0	208,0,16,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cTt/cCt	L297P	nsp3	0.003189	0.071429	1	1	T>C
ERR5749249	4578	PASS	TTAACGATC	T	470	0.082979	0	0,431,0,39	HIGH	NONE	FRAME_SHIFT	ORF1ab	aacgatctaaat/	NDLN621	nsp3	0.000519	0.082979	2	2	TTAACGATC>T
ERR5749249	5388	PASS	C	A	154	0.967532	2147483647	0,0,154,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749249	5560	PASS	A	T	154	0.987013	2147483647	0,0,0,154	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtA/gtT	V947	nsp3	0.987013	0.987013	1	1	A>T
ERR5749249	5986	PASS	C	T	516	0.98062	2147483647	0,0,516,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749249	6159	PASS	G	A	516	0.05814	0	0,484,0,32	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGt/gAt	G1147D	nsp3	0.05814	0.05814	1	1	G>A
ERR5749249	6578	PASS	C	T	411	0.944039	2147483647	0,0,410,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Ttt	L1287F	nsp3	0.035115	0.944039	1	1	C>T
ERR5749249	6696	PASS	C	CT	409	0.08313	0	0,375,0,34	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L1328S?	nsp3	0.000731	0.14377	4	2	C>CT
ERR5749249	6954	PASS	T	C	850	0.8	2147483647	0,0,0,845	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749249	7735	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	938	0.034115	0	902,0,35,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I1672	nsp3	0.000658	0.954659	3	2	C>T
ERR5749249	11173	PASS	C	T	2708	0.587518	2147483647	0,0,2664,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ctC/ctT	L67	nsp6	0.00115	0.587518	1	1	C>T
ERR5749249	11287	PASS	GTCTGGTTTT	G	2711	0.998893	0	0,3,0,2708	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749249	14408	PASS	C	T	35	0.771429	0	0,0,17,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749249	14676	PASS	C	T	401	0.840399	2147483647	0,0,399,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749249	15279	PASS	C	T	539	0.855288	2147483647	0,0,538,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749249	16176	PASS	T	C	537	0.990689	0	0,0,164,373	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749249	17717	PASS	G	A	1120	0.057143	157	590,464,66,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGc/gAc	G494D	helicase	0.000541	0.057143	2	2	G>A
ERR5749249	20857	PASS	GT	G	1892	0.099366	67	1558,146,188,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/	V67	MethTr	0.000531	0.099366	2	2	GT>G
ERR5749249	21188	PASS	A	G	1718	0.977881	2147483647	0,0,1717,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAt/aGt	N177S	MethTr	0.001259	0.977881	1	1	A>G
ERR5749249	21764	PASS	ATACATG	A	967	1.0	2147483647	0,0,967,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749249	21990	PASS	TTTA	T	968	0.998967	0	0,1,1,966	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749249	22690	PASS	T	C	3547	0.051311	0	3302,0,204,0	LOW	SILENT	SYNONYMOUS_CODING	S	acT/acC	T376	S	0.000815	0.051311	2	1	T>C
ERR5749249	23063	PASS	A	T	353	0.847026	2147483647	0,0,0,351	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749249	23271	PASS	C	A	789	0.897338	2147483647	0,0,789,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749249	23403	PASS	A	G	788	0.97335	2147483647	0,0,0,788	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749249	23604	PASS	C	A	451	0.944568	0	1,0,450,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749249	23709	PASS	C	T	450	0.928889	2147483647	0,0,0,449	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749249	23817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	663	0.024133	26	212,434,0,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTt/cCt	L752P	S	0.000646	0.066832	1	1	T>C
ERR5749249	24506	PASS	T	G	792	0.97601	2147483647	0,0,792,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749249	24914	PASS	G	C	2838	0.963354	0	0,0,1413,1424	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749249	26526	PASS	G	T	700	0.947143	2147483647	0,0,0,699	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Gca/Tca	A2S	M	0.001224	0.951192	3	1	G>T
ERR5749249	26631	PASS	T	C	390	0.051282	0	368,0,21,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Ttt/Ctt	F37L	M	0.051282	0.051282	1	1	T>C
ERR5749249	27312	PASS	T	TA	1187	0.088458	0	1082,0,105,0	HIGH	NONE	FRAME_SHIFT	ORF6	aat/aaAt	N39K?	orf6	0.000911	0.088458	4	2	T>TA
ERR5749249	27765	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1927	0.025947	0	0,1873,0,53	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7b	Ctt/Ttt	L4F	orf7b	0.00109	0.970449	1	1	C>T
ERR5749249	27972	PASS	C	T	92	0.913043	0	0,0,91,1	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749249	28048	PASS	G	T	91	0.945055	2147483647	0,0,0,91	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749249	28111	PASS	A	G	3657	0.978944	0	0,0,3565,91	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749249	28227	PASS	C	T	3566	0.951206	2147483647	0,0,3557,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	Cat/Tat	H112Y	orf8	0.000906	0.951206	2	2	C>T
ERR5749249	28270	PASS	TA	T	6909	0.995079	109	38,0,3513,3362	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749249	28280	PASS	G	C	6896	0.93489	0	0,0,3526,3358	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749249	28281	PASS	A	T	6896	0.926044	3	2,0,3524,3362	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749249	28282	PASS	T	A	6896	0.916328	2	3,1,3509,3359	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749249	28292	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	7087	0.001834	0	3528,3546,6,7	HIGH	NONE	FRAME_SHIFT	N	aat/	N8	N	0.000304	0.055324	4	2	CA>C
ERR5749249	28881	PASS	G	A	108	0.759259	0	0,0,52,53	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749249	28882	PASS	G	A	108	0.805556	0	0,0,54,53	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749249	28883	PASS	G	C	108	0.944444	0	0,0,54,54	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749249	28977	PASS	C	T	55	0.909091	2147483647	0,0,0,55	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749250	71	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	510	0.017647	0	500,0,9,0	.	.	.	.	.	.	.	0.002088	0.926791	2	1	C>T
ERR5749250	241	PASS	C	T	320	0.85625	0	0,0,159,159	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749250	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	851	0.011751	0	839,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749250	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	2173	0.002761	10	1315,852,6,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749250	913	PASS	C	T	1320	0.936364	0	0,1,0,1317	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749250	1059	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2222	0.0045	0	2209,0,11,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCc/aTc	T85I	nsp2	0.001728	0.920973	1	1	C>T
ERR5749250	1813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAA	T	3821	0.006019	0	0,3790,0,23	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K338	nsp2	0.001022	0.152738	4	2	TAA>T
ERR5749250	2862	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	2737	0.007673	14	459,2257,0,21	HIGH	NONE	FRAME_SHIFT	ORF1ab	gaa/	E49	nsp3	0.000547	0.850688	4	2	CAG>C
ERR5749250	3037	PASS	C	T	914	0.804158	0	0,0,458,449	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749250	3177	PASS	C	T	1627	0.882606	0	0,0,1168,459	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P153L	nsp3	0.000773	0.96008	3	2	C>T
ERR5749250	3267	PASS	C	T	1169	0.957228	0	1,0,1167,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749250	5388	PASS	C	A	428	0.969626	2147483647	0,0,428,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749250	5986	PASS	C	T	1259	0.975377	2147483647	0,0,1258,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749250	6539	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1405	0.007117	0	1395,0,10,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cac/Tac	H1274Y	nsp3	0.001998	0.979821	1	1	C>T
ERR5749250	6573	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1405	0.017082	0	1378,0,24,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S1285F	nsp3	0.001862	0.957014	1	1	C>T
ERR5749250	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	1402	0.007133	0	0,1392,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L1328S?	nsp3	0.000731	0.14377	4	2	C>CT
ERR5749250	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1402	0.004993	0	0,1380,0,12	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749250	6954	PASS	T	C	3666	0.815876	2147483647	0,0,0,3643	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749250	7564	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	1824	0.011513	0	0,1803,0,21	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/	Y1617	nsp3	0.000586	0.056194	4	2	CT>C
ERR5749250	9402	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	314	0.015924	0	153,150,4,4	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S283F	nsp4	0.000453	0.058824	2	2	C>T
ERR5749250	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	2444	0.006137	2	2271,158,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749250	11104	PASS	T	C	7126	0.675414	0	1856,0,5249,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccT/ccC	P44	nsp6	0.000866	0.675414	2	1	T>C
ERR5749250	11287	PASS	GTCTGGTTTT	G	7123	0.999017	0	0,7,0,7116	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749250	12374	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2964	0.008772	0	0,2936,0,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Ttt	L95F	nsp8	0.001063	0.932196	1	1	C>T
ERR5749250	14408	PASS	C	T	202	0.861386	0	0,0,100,98	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749250	14676	PASS	C	T	877	0.77081	0	1,0,872,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749250	15279	PASS	C	T	1787	0.904309	2147483647	0,0,1785,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749250	15960	PASS	C	T	1044	0.793103	2147483647	0,0,1042,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A840	RdRp	0.001581	0.81574	1	1	C>T
ERR5749250	16176	PASS	T	C	1626	0.985855	0	0,0,582,1044	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749250	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	3377	0.002665	0	3363,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749250	18457	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2707	0.019209	0	2643,0,58,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cca/Tca	P140S	ExoN	0.001253	0.951352	2	1	C>T
ERR5749250	18636	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	2729	0.005863	0	12,2699,0,17	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtG/gtA	V199	ExoN	0.00055	0.963467	3	2	G>A
ERR5749250	20445	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	8465	0.002835	0	0,8438,0,26	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtT/gtG	V275	endoR	0.000518	0.059736	4	2	T>G
ERR5749250	21736	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2531	0.005927	0	2511,2,15,0	LOW	SILENT	SYNONYMOUS_CODING	S	ttC/ttT	F58	S	0.001596	0.804427	3	2	C>T
ERR5749250	21764	PASS	ATACATG	A	2529	0.998418	0	4,0,2525,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749250	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	2529	0.00435	0	2518,0,11,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749250	21846	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5049	0.00812	0	2496,2491,28,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCt/aTt	T95I	S	0.001104	0.788523	1	1	C>T
ERR5749250	21990	PASS	TTTA	T	2528	0.998418	0	0,4,0,2524	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749250	22293	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TACATA	T	7158	0.002794	98	2297,4841,20,0	HIGH	NONE	FRAME_SHIFT	S	ttacataga/	LHR244	S	0.000308	0.160511	4	1	TACATA>T
ERR5749250	22792	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	G	7659	0.004831	0	0,7617,0,41	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	atC/atG	I410M	S	0.000722	0.949572	3	3	C>G
ERR5749250	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	7659	0.001697	0	0,7641,0,13	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749250	23063	PASS	A	T	2240	0.870536	2147483647	0,0,0,2234	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749250	23086	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	2245	0.004009	0	0,2236,0,9	HIGH	NONE	FRAME_SHIFT	S	agagta/	RV509	S	0.00176	0.131707	2	2	CAG>C
ERR5749250	23271	PASS	C	A	1642	0.910475	2147483647	0,0,1640,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749250	23403	PASS	A	G	1641	0.969531	2147483647	0,0,0,1641	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749250	23604	PASS	C	A	2467	0.968383	2147483647	0,0,2466,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749250	23606	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2467	0.005675	0	2452,0,15,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Cgg/Tgg	R682W	S	0.001401	0.064309	2	2	C>T
ERR5749250	23709	PASS	C	T	2466	0.937551	0	0,2,0,2459	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749250	24432	PASS	A	T	5281	0.938269	0	1,0,3169,2108	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cAa/cTa	Q957L	S	0.935743	0.949489	1	1	A>T
ERR5749250	24506	PASS	T	G	3170	0.974763	0	1,0,3169,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749250	24914	PASS	G	C	8215	0.957395	0	0,0,4099,4113	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749250	25019	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GATAA	G	5039	0.002183	6	911,4117,0,11	HIGH	NONE	FRAME_SHIFT	S	aaatat/	KY1154	S	0.00048	0.981297	3	2	GATAA>G
ERR5749250	25495	PASS	A	G	13986	0.903904	3	1,0,6959,7010	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Ata/Gta	I35V	orf3a	0.000735	0.911134	2	1	A>G
ERR5749250	26013	PASS	C	T	7028	0.969266	2147483647	0,0,7025,0	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	ttC/ttT	F207	orf3a	0.000839	0.974528	1	1	C>T
ERR5749250	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	7014	0.001853	0	0,7001,0,13	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749250	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	2337	0.002567	0	0,2331,0,6	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749250	27240	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAT	G	6372	0.003296	0	6351,0,21,0	HIGH	NONE	FRAME_SHIFT	ORF6	atatta/	IL14	orf6	0.000521	0.117458	2	2	GAT>G
ERR5749250	27312	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	6367	0.00267	0	6347,0,19,0	LOW	SILENT	SYNONYMOUS_CODING	ORF6	atT/atA	I37	orf6	0.000911	0.088458	4	2	T>A
ERR5749250	27552	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	AT	7796	0.001283	0	7786,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF7a	gca/Tgca	A55C?	orf7a	0.000563	0.985801	6	1	A>AT
ERR5749250	27955	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	886	0.005643	0	881,0,5,0	HIGH	NONE	FRAME_SHIFT	ORF8	tta/	L22	orf8	0.001684	0.879424	3	2	GT>G
ERR5749250	27972	PASS	C	T	890	0.913483	0	0,0,882,5	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749250	28048	PASS	G	T	884	0.927602	0	0,1,0,883	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749250	28111	PASS	A	G	9978	0.978352	0	3,0,9086,887	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749250	28239	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	9088	0.003081	0	9054,0,28,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	Gtt/Att	V116I	orf8	0.000417	0.984998	9	2	G>A
ERR5749250	28270	PASS	TA	T	17607	0.995513	166	75,4,8973,8555	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749250	28280	PASS	G	C	17573	0.936721	2	3,1,8993,8548	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749250	28281	PASS	A	T	17573	0.91908	18	14,3,8979,8548	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749250	28282	PASS	T	A	17573	0.907927	1	6,7,8965,8553	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749250	28292	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	18069	0.002601	14	8983,9005,30,50	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Caa/Aaa	Q7K	N	0.000304	0.055324	4	2	C>A
ERR5749250	28881	PASS	G	A	1361	0.781778	0	1,0,677,667	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749250	28882	PASS	G	A	1360	0.843382	0	0,0,682,665	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749250	28883	PASS	G	C	1360	0.938235	0	0,0,684,676	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749250	28977	PASS	C	T	701	0.938659	2147483647	0,0,0,700	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749250	29686	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3158	0.003167	0	1568,1572,7,7	.	.	.	.	.	.	.	0.001045	0.802514	2	1	C>T
ERR5749251	241	PASS	C	T	14988	0.860822	0	0,0,7459,7458	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749251	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	8427	0.002017	0	7764,0,646,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749251	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21939	0.001048	0	0,21894,0,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749251	913	PASS	C	T	21940	0.908523	0	0,14,0,21885	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749251	2453	PASS	C	T	13781	0.74073	0	0,14,0,13581	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L550F	nsp2	0.00429	0.842201	2	2	C>T
ERR5749251	2494	PASS	G	T	13800	0.947319	0	0,7,0,13783	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gaG/gaT	E563D	nsp2	0.002624	0.951457	2	2	G>T
ERR5749251	3037	PASS	C	T	20051	0.817665	51	0,17,10021,9889	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749251	3267	PASS	C	T	21867	0.972241	0	2,0,21856,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749251	5178	PASS	C	T	10679	0.878172	0	0,10,0,10599	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T820I	nsp3	0.00175	0.88249	2	1	C>T
ERR5749251	5388	PASS	C	A	4895	0.954035	2147483647	0,0,4892,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749251	5986	PASS	C	T	13834	0.975061	0	1,0,13822,2	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749251	6954	PASS	T	C	22884	0.815723	0	0,1,0,22770	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749251	7564	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	16268	6.76E-4	0	0,16257,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/	Y1617	nsp3	0.000586	0.056194	4	2	CT>C
ERR5749251	7945	PASS	C	T	21687	0.921335	438	13,3,0,21651	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y1742	nsp3	0.001244	0.950558	2	2	C>T
ERR5749251	8141	PASS	T	A	63	0.238095	63	13,12,0,38	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tta/Ata	L1808I	nsp3	0.164557	0.238095	1	1	T>A
ERR5749251	8512	PASS	A	G	11640	0.815464	0	0,2,0,11550	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caA/caG	Q1931	nsp3	0.8	0.822278	1	1	A>G
ERR5749251	8692	PASS	C	T	25482	0.975512	0	3,0,25454,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y46	nsp4	0.967679	0.97884	1	1	C>T
ERR5749251	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	28560	9.8E-4	73	15226,13306,28,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749251	10077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	6903	0.003042	453	10,6834,19,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTc/tCc	F8S	3Cpro	0.001833	0.454545	1	1	T>C
ERR5749251	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20650	0.001356	0	20587,3,30,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749251	11287	PASS	GTCTGGTTTT	G	20633	0.998594	0	0,28,0,20604	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749251	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	36671	7.91E-4	0	24513,12102,20,9	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749251	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	37504	0.001866	0	18722,18666,36,36	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749251	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	11844	0.003799	2502	11618,87,3,135	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749251	14408	PASS	C	T	23103	0.841666	3	0,1,11551,11403	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749251	14676	PASS	C	T	13471	0.813822	0	8,0,13427,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749251	15279	PASS	C	T	21208	0.889853	2147483647	0,0,21178,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749251	16176	PASS	T	C	18553	0.981189	0	0,1,7693,10845	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749251	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29089	0.002028	0	29015,0,61,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749251	21764	PASS	ATACATG	A	13790	0.997462	0	35,0,13755,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749251	21990	PASS	TTTA	T	13792	0.997317	0	0,37,1,13754	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749251	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	31418	8.59E-4	1	14142,17230,14,14	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749251	23063	PASS	A	T	14136	0.844086	2147483647	0,0,0,14057	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749251	23271	PASS	C	A	23663	0.911465	0	2,0,23628,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749251	23403	PASS	A	G	23637	0.968185	0	0,1,0,23617	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749251	23604	PASS	C	A	16366	0.940303	0	10,0,16346,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749251	23709	PASS	C	T	16342	0.933301	0	0,6,2,16305	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749251	24506	PASS	T	G	15770	0.97565	0	11,0,15755,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749251	24914	PASS	G	C	34863	0.959011	0	0,1,17380,17464	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749251	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	26771	0.001083	46	19183,7545,33,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749251	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	20124	0.001441	390	20055,7,15,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749251	27972	PASS	C	T	11161	0.90637	0	0,0,11074,55	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749251	28048	PASS	G	T	11106	0.926886	0	0,14,0,11090	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749251	28111	PASS	A	G	33645	0.975241	7	6,0,22511,11115	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749251	28270	PASS	TA	T	43609	0.994841	473	222,13,22193,21191	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749251	28280	PASS	G	C	43516	0.942963	8	12,5,22242,21178	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749251	28281	PASS	A	T	43516	0.920466	33	32,9,22236,21182	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749251	28282	PASS	T	A	43517	0.909759	2	19,15,22203,21183	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749251	28881	PASS	G	A	14302	0.774927	6	2,0,7041,7085	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749251	28882	PASS	G	A	14302	0.821983	6	5,1,7107,7051	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749251	28883	PASS	G	C	14302	0.94728	0	0,1,7114,7170	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749251	28977	PASS	C	T	7180	0.932451	0	0,2,0,7172	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749251	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	64190	0.001059	0	32235,31846,45,42	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749252	241	PASS	C	T	8191	0.872055	0	0,0,4082,4086	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749252	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	10346	0.002996	0	10317,2,31,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749252	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	10346	0.001353	0	10232,2,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749252	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	10346	0.003383	0	10232,2,35,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749252	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	10346	0.005896	0	10232,2,61,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749252	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10343	0.00174	0	9432,9,737,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749252	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	10343	0.00203	0	10313,9,21,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749252	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	10342	0.001064	0	10317,8,11,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttatg/gtg	VM84V	leader	0.000554	0.991848	4	1	GTTA>G
ERR5749252	635	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10362	0.00193	0	0,10336,0,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgt/Tgt	R124C	leader	0.00148	0.880435	1	1	C>T
ERR5749252	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	25887	0.001584	12	15483,10355,31,10	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749252	913	PASS	C	T	15514	0.896996	0	0,11,0,15476	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749252	3037	PASS	C	T	14481	0.806919	63	0,21,7237,7120	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749252	3177	PASS	C	T	25844	0.911159	0	6,2,18532,7276	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P153L	nsp3	0.000773	0.96008	3	2	C>T
ERR5749252	3267	PASS	C	T	18548	0.972773	0	2,0,18535,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749252	3787	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9347	0.002354	0	6,9319,0,22	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y356	nsp3	0.002354	0.956541	1	1	C>T
ERR5749252	5388	PASS	C	A	5024	0.962381	2147483647	0,0,5022,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749252	5986	PASS	C	T	11191	0.974086	2147483647	0,0,11188,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749252	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10783	0.001762	0	5,10649,0,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749252	6954	PASS	T	C	21723	0.816508	0	0,1,0,21593	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749252	7070	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	35163	0.003498	424	13231,21796,126,8	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggc/Tgc	G1451C	nsp3	0.000698	0.101434	3	1	G>T
ERR5749252	7528	PASS	C	T	15526	0.901971	0	0,3,65,15425	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V1603	nsp3	0.002527	0.916131	1	1	C>T
ERR5749252	8084	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	22118	5.43E-4	0	22108,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1790	nsp3	0.000543	0.923413	4	2	GA>G
ERR5749252	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	21560	0.001948	71	14436,7082,42,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749252	9802	PASS	G	T	14479	0.948822	0	0,2,1,14472	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcG/gcT	A416	nsp4	0.948822	0.951137	1	1	G>T
ERR5749252	10323	PASS	A	G	17237	0.955097	0	0,1,0,17219	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749252	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	23174	0.002028	0	22455,1,47,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749252	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	23159	0.001641	0	23091,0,56,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749252	11287	PASS	GTCTGGTTTT	G	23155	0.995724	0	0,99,0,23056	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749252	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	38016	0.001289	1	18984,18925,26,28	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749252	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	5381	0.005018	1507	5228,61,1,89	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749252	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	10416	9.6E-4	0	5221,5191,5,5	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749252	14408	PASS	C	T	10416	0.836021	0	0,0,5200,5129	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749252	14676	PASS	C	T	12025	0.754927	0	4,0,11979,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749252	15279	PASS	C	T	18103	0.888803	0	2,0,18079,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749252	16176	PASS	T	C	17777	0.979805	0	0,0,7569,10200	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749252	16647	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	22617	9.73E-4	0	4,22440,0,26	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acG/acA	T137	helicase	0.000746	0.885245	2	1	G>A
ERR5749252	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	24267	6.18E-4	0	24252,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749252	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21144	0.001655	0	21098,0,35,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749252	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22061	0.001179	0	22004,0,26,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749252	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	33870	0.001329	0	16572,16877,26,28	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749252	21764	PASS	ATACATG	A	11560	0.996107	0	45,0,11515,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749252	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	11558	8.65E-4	0	11548,0,10,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749252	21990	PASS	TTTA	T	11569	0.997926	0	0,24,8,11537	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749252	22450	PASS	C	T	8863	0.786303	0	3,0,8697,46	LOW	SILENT	SYNONYMOUS_CODING	S	ctC/ctT	L296	S	0.00215	0.803846	1	1	C>T
ERR5749252	23063	PASS	A	T	13501	0.866454	0	0,5,0,13418	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749252	23271	PASS	C	A	18958	0.917713	0	1,0,18940,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749252	23403	PASS	A	G	18950	0.961847	0	0,6,0,18926	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749252	23595	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14112	0.003401	0	14056,0,52,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCt/aTt	T678I	S	0.003401	0.86771	1	1	C>T
ERR5749252	23604	PASS	C	A	14110	0.943444	0	18,0,14086,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749252	23709	PASS	C	T	14091	0.933859	0	0,1,1,14069	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749252	23817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	27930	0.001038	20	13789,14099,22,8	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTt/cCt	L752P	S	0.000646	0.066832	1	1	T>C
ERR5749252	24506	PASS	T	G	17100	0.977544	0	5,0,17091,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749252	24914	PASS	G	C	36542	0.958869	0	0,0,18201,18319	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749252	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	24806	9.68E-4	38	17668,7103,27,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749252	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	13996	0.001858	604	13760,82,86,45	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749252	26456	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11655	0.001544	0	0,11612,0,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	cCt/cTt	P71L	E	0.001544	0.927736	1	1	C>T
ERR5749252	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	11894	7.57E-4	0	1,11880,0,9	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749252	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	11894	0.002438	0	0,11853,0,29	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749252	27346	PASS	T	C	38123	0.051754	0	17889,17820,1119,1121	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF6	Tat/Cat	Y49H	orf6	0.000895	0.888737	2	1	T>C
ERR5749252	27972	PASS	C	T	8254	0.907681	19	1,1,8182,41	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749252	28048	PASS	G	T	8219	0.926025	0	0,13,0,8200	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749252	28111	PASS	A	G	29999	0.978499	4	5,0,21759,8219	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749252	28250	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TCTG	21755	5.52E-4	0	21744,4,12,0	MODERATE	NONE	CODON_INSERTION	ORF8	ttc/CTGttc	F120LF	orf8	0.000494	0.993968	5	3	T>TCTG
ERR5749252	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21751	0.001287	0	21665,4,33,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749252	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	21748	5.98E-4	0	21734,4,13,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749252	28270	PASS	TA	T	42136	0.994874	533	221,7,21468,20452	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749252	28280	PASS	G	C	42045	0.937044	27	18,3,21522,20429	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749252	28281	PASS	A	T	42045	0.919562	40	30,6,21513,20425	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749252	28282	PASS	T	A	42050	0.91346	1	25,21,21464,20438	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749252	28657	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18310	0.007045	0	2,18142,0,148	LOW	SILENT	SYNONYMOUS_CODING	N	gaC/gaT	D128	N	0.00124	0.862766	1	1	C>T
ERR5749252	28881	PASS	G	A	11857	0.760563	21	8,0,5882,5800	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749252	28882	PASS	G	A	11856	0.831562	3	2,0,5938,5808	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749252	28883	PASS	G	C	11856	0.943404	0	1,1,5949,5890	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749252	28977	PASS	C	T	6045	0.922415	0	0,3,0,6026	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749252	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	55737	0.00174	0	27965,27621,60,59	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749253	241	PASS	C	T	6015	0.870657	0	0,0,2994,2998	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749253	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	5314	0.003575	0	5296,0,19,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749253	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	5314	0.001694	0	5261,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749253	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	5314	0.001317	0	5261,0,7,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749253	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	5314	0.006586	0	5261,0,35,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749253	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	5314	0.002823	0	5294,5,15,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749253	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	5314	0.001317	0	5297,5,7,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749253	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	24627	0.001868	9	19246,5322,41,5	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749253	714	PASS	G	T	19304	0.984148	60	4,2,19284,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGc/gTc	G150V	leader	0.001941	0.984148	2	1	G>T
ERR5749253	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19285	0.001296	0	0,19237,0,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749253	913	PASS	C	T	19285	0.914597	0	0,14,0,19242	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749253	2151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATTGGC	A	20716	8.69E-4	0	1,20691,0,18	HIGH	NONE	FRAME_SHIFT	ORF1ab	tggcttgaa/	WLE450	nsp2	0.000402	0.971954	3	2	ATTGGC>A
ERR5749253	3037	PASS	C	T	16150	0.82	36	0,12,8073,7952	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749253	3267	PASS	C	T	21022	0.971744	0	4,0,21010,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749253	3310	PASS	A	G	21009	0.952116	0	5,0,21000,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaA/gaG	E197	nsp3	0.938803	0.952297	1	1	A>G
ERR5749253	4237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTA	T	34371	4.66E-4	0	17205,17151,8,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	ata/	I508	nsp3	0.000302	0.918634	2	2	TTA>T
ERR5749253	5388	PASS	C	A	4311	0.96103	2147483647	0,0,4311,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749253	5986	PASS	C	T	11065	0.974243	2147483647	0,0,11053,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749253	6414	PASS	A	G	24243	0.930413	0	0,0,1,24212	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gAa/gGa	E1232G	nsp3	0.000549	0.930413	2	2	A>G
ERR5749253	6954	PASS	T	C	20071	0.812117	0	0,5,7,19925	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749253	7070	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	30991	0.001581	186	10709,20121,49,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggc/Agc	G1451S	nsp3	0.000698	0.101434	3	1	G>A
ERR5749253	7070	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	30991	0.003259	375	10709,20121,102,7	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggc/Tgc	G1451C	nsp3	0.000698	0.101434	3	1	G>T
ERR5749253	8092	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	21706	0.00106	0	21654,0,49,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ctC/ctA	L1791	nsp3	0.000539	0.063953	3	2	C>A
ERR5749253	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	19714	5.07E-4	17	12671,7033,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749253	10193	PASS	G	A	16770	0.855874	0	1,0,16743,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E47K	3Cpro	0.000774	0.869819	2	2	G>A
ERR5749253	10195	PASS	A	T	16770	0.951998	0	12,0,16745,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gaA/gaT	E47D	3Cpro	0.951998	0.969772	1	1	A>T
ERR5749253	10595	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	16339	0.001102	0	19,16280,0,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F181L	3Cpro	0.000964	0.076408	1	1	T>C
ERR5749253	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21262	0.001881	0	21163,1,46,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749253	11287	PASS	GTCTGGTTTT	G	21245	0.995623	0	0,93,0,21152	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749253	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27414	0.001459	0	13675,13654,23,24	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749253	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	4310	0.003944	1385	4162,55,4,88	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749253	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	8281	0.003985	0	4141,4113,17,16	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749253	14408	PASS	C	T	8281	0.845429	0	0,0,4115,4076	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749253	14676	PASS	C	T	12192	0.826526	0	2,0,12153,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749253	15279	PASS	C	T	17289	0.879403	0	2,0,17258,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749253	16176	PASS	T	C	16614	0.981883	2	0,2,6028,10578	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749253	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	20318	0.001673	0	20284,0,34,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749253	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20771	0.001829	0	20718,0,42,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749253	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29399	0.001191	0	29321,0,36,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749253	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	23107	0.001212	0	0,23060,0,32	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acA	T136	MethTr	0.000447	0.081824	3	2	T>A
ERR5749253	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	32125	7.16E-4	1	15783,16025,13,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749253	21764	PASS	ATACATG	A	11910	0.996809	0	39,0,11872,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749253	21990	PASS	TTTA	T	11915	0.997902	0	0,25,3,11887	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749253	23063	PASS	A	T	12795	0.863072	0	0,8,0,12718	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749253	23271	PASS	C	A	23952	0.919339	0	5,0,23922,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749253	23403	PASS	A	G	23933	0.968746	0	0,8,0,23909	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749253	23604	PASS	C	A	13938	0.935213	0	16,0,13915,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749253	23709	PASS	C	T	13925	0.930987	0	0,4,7,13895	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749253	24506	PASS	T	G	15052	0.974156	0	3,0,15046,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749253	24914	PASS	G	C	36096	0.960494	0	0,0,17975,18090	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749253	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	11966	0.002006	292	11911,15,11,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749253	26158	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	38197	4.19E-4	0	3,38177,0,16	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF3a	gttaat/gat	VN256D	orf3a	0.000297	0.905181	6	2	GTTA>G
ERR5749253	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	12132	8.24E-4	0	5,12115,0,10	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749253	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	12131	0.003215	0	0,12088,0,39	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749253	27506	PASS	G	A	37734	0.980893	1	4,2,19074,18638	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	gGa/gAa	G38E	orf7a	0.000715	0.985435	4	2	G>A
ERR5749253	27972	PASS	C	T	8539	0.907718	0	0,0,8463,48	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749253	28048	PASS	G	T	8494	0.917942	0	0,10,0,8478	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749253	28111	PASS	A	G	30045	0.978765	1	6,1,21516,8505	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749253	28270	PASS	TA	T	41721	0.994847	475	216,11,21231,20275	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749253	28280	PASS	G	C	41638	0.93859	32	15,1,21275,20267	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749253	28281	PASS	A	T	41638	0.915606	19	28,11,21269,20255	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749253	28282	PASS	T	A	41646	0.909379	1	27,23,21238,20267	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749253	28881	PASS	G	A	16332	0.781288	9	4,0,8098,8044	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749253	28882	PASS	G	A	16331	0.826098	6	3,0,8171,8025	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749253	28883	PASS	G	C	16331	0.943972	0	0,0,8176,8133	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749253	28977	PASS	C	T	8296	0.932859	2147483647	0,0,0,8272	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749253	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	63797	0.00105	0	32030,31651,44,43	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749253	29779	PASS	G	T	7792	0.95367	0	0,3,0,7786	.	.	.	.	.	.	.	0.001489	0.975228	1	1	G>T
ERR5749254	241	PASS	C	T	19510	0.856945	15	0,6,9711,9727	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749254	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	12062	0.001658	0	12043,0,20,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749254	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	12064	9.95E-4	0	11986,3,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749254	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	12064	8.29E-4	0	11986,3,10,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749254	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	12064	0.004476	0	11986,3,54,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749254	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12060	0.001078	0	11309,3,636,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749254	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	12060	9.95E-4	0	12045,3,12,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749254	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	12058	8.29E-4	26	12039,2,9,1	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749254	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	35061	5.99E-4	35	22956,12082,21,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749254	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	35060	0.001768	7	22927,12065,46,16	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749254	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22963	0.00135	0	0,22915,0,32	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749254	913	PASS	C	T	22965	0.914783	0	0,16,0,22915	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749254	3037	PASS	C	T	19087	0.849479	23	2,13,9520,9460	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749254	3095	PASS	T	C	9635	0.945407	2147483647	0,0,0,9629	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tca/Cca	S126P	nsp3	0.937591	0.970297	1	1	T>C
ERR5749254	3177	PASS	C	T	31301	0.899109	0	4,2,21619,9620	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P153L	nsp3	0.000773	0.96008	3	2	C>T
ERR5749254	3267	PASS	C	T	21658	0.969342	2147483647	0,0,21640,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749254	4331	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	33125	0.001328	2	15410,17633,25,24	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L538	nsp3	0.000987	0.928955	1	1	C>T
ERR5749254	5388	PASS	C	A	5628	0.961087	0	1,0,5623,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749254	5986	PASS	C	T	12628	0.97854	0	1,0,12618,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749254	6954	PASS	T	C	23608	0.820654	0	0,2,3,23481	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749254	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	33504	4.48E-4	50	15450,18038,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749254	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	18942	0.00132	0	18891,0,38,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749254	11287	PASS	GTCTGGTTTT	G	18938	0.997413	0	0,49,0,18889	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749254	12513	PASS	C	T	16723	0.948693	0	597,0,16115,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aTg	T141M	nsp8	0.000794	0.984064	2	2	C>T
ERR5749254	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30989	0.001226	0	15477,15434,21,21	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749254	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	11348	0.003701	2637	11124,67,9,144	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749254	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	22140	7.23E-4	0	11107,11038,9,7	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749254	14408	PASS	C	T	22140	0.844941	21	0,7,11051,10912	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749254	14676	PASS	C	T	14028	0.81872	0	11,0,13981,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749254	15279	PASS	C	T	24315	0.92371	0	1,0,24286,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749254	15960	PASS	C	T	10703	0.796599	0	4,0,10652,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A840	RdRp	0.001581	0.81574	1	1	C>T
ERR5749254	16176	PASS	T	C	19949	0.982405	0	0,0,9215,10725	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749254	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	23381	5.13E-4	0	23369,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749254	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29909	0.001404	0	29848,0,45,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749254	21764	PASS	ATACATG	A	12393	0.997176	0	35,0,12358,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749254	21990	PASS	TTTA	T	12394	0.997418	0	0,32,1,12361	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749254	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27910	9.67E-4	4	11808,16055,9,19	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749254	23063	PASS	A	T	11806	0.873793	0	0,1,0,11750	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749254	23271	PASS	C	A	23604	0.921666	0	1,0,23578,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749254	23403	PASS	A	G	23599	0.968431	0	0,1,0,23576	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749254	23604	PASS	C	A	15649	0.943894	0	10,0,15628,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749254	23709	PASS	C	T	15638	0.941361	0	0,10,2,15606	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749254	24432	PASS	A	T	29540	0.942688	13	7,0,17581,11938	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cAa/cTa	Q957L	S	0.935743	0.949489	1	1	A>T
ERR5749254	24506	PASS	T	G	17586	0.974127	0	7,0,17573,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749254	24914	PASS	G	C	34619	0.963633	0	0,0,17240,17357	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749254	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	24872	0.001528	71	16716,8105,43,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749254	25495	PASS	A	G	33641	0.897952	0	4,4,16730,16865	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Ata/Gta	I35V	orf3a	0.000735	0.911134	2	1	A>G
ERR5749254	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	26981	0.001186	296	26882,22,21,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749254	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	27008	9.26E-4	0	26983,0,25,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749254	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	27209	9.92E-4	1210	26789,180,131,88	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749254	26013	PASS	C	T	51689	0.962004	0	10,0,51643,0	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	ttC/ttT	F207	orf3a	0.000839	0.974528	1	1	C>T
ERR5749254	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	11557	0.001817	0	4,11529,0,21	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749254	27972	PASS	C	T	10853	0.907767	57	2,3,10756,57	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749254	28048	PASS	G	T	10804	0.925213	0	0,18,0,10783	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749254	28111	PASS	A	G	32979	0.978259	0	4,2,22154,10806	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749254	28250	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TCTG	22140	0.002575	0	22085,0,57,0	MODERATE	NONE	CODON_INSERTION	ORF8	ttc/CTGttc	F120LF	orf8	0.000494	0.993968	5	3	T>TCTG
ERR5749254	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	22133	0.002846	0	22076,0,63,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749254	28270	PASS	TA	T	43029	0.995236	493	206,7,21877,20947	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749254	28280	PASS	G	C	42943	0.938174	9	8,2,21926,20922	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749254	28281	PASS	A	T	42943	0.914747	12	19,8,21913,20928	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749254	28282	PASS	T	A	42946	0.9148	1	21,18,21887,20936	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749254	28881	PASS	G	A	18026	0.780206	11	7,1,8916,8880	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749254	28882	PASS	G	A	18024	0.83117	6	5,1,9013,8862	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749254	28883	PASS	G	C	18024	0.948291	6	0,2,9023,8985	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749254	28977	PASS	C	T	9158	0.932955	0	0,3,0,9136	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749254	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	33641	0.00113	154	24444,9109,6,38	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749254	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	48626	8.43E-4	0	24414,24140,30,28	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749255	241	PASS	C	T	27148	0.847245	0	1,2,13502,13518	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749255	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	13279	0.001205	0	13265,1,16,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749255	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	13280	0.001054	0	13258,2,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749255	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	13263	0.002564	0	12124,3,1091,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749255	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	42862	6.07E-4	0	29535,13298,18,8	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749255	913	PASS	C	T	29542	0.927256	0	0,15,0,29488	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749255	1510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	29845	0.005596	0	0,29361,0,180	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G235	nsp2	0.002159	0.937304	1	1	T>C
ERR5749255	1813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	17538	0.00114	0	0,17503,0,23	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcA	A336	nsp2	0.001022	0.152738	4	2	T>A
ERR5749255	2453	PASS	C	T	18663	0.842201	0	0,15,0,18539	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L550F	nsp2	0.00429	0.842201	2	2	C>T
ERR5749255	2494	PASS	G	T	18690	0.94152	0	0,7,2,18664	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gaG/gaT	E563D	nsp2	0.002624	0.951457	2	2	G>T
ERR5749255	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	105685	0.001561	2147483647	52777,49349,82,3232	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749255	3037	PASS	C	T	23454	0.810054	46	3,24,11708,11525	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749255	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	11861	0.002698	813	6,11814,32,7	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749255	3267	PASS	C	T	28565	0.971994	2147483647	0,0,28548,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749255	3575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	13232	6.8E-4	0	13223,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/ttTa	L287F?	nsp3	0.000594	0.059126	3	1	G>GT
ERR5749255	5170	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	16037	7.48E-4	0	0,16025,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T819	nsp3	0.000565	0.894036	2	2	CCA>C
ERR5749255	5178	PASS	C	T	16037	0.870986	0	0,17,0,15898	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T820I	nsp3	0.00175	0.88249	2	1	C>T
ERR5749255	5388	PASS	C	A	7516	0.961682	0	1,0,7508,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749255	5986	PASS	C	T	15114	0.975321	2147483647	0,0,15106,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749255	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14490	0.001311	0	5,14333,0,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749255	6954	PASS	T	C	31904	0.806137	0	0,6,0,31692	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749255	7945	PASS	C	T	24400	0.934303	343	10,4,0,24367	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y1742	nsp3	0.001244	0.950558	2	2	C>T
ERR5749255	8512	PASS	A	G	14019	0.814823	0	0,2,0,13912	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caA/caG	Q1931	nsp3	0.8	0.822278	1	1	A>G
ERR5749255	8692	PASS	C	T	37251	0.967679	0	4,0,37200,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y46	nsp4	0.967679	0.97884	1	1	C>T
ERR5749255	11287	PASS	GTCTGGTTTT	G	22869	0.998295	0	0,38,0,22830	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749255	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	18573	0.0014	0	18524,0,26,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749255	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	40498	0.001235	0	20228,20161,27,28	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749255	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	14107	0.003828	2147483647	13828,88,6,182	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749255	14408	PASS	C	T	27523	0.836646	2	3,5,13743,13581	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749255	14676	PASS	C	T	18424	0.729266	0	6,0,18341,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749255	15279	PASS	C	T	32020	0.878982	0	7,0,31957,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749255	16176	PASS	T	C	24005	0.981546	2	0,2,10287,13701	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749255	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	34400	6.1E-4	0	0,34379,0,21	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749255	19404	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	21426	8.4E-4	0	21051,1,362,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H455Q	ExoN	0.00084	0.697695	2	2	T>G
ERR5749255	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34644	0.001732	0	34557,0,68,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749255	20786	PASS	A	T	20	0.7	45	0,6,14,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAt/aTt	N43I	MethTr	0.001392	1	1	1	A>T
ERR5749255	21762	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTATACA	C	14536	0.001926	0	14509,0,28,0	MODERATE	NONE	CODON_DELETION	S	atacat/	IH68	S	0.001297	0.875707	2	2	CTATACA>C
ERR5749255	21764	PASS	ATACATG	A	14536	0.997179	0	41,0,14495,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749255	21990	PASS	TTTA	T	14545	0.998281	0	0,25,6,14514	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749255	23063	PASS	A	T	13413	0.870275	0	0,2,0,13347	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749255	23271	PASS	C	A	30432	0.920018	2147483647	0,0,30401,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749255	23403	PASS	A	G	30423	0.969102	0	0,1,0,30399	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749255	23604	PASS	C	A	17800	0.929326	0	17,0,17768,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749255	23709	PASS	C	T	17768	0.940792	0	0,3,1,17746	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749255	24237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13368	0.00202	0	13332,0,28,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gTt	A892V	S	0.001242	0.889739	1	1	C>T
ERR5749255	24506	PASS	T	G	24325	0.975745	0	12,0,24306,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749255	24914	PASS	G	C	37962	0.958511	9	3,0,18903,19020	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749255	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	30405	0.002532	157	19826,10468,103,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749255	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	36968	0.001325	747	36834,27,20,30	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749255	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	36909	8.13E-4	0	36879,0,30,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749255	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	37126	0.001347	1453	36524,213,235,111	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749255	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	12751	6.27E-4	0	1,12741,0,8	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749255	27297	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20458	9.78E-4	0	20410,0,20,0	LOW	SILENT	SYNONYMOUS_CODING	ORF6	atC/atT	I32	orf6	0.000978	0.91266	1	1	C>T
ERR5749255	27972	PASS	C	T	12884	0.90624	0	0,0,12783,58	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749255	28048	PASS	G	T	12850	0.921946	0	0,10,0,12832	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749255	28111	PASS	A	G	40738	0.977638	1	7,2,27865,12849	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749255	28270	PASS	TA	T	53935	0.994475	710	298,10,27463,26174	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749255	28271	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AA	A	53927	4.82E-4	74	27721,26184,26,0	.	.	.	.	.	.	.	0.000482	0.924941	3	2	AA>A
ERR5749255	28280	PASS	G	C	53812	0.938675	36	19,2,27534,26157	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749255	28281	PASS	A	T	53812	0.908589	93	47,4,27512,26143	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749255	28282	PASS	T	A	53818	0.911572	13	36,19,27465,26162	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749255	28881	PASS	G	A	23980	0.781359	9	4,0,11900,11800	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749255	28882	PASS	G	A	23980	0.823478	9	6,1,11973,11766	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749255	28883	PASS	G	C	23980	0.941368	4	1,3,12004,11939	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749255	28977	PASS	C	T	12219	0.932728	0	0,0,5,12199	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749255	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	40204	8.95E-4	117	27961,12169,7,35	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749255	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	55532	0.001225	0	27889,27530,43,40	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749256	241	PASS	C	T	4495	0.859177	3	0,1,2242,2236	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749256	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	8255	8.48E-4	0	8253,0,7,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749256	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	8255	0.00109	0	8242,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749256	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	8253	0.002423	0	7612,0,605,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749256	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	8253	0.001454	0	8241,0,12,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749256	656	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	8275	0.0029	0	1,8239,0,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gct/Cct	A131P	leader	0.001202	0.131429	1	1	G>C
ERR5749256	657	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8275	0.002175	0	1,8251,0,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A131V	leader	0.001202	0.365979	3	1	C>T
ERR5749256	673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	20363	6.38E-4	50	12089,8261,0,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggc/	G137	leader	0.000454	0.602236	3	2	CG>C
ERR5749256	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	20363	0.002161	22	12052,8265,35,9	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749256	751	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	12089	6.62E-4	0	12081,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T163	leader	0.000662	0.943591	2	2	CA>C
ERR5749256	913	PASS	C	T	12086	0.909399	0	0,10,0,12065	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749256	3037	PASS	C	T	13562	0.79767	41	1,17,6770,6636	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749256	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	6853	0.002335	411	2,6832,15,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749256	3267	PASS	C	T	16268	0.968957	0	1,0,16256,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749256	3802	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	19872	5.54E-4	15	12367,7492,3,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N363	nsp3	0.000554	0.064198	4	2	TA>T
ERR5749256	4237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTA	T	30075	3.99E-4	0	15062,15001,6,6	HIGH	NONE	FRAME_SHIFT	ORF1ab	ata/	I508	nsp3	0.000302	0.918634	2	2	TTA>T
ERR5749256	5388	PASS	C	A	3849	0.952975	2147483647	0,0,3848,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749256	5986	PASS	C	T	9705	0.974137	2147483647	0,0,9694,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749256	6516	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	31285	4.79E-4	23	9721,21549,0,15	HIGH	NONE	FRAME_SHIFT	ORF1ab	att/aAtt	I1268N?	nsp3	0.000479	0.186047	4	2	T>TA
ERR5749256	6706	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	9691	9.29E-4	0	0,9682,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1330	nsp3	0.000687	0.883999	2	2	CA>C
ERR5749256	6954	PASS	T	C	21496	0.80187	0	0,6,17,21311	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749256	7070	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	28148	0.006182	1114	6420,21535,182,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggc/Agc	G1451S	nsp3	0.000698	0.101434	3	1	G>A
ERR5749256	8123	PASS	C	T	18757	0.778589	0	1,0,18569,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Ttt	L1802F	nsp3	0.001144	0.778589	1	1	C>T
ERR5749256	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	15958	0.003133	46	12707,3198,50,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749256	10165	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTG	C	16739	0.001135	0	16713,7,19,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tgt/	C38	3Cpro	0.000632	0.976163	2	2	CTG>C
ERR5749256	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	27265	0.002861	0	26400,0,78,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749256	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTA	G	27257	4.77E-4	0	27245,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/	Y38	nsp6	0.000477	0.901695	5	2	GTA>G
ERR5749256	11199	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	54278	9.4E-4	0	26950,27097,26,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCc/gTc	A76V	nsp6	0.000309	0.056758	3	2	C>T
ERR5749256	11287	PASS	GTCTGGTTTT	G	27251	0.997028	0	0,81,0,27170	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749256	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	30283	8.59E-4	8	20935,9300,23,5	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749256	11690	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	20976	9.53E-4	0	20922,4,20,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggt/Cgt	G240R	nsp6	0.000953	0.091324	4	2	G>C
ERR5749256	13059	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTG	C	23135	5.62E-4	54	14298,8824,0,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	gta/	V13	nsp10	0.000448	0.855104	3	2	CTG>C
ERR5749256	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28366	9.87E-4	0	14173,14129,15,16	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749256	14097	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	18412	8.69E-4	0	18378,18,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggt/	G220	RdRp	0.000613	0.981481	2	2	CG>C
ERR5749256	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	3011	0.005314	977	2920,26,5,60	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749256	14408	PASS	C	T	5811	0.848735	6	0,2,2903,2863	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749256	14676	PASS	C	T	9871	0.802148	0	2,0,9848,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749256	15237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	14792	0.001014	0	14768,9,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aac/	N600	RdRp	0.001014	0.955128	2	2	CA>C
ERR5749256	15279	PASS	C	T	14783	0.887506	0	1,0,14758,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749256	16176	PASS	T	C	14665	0.978588	0	0,0,5441,9219	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749256	16573	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	25004	6.0E-4	0	24989,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gac/	D113	helicase	0.000597	0.156477	4	2	GA>G
ERR5749256	16689	PASS	T	A	24958	0.885448	0	0,19,0,24889	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atT/atA	I151	helicase	0.00155	0.885448	2	2	T>A
ERR5749256	17615	PASS	A	G	14361	0.897988	2147483647	0,0,0,14312	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749256	17626	PASS	C	T	14368	0.942024	0	0,23,0,14315	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cat/Tat	H464Y	helicase	0.001039	0.946125	2	2	C>T
ERR5749256	18674	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	24185	4.13E-4	0	24175,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aga/	R212	ExoN	0.000413	0.056921	3	2	GA>G
ERR5749256	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	24185	5.79E-4	0	24171,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749256	18756	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	24178	7.03E-4	0	24161,0,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F240	ExoN	0.000392	0.942688	3	2	GT>G
ERR5749256	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	22683	7.05E-4	0	0,22667,0,16	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749256	19296	PASS	G	A	13915	0.974344	220	0,6,13908,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttG/ttA	L419	ExoN	0.000586	0.977017	2	2	G>A
ERR5749256	19524	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13906	0.003955	0	0,13839,0,57	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ctC/ctT	L495	ExoN	0.000745	0.953697	2	2	C>T
ERR5749256	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14138	0.002122	0	14100,0,31,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749256	20857	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	39681	6.55E-4	57	23278,16377,26,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/	V67	MethTr	0.000531	0.099366	2	2	GT>G
ERR5749256	21304	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	26781	4.11E-4	0	0,26770,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	cgc/	R216	MethTr	0.000411	0.605296	3	2	CG>C
ERR5749256	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30027	0.002231	2	14707,14952,35,41	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749256	21764	PASS	ATACATG	A	11352	0.995684	0	45,0,11303,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749256	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	11352	7.93E-4	0	11343,0,9,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749256	21817	PASS	A	G	11348	0.959376	0	4,0,11334,0	LOW	SILENT	SYNONYMOUS_CODING	S	ccA/ccG	P85	S	0.000689	0.961354	3	2	A>G
ERR5749256	21846	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22646	0.001104	0	11316,11270,15,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCt/aTt	T95I	S	0.001104	0.788523	1	1	C>T
ERR5749256	21990	PASS	TTTA	T	11352	0.998326	0	0,19,0,11333	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749256	22289	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GC	G	24657	4.46E-4	0	4,24642,0,11	HIGH	NONE	FRAME_SHIFT	S	gct/	A243	S	0.000446	0.915917	3	2	GC>G
ERR5749256	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	22440	0.001292	0	0,22403,0,30	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749256	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	36265	0.00102	8	13797,22410,20,20	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749256	23063	PASS	A	T	13804	0.868951	0	0,3,0,13728	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749256	23271	PASS	C	A	17373	0.925804	0	2,0,17350,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749256	23403	PASS	A	G	17367	0.970461	0	0,2,0,17349	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749256	23604	PASS	C	A	13508	0.947068	0	4,0,13499,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749256	23709	PASS	C	T	13501	0.932672	0	0,6,0,13481	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749256	24010	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	11331	0.00203	189	80,11202,12,12	LOW	SILENT	SYNONYMOUS_CODING	S	tcA/tcG	S816	S	0.000455	0.926398	4	2	A>G
ERR5749256	24506	PASS	T	G	17520	0.973801	0	4,0,17514,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749256	24914	PASS	G	C	38280	0.956714	0	1,1,19051,19170	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749256	25555	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTTT	G	19923	5.52E-4	0	0,19909,0,11	HIGH	NONE	FRAME_SHIFT	ORF3a	gttttt/	VF55	orf3a	0.000552	0.900573	5	2	GTTTT>G
ERR5749256	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	8934	0.002351	467	8870,25,1,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749256	25690	PASS	G	T	8916	0.971288	0	2,0,8908,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Ggc/Tgc	G100C	orf3a	0.971091	0.979849	1	1	G>T
ERR5749256	26151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	34436	5.23E-4	0	0,34418,0,18	HIGH	NONE	FRAME_SHIFT	ORF3a	gga/	G254	orf3a	0.000501	0.913698	4	2	CG>C
ERR5749256	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	34442	3.48E-4	0	0,34430,0,12	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749256	26526	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	11870	0.001348	0	0,11849,0,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Gca/Aca	A2T	M	0.001224	0.951192	3	1	G>A
ERR5749256	26571	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11513	0.007904	0	11407,6,96,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Ctt/Ttt	L17F	M	0.000508	0.905823	3	2	C>T
ERR5749256	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	11499	9.57E-4	0	1,11486,0,11	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749256	27513	PASS	C	T	23630	0.97884	0	1,0,23600,0	LOW	SILENT	SYNONYMOUS_CODING	ORF7a	taC/taT	Y40	orf7a	0.001863	0.982462	2	2	C>T
ERR5749256	27972	PASS	C	T	7428	0.90657	0	0,0,7334,54	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749256	28048	PASS	G	T	7375	0.93261	0	0,4,0,7369	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749256	28111	PASS	A	G	35449	0.978279	11	4,4,28057,7378	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749256	28147	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTTTTACAA	C	28073	8.55E-4	0	28030,5,24,0	HIGH	NONE	FRAME_SHIFT	ORF8	tttacaatt/	FTI86	orf8	0.000438	0.981624	4	2	CTTTTACAA>C
ERR5749256	28270	PASS	TA	T	54369	0.995475	576	249,10,27712,26411	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749256	28280	PASS	G	C	54269	0.936041	27	29,9,27749,26386	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749256	28281	PASS	A	T	54269	0.917356	21	33,13,27750,26382	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749256	28282	PASS	T	A	54272	0.910506	0	25,22,27689,26387	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749256	28292	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	55832	3.04E-4	0	27810,27949,9,8	HIGH	NONE	FRAME_SHIFT	N	aat/	N8	N	0.000304	0.055324	4	2	CAA>C
ERR5749256	28881	PASS	G	A	8516	0.702208	6	3,0,4172,4160	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749256	28882	PASS	G	A	8516	0.796383	9	4,0,4247,4148	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749256	28883	PASS	G	C	8516	0.937529	3	0,1,4258,4249	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749256	28977	PASS	C	T	4357	0.927473	2147483647	0,0,0,4348	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749256	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	57687	0.001196	0	28975,28605,44,43	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749256	29686	PASS	C	T	13040	0.783742	2	1,2,6495,6347	.	.	.	.	.	.	.	0.001045	0.802514	2	1	C>T
ERR5749256	29688	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	13059	0.002374	0	6500,6490,18,17	.	.	.	.	.	.	.	0.002374	0.664502	2	1	G>A
ERR5749257	241	PASS	C	T	12569	0.853926	0	2,3,6181,6350	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749257	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	13089	0.004049	0	13030,5,53,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749257	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	13089	9.93E-4	0	12942,5,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749257	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	13089	0.003362	0	12942,5,44,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749257	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	13089	0.006188	0	12942,5,81,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749257	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	13081	0.001988	0	11976,7,859,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749257	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	13081	0.00344	16	13030,6,44,1	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749257	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	13080	9.94E-4	0	13044,7,13,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttatg/gtg	VM84V	leader	0.000554	0.991848	4	1	GTTA>G
ERR5749257	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	13080	0.001147	0	13044,7,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749257	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	13079	7.65E-4	0	13046,8,10,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749257	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATGGTTG	T	13079	0.00107	0	13046,8,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	atggttgag/	MVE85	leader	0.000587	0.476744	4	1	TATGGTTG>T
ERR5749257	520	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTT	G	13103	0.001145	0	13055,33,15,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttgag/gag	VE86E	leader	0.000583	0.051154	1	1	GGTT>G
ERR5749257	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	33331	4.2E-4	12	20216,13099,12,2	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749257	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	33332	7.2E-4	10	20135,13074,19,5	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749257	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	33332	0.00285	26	20135,13074,72,23	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749257	913	PASS	C	T	20219	0.91231	0	0,6,0,20186	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749257	3037	PASS	C	T	19564	0.811899	76	1,29,9762,9621	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749257	3177	PASS	C	T	28559	0.895725	20	1,6,18690,9825	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P153L	nsp3	0.000773	0.96008	3	2	C>T
ERR5749257	3250	PASS	G	T	18706	0.921255	0	10,0,18692,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gaG/gaT	E177D	nsp3	0.001378	0.921255	2	2	G>T
ERR5749257	3267	PASS	C	T	18705	0.968137	0	5,0,18686,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749257	3754	PASS	A	C	11897	0.935446	0	0,12,0,11879	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	agA/agC	R345S	nsp3	0.935446	0.935446	1	1	A>C
ERR5749257	5077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	10766	0.001393	0	10718,0,17,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtT/gtC	V786	nsp3	0.001393	0.168205	1	1	T>C
ERR5749257	5388	PASS	C	A	5639	0.95673	2147483647	0,0,5635,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749257	5986	PASS	C	T	12736	0.975738	2147483647	0,0,12729,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749257	6954	PASS	T	C	20721	0.823947	0	0,1,4,20608	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749257	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	32350	0.001206	119	15978,16333,39,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749257	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	17398	0.003851	0	17304,0,79,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749257	11095	PASS	C	T	17392	0.887707	0	47,0,17304,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A41	nsp6	0.000515	0.887707	7	2	C>T
ERR5749257	11095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	17392	0.002185	0	17354,0,38,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/ttTa	L43F?	nsp6	0.000515	0.887707	7	2	C>CT
ERR5749257	11287	PASS	GTCTGGTTTT	G	17396	0.995056	0	0,85,0,17310	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749257	12781	PASS	C	T	15365	0.974683	0	1,0,15327,8	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y32	nsp9	0.001869	0.974683	2	2	C>T
ERR5749257	13176	PASS	C	T	9483	0.919962	0	0,0,9468,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T51I	nsp10	0.002004	0.919962	2	1	C>T
ERR5749257	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27863	0.00201	0	13902,13860,31,31	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749257	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	14562	0.005494	2147483647	14183,127,8,233	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749257	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	28255	0.001026	1	14162,14082,16,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749257	14408	PASS	C	T	28255	0.842223	8	3,8,14100,13941	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749257	14676	PASS	C	T	12659	0.809622	0	8,0,12624,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749257	15279	PASS	C	T	21702	0.906276	0	4,0,21658,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749257	16176	PASS	T	C	19527	0.979362	6	0,2,9766,9745	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749257	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	24381	4.92E-4	0	24368,1,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749257	19269	PASS	C	T	40555	0.954777	1	2,4,17374,23153	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N410	ExoN	0.000773	0.954777	2	2	C>T
ERR5749257	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30137	0.002057	0	30045,0,63,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749257	20718	PASS	G	T	27448	0.920213	0	0,5,6,27407	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atT	M20I	MethTr	0.000898	0.920213	3	1	G>T
ERR5749257	21764	PASS	ATACATG	A	12540	0.995056	0	60,0,12478,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749257	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	12537	6.38E-4	0	12529,0,8,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749257	21990	PASS	TTTA	T	12547	0.998087	0	0,24,10,12513	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749257	23063	PASS	A	T	11426	0.866532	2147483647	0,0,0,11370	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749257	23271	PASS	C	A	20926	0.921629	0	5,0,20901,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749257	23403	PASS	A	G	20922	0.970318	0	0,2,0,20910	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749257	23604	PASS	C	A	15197	0.934527	0	15,0,15169,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749257	23709	PASS	C	T	15190	0.941935	0	0,6,8,15150	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749257	24127	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	26957	5.56E-4	0	9712,17238,5,10	HIGH	NONE	FRAME_SHIFT	S	aac/	N856	S	0.000324	0.111888	4	1	TA>T
ERR5749257	24506	PASS	T	G	16529	0.974409	0	9,0,16515,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749257	24712	PASS	G	T	16571	0.796995	814	41,107,4,16412	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	atG/atT	M1050I	S	0.005726	0.796995	2	1	G>T
ERR5749257	24914	PASS	G	C	14839	0.964351	0	0,0,16,14813	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749257	25429	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTAACTT	G	17812	8.98E-4	0	17794,1,16,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF3a	gtaactttg/gtg	VTL13V	orf3a	0.00064	0.906678	5	2	GTAACTT>G
ERR5749257	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	52584	5.32E-4	0	5,52546,0,28	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749257	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	10630	0.001129	0	5,10612,0,12	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749257	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	10631	0.003763	0	4,10585,0,40	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749257	27297	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16349	0.001468	0	16295,1,25,0	LOW	SILENT	SYNONYMOUS_CODING	ORF6	atC/atT	I32	orf6	0.000978	0.91266	1	1	C>T
ERR5749257	27972	PASS	C	T	9786	0.900777	20	1,1,9705,43	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749257	28048	PASS	G	T	9754	0.909883	0	0,13,0,9734	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749257	28111	PASS	A	G	25055	0.979405	0	6,3,15283,9753	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749257	28270	PASS	TA	T	29574	0.994691	344	152,7,15071,14346	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749257	28280	PASS	G	C	29521	0.938891	0	5,4,15116,14323	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749257	28281	PASS	A	T	29521	0.916128	8	15,7,15111,14330	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749257	28282	PASS	T	A	29524	0.90672	4	18,12,15081,14339	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749257	28881	PASS	G	A	12512	0.76031	30	11,0,6183,6123	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749257	28882	PASS	G	A	12509	0.821089	2	3,1,6254,6105	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749257	28883	PASS	G	C	12508	0.943476	0	0,0,6268,6228	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749257	28977	PASS	C	T	6375	0.925176	0	0,0,4,6357	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749257	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	38942	8.99E-4	1	19551,19330,26,23	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749257	29803	PASS	C	T	7958	0.886529	0	0,2,1,7952	.	.	.	.	.	.	.	0.002474	0.886529	2	1	C>T
ERR5749258	241	PASS	C	T	16510	0.868201	0	0,0,8194,8267	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749258	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	13996	0.001143	0	13982,1,16,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749258	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	13996	0.002215	0	13954,1,31,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749258	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	13987	0.002574	0	12817,4,1094,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749258	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	13985	7.87E-4	24	13971,4,10,1	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749258	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	43574	4.13E-4	11	29538,14016,16,2	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749258	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29552	9.14E-4	0	0,29504,0,28	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749258	913	PASS	C	T	29552	0.918753	0	0,11,0,29491	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749258	1510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	28719	0.004875	0	0,28286,0,156	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G235	nsp2	0.002159	0.937304	1	1	T>C
ERR5749258	2453	PASS	C	T	19004	0.746106	0	0,12,2,18775	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L550F	nsp2	0.00429	0.842201	2	2	C>T
ERR5749258	2494	PASS	G	T	19033	0.951453	0	0,6,2,19007	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gaG/gaT	E563D	nsp2	0.002624	0.951457	2	2	G>T
ERR5749258	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	99405	0.001278	2147483647	49578,46679,98,2796	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749258	3037	PASS	C	T	24599	0.817757	63	0,21,12291,12131	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749258	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12406	0.001773	623	2,12376,22,4	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749258	3267	PASS	C	T	28212	0.969942	0	4,0,28187,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749258	5170	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	14975	0.001002	0	0,14960,0,15	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T819	nsp3	0.000565	0.894036	2	2	CCA>C
ERR5749258	5178	PASS	C	T	14975	0.872588	0	0,4,0,14857	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T820I	nsp3	0.00175	0.88249	2	1	C>T
ERR5749258	5388	PASS	C	A	7786	0.959928	2147483647	0,0,7781,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749258	5986	PASS	C	T	16090	0.97688	0	1,0,16079,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749258	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14888	0.001142	0	3,14722,0,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749258	6954	PASS	T	C	30749	0.828124	0	0,8,0,30602	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749258	7945	PASS	C	T	26517	0.930724	784	24,2,1,26463	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y1742	nsp3	0.001244	0.950558	2	2	C>T
ERR5749258	8512	PASS	A	G	14714	0.822278	0	0,2,0,14600	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caA/caG	Q1931	nsp3	0.8	0.822278	1	1	A>G
ERR5749258	8692	PASS	C	T	35886	0.970824	0	1,0,35848,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y46	nsp4	0.967679	0.97884	1	1	C>T
ERR5749258	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	40807	3.68E-4	48	19369,21423,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749258	10323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	21067	0.001661	0	0,20979,0,38	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749258	11082	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	25769	4.27E-4	0	25763,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000427	0.179468	2	1	TG>T
ERR5749258	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	25769	0.003493	0	25634,0,117,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749258	11287	PASS	GTCTGGTTTT	G	25764	0.99837	0	0,42,0,25722	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749258	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	37928	0.001318	0	18942,18874,28,28	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749258	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	14812	0.003578	2147483647	14517,111,5,173	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749258	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	28908	6.57E-4	0	14496,14416,10,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749258	14408	PASS	C	T	28908	0.852947	16	2,10,14430,14276	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749258	14676	PASS	C	T	17111	0.701186	0	2,0,17026,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749258	15279	PASS	C	T	29459	0.897077	0	3,0,29408,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749258	16176	PASS	T	C	25250	0.981465	12	4,0,11954,13287	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749258	16274	PASS	C	T	11961	0.135942	0	10127,2,1812,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCa/tTa	S13L	helicase	0.001644	0.135942	2	2	C>T
ERR5749258	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	33741	3.85E-4	0	0,33728,0,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749258	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	37082	0.0024	0	36960,0,93,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749258	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	42733	7.72E-4	2	20899,21331,19,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749258	21764	PASS	ATACATG	A	15564	0.997558	26	37,1,15526,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749258	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	15563	7.71E-4	0	15551,0,12,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749258	21990	PASS	TTTA	T	15572	0.997431	0	0,40,7,15525	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749258	22290	PASS	C	T	28280	0.578006	4	1,10305,0,17935	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gTt	A243V	S	0.000389	0.578006	2	2	C>T
ERR5749258	22451	PASS	T	A	107	0.056075	6	1,18,0,71	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Aca	S297T	S	0.001815	0.056075	2	1	T>A
ERR5749258	22716	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	40549	0.010925	0	20000,19968,292,285	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCt/aAt	T385N	S	0.000738	0.865911	1	1	C>A
ERR5749258	22717	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	40550	0.011418	0	19977,19956,252,257	LOW	SILENT	SYNONYMOUS_CODING	S	acT/acC	T385	S	0.000395	0.918478	3	2	T>C
ERR5749258	23063	PASS	A	T	16874	0.860614	0	0,4,0,16796	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749258	23271	PASS	C	A	29786	0.89579	0	1,0,29745,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749258	23403	PASS	A	G	29776	0.967759	0	0,5,0,29745	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749258	23604	PASS	C	A	19173	0.940281	0	19,0,19148,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749258	23709	PASS	C	T	19164	0.936652	0	0,5,5,19118	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749258	24506	PASS	T	G	23213	0.975617	0	10,0,23197,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749258	24914	PASS	G	C	43588	0.958888	3	0,2,21723,21832	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749258	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	30142	0.002754	130	21141,8885,96,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749258	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	35035	0.001028	503	34924,28,21,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749258	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	34983	9.72E-4	0	34949,0,34,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749258	26091	PASS	CAAT	C	64323	0.128212	0	56077,4,8247,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF3a	aataaa/aaa	NK234K	orf3a	0.000569	0.128212	4	2	CAAT>C
ERR5749258	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	64300	2.49E-4	0	7,64277,0,16	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749258	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	13804	0.001666	0	2,13777,0,23	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749258	27972	PASS	C	T	13775	0.901851	37	2,2,13654,74	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749258	28001	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	27382	9.86E-4	0	13652,13663,16,17	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ccG/ccA	P36	orf8	0.00085	0.830607	2	1	G>A
ERR5749258	28048	PASS	G	T	13719	0.938625	0	0,12,0,13699	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749258	28111	PASS	A	G	37887	0.978251	0	3,1,24150,13717	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749258	28270	PASS	TA	T	46771	0.99504	595	234,5,23828,22711	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749258	28280	PASS	G	C	46669	0.939639	27	20,4,23870,22685	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749258	28281	PASS	A	T	46669	0.910754	23	33,12,23860,22680	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749258	28282	PASS	T	A	46676	0.91291	12	41,24,23791,22692	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749258	28881	PASS	G	A	23242	0.773298	18	7,0,11496,11412	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749258	28882	PASS	G	A	23242	0.846442	1	4,2,11632,11438	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749258	28883	PASS	G	C	23243	0.945919	1	3,4,11652,11563	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749258	28977	PASS	C	T	11817	0.925785	0	0,3,9,11782	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749258	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	54750	8.77E-4	0	27491,27185,28,27	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749259	241	PASS	C	T	4743	0.868016	0	0,0,2365,2369	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749259	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	9536	0.001783	0	9519,0,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749259	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	9532	0.001993	0	8843,0,659,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749259	560	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9536	0.002097	0	0,9511,0,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgt/Tgt	R99C	leader	0.002097	0.070839	1	1	C>T
ERR5749259	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	25062	4.79E-4	1	15503,9543,7,5	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749259	913	PASS	C	T	15506	0.914614	0	0,9,1,15479	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749259	1368	PASS	T	C	15952	0.945837	0	2,0,15933,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTt/aCt	I188T	nsp2	0.925045	0.945837	1	1	T>C
ERR5749259	3037	PASS	C	T	14501	0.862837	9	2,7,7241,7186	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749259	3267	PASS	C	T	17374	0.969725	0	4,0,17358,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749259	3671	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GA	20508	5.85E-4	0	10260,10242,6,6	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/aaAt	N319K?	nsp3	0.000351	0.0625	6	2	G>GA
ERR5749259	5388	PASS	C	A	3905	0.963892	2147483647	0,0,3902,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749259	5497	PASS	C	T	3902	0.897745	0	0,1,0,3893	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C926	nsp3	0.000964	0.897745	3	2	C>T
ERR5749259	5784	PASS	C	T	28369	0.907998	12	0,5,14002,14326	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T1022I	nsp3	0.001294	0.919357	2	1	C>T
ERR5749259	5986	PASS	C	T	10661	0.976081	0	1,0,10650,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749259	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10483	0.002003	0	4,10352,0,28	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749259	6954	PASS	T	C	19566	0.823316	0	0,1,0,19471	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749259	8964	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	16590	6.63E-4	0	16573,6,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K138	nsp4	0.000553	0.981649	4	2	CA>C
ERR5749259	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	17986	5.56E-4	11	13306,4670,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749259	9661	PASS	C	T	25822	0.920378	24	2,13,13275,12477	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F369	nsp4	0.000584	0.920378	2	2	C>T
ERR5749259	10116	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23840	0.001888	4	17971,5809,32,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T21I	3Cpro	0.001266	0.952096	1	1	C>T
ERR5749259	10595	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	15777	0.001141	0	4,15729,0,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F181L	3Cpro	0.000964	0.076408	1	1	T>C
ERR5749259	11287	PASS	GTCTGGTTTT	G	21688	0.998432	0	0,34,0,21654	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749259	11761	PASS	G	T	38711	0.354576	1	10491,10500,8842,8792	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaG/aaT	K263N	nsp6	0.000786	0.354576	2	2	G>T
ERR5749259	12269	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	18229	6.03E-4	0	18216,2,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aag/	K61	nsp8	0.000434	0.213333	2	1	GA>G
ERR5749259	13468	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	12624	7.13E-4	0	12615,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggg/	G10	nsp11	0.000713	0.076498	2	2	CG>C
ERR5749259	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25223	0.001189	0	12601,12562,17,18	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749259	14408	PASS	C	T	6517	0.859445	3	0,1,3257,3232	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749259	14676	PASS	C	T	11082	0.818986	0	4,0,11046,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749259	15279	PASS	C	T	15385	0.888593	0	2,0,15363,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749259	16176	PASS	T	C	15757	0.980263	0	0,0,6186,9566	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749259	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	19237	0.001923	0	19198,0,37,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749259	18403	PASS	A	G	26898	0.975463	0	12,0,26863,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Aca/Gca	T122A	ExoN	0.975463	0.978459	1	1	A>G
ERR5749259	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	26282	9.51E-4	0	26257,0,25,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749259	18756	PASS	G	T	26277	0.942688	0	24,0,26199,7	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccG/ccT	P239	ExoN	0.000392	0.942688	3	2	G>T
ERR5749259	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	25080	0.001236	0	0,25049,0,31	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749259	19328	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	15566	9.64E-4	0	15551,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F431	ExoN	0.000459	0.937906	4	2	CT>C
ERR5749259	19343	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	15566	7.71E-4	0	15551,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F436	ExoN	0.000519	0.192257	7	2	CT>C
ERR5749259	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20147	0.002432	0	20085,0,50,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749259	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	21977	9.1E-4	0	0,21957,0,20	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TA>T
ERR5749259	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	27489	0.021063	1772	13729,13125,0,579	HIGH	NONE	FRAME_SHIFT	S	ctt/Tctt	L5S?	S	0.000394	0.091869	4	1	G>GT
ERR5749259	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GTT	27489	0.001637	139	13729,13125,0,45	HIGH	NONE	FRAME_SHIFT	S	ctt/TTctt	L5F?	S	0.000394	0.091869	4	1	G>GTT
ERR5749259	21575	PASS	C	T	26672	0.86094	2	1,3,12654,13608	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749259	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	26661	0.002401	180	12886,13706,0,64	HIGH	NONE	FRAME_SHIFT	S	gtt/Tgtt	V6C?	S	0.000619	0.877942	3	2	C>CT
ERR5749259	21764	PASS	ATACATG	A	12264	0.997228	0	34,0,12230,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749259	21990	PASS	TTTA	T	12268	0.99837	0	0,20,2,12246	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749259	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	16632	0.001263	0	0,16604,0,23	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749259	23063	PASS	A	T	13489	0.873378	0	0,3,0,13429	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749259	23271	PASS	C	A	19134	0.91408	0	1,0,19113,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749259	23403	PASS	A	G	19127	0.970983	0	0,3,0,19109	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749259	23604	PASS	C	A	14126	0.942447	0	12,0,14107,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749259	23709	PASS	C	T	14113	0.944874	0	0,6,1,14090	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749259	24382	PASS	C	T	10491	0.918978	0	0,3,0,10474	LOW	SILENT	SYNONYMOUS_CODING	S	tcC/tcT	S940	S	0.002118	0.920404	2	1	C>T
ERR5749259	24506	PASS	T	G	15421	0.975618	0	6,0,15413,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749259	24914	PASS	G	C	41614	0.962681	0	0,1,20743,20845	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749259	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	25502	0.002117	73	19358,6074,63,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749259	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	10284	0.001653	325	10230,20,4,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749259	25685	PASS	C	T	10250	0.95239	0	1,0,10238,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	gCt/gTt	A98V	orf3a	0.002048	0.964351	1	1	C>T
ERR5749259	26461	PASS	C	T	11204	0.928597	2147483647	0,0,0,11188	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	Ctt/Ttt	L73F	E	0.001401	0.928597	1	1	C>T
ERR5749259	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	12227	9.0E-4	0	0,12216,0,11	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749259	27972	PASS	C	T	7652	0.90081	0	1,0,7609,25	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749259	28048	PASS	G	T	7634	0.930181	0	0,6,0,7621	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749259	28111	PASS	A	G	28964	0.979354	0	2,0,21310,7638	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749259	28270	PASS	TA	T	41496	0.995518	494	192,4,21048,20262	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749259	28280	PASS	G	C	41412	0.938472	25	17,3,21082,20241	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749259	28281	PASS	A	T	41412	0.920917	24	29,10,21066,20241	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749259	28282	PASS	T	A	41413	0.915896	5	19,12,21022,20249	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749259	28881	PASS	G	A	9364	0.780542	3	2,0,4636,4624	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749259	28882	PASS	G	A	9363	0.840115	0	1,1,4681,4611	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749259	28883	PASS	G	C	9363	0.945637	0	1,0,4682,4675	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749259	28977	PASS	C	T	4747	0.930904	2147483647	0,0,0,4738	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749259	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	37449	0.001549	403	32664,4672,8,55	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749259	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	64941	0.001601	0	32603,32201,61,60	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749260	241	PASS	C	T	19456	0.872995	0	0,1,9694,9702	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749260	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	10407	9.61E-4	0	10390,1,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749260	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10395	0.001539	0	9596,1,765,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749260	913	PASS	C	T	22954	0.908556	0	0,6,0,22921	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749260	3037	PASS	C	T	22312	0.820411	39	2,19,11146,10985	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749260	3177	PASS	C	T	33795	0.892972	2	6,5,22557,11196	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P153L	nsp3	0.000773	0.96008	3	2	C>T
ERR5749260	3267	PASS	C	T	22572	0.969077	0	33,0,22526,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749260	5388	PASS	C	A	6928	0.963193	2147483647	0,0,6924,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749260	5822	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19277	0.002438	0	2,19190,0,54	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Ttt	L1035F	nsp3	0.002438	0.069663	1	1	C>T
ERR5749260	5986	PASS	C	T	14910	0.978135	0	2,0,14897,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749260	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14380	0.001182	0	1,14211,0,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749260	6954	PASS	T	C	23276	0.830899	0	0,2,0,23170	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749260	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	34516	5.21E-4	51	17380,17118,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749260	10077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	6644	0.002258	301	5,6597,12,4	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTc/tCc	F8S	3Cpro	0.001833	0.454545	1	1	T>C
ERR5749260	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	19613	0.00209	0	19091,2,41,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749260	11287	PASS	GTCTGGTTTT	G	19603	0.998572	0	0,28,0,19575	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749260	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29210	0.001404	0	14590,14542,23,23	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749260	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12160	0.004194	2934	11856,111,13,174	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749260	14408	PASS	C	T	23646	0.854944	12	0,4,11812,11692	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749260	14676	PASS	C	T	13560	0.791077	0	6,0,13518,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749260	15279	PASS	C	T	22611	0.894565	0	5,0,22585,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749260	16176	PASS	T	C	20227	0.978939	0	0,0,9794,10421	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749260	17135	PASS	C	T	14268	0.96005	355	3,11,14248,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P300L	helicase	0.010417	0.96005	2	2	C>T
ERR5749260	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	23982	4.59E-4	0	23971,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749260	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34612	0.001473	0	34552,0,51,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749260	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	35200	8.52E-4	0	35110,1,31,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749260	21764	PASS	ATACATG	A	15076	0.997811	0	33,0,15043,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749260	21990	PASS	TTTA	T	15086	0.997349	18	1,39,5,15041	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749260	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	16582	0.001508	0	0,16547,0,26	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749260	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30632	0.001143	2	14028,16560,18,18	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749260	22927	PASS	G	T	14049	0.899566	0	33,0,14002,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	ttG/ttT	L455F	S	0.000791	0.909717	4	3	G>T
ERR5749260	22927	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	14049	0.001851	0	14023,0,26,0	HIGH	NONE	FRAME_SHIFT+STOP_GAINED	S	agg/Tagg	R457*?	S	0.000791	0.909717	4	3	G>GT
ERR5749260	23063	PASS	A	T	14027	0.864262	0	0,2,0,13955	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749260	23271	PASS	C	A	23207	0.919593	0	1,0,23184,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749260	23403	PASS	A	G	23205	0.968929	0	0,4,2,23188	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749260	23604	PASS	C	A	17644	0.94304	0	13,0,17621,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749260	23709	PASS	C	T	17629	0.942878	0	0,7,0,17592	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749260	24506	PASS	T	G	17507	0.973439	0	9,0,17494,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749260	24902	PASS	A	G	35648	0.759959	39	13,0,17652,17806	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Atc/Gtc	I1114V	S	0.000992	0.759959	2	1	A>G
ERR5749260	24914	PASS	G	C	35576	0.958708	3	1,0,17723,17837	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749260	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	26064	0.001113	34	20361,5665,36,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749260	25350	PASS	C	T	20563	0.97904	37	3,1,20551,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCa/cTa	P1263L	S	0.000626	0.97904	4	2	C>T
ERR5749260	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	26620	0.001014	459	26522,18,12,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749260	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	26583	0.001016	0	26556,0,27,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749260	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	26742	0.00101	910	26307,157,176,72	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749260	26151	PASS	C	T	60543	0.913698	0	0,29,4,60360	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	tcC/tcT	S253	orf3a	0.000501	0.913698	4	2	C>T
ERR5749260	26690	PASS	G	T	14044	0.753489	0	155,0,13852,21	LOW	SILENT	SYNONYMOUS_CODING	M	ctG/ctT	L56	M	0.002912	0.753489	2	1	G>T
ERR5749260	27972	PASS	C	T	13411	0.892029	19	1,1,13298,66	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749260	28001	PASS	G	A	26452	0.815515	12	4,0,13103,13171	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ccG/ccA	P36	orf8	0.00085	0.830607	2	1	G>A
ERR5749260	28048	PASS	G	T	13348	0.91804	0	0,21,0,13325	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749260	28111	PASS	A	G	34855	0.979544	0	2,1,21487,13355	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749260	28270	PASS	TA	T	41617	0.995579	420	184,8,21237,20196	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749260	28280	PASS	G	C	41545	0.937658	31	17,2,21269,20178	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749260	28281	PASS	A	T	41545	0.913491	21	21,6,21262,20174	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749260	28282	PASS	T	A	41550	0.913213	12	23,11,21218,20197	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749260	28881	PASS	G	A	19778	0.773587	0	1,0,9808,9698	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749260	28882	PASS	G	A	19778	0.827687	0	0,0,9902,9686	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749260	28883	PASS	G	C	19778	0.945141	6	0,2,9912,9840	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749260	28977	PASS	C	T	10050	0.924279	29	1,3,2,10029	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749260	29171	PASS	C	T	30286	0.854685	0	4,0,30130,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Cat/Tat	H300Y	N	0.00121	0.854685	2	2	C>T
ERR5749260	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	60226	0.001096	0	30226,29901,38,37	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749261	13	PASS	T	C	35	1.0	2147483647	0,0,35,0	.	.	.	.	.	.	.	1	1	1	1	T>C
ERR5749261	241	PASS	C	T	22134	0.865094	0	3,4,10932,11096	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749261	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	12307	0.007963	0	12206,4,98,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749261	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	12312	0.001381	0	12105,13,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749261	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	12312	0.001787	0	12105,13,22,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749261	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	12312	0.01194	0	12105,13,147,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749261	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12305	0.001056	2	11058,16,871,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749261	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	12305	0.005445	24	12224,14,65,2	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749261	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	12303	0.001057	0	12260,16,13,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttatg/gtg	VM84V	leader	0.000554	0.991848	4	1	GTTA>G
ERR5749261	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	12303	0.001057	0	12260,16,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749261	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	12306	0.001463	0	12246,20,18,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749261	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATGGTTG	T	12306	0.0013	0	12246,20,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	atggttgag/	MVE85	leader	0.000587	0.476744	4	1	TATGGTTG>T
ERR5749261	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	40065	0.001123	56	27701,12314,44,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749261	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	40064	6.74E-4	10	27612,12293,23,4	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749261	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	40064	0.00307	43	27612,12293,105,18	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749261	714	PASS	G	T	27757	0.97334	277	1,8,27735,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGc/gTc	G150V	leader	0.001941	0.984148	2	1	G>T
ERR5749261	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27733	9.74E-4	0	1,27663,0,28	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749261	913	PASS	C	T	27733	0.910828	0	0,15,1,27688	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749261	1510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	25838	0.003599	0	0,25502,0,105	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G235	nsp2	0.002159	0.937304	1	1	T>C
ERR5749261	2702	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	45463	8.36E-4	2488	45095,90,68,121	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F633V	nsp2	0.000632	0.333333	1	1	T>G
ERR5749261	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	90099	0.001576	2147483647	44953,42039,86,2774	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749261	3037	PASS	C	T	25182	0.816814	58	2,26,12573,12415	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749261	3096	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12666	0.003553	0	0,12599,0,46	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCa/tTa	S126L	nsp3	0.001801	0.932094	1	1	C>T
ERR5749261	3267	PASS	C	T	26244	0.97207	0	2,0,26227,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749261	3310	PASS	A	G	26234	0.952123	0	4,0,26222,2	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaA/gaG	E197	nsp3	0.938803	0.952297	1	1	A>G
ERR5749261	3998	PASS	G	C	33647	0.060629	0	3,31435,0,2140	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Caa	E427Q	nsp3	0.009351	0.060629	2	1	G>C
ERR5749261	5388	PASS	C	A	6939	0.961234	2147483647	0,0,6937,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749261	5986	PASS	C	T	16080	0.97357	2147483647	0,0,16073,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749261	6414	PASS	A	G	28732	0.921098	0	0,3,1,28685	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gAa/gGa	E1232G	nsp3	0.000549	0.930413	2	2	A>G
ERR5749261	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15426	0.001167	0	25,15214,0,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749261	6954	PASS	T	C	27385	0.814862	0	0,4,2,27237	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749261	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	40118	4.74E-4	61	19115,20984,19,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749261	10138	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29598	8.78E-4	2	21157,8400,17,9	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N28	3Cpro	0.000458	0.983567	3	3	C>T
ERR5749261	10193	PASS	G	A	21187	0.863407	0	1,0,21154,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E47K	3Cpro	0.000774	0.869819	2	2	G>A
ERR5749261	10195	PASS	A	T	21187	0.96158	0	15,0,21154,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gaA/gaT	E47D	3Cpro	0.951998	0.969772	1	1	A>T
ERR5749261	11082	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	24265	4.95E-4	0	24259,2,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000427	0.179468	2	1	TG>T
ERR5749261	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	24265	0.002596	0	24160,2,77,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749261	11287	PASS	GTCTGGTTTT	G	24265	0.995302	0	0,114,0,24151	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749261	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	44939	8.23E-4	3	28651,16215,22,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749261	12125	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	19006	0.001052	0	12,18906,0,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y12H	nsp8	0.000847	0.113436	1	1	T>C
ERR5749261	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	39178	0.001685	0	19560,19503,35,36	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749261	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	17158	0.004488	2147483647	16708,161,5,281	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749261	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	33260	0.003007	2	16643,16541,53,47	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749261	14408	PASS	C	T	33260	0.839537	11	2,8,16564,16383	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749261	14676	PASS	C	T	16873	0.714396	0	6,0,16779,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749261	15279	PASS	C	T	29325	0.880341	0	7,0,29267,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749261	16176	PASS	T	C	24298	0.981645	0	0,1,10667,13621	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749261	16647	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	28091	8.19E-4	0	5,27941,0,25	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acG/acA	T137	helicase	0.000746	0.885245	2	1	G>A
ERR5749261	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	36861	0.001465	0	36779,0,59,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749261	21764	PASS	ATACATG	A	15671	0.997256	0	42,0,15628,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749261	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	15671	7.66E-4	0	15659,0,12,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749261	21990	PASS	TTTA	T	15678	0.997002	0	0,47,6,15625	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749261	22290	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	27360	5.48E-4	0	1,27342,0,15	HIGH	NONE	FRAME_SHIFT	S	tta/	L244	S	0.000389	0.578006	2	2	CT>C
ERR5749261	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	19204	0.001198	0	0,19177,0,23	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749261	23063	PASS	A	T	91	0.791209	2147483647	0,0,0,91	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749261	23271	PASS	C	A	28620	0.921419	0	2,0,28593,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749261	23403	PASS	A	G	28610	0.967599	2147483647	0,0,0,28589	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749261	23522	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTA	G	18631	5.37E-4	0	18612,1,10,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	gaacatgtcaacaactcatatgagtgtgacatacccattggtgcaggtata/gta	EHVNNSYECDIPIGAGI654V	S	0.00053	0.959726	5	2	GAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTA>G
ERR5749261	23604	PASS	C	A	18625	0.943141	0	12,0,18601,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749261	23709	PASS	C	T	18627	0.942771	0	0,6,17,18579	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749261	24010	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATTTATTGAAGATCTAC	A	23616	7.2E-4	0	182,23424,0,17	HIGH	NONE	FRAME_SHIFT	S	attgaagatctacttttc/	IEDLLF818	S	0.000455	0.926398	4	2	ATTTATTGAAGATCTAC>A
ERR5749261	24127	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TTTG	38104	5.77E-4	45	14652,23452,0,22	MODERATE	NONE	CODON_INSERTION	S	aac/TTGaac	N856LN	S	0.000324	0.111888	4	1	T>TTTG
ERR5749261	24127	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	38104	3.41E-4	1	14640,23483,4,9	HIGH	NONE	FRAME_SHIFT	S	aac/	N856	S	0.000324	0.111888	4	1	TA>T
ERR5749261	24506	PASS	T	G	23272	0.97555	0	9,0,23251,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749261	24914	PASS	G	C	40985	0.960791	0	0,1,20429,20522	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749261	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	30872	0.001749	101	21100,9695,64,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749261	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	30641	8.81E-4	0	30614,0,27,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749261	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	30874	0.001263	1224	30406,213,130,89	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749261	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	63266	9.8E-4	0	2,63192,0,62	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749261	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	14548	0.001993	0	3,14507,0,29	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749261	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	14548	0.001787	0	3,14518,0,26	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749261	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	14550	0.005842	0	3,14453,0,85	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749261	27494	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	48202	0.002967	10	25613,22408,68,80	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	cCt/cTt	P34L	orf7a	0.000672	0.961447	2	2	C>T
ERR5749261	27506	PASS	G	A	48199	0.985435	11	5,0,25688,22491	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	gGa/gAa	G38E	orf7a	0.000715	0.985435	4	2	G>A
ERR5749261	27972	PASS	C	T	13536	0.908245	18	1,1,13400,91	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749261	28048	PASS	G	T	13468	0.92174	0	0,13,2,13444	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749261	28111	PASS	A	G	38245	0.980468	0	3,1,24761,13468	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749261	28270	PASS	TA	T	47943	0.995077	617	242,5,24429,23278	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749261	28280	PASS	G	C	47862	0.934792	12	11,3,24497,23247	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749261	28281	PASS	A	T	47862	0.914922	25	30,10,24485,23260	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749261	28282	PASS	T	A	47866	0.910918	9	25,14,24429,23273	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749261	28406	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTACCCAATA	T	24789	6.86E-4	0	20,24751,0,17	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	N	ttacccaataat/tat	LPNN45Y	N	0.00043	0.921074	3	2	TTACCCAATA>T
ERR5749261	28881	PASS	G	A	20595	0.751687	27	10,0,10164,10105	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749261	28882	PASS	G	A	20594	0.822327	0	1,0,10306,10082	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749261	28883	PASS	G	C	20594	0.939351	0	2,1,10322,10246	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749261	28977	PASS	C	T	10523	0.923026	0	0,2,0,10498	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749261	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	40593	0.001109	158	30027,10470,9,41	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749261	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	59674	0.00114	0	29977,29598,37,38	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749261	29779	PASS	G	T	11561	0.961249	0	0,4,0,11547	.	.	.	.	.	.	.	0.001489	0.975228	1	1	G>T
ERR5749262	241	PASS	C	T	15504	0.857908	0	3,4,7678,7749	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749262	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	15439	0.001814	0	15416,0,28,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749262	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	15440	7.12E-4	0	15358,1,11,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749262	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	15440	0.003627	0	15358,1,56,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749262	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	15427	0.001426	0	15403,2,22,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749262	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	15427	7.13E-4	0	15403,3,11,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749262	520	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTT	G	15442	5.83E-4	0	15415,18,9,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttgag/gag	VE86E	leader	0.000583	0.051154	1	1	GGTT>G
ERR5749262	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	36932	3.25E-4	27	21447,15469,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749262	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	36934	3.52E-4	2	21420,15451,9,4	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749262	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	36934	0.00111	6	21420,15451,28,13	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749262	913	PASS	C	T	21463	0.92317	0	0,21,0,21412	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749262	1510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	21686	0.002721	0	0,21421,0,67	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G235	nsp2	0.002159	0.937304	1	1	T>C
ERR5749262	1573	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	21751	0.001287	759	7,21687,26,3	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acA/acG	T256	nsp2	0.001231	0.75	1	1	A>G
ERR5749262	3037	PASS	C	T	22819	0.804242	78	1,30,11390,11210	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749262	3267	PASS	C	T	19897	0.96884	0	0,0,19882,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749262	3575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	15880	6.3E-4	0	15870,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/ttTa	L287F?	nsp3	0.000594	0.059126	3	1	G>GT
ERR5749262	4255	PASS	G	A	42720	0.834902	82	36,2,21242,21217	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccG/ccA	P512	nsp3	0.001102	0.871853	2	1	G>A
ERR5749262	5170	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	12526	7.98E-4	0	2,12514,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T819	nsp3	0.000565	0.894036	2	2	CCA>C
ERR5749262	5388	PASS	C	A	8305	0.959663	2147483647	0,0,8303,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749262	5497	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	8300	9.64E-4	0	0,8291,0,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	aga/	R928	nsp3	0.000964	0.897745	3	2	CA>C
ERR5749262	5986	PASS	C	T	15053	0.972696	0	1,0,15038,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749262	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14440	0.001454	0	6,14291,0,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749262	6954	PASS	T	C	22290	0.820502	0	0,8,1,22165	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749262	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	19687	0.001422	0	19631,0,47,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749262	11287	PASS	GTCTGGTTTT	G	19688	0.997511	0	0,49,0,19639	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749262	11507	PASS	G	A	32966	0.906874	6	3,0,16477,16403	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Att	V179I	nsp6	0.007744	0.914418	2	2	G>A
ERR5749262	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	20981	0.001239	0	20935,0,27,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749262	12513	PASS	C	T	20981	0.983652	0	1,0,20965,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aTg	T141M	nsp8	0.000794	0.984064	2	2	C>T
ERR5749262	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	39772	0.001358	0	19856,19814,29,31	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749262	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	17543	0.004389	2147483647	17134,126,11,263	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749262	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	34144	7.91E-4	1	17120,17015,15,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749262	14408	PASS	C	T	34144	0.847411	11	1,6,17036,16851	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749262	14676	PASS	C	T	13643	0.790662	0	6,0,13598,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749262	15279	PASS	C	T	23264	0.886219	0	1,0,23235,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749262	16176	PASS	T	C	23834	0.981161	4	1,3,12623,11198	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749262	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34305	0.002128	0	34206,0,75,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749262	21304	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	32465	0.001602	0	6,32382,0,64	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgc/Agc	R216S	MethTr	0.000411	0.605296	3	2	C>A
ERR5749262	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	32699	8.26E-4	2	15946,16325,14,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749262	21764	PASS	ATACATG	A	15050	0.996944	0	45,0,15004,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749262	21990	PASS	TTTA	T	15062	0.998539	0	0,22,6,15034	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749262	22484	PASS	G	T	11069	0.713344	0	0,9,87,10854	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gta/Tta	V308L	S	0.003485	0.765485	2	1	G>T
ERR5749262	23063	PASS	A	T	15044	0.865129	0	0,2,0,14979	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749262	23271	PASS	C	A	22296	0.922363	0	2,0,22270,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749262	23403	PASS	A	G	22302	0.966505	0	0,7,0,22273	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749262	23604	PASS	C	A	18588	0.943135	0	12,0,18564,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749262	23709	PASS	C	T	18564	0.928571	0	0,6,5,18517	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749262	24506	PASS	T	G	18735	0.97502	0	11,0,18718,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749262	24914	PASS	G	C	42347	0.954282	3	0,2,21089,21229	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749262	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	28630	0.001327	85	19850,8713,55,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749262	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	23784	0.001387	375	23673,31,18,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749262	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	23737	5.9E-4	0	23722,1,14,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749262	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	23884	0.001172	960	23448,167,150,76	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749262	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	58331	3.26E-4	0	6,58300,0,19	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749262	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	14172	0.001693	0	2,14139,0,24	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749262	26936	PASS	C	T	33298	0.955072	0	1,0,33255,0	LOW	SILENT	SYNONYMOUS_CODING	M	ctC/ctT	L138	M	0.001308	0.968147	2	1	C>T
ERR5749262	27972	PASS	C	T	12598	0.900064	78	3,4,12492,53	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749262	28048	PASS	G	T	12570	0.923071	0	0,15,0,12544	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749262	28111	PASS	A	G	30638	0.979764	5	3,5,18047,12574	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749262	28270	PASS	TA	T	34997	0.9944	502	201,5,17774,17027	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749262	28280	PASS	G	C	34920	0.936541	10	13,5,17828,17013	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749262	28281	PASS	A	T	34920	0.912572	40	32,7,17807,17018	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749262	28282	PASS	T	A	34920	0.911226	30	25,6,17774,17024	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749262	28881	PASS	G	A	16270	0.753227	1	4,2,8005,7998	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749262	28882	PASS	G	A	16270	0.827843	12	5,0,8126,8002	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749262	28883	PASS	G	C	16270	0.943884	12	5,0,8138,8117	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749262	28977	PASS	C	T	8319	0.929919	0	0,2,0,8302	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749262	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	36291	0.001102	181	27938,8275,6,38	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749262	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	55489	0.001225	0	27859,27512,48,47	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749263	241	PASS	C	T	7053	0.845739	6	0,2,3512,3502	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749263	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	12961	0.003163	0	12920,4,41,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749263	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	12961	0.001234	0	12879,4,16,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749263	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	12961	0.004166	0	12879,4,54,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749263	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12943	0.002395	0	11935,5,862,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749263	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	12943	0.001777	0	12915,5,23,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749263	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	12942	7.73E-4	0	12921,6,10,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749263	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	30169	6.63E-4	2	17164,12980,13,7	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749263	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	30169	4.31E-4	5	17126,12965,5,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749263	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	30169	0.001823	24	17126,12965,42,13	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749263	913	PASS	C	T	17173	0.913702	0	0,10,0,17137	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749263	3037	PASS	C	T	19447	0.814059	21	3,14,9712,9570	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749263	3267	PASS	C	T	17080	0.965105	0	3,0,17068,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749263	4578	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTAACGATC	T	12323	6.49E-4	0	0,12315,0,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	aacgatctaaat/	NDLN621	nsp3	0.000519	0.082979	2	2	TTAACGATC>T
ERR5749263	5388	PASS	C	A	6338	0.958504	2147483647	0,0,6337,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749263	5986	PASS	C	T	12389	0.974978	0	1,0,12380,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749263	6954	PASS	T	C	18025	0.822136	0	0,2,0,17919	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749263	7564	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	13961	7.88E-4	0	1,13949,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/	Y1617	nsp3	0.000586	0.056194	4	2	CT>C
ERR5749263	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	24698	8.5E-4	32	16726,7951,21,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749263	10323	PASS	A	G	18152	0.955267	0	0,4,0,18126	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749263	10615	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15080	0.012069	0	5,14853,0,213	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D187	3Cpro	0.001623	0.865067	1	1	C>T
ERR5749263	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	17793	0.001517	0	17736,0,43,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749263	11287	PASS	GTCTGGTTTT	G	17790	0.997527	0	0,44,0,17746	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749263	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	19538	0.001126	0	19495,0,22,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749263	13329	PASS	C	T	14072	0.882106	450	14,2,0,14045	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T102I	nsp10	0.000676	0.882106	2	2	C>T
ERR5749263	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14721	0.001902	0	14,14658,0,31	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749263	13712	PASS	A	G	18537	0.300156	0	12739,0,5790,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K91R	RdRp	0.001252	0.300156	1	1	A>G
ERR5749263	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	9429	0.005621	2872	9172,84,3,166	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749263	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	18258	9.86E-4	0	9154,9097,9,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749263	14408	PASS	C	T	18258	0.837222	4	1,3,9110,8998	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749263	14676	PASS	C	T	11555	0.763133	0	12,0,11493,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749263	15096	PASS	T	C	19253	0.964213	0	0,3,28,19210	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaT/aaC	N552	RdRp	0.941667	0.970182	1	1	T>C
ERR5749263	15279	PASS	C	T	18814	0.894653	0	3,0,18775,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749263	16176	PASS	T	C	19766	0.980826	0	1,0,10119,9630	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749263	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	25492	5.1E-4	0	25479,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749263	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27580	0.002067	0	27505,1,60,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749263	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	18375	6.53E-4	0	0,18362,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TA>T
ERR5749263	21764	PASS	ATACATG	A	13348	0.997303	0	36,0,13312,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749263	21990	PASS	TTTA	T	13355	0.997754	0	0,30,6,13319	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749263	23063	PASS	A	T	14148	0.85998	0	0,0,1,14069	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749263	23271	PASS	C	A	18917	0.925675	0	3,0,18895,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749263	23403	PASS	A	G	18914	0.970921	0	0,6,0,18898	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749263	23604	PASS	C	A	16353	0.948389	0	12,0,16335,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749263	23709	PASS	C	T	16329	0.935513	0	0,9,2,16299	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749263	24506	PASS	T	G	15321	0.971281	0	5,0,15313,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749263	24914	PASS	G	C	38564	0.957188	3	1,0,19219,19312	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749263	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	26131	0.001569	49	18388,7678,47,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749263	25437	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	18612	0.001128	0	18573,0,32,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	ttG/ttT	L15F	orf3a	0.001128	0.971411	2	2	G>T
ERR5749263	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	13779	0.002468	597	13701,22,9,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749263	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	13945	0.001004	0	13931,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749263	26209	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	48000	7.92E-4	0	2,47904,0,50	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gtg/Atg	V273M	orf3a	0.000792	0.234679	3	1	G>A
ERR5749263	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	13810	9.41E-4	0	4,13776,0,13	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749263	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	13808	0.002462	0	0,13764,0,34	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749263	27684	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTCTCCAATTTT	C	17787	0.001912	0	10,17743,0,34	HIGH	NONE	FRAME_SHIFT	ORF7a	ccaatttttctt/	PIFL99	orf7a	0.000478	0.90411	2	2	CTCTCCAATTTT>C
ERR5749263	27972	PASS	C	T	9587	0.90581	19	1,1,9496,49	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749263	28048	PASS	G	T	9547	0.91369	0	0,6,0,9537	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749263	28095	PASS	A	T	9558	0.963068	71	2,1,0,9540	HIGH	NONSENSE	STOP_GAINED	ORF8	Aaa/Taa	K68*	orf8	0.002672	0.967672	2	2	A>T
ERR5749263	28111	PASS	A	G	25315	0.977642	0	1,0,15749,9553	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749263	28270	PASS	TA	T	30434	0.994316	400	173,7,15504,14757	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749263	28280	PASS	G	C	30364	0.93489	7	7,2,15549,14741	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749263	28281	PASS	A	T	30364	0.913714	25	17,3,15541,14742	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749263	28282	PASS	T	A	30366	0.906046	2	14,10,15522,14756	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749263	28881	PASS	G	A	14632	0.750683	7	7,2,7213,7173	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749263	28882	PASS	G	A	14632	0.822512	3	2,0,7326,7164	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749263	28883	PASS	G	C	14632	0.942387	0	1,1,7339,7278	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749263	28977	PASS	C	T	7451	0.922427	2147483647	0,0,0,7435	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749263	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	60342	9.11E-4	0	30329,29923,34,32	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749264	241	PASS	C	T	13395	0.866592	0	1,1,6655,6687	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749264	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	13885	0.001224	0	13847,11,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749264	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	13885	0.002017	2	12830,14,994,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749264	520	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTT	G	13892	7.92E-4	0	13859,22,11,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttgag/gag	VE86E	leader	0.000583	0.051154	1	1	GGTT>G
ERR5749264	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	33316	9.0E-4	8	19405,13881,22,8	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749264	913	PASS	C	T	19416	0.91919	0	0,8,0,19380	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749264	1059	PASS	C	T	15069	0.695335	0	3797,0,11258,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCc/aTc	T85I	nsp2	0.001728	0.920973	1	1	C>T
ERR5749264	3037	PASS	C	T	21892	0.806961	58	1,23,10945,10756	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749264	3267	PASS	C	T	18903	0.971433	0	1,0,18897,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749264	5388	PASS	C	A	6952	0.964039	2147483647	0,0,6946,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749264	5986	PASS	C	T	13115	0.976592	0	2,0,13106,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749264	6813	PASS	C	T	32965	0.954376	0	3,1,19962,12974	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T1365I	nsp3	0.001082	0.95799	2	1	C>T
ERR5749264	6954	PASS	T	C	19925	0.806775	0	0,3,0,19798	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749264	8092	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23662	0.013904	0	23277,0,354,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ctC/ctT	L1791	nsp3	0.000539	0.063953	3	2	C>T
ERR5749264	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	31842	0.001131	90	17631,14176,36,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749264	10244	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18454	0.004823	0	18348,1,94,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cat/Tat	H64Y	3Cpro	0.001845	0.074194	2	2	C>T
ERR5749264	10323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	18444	0.001627	0	0,18374,0,36	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749264	11287	PASS	GTCTGGTTTT	G	18048	0.998393	0	0,28,0,18019	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749264	11442	PASS	C	T	15785	0.064428	0	14717,0,1046,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A157V	nsp6	0.00069	0.064428	2	2	C>T
ERR5749264	11507	PASS	G	A	31427	0.900086	1	4,2,15724,15615	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Att	V179I	nsp6	0.007744	0.914418	2	2	G>A
ERR5749264	12318	PASS	C	T	45505	0.097044	1	20100,20129,2570,2600	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S76F	nsp8	0.003407	0.097044	1	1	C>T
ERR5749264	12870	PASS	C	T	14738	0.833899	0	1,0,14689,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T62I	nsp9	0.773252	0.848527	1	1	C>T
ERR5749264	12884	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	14738	0.005021	0	14636,0,81,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Aca/Gca	T67A	nsp9	0.001655	0.08541	1	1	A>G
ERR5749264	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	13494	0.004669	2147483647	13212,81,5,192	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749264	14408	PASS	C	T	26309	0.856551	11	1,6,13147,12994	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749264	14676	PASS	C	T	12464	0.757381	0	5,0,12411,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749264	15279	PASS	C	T	20949	0.906821	2147483647	0,0,20920,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749264	16176	PASS	T	C	20583	0.979595	6	0,2,10735,9832	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749264	17999	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24945	0.003728	0	12494,12341,46,48	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T588I	helicase	0.001094	0.974498	2	1	C>T
ERR5749264	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	25583	7.43E-4	0	25564,0,19,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749264	18897	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	25598	0.001367	0	9,25535,0,41	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttT/ttC	F286	ExoN	0.00046	0.060685	3	3	T>C
ERR5749264	19401	PASS	T	A	18384	0.916177	0	11,0,18333,2	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcT/tcA	S454	ExoN	0.913864	0.918286	1	1	T>A
ERR5749264	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	31771	0.001228	0	31711,0,40,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749264	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30445	0.002956	4	14876,15132,47,58	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749264	21637	PASS	C	T	15290	0.958404	0	0,4,0,15281	LOW	SILENT	SYNONYMOUS_CODING	S	ccC/ccT	P25	S	0.954687	0.96491	1	1	C>T
ERR5749264	21764	PASS	ATACATG	A	13651	0.996264	0	50,0,13600,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749264	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	13651	8.79E-4	0	13639,0,12,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749264	21990	PASS	TTTA	T	13653	0.998755	0	0,17,2,13634	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749264	23063	PASS	A	T	13711	0.872584	0	0,1,0,13663	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749264	23271	PASS	C	A	20473	0.94505	0	2,0,20457,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749264	23403	PASS	A	G	20464	0.969703	0	0,4,0,20448	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749264	23406	PASS	T	C	20464	0.950987	0	0,9,0,20446	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gTt/gCt	V615A	S	0.949411	0.956636	1	1	T>C
ERR5749264	23604	PASS	C	A	16712	0.958832	0	12,0,16693,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749264	23709	PASS	C	T	16703	0.945279	0	0,5,1,16672	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749264	24506	PASS	T	G	15879	0.974558	0	2,0,15876,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749264	24835	PASS	T	C	19541	0.740648	0	4798,0,14736,0	LOW	SILENT	SYNONYMOUS_CODING	S	cgT/cgC	R1091	S	0.002491	0.740648	1	1	T>C
ERR5749264	24914	PASS	G	C	38844	0.956467	0	0,0,19330,19467	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749264	25207	PASS	C	T	7359	0.799565	0	0,18,0,7306	LOW	SILENT	SYNONYMOUS_CODING	S	taC/taT	Y1215	S	0.004687	0.815232	1	1	C>T
ERR5749264	25496	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	37348	0.010951	1	18261,18202,211,219	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aTa/aCa	I35T	orf3a	0.000369	0.96555	3	2	T>C
ERR5749264	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	13284	0.001129	0	0,13268,0,15	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749264	27972	PASS	C	T	11879	0.908747	0	0,0,11804,47	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749264	28048	PASS	G	T	11838	0.928366	0	0,12,0,11823	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749264	28077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	11844	0.00228	0	0,11811,0,33	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	Gtg/Ttg	V62L	orf8	0.00228	0.974466	2	1	G>T
ERR5749264	28111	PASS	A	G	29359	0.977077	0	2,2,17508,11839	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749264	28270	PASS	TA	T	33969	0.994436	470	194,6,17264,16516	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749264	28280	PASS	G	C	33887	0.93741	16	9,1,17308,16492	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749264	28281	PASS	A	T	33887	0.904329	19	18,5,17295,16501	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749264	28282	PASS	T	A	33888	0.882761	4	20,14,17220,16503	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749264	28881	PASS	G	A	15915	0.753252	19	10,1,7857,7811	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749264	28882	PASS	G	A	15915	0.824568	11	7,1,7965,7796	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749264	28883	PASS	G	C	15915	0.941502	0	1,0,7985,7915	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749264	28977	PASS	C	T	8095	0.929833	0	0,2,0,8085	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749264	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	56787	7.22E-4	0	28537,28191,25,24	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749265	241	PASS	C	T	12574	0.864562	0	1,2,6260,6262	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749265	913	PASS	C	T	18865	0.913173	0	0,13,0,18820	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749265	3037	PASS	C	T	13818	0.811188	19	2,11,6906,6806	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749265	3267	PASS	C	T	18801	0.969257	0	1,0,18787,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749265	5388	PASS	C	A	4553	0.960466	2147483647	0,0,4550,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749265	5986	PASS	C	T	9628	0.973411	2147483647	0,0,9621,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749265	6954	PASS	T	C	20712	0.824256	2147483647	0,0,0,20595	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749265	7070	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	36943	8.66E-4	109	16116,20774,34,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggc/Agc	G1451S	nsp3	0.000698	0.101434	3	1	G>A
ERR5749265	7716	PASS	C	T	16359	0.068036	0	15221,0,1127,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T1666I	nsp3	0.068036	0.068036	1	1	C>T
ERR5749265	7764	PASS	C	T	16355	0.961847	0	2,0,16340,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCc/tTc	S1682F	nsp3	0.001052	0.964731	1	1	C>T
ERR5749265	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	25903	0.00166	124	13217,12643,43,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749265	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	20323	0.002116	0	19786,2,43,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749265	11287	PASS	GTCTGGTTTT	G	20310	0.998917	0	0,21,0,20288	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749265	11464	PASS	G	T	11656	0.906658	0	12,0,11626,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atT	M164I	nsp6	0.001064	0.906658	2	2	G>T
ERR5749265	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	36601	0.001284	0	18278,18227,26,25	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749265	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	8082	0.004331	2088	7889,62,6,119	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749265	14408	PASS	C	T	15711	0.85106	4	1,3,7844,7761	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749265	14676	PASS	C	T	12892	0.797549	0	2,0,12862,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749265	15279	PASS	C	T	21302	0.888133	0	3,0,21277,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749265	16176	PASS	T	C	18554	0.981729	0	0,1,7901,10649	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749265	17024	PASS	C	T	16096	0.069148	0	0,14881,0,1194	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S263F	helicase	0.069148	0.069148	1	1	C>T
ERR5749265	17799	PASS	A	G	12700	0.977795	0	1,0,12691,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtA/gtG	V521	helicase	0.001548	0.98027	1	1	A>G
ERR5749265	18457	PASS	C	T	27360	0.946966	0	4,0,27318,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cca/Tca	P140S	ExoN	0.001253	0.951352	2	1	C>T
ERR5749265	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21623	0.001989	0	21573,0,44,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749265	21764	PASS	ATACATG	A	9930	0.997281	0	27,0,9903,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749265	21990	PASS	TTTA	T	9937	0.997484	0	0,25,5,9907	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749265	23063	PASS	A	T	11452	0.862906	0	0,1,0,11388	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749265	23271	PASS	C	A	21245	0.922476	0	1,0,21227,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749265	23403	PASS	A	G	21243	0.970437	0	0,7,0,21220	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749265	23541	PASS	A	T	12463	0.950734	0	8,0,12446,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tAt/tTt	Y660F	S	0.000911	0.950734	4	2	A>T
ERR5749265	23604	PASS	C	A	12461	0.940454	0	9,0,12444,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749265	23709	PASS	C	T	12442	0.941569	0	0,3,2,12424	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749265	24506	PASS	T	G	17400	0.976609	0	1,0,17396,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749265	24914	PASS	G	C	31998	0.959935	3	1,0,15945,16032	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749265	25555	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	14396	0.003751	0	1,14323,0,66	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gtt/Ttt	V55F	orf3a	0.000552	0.900573	5	2	G>T
ERR5749265	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	16316	0.00141	392	16258,9,8,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749265	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	16378	0.001404	926	16165,71,66,58	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749265	27972	PASS	C	T	7358	0.904186	0	0,0,7302,29	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749265	28048	PASS	G	T	7333	0.918314	0	0,7,0,7324	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749265	28111	PASS	A	G	27492	0.977157	7	3,3,20140,7337	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749265	28270	PASS	TA	T	38980	0.994869	411	196,12,19868,18912	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749265	28280	PASS	G	C	38917	0.93612	9	11,4,19922,18901	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749265	28281	PASS	A	T	38917	0.919136	52	33,5,19911,18904	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749265	28282	PASS	T	A	38919	0.91007	21	26,9,19875,18918	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749265	28396	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GC	G	20162	4.96E-4	0	11,20141,0,10	HIGH	NONE	FRAME_SHIFT	N	caa/	Q43	N	0.000496	0.946059	5	2	GC>G
ERR5749265	28881	PASS	G	A	15898	0.78123	2	3,1,7892,7810	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749265	28882	PASS	G	A	15898	0.826142	0	1,1,7973,7771	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749265	28883	PASS	G	C	15898	0.94515	3	0,1,7976,7907	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749265	28977	PASS	C	T	8080	0.905569	0	0,6,0,8055	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749265	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	48513	0.001525	0	24336,24070,43,42	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749266	239	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTC	T	15990	6.25E-4	0	7953,8027,5,5	.	.	.	.	.	.	.	0.000495	0.25	4	1	TTC>T
ERR5749266	241	PASS	C	T	15987	0.866704	0	0,1,7937,7987	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749266	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	11564	0.001643	0	11544,3,19,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749266	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	11558	0.00225	0	11521,3,26,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749266	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	32303	6.19E-4	17	20699,11579,18,2	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749266	913	PASS	C	T	20708	0.918148	0	0,5,0,20668	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749266	3037	PASS	C	T	16878	0.808923	39	0,13,8442,8303	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749266	3267	PASS	C	T	18890	0.972896	0	1,0,18875,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749266	4276	PASS	C	T	13084	0.790737	0	0,1,0,12965	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y519	nsp3	0.00102	0.812261	1	1	C>T
ERR5749266	5170	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	11987	0.001085	0	4,11970,0,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T819	nsp3	0.000565	0.894036	2	2	CCA>C
ERR5749266	5388	PASS	C	A	5409	0.95452	2147483647	0,0,5408,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749266	5986	PASS	C	T	10385	0.978142	0	3,0,10376,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749266	6954	PASS	T	C	20933	0.810061	0	0,4,0,20826	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749266	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	30379	9.88E-4	112	12817,17532,30,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749266	11287	PASS	GTCTGGTTTT	G	15690	0.997514	0	0,39,0,15651	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749266	11507	PASS	G	A	21681	0.898713	4	4,1,10844,10760	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Att	V179I	nsp6	0.007744	0.914418	2	2	G>A
ERR5749266	11782	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	20477	0.00669	0	14,20136,0,144	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaA/aaG	K270	nsp6	0.001073	0.917917	2	2	A>G
ERR5749266	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29855	0.002043	0	14903,14848,34,33	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749266	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	11021	0.005444	2147483647	10777,49,5,187	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749266	14408	PASS	C	T	21434	0.833535	6	1,4,10710,10558	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749266	14676	PASS	C	T	12826	0.752144	0	5,0,12782,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749266	15279	PASS	C	T	22539	0.899818	0	3,0,22514,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749266	16176	PASS	T	C	17893	0.980216	0	1,2,7915,9967	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749266	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	20217	6.43E-4	0	20204,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749266	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	23159	4.32E-4	0	0,23149,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749266	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23960	0.002462	0	23892,0,60,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749266	21764	PASS	ATACATG	A	11118	0.995863	0	46,0,11072,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749266	21812	PASS	C	T	11118	0.06449	0	10369,0,739,0	LOW	SILENT	SYNONYMOUS_CODING	S	Cta/Tta	L84	S	0.001506	0.06449	1	1	C>T
ERR5749266	21990	PASS	TTTA	T	11125	0.997843	0	0,24,7,11094	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749266	23063	PASS	A	T	8535	0.855185	0	0,1,0,8479	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749266	23271	PASS	C	A	20863	0.921152	0	2,0,20843,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749266	23403	PASS	A	G	20850	0.974101	0	0,2,0,20833	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749266	23604	PASS	C	A	12785	0.935628	0	7,0,12771,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749266	23709	PASS	C	T	12766	0.935689	0	0,4,1,12749	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749266	24506	PASS	T	G	16556	0.972095	0	3,0,16550,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749266	24914	PASS	G	C	26721	0.958984	3	1,0,13320,13386	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749266	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	25816	0.001433	1433	25383,165,135,102	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749266	26257	PASS	G	A	57806	0.942999	5	2,3,11870,45865	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	Gtt/Att	V5I	E	0.000247	0.948926	4	2	G>A
ERR5749266	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	8572	0.00105	0	0,8562,0,9	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749266	27972	PASS	C	T	7943	0.902178	0	0,0,7884,33	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749266	28048	PASS	G	T	7913	0.916214	0	0,6,0,7905	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749266	28111	PASS	A	G	24855	0.977872	2	2,2,16928,7915	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749266	28270	PASS	TA	T	32718	0.99514	367	165,8,16708,15851	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749266	28280	PASS	G	C	32650	0.935896	19	10,1,16729,15836	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749266	28281	PASS	A	T	32650	0.911884	32	26,6,16726,15835	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749266	28282	PASS	T	A	32656	0.907276	6	25,15,16699,15846	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749266	28412	PASS	A	T	16945	0.955798	63	2,2,3,16926	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Aat/Tat	N47Y	N	0.00198	0.965453	2	1	A>T
ERR5749266	28881	PASS	G	A	12716	0.7581	12	5,0,6321,6216	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749266	28882	PASS	G	A	12716	0.820698	9	4,0,6388,6198	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749266	28883	PASS	G	C	12716	0.945816	0	1,0,6402,6308	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749266	28977	PASS	C	T	6451	0.926213	0	0,1,0,6443	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749266	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	45043	0.001332	0	22627,22325,36,34	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749267	241	PASS	C	T	644	0.881988	0	0,0,320,322	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749267	673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10430	0.002397	109	7573,2825,3,25	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y136	leader	0.000454	0.602236	3	2	C>T
ERR5749267	913	PASS	C	T	7575	0.912343	0	0,4,0,7564	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749267	1461	PASS	A	G	12031	0.900091	1	3,2,5944,6041	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K219R	nsp2	0.000518	0.90899	2	2	A>G
ERR5749267	1599	PASS	G	T	16048	0.964482	14	1,5,9929,6110	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGt/gTt	G265V	nsp2	0.001427	0.96468	2	1	G>T
ERR5749267	1685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	9923	0.001915	0	9894,0,28,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gcc/Tcc	A294S	nsp2	0.001379	0.231183	3	2	G>T
ERR5749267	1813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	9913	0.001614	0	0,9886,0,20	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcA	A336	nsp2	0.001022	0.152738	4	2	T>A
ERR5749267	1874	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	9930	0.001611	0	0,9906,0,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gca/Tca	A357S	nsp2	0.001611	0.344371	2	1	G>T
ERR5749267	2232	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	13166	7.6E-4	21	5558,7598,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	tgt/	C477	nsp2	0.000499	0.381237	2	2	CT>C
ERR5749267	2506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	5559	0.002339	0	3,5539,0,13	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ctT/ctC	L567	nsp2	0.002339	0.065476	2	2	T>C
ERR5749267	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	24951	0.001242	1870	12457,11666,29,749	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749267	3037	PASS	C	T	4876	0.814397	9	0,3,2437,2402	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749267	3047	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	2481	0.007658	92	22,2429,8,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gat/Tat	D110Y	nsp3	0.004044	0.233775	2	1	G>T
ERR5749267	3177	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	10689	0.001403	16	8217,2454,18,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cAt	P153H	nsp3	0.000773	0.96008	3	2	C>A
ERR5749267	3267	PASS	C	T	8236	0.971588	2147483647	0,0,8216,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749267	3335	PASS	G	A	15989	0.888736	1	4,2,8208,7722	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E206K	nsp3	0.001289	0.891976	4	3	G>A
ERR5749267	3741	PASS	T	C	4537	0.968922	2147483647	0,0,0,4536	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I341T	nsp3	0.000648	0.968922	2	2	T>C
ERR5749267	3802	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	7832	0.001277	1	3288,4534,5,5	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N363	nsp3	0.000554	0.064198	4	2	TA>T
ERR5749267	4999	PASS	C	T	5508	0.936093	2147483647	0,0,5505,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N760	nsp3	0.001692	0.947468	1	1	C>T
ERR5749267	5206	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	5506	0.002361	0	0,5469,0,28	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atT	M829I	nsp3	0.001901	0.0725	2	1	G>T
ERR5749267	5388	PASS	C	A	1272	0.958333	2147483647	0,0,1272,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749267	5628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	7121	0.003089	0	7099,0,22,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acg/	T970	nsp3	0.000561	0.973644	3	2	CG>C
ERR5749267	5986	PASS	C	T	4411	0.978463	2147483647	0,0,4409,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749267	6813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	15000	0.001533	41	10524,4440,35,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aAt	T1365N	nsp3	0.001082	0.95799	2	1	C>A
ERR5749267	6954	PASS	T	C	10528	0.821809	2147483647	0,0,0,10470	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749267	7564	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	7196	0.003613	0	0,7170,0,26	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/	Y1617	nsp3	0.000586	0.056194	4	2	CT>C
ERR5749267	7860	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11769	0.002719	0	0,11711,0,47	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T1714I	nsp3	0.000611	0.666818	2	2	C>T
ERR5749267	9541	PASS	C	T	6867	0.947284	0	5,0,6146,716	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ctC/ctT	L329	nsp4	0.000346	0.955771	2	2	C>T
ERR5749267	10165	PASS	C	T	10432	0.972297	139	1,4,10419,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y37	3Cpro	0.000632	0.976163	2	2	C>T
ERR5749267	10350	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10428	0.001438	0	0,10403,0,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P99L	3Cpro	0.001438	0.208333	1	1	C>T
ERR5749267	10502	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10202	0.002549	0	10162,0,40,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Gtt	F150V	3Cpro	0.000992	0.998494	3	2	T>G
ERR5749267	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18249	0.001644	0	18186,0,36,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749267	11095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	18237	0.001864	0	18203,0,34,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L43	nsp6	0.000515	0.887707	7	2	CT>C
ERR5749267	11287	PASS	GTCTGGTTTT	G	18245	0.99852	0	0,26,0,18218	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749267	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	11434	0.002012	36	7934,3470,24,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749267	12020	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	14193	0.001691	0	14132,0,56,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Att	L60I	nsp7	0.000994	0.968243	3	2	C>A
ERR5749267	14028	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	8315	0.002405	0	8288,0,27,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atT	M196I	RdRp	0.002405	0.051178	1	1	G>T
ERR5749267	14087	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	8312	0.001684	0	8290,0,18,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tGg/tCg	W216S	RdRp	0.001684	0.130841	2	1	G>C
ERR5749267	14408	PASS	C	T	568	0.822183	0	1,1,280,279	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749267	14676	PASS	C	T	5100	0.80451	2147483647	0,0,5082,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749267	15279	PASS	C	T	7206	0.873994	0	1,0,7192,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749267	15708	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	10371	0.002314	0	0,10330,0,40	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atT	M756I	RdRp	0.001488	0.095967	1	1	G>T
ERR5749267	16176	PASS	T	C	7487	0.982503	0	0,0,1510,5974	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749267	16647	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	13270	0.002788	0	1,13155,0,91	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acG/acT	T137	helicase	0.000746	0.885245	2	1	G>T
ERR5749267	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	8315	0.002766	0	8292,0,23,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749267	17615	PASS	A	G	6744	0.905397	0	0,1,0,6724	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749267	17756	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	6182	0.002426	0	6165,0,15,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aGa/aAa	R507K	helicase	0.000865	0.165644	4	2	G>A
ERR5749267	18498	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	14057	0.002348	0	0,13967,0,34	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atA	M153I	ExoN	0.001072	0.080328	3	1	G>A
ERR5749267	19329	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	7692	0.00338	0	7664,0,26,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcC	A430	ExoN	0.001217	0.228916	1	1	T>C
ERR5749267	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	13317	0.001877	0	0,13292,0,25	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TA>T
ERR5749267	21123	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	25163	9.14E-4	63	11841,13299,0,23	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F156	MethTr	0.000257	0.90982	5	2	GT>G
ERR5749267	21255	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	22767	0.00101	0	11810,10922,17,15	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcG/gcA	A199	MethTr	0.000341	0.917425	4	2	G>A
ERR5749267	21302	PASS	C	T	11768	0.832852	0	0,11,0,11690	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCa/cTa	P215L	MethTr	0.001031	0.843069	1	1	C>T
ERR5749267	21304	PASS	C	A	11768	0.596958	0	0,452,0,11307	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgc/Agc	R216S	MethTr	0.000411	0.605296	3	2	C>A
ERR5749267	21305	PASS	G	A	11768	0.703943	0	0,1,0,11563	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cGc/cAc	R216H	MethTr	0.000727	0.703943	1	1	G>A
ERR5749267	21375	PASS	G	A	11862	0.858793	125	5,2,17,11795	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttG/ttA	L239	MethTr	0.002365	0.858793	2	2	G>A
ERR5749267	21727	PASS	C	T	6769	0.869257	38	0,1,6763,0	LOW	SILENT	SYNONYMOUS_CODING	S	ttC/ttT	F55	S	0.000896	0.878141	2	2	C>T
ERR5749267	21764	PASS	ATACATG	A	6768	0.997784	0	15,0,6753,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749267	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	6768	0.001625	0	6757,0,11,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749267	21913	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	6766	0.003104	0	0,6735,0,23	LOW	SILENT	SYNONYMOUS_CODING	S	ctA/ctG	L117	S	0.003104	0.904899	1	1	A>G
ERR5749267	21990	PASS	TTTA	T	6773	0.998376	0	0,11,4,6758	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749267	22225	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	12996	0.025854	0	0,12626,0,369	LOW	SILENT	SYNONYMOUS_CODING	S	tcG/tcT	S221	S	0.001195	0.94526	3	1	G>T
ERR5749267	22280	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ACTTTACTTG	A	12997	0.002616	0	0,12963,0,34	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	cttgctttacat/cat	LALH242H	S	0.00046	0.997799	1	1	ACTTTACTTG>A
ERR5749267	22690	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	13828	0.00188	0	13519,0,32,0	LOW	SILENT	SYNONYMOUS_CODING	S	acT/acC	T376	S	0.000815	0.051311	2	1	T>C
ERR5749267	22759	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	13836	0.002746	0	0,13778,0,46	LOW	SILENT	SYNONYMOUS_CODING	S	tcA/tcT	S399	S	0.000578	0.12649	2	2	A>T
ERR5749267	23063	PASS	A	T	342	0.862573	2147483647	0,0,0,341	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749267	23191	PASS	C	T	9776	0.956322	39	0,1,9771,0	LOW	SILENT	SYNONYMOUS_CODING	S	ttC/ttT	F543	S	0.000538	0.973337	2	2	C>T
ERR5749267	23255	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	9773	0.001637	0	9695,0,29,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ttt/Att	F565I	S	0.001637	0.921001	2	1	T>A
ERR5749267	23271	PASS	C	A	9768	0.910729	2147483647	0,0,9766,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749267	23403	PASS	A	G	9772	0.969812	0	0,2,0,9765	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749267	23604	PASS	C	A	6909	0.940078	0	6,0,6902,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749267	23709	PASS	C	T	6897	0.944324	0	0,1,0,6890	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749267	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10328	0.002614	44	3420,6878,0,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L752F	S	0.000334	0.080808	2	2	C>T
ERR5749267	24320	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	5137	0.003309	0	0,5120,0,17	HIGH	NONE	FRAME_SHIFT	S	aaa/	K921	S	0.000763	0.138365	4	2	CA>C
ERR5749267	24506	PASS	T	G	9135	0.978106	0	2,0,9130,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749267	24745	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22317	0.001075	54	13155,9133,25,0	LOW	SILENT	SYNONYMOUS_CODING	S	gtC/gtT	V1061	S	0.00048	0.961619	3	2	C>T
ERR5749267	24914	PASS	G	C	26196	0.959918	0	0,0,13048,13132	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749267	25135	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	3657	0.003281	0	3626,0,13,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aaG/aaC	K1191N	S	0.003281	0.884331	3	2	G>C
ERR5749267	25135	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	3657	0.003281	0	3626,0,18,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aaG/aaT	K1191N	S	0.003281	0.884331	3	2	G>T
ERR5749267	25391	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTA	T	14460	0.002835	0	14419,0,41,0	HIGH	NONE	FRAME_SHIFT+START_LOST	ORF3a	atg/	M1	orf3a	0.000585	0.191026	1	1	TTA>T
ERR5749267	25510	PASS	T	G	14458	0.96355	0	0,3,33,14406	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Tca/Gca	S40A	orf3a	0.001771	0.96355	3	1	T>G
ERR5749267	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	1550	0.006452	154	1520,18,1,9	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749267	26256	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22000	0.001182	8	7910,14046,13,13	LOW	SILENT	SYNONYMOUS_CODING	E	ttC/ttT	F4	E	0.000748	0.969561	2	2	C>T
ERR5749267	26270	PASS	C	T	22000	0.926045	5	0,4,7915,14061	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	aCa/aTa	T9I	E	0.000586	0.930791	3	2	C>T
ERR5749267	27476	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25105	9.96E-4	36	12862,12211,4,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	aCa/aTa	T28I	orf7a	0.000547	0.22827	4	2	C>T
ERR5749267	27604	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	12894	0.001008	0	12881,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF7a	gta/gtTa	V71V?	orf7a	0.001008	0.967671	3	2	G>GT
ERR5749267	27643	PASS	C	T	12869	0.741394	2147483647	0,0,12756,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Cct/Tct	P84S	orf7a	0.00166	0.858006	2	1	C>T
ERR5749267	27737	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	12891	0.001474	0	0,12872,0,19	HIGH	NONE	FRAME_SHIFT	ORF7a	aca/	T115	orf7a	0.001474	0.817082	2	2	CA>C
ERR5749267	27752	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	12892	0.001241	0	0,12876,0,16	HIGH	NONE	FRAME_SHIFT	ORF7a	gaa/	E121	orf7a	0.000582	0.943806	2	2	CAG>C
ERR5749267	27972	PASS	C	T	2165	0.902079	0	0,0,2153,6	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749267	28048	PASS	G	T	2159	0.925428	0	0,2,0,2156	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749267	28111	PASS	A	G	20330	0.978701	6	1,1,18153,2160	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749267	28239	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	18162	0.001156	0	18131,0,27,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	Gtt/Ttt	V116F	orf8	0.000417	0.984998	9	2	G>T
ERR5749267	28270	PASS	TA	T	35019	0.995717	324	146,7,17941,16928	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749267	28280	PASS	G	C	34953	0.94012	16	9,1,17961,16921	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749267	28281	PASS	A	T	34954	0.91094	21	24,8,17950,16910	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749267	28282	PASS	T	A	34956	0.91146	19	20,6,17919,16929	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749267	28292	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	36127	0.00108	7	17981,18063,33,46	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Caa/Aaa	Q7K	N	0.000304	0.055324	4	2	C>A
ERR5749267	28881	PASS	G	A	2559	0.794842	3	1,0,1263,1267	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749267	28882	PASS	G	A	2559	0.833138	0	0,0,1281,1261	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749267	28883	PASS	G	C	2559	0.943728	0	0,0,1279,1276	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749267	28977	PASS	C	T	1303	0.919417	2147483647	0,0,0,1301	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749267	29077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16879	0.001244	0	16848,0,22,0	LOW	SILENT	SYNONYMOUS_CODING	N	taC/taT	Y268	N	0.000408	0.88565	3	2	C>T
ERR5749267	29095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	16878	9.48E-4	0	16862,0,16,0	HIGH	NONE	FRAME_SHIFT	N	ggc/	G275	N	0.000792	0.961279	2	2	CG>C
ERR5749267	29140	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	16875	0.0016	0	16844,0,27,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	caG/caC	Q289H	N	0.000955	0.888232	2	1	G>C
ERR5749268	71	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2656	0.007907	0	2632,0,21,0	.	.	.	.	.	.	.	0.002088	0.926791	2	1	C>T
ERR5749268	241	PASS	C	T	4778	0.868774	0	0,0,2376,2385	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749268	283	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	2400	0.0025	0	0,2394,0,6	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggt/	G7	leader	0.0025	0.984848	2	2	TG>T
ERR5749268	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	20934	0.001099	7	14448,6463,19,4	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749268	913	PASS	C	T	14460	0.922614	0	0,9,0,14428	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749268	1357	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	10134	8.88E-4	0	10125,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/	V185	nsp2	0.000493	0.077966	3	2	TG>T
ERR5749268	3037	PASS	C	T	8765	0.817912	24	0,8,4381,4320	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749268	3047	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	4451	0.004044	133	34,4369,9,11	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gat/Cat	D110H	nsp3	0.004044	0.233775	2	1	G>C
ERR5749268	3253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	13086	7.64E-4	0	13076,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N179	nsp3	0.000764	0.07578	1	1	CA>C
ERR5749268	3267	PASS	C	T	13085	0.967596	2147483647	0,0,13080,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749268	3802	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	11362	7.92E-4	1	5195,6158,5,4	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N363	nsp3	0.000554	0.064198	4	2	TA>T
ERR5749268	4136	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	17025	8.81E-4	20	11810,5200,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	caa/Tcaa	Q474S?	nsp3	0.00075	0.974623	4	2	G>GT
ERR5749268	4423	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	9841	8.13E-4	0	9825,8,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K569	nsp3	0.00063	0.953796	2	2	CA>C
ERR5749268	4693	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	9463	7.4E-4	0	9456,0,7,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/	V659	nsp3	0.000654	0.078873	1	1	TG>T
ERR5749268	5184	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6249	0.006401	0	0,6195,0,44	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P822L	nsp3	0.004643	0.894684	2	2	C>T
ERR5749268	5388	PASS	C	A	2477	0.962858	2147483647	0,0,2476,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749268	5986	PASS	C	T	5221	0.973377	2147483647	0,0,5216,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749268	6337	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	14430	0.00104	0	14415,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F1207	nsp3	0.000579	0.91624	3	2	GT>G
ERR5749268	6813	PASS	C	T	16734	0.95799	0	1,0,10453,6269	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T1365I	nsp3	0.001082	0.95799	2	1	C>T
ERR5749268	6954	PASS	T	C	10434	0.829308	0	0,1,0,10381	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749268	7564	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	9368	9.61E-4	0	0,9359,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/	Y1617	nsp3	0.000586	0.056194	4	2	CT>C
ERR5749268	8084	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	12000	0.001167	0	11969,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1790	nsp3	0.000543	0.923413	4	2	GA>G
ERR5749268	8084	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAA	G	12000	0.0015	0	11969,0,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1790	nsp3	0.000543	0.923413	4	2	GAA>G
ERR5749268	8796	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	12801	0.00164	1	6388,6366,19,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aGt/aTt	S81I	nsp4	0.000257	0.25	2	2	G>T
ERR5749268	8964	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	12122	0.0033	0	12077,5,40,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K138	nsp4	0.000553	0.981649	4	2	CA>C
ERR5749268	9130	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	12112	0.001321	0	0,12081,0,19	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtG/gtC	V192	nsp4	0.001321	0.963415	2	1	G>C
ERR5749268	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	13721	0.001239	25	9316,4388,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749268	10263	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGG	C	23582	0.001611	0	11796,11749,20,18	MODERATE	NONE	CODON_DELETION	ORF1ab	ggt/	G71	3Cpro	0.000593	0.192529	3	2	CTGG>C
ERR5749268	10323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	11819	0.002369	0	0,11764,0,28	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749268	10675	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	11074	0.001625	0	36,11004,0,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tgG/tgC	W207C	3Cpro	0.001625	0.134146	2	1	G>C
ERR5749268	11287	PASS	GTCTGGTTTT	G	15444	0.998576	0	0,22,0,15422	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749268	11507	PASS	G	A	9523	0.914418	2	3,1,4768,4732	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Att	V179I	nsp6	0.007744	0.914418	2	2	G>A
ERR5749268	12513	PASS	C	T	13026	0.222708	0	10068,0,2952,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aTg	T141M	nsp8	0.000794	0.984064	2	2	C>T
ERR5749268	12870	PASS	C	T	5381	0.8294	0	1,0,5360,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T62I	nsp9	0.773252	0.848527	1	1	C>T
ERR5749268	13208	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAT	A	20539	0.001071	0	10261,10256,11,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	atg/	M63	nsp10	0.000407	0.953357	4	2	AAT>A
ERR5749268	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18794	0.001703	0	9376,9355,19,19	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749268	14098	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	8432	0.001779	0	8356,52,20,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggt/Tgt	G220C	RdRp	0.000806	0.065317	4	2	G>T
ERR5749268	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10091	0.003568	2015	9866,97,6,116	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749268	14408	PASS	C	T	19670	0.845297	15	0,5,9819,9723	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749268	14676	PASS	C	T	8179	0.826018	0	6,0,8155,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749268	15279	PASS	C	T	8520	0.876878	0	9,0,8489,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749268	15983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	7423	0.001078	0	7416,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T850	RdRp	0.000701	0.338235	2	1	TA>T
ERR5749268	16176	PASS	T	C	11814	0.984341	0	0,0,4380,7430	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749268	16974	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	13101	7.63E-4	0	0,13091,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/	V247	helicase	0.000586	0.055482	2	2	TG>T
ERR5749268	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	19372	5.68E-4	0	19361,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749268	18756	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	19367	6.71E-4	0	19354,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F240	ExoN	0.000392	0.942688	3	2	GT>G
ERR5749268	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	16011	6.87E-4	0	0,16000,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749268	19401	PASS	T	A	8662	0.915839	0	4,0,8643,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcT/tcA	S454	ExoN	0.913864	0.918286	1	1	T>A
ERR5749268	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12261	0.002773	0	12220,0,34,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749268	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTT	C	12260	0.001713	0	12199,0,21,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F123	endoR	0.000884	0.981982	5	2	CTT>C
ERR5749268	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19329	0.001552	0	19275,0,30,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749268	20853	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	33881	8.56E-4	2	14526,19314,20,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atT	M65I	MethTr	0.000856	0.198276	2	1	G>T
ERR5749268	20857	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	33881	5.31E-4	43	14546,19317,0,18	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/	V67	MethTr	0.000531	0.099366	2	2	GT>G
ERR5749268	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	14540	0.002063	0	0,14510,0,30	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TA>T
ERR5749268	21462	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	8979	7.8E-4	0	8972,0,7,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gat/	D269	MethTr	0.00078	0.959051	2	2	TG>T
ERR5749268	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	17888	9.5E-4	8	8922,8949,5,12	HIGH	NONE	FRAME_SHIFT	S	ctt/Tctt	L5S?	S	0.000394	0.091869	4	1	G>GT
ERR5749268	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17876	0.005594	2	8748,8854,56,64	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749268	21637	PASS	C	T	8977	0.96491	0	0,3,0,8964	LOW	SILENT	SYNONYMOUS_CODING	S	ccC/ccT	P25	S	0.954687	0.96491	1	1	C>T
ERR5749268	21764	PASS	ATACATG	A	7945	0.993707	0	50,0,7895,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749268	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	7945	8.81E-4	0	7938,0,7,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749268	21990	PASS	TTTA	T	7948	0.998364	0	0,13,2,7933	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749268	22792	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	11087	7.22E-4	0	0,11079,0,8	HIGH	NONE	FRAME_SHIFT	S	gct/	A411	S	0.000722	0.949572	3	3	CG>C
ERR5749268	23063	PASS	A	T	9187	0.87515	0	0,1,0,9159	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749268	23271	PASS	C	A	18350	0.945559	2147483647	0,0,18337,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749268	23401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGA	G	18333	4.91E-4	0	0,18324,0,9	HIGH	NONE	FRAME_SHIFT	S	gat/	D614	S	0.000491	0.839283	2	2	GGA>G
ERR5749268	23403	PASS	A	G	18333	0.973981	0	0,1,0,18313	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749268	23406	PASS	T	C	18333	0.956636	0	0,10,0,18315	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gTt/gCt	V615A	S	0.949411	0.956636	1	1	T>C
ERR5749268	23460	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	18359	0.001089	0	4,18324,0,23	HIGH	NONSENSE	STOP_GAINED	S	tGg/tAg	W633*	S	0.001089	0.052716	2	2	G>A
ERR5749268	23604	PASS	C	A	8656	0.934958	0	7,0,8642,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749268	23709	PASS	C	T	8649	0.946121	0	0,1,0,8639	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749268	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	14039	7.12E-4	20	5381,8648,0,10	HIGH	NONE	FRAME_SHIFT	S	ttg/	L753	S	0.000334	0.080808	2	2	CT>C
ERR5749268	24506	PASS	T	G	9875	0.97681	0	2,0,9873,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749268	24914	PASS	G	C	33174	0.963194	0	0,1,16516,16628	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749268	25207	PASS	C	T	5239	0.815232	0	0,4,0,5200	LOW	SILENT	SYNONYMOUS_CODING	S	taC/taT	Y1215	S	0.004687	0.815232	1	1	C>T
ERR5749268	25350	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	14374	6.26E-4	0	14363,2,9,0	HIGH	NONE	FRAME_SHIFT	S	ccagtg/	PV1263	S	0.000626	0.97904	4	2	CAG>C
ERR5749268	26159	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	19570	9.71E-4	0	0,19501,0,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	gTt/gCt	V256A	orf3a	0.000311	0.053032	2	2	T>C
ERR5749268	26985	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20651	0.001017	0	20608,0,25,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Cat/Tat	H155Y	M	0.001017	0.889358	1	1	C>T
ERR5749268	27972	PASS	C	T	4909	0.903646	36	2,2,4859,28	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749268	28048	PASS	G	T	4888	0.922872	0	0,4,0,4882	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749268	28111	PASS	A	G	19798	0.979493	0	3,0,14901,4888	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749268	28270	PASS	TA	T	28950	0.994819	335	148,7,14690,14110	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749268	28280	PASS	G	C	28894	0.940264	35	13,0,14716,14098	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749268	28281	PASS	A	T	28894	0.915657	30	27,7,14714,14103	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749268	28282	PASS	T	A	28895	0.914034	13	24,11,14681,14104	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749268	28512	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	15736	6.99E-4	0	15725,0,11,0	HIGH	NONE	FRAME_SHIFT	N	gat/	D81	N	0.000621	0.172671	3	2	CAG>C
ERR5749268	28881	PASS	G	A	1121	0.817128	3	2,0,555,557	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749268	28882	PASS	G	A	1119	0.856122	0	0,0,557,555	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749268	28883	PASS	G	C	1119	0.959786	0	0,0,557,559	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749268	28977	PASS	C	T	562	0.959075	2147483647	0,0,0,562	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749268	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	50226	0.001414	0	25193,24920,44,44	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749269	241	PASS	C	T	17983	0.852027	2	1,2,8945,8931	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749269	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	14392	0.00139	0	14375,0,20,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749269	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	14392	0.00132	0	14363,0,19,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749269	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	14378	0.002017	0	13312,0,997,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749269	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	14378	6.26E-4	0	14368,0,9,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749269	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	37928	3.16E-4	23	23497,14417,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749269	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	37927	6.06E-4	12	23490,14413,19,4	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749269	913	PASS	C	T	23491	0.900558	0	0,13,0,23441	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749269	1461	PASS	A	G	41834	0.905986	1	3,5,20674,21009	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K219R	nsp2	0.000518	0.90899	2	2	A>G
ERR5749269	1599	PASS	G	T	44894	0.961331	32	1,13,23547,21314	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGt/gTt	G265V	nsp2	0.001427	0.96468	2	1	G>T
ERR5749269	2305	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTAAATAAATTTTTGGCTTTGTGTGCTGACTCTATCATTATTGGTGGAGCTAAACTTAAAGC	G	11380	7.03E-4	0	11372,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtaaataaatttttggctttgtgtgctgactctatcattattggtggagctaaacttaaagccttg/	VNKFLALCADSIIIGGAKLKAL502	nsp2	0.000443	0.070409	4	3	GCTTGTAAATAAATTTTTGGCTTTGTGTGCTGACTCTATCATTATTGGTGGAGCTAAACTTAAAGC>G
ERR5749269	3037	PASS	C	T	18254	0.805686	64	0,21,9129,8958	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749269	3267	PASS	C	T	24021	0.971733	0	2,0,24010,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749269	3335	PASS	G	A	46477	0.881856	9	21,10,23903,22383	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E206K	nsp3	0.001289	0.891976	4	3	G>A
ERR5749269	3671	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GA	15163	6.6E-4	0	7588,7571,5,5	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/aaAt	N319K?	nsp3	0.000351	0.0625	6	2	G>GA
ERR5749269	3832	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	18877	6.89E-4	0	18864,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L373	nsp3	0.000689	0.327273	4	2	CT>C
ERR5749269	4504	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	30566	0.001014	2	15227,15254,43,37	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gaG/gaT	E595D	nsp3	0.001014	0.846766	1	1	G>T
ERR5749269	4999	PASS	C	T	10137	0.942488	77	0,2,10123,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N760	nsp3	0.001692	0.947468	1	1	C>T
ERR5749269	5170	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	10111	0.001582	0	4,10091,0,16	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T819	nsp3	0.000565	0.894036	2	2	CCA>C
ERR5749269	5388	PASS	C	A	5024	0.958201	0	1,0,5019,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749269	5986	PASS	C	T	7175	0.971847	0	4,0,7165,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749269	6706	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	6824	0.001172	0	0,6816,0,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1330	nsp3	0.000687	0.883999	2	2	CA>C
ERR5749269	6954	PASS	T	C	12576	0.818146	0	0,1,3,12511	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749269	9541	PASS	C	T	29680	0.949562	10	0,3,16871,12776	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ctC/ctT	L329	nsp4	0.000346	0.955771	2	2	C>T
ERR5749269	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	29680	0.002628	189	16818,12784,78,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749269	10077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	6525	0.002912	441	3,6483,17,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTc/tCc	F8S	3Cpro	0.001833	0.454545	1	1	T>C
ERR5749269	10165	PASS	C	T	19046	0.976163	110	2,3,19014,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y37	3Cpro	0.000632	0.976163	2	2	C>T
ERR5749269	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22772	0.001098	0	22708,4,27,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749269	11199	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	45335	3.09E-4	0	22639,22689,7,7	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T77	nsp6	0.000309	0.056758	3	2	CCA>C
ERR5749269	11287	PASS	GTCTGGTTTT	G	22762	0.997276	0	0,62,0,22700	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749269	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	21318	0.001454	0	21264,0,35,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749269	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	16400	7.32E-4	0	16385,3,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749269	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30301	0.001353	1	15125,15082,23,25	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749269	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	16932	0.007146	2147483647	16482,103,7,328	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749269	14408	PASS	C	T	32803	0.834893	18	0,6,16396,16159	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749269	14676	PASS	C	T	12474	0.743627	0	7,0,12414,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749269	15279	PASS	C	T	21886	0.886	0	1,0,21854,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749269	16176	PASS	T	C	20336	0.979249	3	1,0,8909,11418	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749269	17615	PASS	A	G	16610	0.900301	2147483647	0,0,0,16558	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749269	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	28455	8.08E-4	0	28431,1,23,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749269	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11745	0.002043	0	11711,2,26,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749269	21302	PASS	C	T	27843	0.819811	0	0,41,0,27646	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCa/cTa	P215L	MethTr	0.001031	0.843069	1	1	C>T
ERR5749269	21304	PASS	C	A	27843	0.568653	0	0,1215,0,26619	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgc/Agc	R216S	MethTr	0.000411	0.605296	3	2	C>A
ERR5749269	21305	PASS	G	A	27843	0.660525	0	0,2,0,27229	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cGc/cAc	R216H	MethTr	0.000727	0.703943	1	1	G>A
ERR5749269	21375	PASS	G	A	27954	0.833548	0	0,1,1,27859	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttG/ttA	L239	MethTr	0.002365	0.858793	2	2	G>A
ERR5749269	21727	PASS	C	T	10933	0.859325	0	1,0,10909,0	LOW	SILENT	SYNONYMOUS_CODING	S	ttC/ttT	F55	S	0.000896	0.878141	2	2	C>T
ERR5749269	21764	PASS	ATACATG	A	10932	0.992408	0	83,0,10849,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749269	21817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	10927	7.32E-4	0	10919,0,8,0	HIGH	NONE	FRAME_SHIFT	S	ttt/	F86	S	0.000689	0.961354	3	2	AT>A
ERR5749269	21990	PASS	TTTA	T	10937	0.99808	0	0,21,3,10913	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749269	22225	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	20080	0.001195	0	0,20052,0,28	LOW	SILENT	SYNONYMOUS_CODING	S	tcG/tcT	S221	S	0.001195	0.94526	3	1	G>T
ERR5749269	23063	PASS	A	T	456	0.822368	2147483647	0,0,0,453	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749269	23191	PASS	C	T	27328	0.960224	0	6,0,27305,0	LOW	SILENT	SYNONYMOUS_CODING	S	ttC/ttT	F543	S	0.000538	0.973337	2	2	C>T
ERR5749269	23271	PASS	C	A	27317	0.911484	0	4,0,27279,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749269	23403	PASS	A	G	27296	0.96494	0	0,1,0,27264	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749269	23604	PASS	C	A	14793	0.929764	0	12,0,14769,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749269	23709	PASS	C	T	14795	0.931666	0	0,6,8,14763	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749269	24506	PASS	T	G	18839	0.975636	0	6,0,18823,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749269	24914	PASS	G	C	46630	0.959833	3	1,0,23249,23352	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749269	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	18125	0.001766	363	18043,18,17,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749269	26270	PASS	C	T	60273	0.929471	0	0,4,9763,50444	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	aCa/aTa	T9I	E	0.000586	0.930791	3	2	C>T
ERR5749269	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	G	14697	6.12E-4	0	0,14666,0,9	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/	ACLVGLMWLSYFIASF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT>G
ERR5749269	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	14697	0.001497	0	0,14666,0,22	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749269	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	14697	0.001565	0	0,14667,0,23	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749269	27312	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	21727	0.001289	0	21699,0,28,0	HIGH	NONE	FRAME_SHIFT	ORF6	aat/aaAt	N39K?	orf6	0.000911	0.088458	4	2	T>TA
ERR5749269	27643	PASS	C	T	21173	0.819156	0	1,0,21063,5	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Cct/Tct	P84S	orf7a	0.00166	0.858006	2	1	C>T
ERR5749269	27972	PASS	C	T	9676	0.901819	18	2,1,9600,42	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749269	28048	PASS	G	T	9635	0.913441	0	0,9,0,9623	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749269	28111	PASS	A	G	34428	0.976589	0	9,3,24768,9638	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749269	28270	PASS	TA	T	47901	0.994885	512	230,11,24459,23197	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749269	28280	PASS	G	C	47783	0.935123	26	15,2,24502,23171	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749269	28281	PASS	A	T	47783	0.917314	30	40,14,24471,23172	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749269	28282	PASS	T	A	47786	0.908572	11	30,16,24433,23188	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749269	28674	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23398	0.010215	0	0,23127,0,251	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gCa/gTa	A134V	N	0.001338	0.958634	1	1	C>T
ERR5749269	28739	PASS	G	T	35852	0.951077	0	2,5,12428,23384	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gca/Tca	A156S	N	0.005353	0.951077	1	1	G>T
ERR5749269	28881	PASS	G	A	24382	0.728529	45	16,0,12017,11918	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749269	28882	PASS	G	A	24380	0.816079	15	6,0,12204,11882	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749269	28883	PASS	G	C	24379	0.943804	2	3,1,12221,12129	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749269	28977	PASS	C	T	12436	0.924976	0	0,2,0,12406	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749269	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	41433	0.001207	176	28962,12375,8,49	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749269	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	57509	0.001235	0	28886,28498,43,45	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749269	29749	PASS	ACGATCGAGTG	A	9989	0.997197	0	0,28,0,9961	.	.	.	.	.	.	.	0.00126	0.997197	2	1	ACGATCGAGTG>A
ERR5749270	241	PASS	C	T	1491	0.873239	0	0,0,743,745	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749270	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9624	0.002286	0	0,9589,0,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749270	913	PASS	C	T	9624	0.913549	0	0,4,0,9609	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749270	2185	PASS	G	A	9158	0.963529	0	0,1,0,9149	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaG/gaA	E460	nsp2	0.000441	0.963529	4	3	G>A
ERR5749270	2509	PASS	C	T	2108	0.944972	58	2,1,0,2104	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P568	nsp2	0.001408	0.949382	1	1	C>T
ERR5749270	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	4327	0.002773	0	2,4072,0,246	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749270	3037	PASS	C	T	5782	0.835178	15	0,5,2892,2854	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749270	3267	PASS	C	T	12376	0.971396	0	1,0,12368,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749270	5192	PASS	C	T	6152	0.909785	0	0,4,0,6124	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Ctg/Ttg	L825	nsp3	0.003789	0.912192	1	1	C>T
ERR5749270	5388	PASS	C	A	1542	0.953307	2147483647	0,0,1539,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749270	5986	PASS	C	T	5127	0.974839	0	1,0,5123,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749270	6954	PASS	T	C	10684	0.818233	0	0,2,0,10615	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749270	7926	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	11038	0.002084	0	0,11015,0,23	HIGH	NONE	FRAME_SHIFT	ORF1ab	tca/Atca	S1738I?	nsp3	0.000531	0.97019	5	2	C>CA
ERR5749270	8639	PASS	C	T	3783	0.962464	2147483647	0,0,3778,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cct/Tct	P29S	nsp4	0.962183	0.962789	1	1	C>T
ERR5749270	8964	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	10647	0.002724	0	10618,0,29,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K138	nsp4	0.000553	0.981649	4	2	CA>C
ERR5749270	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	7567	0.001454	4	6630,926,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749270	10386	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	23405	0.002606	85	12509,10835,10,51	HIGH	NONE	FRAME_SHIFT	ORF1ab	tca/	S113	3Cpro	0.000642	0.160456	4	2	CT>C
ERR5749270	10387	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	23405	9.4E-4	46	12505,10803,3,22	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T111	3Cpro	0.00094	0.973895	1	1	T>C
ERR5749270	11095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18666	0.001179	0	18602,0,25,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A41	nsp6	0.000515	0.887707	7	2	C>T
ERR5749270	11287	PASS	GTCTGGTTTT	G	18662	0.999357	0	0,12,0,18650	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749270	12079	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	30486	9.84E-4	1	15193,15192,19,16	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	agG/agA	R79	nsp7	0.000984	0.937056	1	1	G>A
ERR5749270	12125	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	15287	0.001832	0	2,15195,0,30	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y12H	nsp8	0.000847	0.113436	1	1	T>C
ERR5749270	12357	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	6309	0.002061	0	0,6289,0,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aAa	T89K	nsp8	0.000909	0.956941	3	2	C>A
ERR5749270	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	9246	0.001947	0	9225,0,18,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749270	13134	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	11213	0.001694	0	11185,0,27,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCa/cAa	P37Q	nsp10	0.000682	0.107576	2	2	C>A
ERR5749270	13459	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	10952	0.006209	0	10884,0,68,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/ttTa	L8F?	nsp11	0.000691	0.060726	5	2	G>GT
ERR5749270	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21885	9.6E-4	0	10933,10899,12,12	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749270	14408	PASS	C	T	2853	0.871714	3	0,1,1429,1413	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749270	14676	PASS	C	T	7220	0.810803	0	5,0,7191,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749270	14724	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7204	0.001805	0	7181,2,15,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F428	RdRp	0.000952	0.789267	3	2	C>T
ERR5749270	15279	PASS	C	T	6591	0.896526	2147483647	0,0,6585,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749270	15839	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	11448	0.002446	0	1,11412,0,34	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tGg/tTg	W800L	RdRp	0.001405	0.074516	2	1	G>T
ERR5749270	16176	PASS	T	C	9838	0.979569	0	0,0,1992,7841	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749270	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	11111	9.0E-4	0	11101,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749270	18079	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	4666	0.003215	0	4649,0,15,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gta/Ata	V14I	ExoN	0.003215	0.944695	2	1	G>A
ERR5749270	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	20402	7.84E-4	0	20386,0,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749270	18984	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTT	G	17074	0.001464	0	17049,0,25,0	MODERATE	NONE	CODON_DELETION	ORF1ab	gtt/	V317	ExoN	0.000419	0.950929	5	2	GGTT>G
ERR5749270	19328	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	7639	0.001964	0	7624,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F431	ExoN	0.000459	0.937906	4	2	CT>C
ERR5749270	19343	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	7639	0.002487	0	7620,0,19,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F436	ExoN	0.000519	0.192257	7	2	CT>C
ERR5749270	19955	PASS	C	T	5391	0.928399	2147483647	0,0,5381,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T112I	endoR	0.0084	0.934633	1	1	C>T
ERR5749270	20445	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	20996	7.14E-4	0	0,20981,0,15	HIGH	NONE	FRAME_SHIFT	ORF1ab	aac/aaAc	N277K?	endoR	0.000518	0.059736	4	2	T>TA
ERR5749270	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	15245	0.001837	0	0,15217,0,28	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TA>T
ERR5749270	21614	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9067	0.001544	0	0,9042,0,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L18F	S	0.001194	0.949239	2	2	C>T
ERR5749270	21764	PASS	ATACATG	A	7345	0.998094	0	14,0,7331,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749270	21990	PASS	TTTA	T	7352	0.996192	0	0,28,7,7317	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749270	21991	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTA	T	7356	0.001767	0	11,7330,0,13	HIGH	NONE	FRAME_SHIFT	S	tat/	Y144	S	0.00078	0.991378	2	1	TTA>T
ERR5749270	22323	PASS	C	T	18542	0.97627	0	0,1,5341,13198	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCt/tTt	S254F	S	0.000812	0.978946	3	2	C>T
ERR5749270	22600	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	19326	0.001708	32	13952,5341,32,1	HIGH	NONE	FRAME_SHIFT	S	ttt/	F347	S	0.000471	0.963998	3	3	AT>A
ERR5749270	22981	PASS	T	C	6682	0.859922	0	1,0,6653,0	LOW	SILENT	SYNONYMOUS_CODING	S	taT/taC	Y473	S	0.001557	0.861194	3	2	T>C
ERR5749270	23063	PASS	A	T	6679	0.876029	0	0,1,0,6638	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749270	23271	PASS	C	A	14991	0.919752	0	3,0,14968,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749270	23403	PASS	A	G	14988	0.969642	0	0,1,0,14977	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749270	23604	PASS	C	A	6441	0.939295	0	4,0,6415,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749270	23604	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6441	0.003105	0	4,0,22,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cTt	P681L	S	0.003105	0.969595	3	1	C>T
ERR5749270	23709	PASS	C	T	6437	0.947646	0	0,1,0,6425	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749270	23914	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	3354	0.003876	0	3341,0,13,0	LOW	SILENT	SYNONYMOUS_CODING	S	caA/caG	Q784	S	0.003876	0.965493	1	1	A>G
ERR5749270	24320	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	6627	0.001207	0	0,6601,0,8	HIGH	NONE	FRAME_SHIFT	S	aaa/	K921	S	0.000763	0.138365	4	2	CAA>C
ERR5749270	24506	PASS	T	G	9058	0.974056	0	1,0,9056,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749270	24914	PASS	G	C	31388	0.961004	0	1,1,15635,15733	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749270	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	1407	0.008529	164	1361,30,1,11	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749270	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	5746	0.001566	0	0,5737,0,9	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749270	27972	PASS	C	T	1988	0.905433	0	0,0,1980,5	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749270	28048	PASS	G	T	1984	0.931956	0	0,5,0,1979	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749270	28095	PASS	A	T	1988	0.954225	118	4,0,0,1982	HIGH	NONSENSE	STOP_GAINED	ORF8	Aaa/Taa	K68*	orf8	0.002672	0.967672	2	2	A>T
ERR5749270	28111	PASS	A	G	22794	0.979512	0	7,0,20791,1984	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749270	28270	PASS	TA	T	40397	0.995297	479	196,6,20525,19682	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749270	28280	PASS	G	C	40313	0.928807	32	15,1,20561,19669	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749270	28281	PASS	A	T	40313	0.889018	13	18,7,20540,19666	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749270	28282	PASS	T	A	40316	0.887712	0	11,11,20469,19675	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749270	28310	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	20783	0.001059	0	0,20726,0,28	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Ccc/Acc	P13T	N	0.00095	0.92832	2	1	C>A
ERR5749270	28310	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20783	0.001251	0	0,20726,0,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Ccc/Tcc	P13S	N	0.00095	0.92832	2	1	C>T
ERR5749270	28881	PASS	G	A	4059	0.781473	3	2,0,2026,1992	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749270	28882	PASS	G	A	4058	0.835387	2	3,1,2042,1984	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749270	28883	PASS	G	C	4058	0.94825	0	0,0,2044,2012	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749270	28977	PASS	C	T	2073	0.925712	2147483647	0,0,0,2071	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749270	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTC	T	18120	9.38E-4	6	16030,2073,17,0	HIGH	NONE	FRAME_SHIFT	N	tct/	S255	N	0.000601	0.054952	4	2	TTC>T
ERR5749270	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	31851	0.001538	0	15988,15792,29,30	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749270	29803	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	2425	0.002474	0	0,2419,0,6	.	.	.	.	.	.	.	0.002474	0.886529	2	1	C>CT
ERR5749271	241	PASS	C	T	27083	0.862275	6	0,3,13466,13498	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749271	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	15108	0.001655	0	15090,1,25,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749271	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	15110	5.96E-4	0	15056,3,9,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749271	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	15110	0.002316	0	15056,3,35,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749271	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	15103	0.00245	0	13820,4,1184,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749271	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	15103	5.96E-4	0	15090,4,9,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749271	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	41400	8.94E-4	0	26238,15119,23,14	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749271	913	PASS	C	T	26263	0.91429	0	0,13,0,26214	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749271	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	95169	0.001313	2147483647	47460,44633,85,2733	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749271	3037	PASS	C	T	23933	0.822546	44	1,18,11953,11780	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749271	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12083	0.001821	595	11,12038,23,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749271	3267	PASS	C	T	25164	0.971189	2147483647	0,0,25152,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749271	4122	PASS	T	A	54094	0.839982	20	1,15,20192,33740	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aAa	I468K	nsp3	0.002265	0.8595	2	2	T>A
ERR5749271	4276	PASS	C	T	20177	0.812261	0	0,5,4,20037	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y519	nsp3	0.00102	0.812261	1	1	C>T
ERR5749271	5217	PASS	A	G	14537	0.945518	2147483647	0,0,0,14517	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAt/aGt	N833S	nsp3	0.936162	0.945518	1	1	A>G
ERR5749271	5388	PASS	C	A	8341	0.955041	2147483647	0,0,8338,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749271	5986	PASS	C	T	14582	0.976615	0	1,0,14574,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749271	6931	PASS	T	C	57611	0.688428	10	7,16,28382,28630	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaT/aaC	N1404	nsp3	0.684863	0.688428	1	1	T>C
ERR5749271	6954	PASS	T	C	29041	0.819152	0	0,2,2,28890	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749271	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	40208	8.7E-4	122	17904,22266,35,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749271	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	22343	0.001208	0	22285,0,48,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749271	11287	PASS	GTCTGGTTTT	G	22343	0.998299	0	0,38,0,22305	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749271	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	35915	0.001225	0	17933,17887,27,27	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749271	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	14673	0.005043	2147483647	14343,99,6,222	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749271	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	28570	5.6E-4	0	14322,14244,8,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749271	14408	PASS	C	T	28570	0.839972	9	1,5,14274,14101	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749271	14676	PASS	C	T	16534	0.803919	0	4,0,16494,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749271	15279	PASS	C	T	28057	0.879353	0	3,0,27999,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749271	16176	PASS	T	C	24077	0.980895	6	2,0,11344,12720	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749271	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	24946	7.62E-4	0	24927,0,19,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749271	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	30798	3.57E-4	0	2,30785,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749271	19227	PASS	C	T	30823	0.982286	67	2,11,0,30807	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S396	ExoN	0.002586	0.982286	2	2	C>T
ERR5749271	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34209	0.0019	0	34119,0,65,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749271	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	42254	6.63E-4	3	20696,21050,15,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749271	21764	PASS	ATACATG	A	14402	0.996667	0	48,0,14354,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749271	21990	PASS	TTTA	T	14404	0.997987	0	0,29,2,14373	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749271	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	18608	0.00129	0	1,18573,0,25	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749271	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	32581	9.21E-4	4	13951,18577,11,21	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749271	23063	PASS	A	T	13948	0.862919	0	0,3,0,13898	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749271	23271	PASS	C	A	27042	0.913542	0	4,0,27008,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749271	23403	PASS	A	G	27038	0.970449	0	0,2,0,27023	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749271	23604	PASS	C	A	17811	0.939644	0	9,0,17794,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749271	23709	PASS	C	T	17797	0.943642	0	0,6,6,17762	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749271	24506	PASS	T	G	21560	0.974814	0	4,0,21553,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749271	24914	PASS	G	C	39298	0.960889	0	0,0,19563,19705	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749271	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	29095	0.001237	45	19321,9716,43,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749271	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	33141	0.001116	509	33012,29,17,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749271	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	33093	6.35E-4	0	33069,3,21,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749271	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	13046	0.00115	0	0,13028,0,15	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749271	27476	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	45975	0.001784	0	26143,19729,48,37	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	aCa/aTa	T28I	orf7a	0.000547	0.22827	4	2	C>T
ERR5749271	27696	PASS	TCTTATTGTTGCGGCAATAGTGTTTATAACACTTTGCTTCACACTCAAAAGAAAG	T	26018	0.99631	197	9,162,0,25922	MODERATE	NONE	CODON_DELETION	ORF7a	cttattgttgcggcaatagtgtttataacactttgcttcacactcaaaagaaag/	LIVAAIVFITLCFTLKRK102	orf7a	0.000628	0.99631	1	1	TCTTATTGTTGCGGCAATAGTGTTTATAACACTTTGCTTCACACTCAAAAGAAAG>T
ERR5749271	27972	PASS	C	T	12196	0.897507	0	0,0,12086,52	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749271	28048	PASS	G	T	12159	0.930751	0	0,8,0,12145	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749271	28111	PASS	A	G	37522	0.976974	1	4,3,25333,12162	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749271	28270	PASS	TA	T	49221	0.994352	696	279,7,24992,23951	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749271	28280	PASS	G	C	49111	0.939627	14	10,2,25077,23919	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749271	28281	PASS	A	T	49111	0.91674	33	34,10,25048,23925	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749271	28282	PASS	T	A	49113	0.914951	10	33,19,25002,23936	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749271	28881	PASS	G	A	21603	0.769476	12	5,0,10693,10629	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749271	28882	PASS	G	A	21603	0.830857	9	6,1,10801,10593	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749271	28883	PASS	G	C	21603	0.94061	0	1,1,10819,10753	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749271	28977	PASS	C	T	11003	0.938017	0	0,3,0,10990	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749271	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	37718	7.69E-4	122	26687,10963,3,29	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749271	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	53040	7.92E-4	1	26644,26329,27,24	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749271	29635	PASS	C	T	21492	0.92574	0	1,2,9921,11551	LOW	SILENT	SYNONYMOUS_CODING	ORF10	taC/taT	Y26	orf10	0.001133	0.928275	1	1	C>T
ERR5749272	241	PASS	C	T	16297	0.86476	0	0,1,8060,8186	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749272	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	12175	0.001232	0	12163,0,15,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749272	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	12175	7.39E-4	0	12115,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749272	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	12175	0.001643	0	12115,0,20,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749272	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	12175	0.002136	0	12115,0,26,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749272	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12163	0.002384	0	11155,0,903,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749272	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	35626	0.001067	4	23400,12180,28,10	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749272	913	PASS	C	T	23416	0.907585	0	0,15,0,23364	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749272	2185	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	6	0.666667	0	2,0,4,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaG/gaA	E460	nsp2	0.000441	0.963529	4	3	G>A
ERR5749272	2509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12	0.75	2	3,0,6,3	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P568	nsp2	0.001408	0.949382	1	1	C>T
ERR5749272	2702	PASS	T	G	46	0.173913	17	3,10,0,33	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F633V	nsp2	0.000632	0.333333	1	1	T>G
ERR5749272	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	13472	0.00245	0	3,12703,0,754	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749272	3037	PASS	C	T	20464	0.810154	43	3,23,10226,10078	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749272	3267	PASS	C	T	21474	0.971966	0	2,0,21462,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749272	5192	PASS	C	T	12253	0.905003	0	0,10,1,12200	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Ctg/Ttg	L825	nsp3	0.003789	0.912192	1	1	C>T
ERR5749272	5388	PASS	C	A	6792	0.959658	2147483647	0,0,6787,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749272	5986	PASS	C	T	12212	0.976662	2147483647	0,0,12206,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749272	6954	PASS	T	C	24397	0.799852	0	0,1,3,24226	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749272	7564	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	17046	7.04E-4	0	0,17034,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/	Y1617	nsp3	0.000586	0.056194	4	2	CT>C
ERR5749272	8639	PASS	C	T	29400	0.962789	35	7,1,29371,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cct/Tct	P29S	nsp4	0.962183	0.962789	1	1	C>T
ERR5749272	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	34151	9.37E-4	111	15274,18845,32,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749272	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	17724	0.001411	0	17673,0,46,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749272	11104	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	17720	0.001354	0	17634,0,26,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccT/ccC	P44	nsp6	0.000866	0.675414	2	1	T>C
ERR5749272	11287	PASS	GTCTGGTTTT	G	17717	0.998025	0	0,34,0,17682	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749272	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	35728	9.24E-4	4	23179,12494,21,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749272	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	15793	0.001203	0	15754,0,19,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749272	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30335	0.001187	0	15152,15120,19,20	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749272	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	14572	0.003774	2147483647	14244,106,3,212	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749272	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	28354	7.76E-4	0	14229,14119,11,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749272	14408	PASS	C	T	28354	0.851696	5	2,5,14175,13987	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749272	14676	PASS	C	T	14305	0.760084	0	6,0,14260,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749272	15279	PASS	C	T	23836	0.88874	0	3,0,23803,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749272	16176	PASS	T	C	19965	0.980165	0	0,0,9344,10608	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749272	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	18316	0.001147	0	18292,1,21,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749272	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	24270	0.001277	0	24237,0,31,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749272	19955	PASS	C	T	30612	0.934633	0	1,0,30574,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T112I	endoR	0.0084	0.934633	1	1	C>T
ERR5749272	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30611	0.001829	0	30531,2,59,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749272	21764	PASS	ATACATG	A	12836	0.995637	0	56,0,12780,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749272	21990	PASS	TTTA	T	12844	0.998521	0	0,19,7,12818	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749272	22227	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	21846	5.04E-4	0	1,21832,0,11	HIGH	NONE	FRAME_SHIFT	S	tta/	L223	S	0.000419	0.824305	2	2	CT>C
ERR5749272	22323	PASS	C	T	30160	0.978946	9	0,8,8307,21840	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCt/tTt	S254F	S	0.000812	0.978946	3	2	C>T
ERR5749272	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26703	0.001086	0	10971,15689,13,17	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749272	22981	PASS	T	C	10977	0.850688	0	1,0,10910,1	LOW	SILENT	SYNONYMOUS_CODING	S	taT/taC	Y473	S	0.001557	0.861194	3	2	T>C
ERR5749272	23063	PASS	A	T	10984	0.870812	0	0,5,3,10920	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749272	23271	PASS	C	A	22864	0.926347	0	2,0,22838,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749272	23403	PASS	A	G	22862	0.963127	0	0,3,0,22839	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749272	23604	PASS	C	A	14665	0.952881	0	9,0,14654,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749272	23709	PASS	C	T	14649	0.939382	0	0,4,3,14621	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749272	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	34760	4.03E-4	1	20084,14662,9,5	HIGH	NONE	FRAME_SHIFT	S	ttg/	L753	S	0.000334	0.080808	2	2	CT>C
ERR5749272	24506	PASS	T	G	18766	0.972503	0	7,0,18753,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749272	24914	PASS	G	C	33168	0.957278	0	0,0,16527,16614	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749272	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	29516	0.001016	1233	29056,185,154,91	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749272	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	10008	0.001799	0	0,9988,0,18	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749272	27972	PASS	C	T	9844	0.901056	38	2,2,9769,46	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749272	28048	PASS	G	T	9801	0.924191	0	0,9,1,9787	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749272	28095	PASS	A	T	9821	0.960798	165	5,2,0,9798	HIGH	NONSENSE	STOP_GAINED	ORF8	Aaa/Taa	K68*	orf8	0.002672	0.967672	2	2	A>T
ERR5749272	28111	PASS	A	G	25672	0.978342	0	3,2,15844,9813	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749272	28270	PASS	TA	T	30675	0.995729	284	130,7,15669,14875	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749272	28280	PASS	G	C	30624	0.934953	19	10,1,15691,14859	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749272	28281	PASS	A	T	30625	0.911771	25	19,4,15683,14864	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749272	28282	PASS	T	A	30627	0.913704	8	20,11,15661,14869	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749272	28292	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	31552	6.34E-4	0	15730,15798,10,10	HIGH	NONE	FRAME_SHIFT	N	aat/	N8	N	0.000304	0.055324	4	2	CA>C
ERR5749272	28881	PASS	G	A	15365	0.774748	12	5,0,7639,7551	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749272	28882	PASS	G	A	15365	0.830784	3	2,0,7694,7533	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749272	28883	PASS	G	C	15366	0.939867	3	2,0,7709,7641	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749272	28977	PASS	C	T	7827	0.924748	0	0,0,1,7807	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749272	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	28486	9.48E-4	75	20647,7796,6,22	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749272	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	41011	9.27E-4	0	20600,20348,23,23	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749273	241	PASS	C	T	5315	0.856632	0	0,0,2649,2659	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749273	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	10011	0.001598	0	9990,0,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749273	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10007	0.002298	0	9152,1,806,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749273	913	PASS	C	T	15817	0.914396	0	0,4,0,15793	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749273	3037	PASS	C	T	14870	0.806725	42	0,14,7437,7313	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749273	3267	PASS	C	T	17211	0.969612	0	2,0,17199,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749273	3802	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	21810	6.42E-4	5	11829,9967,10,4	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N363	nsp3	0.000554	0.064198	4	2	TA>T
ERR5749273	4122	PASS	T	A	28242	0.8595	5	3,0,16377,11801	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aAa	I468K	nsp3	0.002265	0.8595	2	2	T>A
ERR5749273	4276	PASS	C	T	16364	0.80176	0	0,2,0,16247	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y519	nsp3	0.00102	0.812261	1	1	C>T
ERR5749273	5144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19838	0.001411	0	9908,9783,15,16	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L809	nsp3	0.000909	0.822022	1	1	C>T
ERR5749273	5217	PASS	A	G	9947	0.936162	2147483647	0,0,0,9938	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAt/aGt	N833S	nsp3	0.936162	0.945518	1	1	A>G
ERR5749273	5388	PASS	C	A	4741	0.956338	2147483647	0,0,4741,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749273	5986	PASS	C	T	11299	0.974334	2147483647	0,0,11293,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749273	6348	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	20928	0.001003	237	20833,37,11,11	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cTg/cCg	L1210P	nsp3	0.001003	0.125	2	1	T>C
ERR5749273	6931	PASS	T	C	39824	0.684863	18	2,12,19595,19820	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaT/aaC	N1404	nsp3	0.684863	0.688428	1	1	T>C
ERR5749273	6954	PASS	T	C	20077	0.827265	0	0,17,0,19958	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749273	9060	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATT	A	16092	6.21E-4	0	16076,7,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tattgt/	YC169	nsp4	0.000621	0.433333	5	2	ATT>A
ERR5749273	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	19375	0.001084	23	14653,4701,21,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749273	10077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	6340	0.002366	398	3,6301,15,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTc/tCc	F8S	3Cpro	0.001833	0.454545	1	1	T>C
ERR5749273	10323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	19049	0.007297	0	0,18871,0,143	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749273	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	21965	0.002367	0	21359,0,52,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749273	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21965	0.001639	0	21898,0,38,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749273	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	21954	0.001139	0	21894,0,42,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749273	11173	PASS	C	T	21887	0.069128	6	19344,16,2423,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ctC/ctT	L67	nsp6	0.00115	0.587518	1	1	C>T
ERR5749273	11287	PASS	GTCTGGTTTT	G	21953	0.997631	0	0,48,0,21901	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749273	12020	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	20128	9.94E-4	0	20107,1,20,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S61	nsp7	0.000994	0.968243	3	2	CT>C
ERR5749273	12459	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	36751	0.001034	22	18414,18289,28,10	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T123I	nsp8	0.000658	0.986093	1	1	C>T
ERR5749273	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	4171	0.003836	895	4079,39,2,51	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749273	14408	PASS	C	T	8111	0.853286	2	1,2,4052,4014	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749273	14676	PASS	C	T	11184	0.821531	0	5,0,11153,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749273	15279	PASS	C	T	15981	0.883111	2147483647	0,0,15954,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749273	16176	PASS	T	C	16917	0.983389	0	0,0,7341,9565	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749273	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	27136	6.63E-4	0	27118,0,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749273	18877	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27130	8.48E-4	0	0,27091,0,25	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L280	ExoN	0.000848	0.953596	2	2	C>T
ERR5749273	19011	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	24498	4.08E-4	0	24488,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttc/Attc	F326I?	ExoN	0.000408	0.975746	4	2	C>CA
ERR5749273	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	24466	7.36E-4	0	1,24447,0,18	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749273	19164	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24470	0.001512	0	1,24420,0,41	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D375	ExoN	0.000358	0.075732	4	2	C>T
ERR5749273	19227	PASS	C	T	24496	0.980568	0	0,5,0,24488	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S396	ExoN	0.002586	0.982286	2	2	C>T
ERR5749273	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18685	0.001338	0	18647,0,25,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749273	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	31956	0.001408	1	15642,15942,24,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749273	21764	PASS	ATACATG	A	13113	0.997026	0	39,0,13074,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749273	21990	PASS	TTTA	T	13120	0.998094	0	0,25,3,13092	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749273	23063	PASS	A	T	14252	0.864159	0	0,1,0,14190	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749273	23271	PASS	C	A	18668	0.921041	0	0,0,18644,5	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749273	23403	PASS	A	G	18650	0.970724	0	0,2,0,18632	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749273	23604	PASS	C	A	14911	0.937697	0	12,0,14894,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749273	23709	PASS	C	T	14889	0.941903	0	0,2,0,14872	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749273	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	26165	5.35E-4	5	11246,14905,8,6	HIGH	NONE	FRAME_SHIFT	S	ttg/	L753	S	0.000334	0.080808	2	2	CT>C
ERR5749273	23817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	26165	9.17E-4	5	11232,14878,8,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTt/cCt	L752P	S	0.000646	0.066832	1	1	T>C
ERR5749273	24237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12381	0.001858	0	12353,0,24,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gTt	A892V	S	0.001242	0.889739	1	1	C>T
ERR5749273	24506	PASS	T	G	15071	0.976843	0	5,0,15065,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749273	24914	PASS	G	C	39976	0.961552	3	1,0,19920,20034	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749273	25302	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	25861	0.001121	43	19774,6030,26,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tGt/tTt	C1247F	S	0.001121	0.05002	1	1	G>T
ERR5749273	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	25862	9.67E-4	33	19767,6061,31,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749273	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	8566	0.002101	403	8514,22,1,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749273	26526	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	11388	0.002371	0	2,11348,0,32	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Gca/Tca	A2S	M	0.001224	0.951192	3	1	G>T
ERR5749273	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	12185	8.21E-4	0	0,12173,0,10	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749273	27389	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20214	0.001237	0	49,20113,0,28	.	.	.	.	.	.	.	0.001157	0.899553	2	1	C>T
ERR5749273	27476	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	40585	0.001725	0	20352,20154,37,36	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	aCa/aTa	T28I	orf7a	0.000547	0.22827	4	2	C>T
ERR5749273	27494	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	40588	7.64E-4	63	20351,20190,29,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	cCt/cTt	P34L	orf7a	0.000672	0.961447	2	2	C>T
ERR5749273	27629	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	40706	7.86E-4	0	20327,20232,18,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	gCc/gTc	A79V	orf7a	0.000786	0.088751	2	1	C>T
ERR5749273	27641	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	40694	9.83E-4	0	20318,20291,22,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	tCa/tTa	S83L	orf7a	0.000983	0.911213	2	2	C>T
ERR5749273	27696	PASS	TCTTATTGTTGCGGCAATAGTGTTTATAACACTTTGCTTCACACTCAAAAGAAAG	T	20285	0.995613	0	0,113,0,20196	MODERATE	NONE	CODON_DELETION	ORF7a	cttattgttgcggcaatagtgtttataacactttgcttcacactcaaaagaaag/	LIVAAIVFITLCFTLKRK102	orf7a	0.000628	0.99631	1	1	TCTTATTGTTGCGGCAATAGTGTTTATAACACTTTGCTTCACACTCAAAAGAAAG>T
ERR5749273	27972	PASS	C	T	6942	0.910112	0	0,0,6874,42	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749273	28048	PASS	G	T	6902	0.9235	0	0,6,0,6891	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749273	28111	PASS	A	G	29029	0.979124	10	4,4,22105,6902	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749273	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22104	0.003393	0	21961,7,80,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749273	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	22101	7.24E-4	0	22081,7,16,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749273	28270	PASS	TA	T	42872	0.994985	504	214,8,21816,20841	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749273	28280	PASS	G	C	42793	0.938401	19	18,5,21871,20819	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749273	28281	PASS	A	T	42793	0.917089	26	30,10,21848,20815	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749273	28282	PASS	T	A	42795	0.908681	23	30,11,21821,20832	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749273	28310	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22109	9.5E-4	0	6,22059,0,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Ccc/Tcc	P13S	N	0.00095	0.92832	2	1	C>T
ERR5749273	28881	PASS	G	A	8598	0.767969	11	7,1,4255,4239	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749273	28882	PASS	G	A	8596	0.832946	2	3,1,4297,4223	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749273	28883	PASS	G	C	8596	0.945556	0	1,0,4296,4277	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749273	28977	PASS	C	T	4378	0.930562	2147483647	0,0,0,4369	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749273	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	57679	0.001231	0	28955,28610,44,42	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749273	29253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29054	0.001377	0	0,28978,0,41	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCg/tTg	S327L	N	0.000361	0.053998	4	2	C>T
ERR5749273	29635	PASS	C	T	14458	0.928275	6	2,0,6764,7667	LOW	SILENT	SYNONYMOUS_CODING	ORF10	taC/taT	Y26	orf10	0.001133	0.928275	1	1	C>T
ERR5749274	241	PASS	C	T	21750	0.861471	0	0,1,10793,10882	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749274	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	17485	0.001716	0	17454,1,30,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749274	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	17487	7.43E-4	0	17399,3,13,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749274	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	17487	0.003374	0	17399,3,59,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749274	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	17477	0.003147	0	16081,5,1248,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749274	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	17477	0.001831	0	17440,5,32,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749274	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	17476	6.29E-4	0	17454,5,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749274	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	17476	7.44E-4	0	17447,6,13,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749274	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	17627	5.67E-4	188	106,17510,9,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749274	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	17627	6.24E-4	34	45,17485,2,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749274	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	17627	0.004595	1345	45,17485,64,17	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749274	913	PASS	C	T	116	0.887931	2147483647	0,0,0,115	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749274	1643	PASS	A	T	22348	0.975389	130	10,4,22327,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Aac/Tac	N280Y	nsp2	0.001863	0.97665	1	1	A>T
ERR5749274	1684	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22342	0.018441	0	21914,0,417,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I293	nsp2	0.000638	0.973136	2	2	C>T
ERR5749274	2245	PASS	C	T	21758	0.985201	223	1,6,21740,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V480	nsp2	0.985201	0.985201	1	1	C>T
ERR5749274	2395	PASS	C	T	42720	0.866198	33	1,14,21503,20978	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V530	nsp2	0.866198	0.866198	1	1	C>T
ERR5749274	3037	PASS	C	T	30647	0.807159	53	3,27,15314,15066	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749274	3267	PASS	C	T	1555	0.973633	2147483647	0,0,1555,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749274	3518	PASS	G	T	17203	0.970993	0	1,0,17194,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Ttt	V267F	nsp3	0.001724	0.970993	2	2	G>T
ERR5749274	5388	PASS	C	A	8044	0.962084	0	1,0,8040,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749274	5986	PASS	C	T	17986	0.974869	0	2,0,17969,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749274	6954	PASS	T	C	28326	0.822001	0	0,3,3,28158	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749274	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	43961	0.001069	134	22700,21214,47,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749274	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	20550	0.001168	0	20502,0,42,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749274	11287	PASS	GTCTGGTTTT	G	20548	0.997859	0	0,43,0,20504	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749274	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	45079	7.54E-4	2	26703,18295,21,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749274	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	35781	0.001146	0	17863,17824,22,22	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749274	14097	PASS	C	T	17673	0.503423	1	8523,5,9119,7	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F219	RdRp	0.000613	0.981481	2	2	C>T
ERR5749274	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	20434	0.005383	2147483647	19913,174,4,336	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749274	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	39676	0.001235	0	19878,19770,25,24	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749274	14408	PASS	C	T	39676	0.844037	7	2,6,19806,19570	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749274	14676	PASS	C	T	16221	0.822082	0	8,0,16177,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749274	15042	PASS	T	C	29649	0.901818	0	3,0,29520,3	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaT/aaC	N534	RdRp	0.002424	0.901818	2	2	T>C
ERR5749274	15279	PASS	C	T	27491	0.893674	0	4,0,27460,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749274	16176	PASS	T	C	26152	0.980078	9	0,3,13630,12509	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749274	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	32835	0.001005	0	32802,0,33,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749274	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	43800	0.002374	0	43663,0,109,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749274	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	39347	8.64E-4	0	39264,2,35,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749274	21764	PASS	ATACATG	A	18611	0.995755	23	76,1,18532,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749274	21990	PASS	TTTA	T	18621	0.998174	0	0,34,11,18576	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749274	22290	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	25413	4.33E-4	0	2,25400,0,11	HIGH	NONE	FRAME_SHIFT	S	tta/	L244	S	0.000389	0.578006	2	2	CT>C
ERR5749274	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	18420	0.001574	0	0,18379,0,29	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749274	23063	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	7	0.571429	0	0,1,0,6	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749274	23271	PASS	C	A	26880	0.920871	0	5,0,26854,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749274	23403	PASS	A	G	26869	0.970226	0	0,3,0,26852	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749274	23604	PASS	C	A	22025	0.949467	0	18,0,21998,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749274	23709	PASS	C	T	22004	0.937784	0	0,6,6,21959	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749274	24506	PASS	T	G	21659	0.97493	0	14,0,21643,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749274	24914	PASS	G	C	48640	0.960629	0	0,0,24223,24390	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749274	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	32263	0.001457	453	32126,28,28,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749274	25690	PASS	G	T	32214	0.974514	0	5,0,32190,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Ggc/Tgc	G100C	orf3a	0.971091	0.979849	1	1	G>T
ERR5749274	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	77494	2.58E-4	0	1,77471,0,20	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749274	26270	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	92458	6.71E-4	0	14767,77592,11,57	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	aCa/aTa	T9I	E	0.000586	0.930791	3	2	C>T
ERR5749274	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	16556	9.66E-4	0	0,16536,0,16	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749274	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	16556	7.25E-4	0	0,16544,0,12	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749274	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	16556	0.00151	0	0,16528,0,25	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749274	27972	PASS	C	T	15162	0.905883	18	1,1,15012,108	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749274	28048	PASS	G	T	15061	0.916008	0	0,18,0,15031	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749274	28095	PASS	A	T	15078	0.959544	296	9,3,0,15030	HIGH	NONSENSE	STOP_GAINED	ORF8	Aaa/Taa	K68*	orf8	0.002672	0.967672	2	2	A>T
ERR5749274	28111	PASS	A	G	34969	0.976951	4	8,3,19884,15064	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749274	28245	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	19880	0.019165	0	19464,1,396,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	Tta/Gta	L118V	orf8	0.019165	0.950471	2	2	T>G
ERR5749274	28249	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	ATC	19855	0.001108	0	19819,1,22,0	HIGH	NONE	FRAME_SHIFT	ORF8	ttc/CTttc	F120L?	orf8	0.000443	0.063605	3	2	A>ATC
ERR5749274	28250	PASS	T	TCTG	19765	0.990387	0	223,0,19574,1	MODERATE	NONE	CODON_INSERTION	ORF8	ttc/CTGttc	F120LF	orf8	0.000494	0.993968	5	3	T>TCTG
ERR5749274	28250	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TATG	19765	0.002125	0	223,0,42,0	MODERATE	NONE	CODON_INSERTION	ORF8	ttc/ATGttc	F120MF	orf8	0.000494	0.993968	5	3	T>TATG
ERR5749274	28253	PASS	CA	C	19765	0.993726	0	124,0,19640,1	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749274	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	19765	0.001568	0	19731,1,31,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/TTatc	I121L?	orf8	0.000422	0.995511	4	3	C>CTT
ERR5749274	28254	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	ATC	19765	0.001164	0	19741,1,23,0	HIGH	NONE	FRAME_SHIFT+STOP_LOST+SPLICE_SITE_REGION	ORF8	taa/tCTaa	*122S?	orf8	0.000541	0.914398	3	2	A>ATC
ERR5749274	28270	PASS	TA	T	38648	0.992833	621	270,12,19480,18891	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749274	28280	PASS	G	C	38502	0.931926	19	10,1,19542,18871	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749274	28281	PASS	A	T	38502	0.916446	39	27,5,19516,18880	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749274	28282	PASS	T	A	38506	0.88768	6	21,13,19508,18887	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749274	28881	PASS	G	A	18757	0.788879	9	4,0,9322,9221	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749274	28882	PASS	G	A	18756	0.829495	2	3,1,9390,9194	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749274	28883	PASS	G	C	18757	0.942155	1	2,3,9403,9330	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749274	28977	PASS	C	T	9549	0.932244	0	0,1,4,9531	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749274	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	63727	0.001114	1	32004,31605,50,46	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749275	241	PASS	C	T	137	0.854015	0	0,0,68,69	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749275	815	PASS	C	T	799	0.125156	0	686,0,113,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgc/Tgc	R4C	nsp2	0.001196	0.125156	1	1	C>T
ERR5749275	913	PASS	C	T	800	0.9225	0	0,1,0,799	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749275	1625	PASS	C	T	743	0.228802	0	569,0,174,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L274F	nsp2	0.228802	0.228802	1	1	C>T
ERR5749275	1820	PASS	G	A	743	0.948856	2147483647	0,0,0,742	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggt/Agt	G339S	nsp2	0.001189	0.949024	2	2	G>A
ERR5749275	2835	PASS	G	T	1923	0.050442	0	0,1816,0,107	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tGc/tTc	C39F	nsp3	0.050442	0.050442	1	1	G>T
ERR5749275	3037	PASS	C	T	405	0.846914	0	0,1,201,200	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749275	3124	PASS	T	C	203	0.950739	2147483647	0,0,0,202	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaT/gaC	D135	nsp3	0.950739	0.954097	1	1	T>C
ERR5749275	3267	PASS	C	T	831	0.968712	2147483647	0,0,831,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749275	3366	PASS	T	C	831	0.050542	0	2,774,0,52	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cTt/cCt	L216P	nsp3	0.001518	0.050542	2	1	T>C
ERR5749275	3817	PASS	C	T	515	0.972816	0	1,0,293,221	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D366	nsp3	0.000777	0.972816	2	2	C>T
ERR5749275	5388	PASS	C	A	153	0.96732	2147483647	0,0,153,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749275	5986	PASS	C	T	468	0.970085	2147483647	0,0,466,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749275	6954	PASS	T	C	1343	0.80417	2147483647	0,0,0,1336	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749275	8603	PASS	T	C	220	0.936364	2147483647	0,0,0,219	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Ctc	F17L	nsp4	0.002607	0.974959	2	1	T>C
ERR5749275	8950	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1656	0.012077	209	1499,137,0,20	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I132	nsp4	0.002808	0.982604	1	1	C>T
ERR5749275	9561	PASS	C	T	643	0.161742	0	526,0,117,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCa/tTa	S336L	nsp4	0.00171	0.161742	2	2	C>T
ERR5749275	9697	PASS	T	C	1274	0.05887	0	598,592,42,41	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taT/taC	Y381	nsp4	0.001995	0.05887	1	1	T>C
ERR5749275	9968	PASS	G	A	282	0.078014	0	260,0,22,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gca/Aca	A472T	nsp4	0.003141	0.078014	2	1	G>A
ERR5749275	10783	PASS	A	G	17	0.882353	2147483647	0,0,16,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acA/acG	T243	3Cpro	0.882353	0.922956	1	1	A>G
ERR5749275	11082	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	3601	0.002499	0	3593,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000427	0.179468	2	1	TG>T
ERR5749275	11083	PASS	G	T	3601	0.06276	0	3352,0,239,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749275	11220	PASS	T	C	6994	0.057907	4	3190,3347,205,237	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTg/aCg	M83T	nsp6	0.000767	0.057907	2	2	T>C
ERR5749275	11287	PASS	GTCTGGTTTT	G	3603	0.999445	0	0,2,0,3601	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749275	14028	PASS	G	T	1231	0.051178	0	1165,0,65,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atT	M196I	RdRp	0.002405	0.051178	1	1	G>T
ERR5749275	14408	PASS	C	T	54	0.833333	0	0,0,27,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749275	14676	PASS	C	T	526	0.676806	2147483647	0,0,522,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749275	15279	PASS	C	T	832	0.903846	2147483647	0,0,831,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749275	16176	PASS	T	C	900	0.98	0	0,0,108,792	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749275	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	1052	0.011407	0	1040,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749275	17615	PASS	A	G	1105	0.912217	2147483647	0,0,0,1102	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749275	17747	PASS	C	T	670	0.058209	0	628,0,40,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P504L	helicase	0.000839	0.968462	2	2	C>T
ERR5749275	17749	PASS	G	T	670	0.095522	0	603,0,67,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gct/Tct	A505S	helicase	0.001521	0.987943	4	2	G>T
ERR5749275	19619	PASS	A	C	997	0.074223	0	921,0,76,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING+SPLICE_SITE_REGION	ORF1ab	cAg/cCg	Q527P	ExoN	0.074223	0.074223	1	1	A>C
ERR5749275	19983	PASS	C	CT	436	0.100917	0	392,0,44,0	HIGH	NONE	FRAME_SHIFT+STOP_GAINED	ORF1ab	gat/Tgat	D124*?	endoR	0.000884	0.981982	5	2	C>CT
ERR5749275	21764	PASS	ATACATG	A	1083	0.996307	0	4,0,1079,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749275	21790	PASS	TA	T	1083	0.063712	0	1014,0,69,0	HIGH	NONE	FRAME_SHIFT	S	aag/	K77	S	0.001442	0.063712	3	2	TA>T
ERR5749275	21846	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2157	0.044506	0	1022,1015,60,60	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCt/aTt	T95I	S	0.001104	0.788523	1	1	C>T
ERR5749275	21990	PASS	TTTA	T	1083	0.999077	0	0,1,0,1082	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749275	22248	PASS	T	C	1838	0.101741	0	0,1644,0,193	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tTg/tCg	L229S	S	0.101741	0.101741	1	1	T>C
ERR5749275	22787	PASS	C	T	2708	0.053914	0	0,2556,0,149	HIGH	NONSENSE	STOP_GAINED	S	Caa/Taa	Q409*	S	0.000599	0.053914	2	2	C>T
ERR5749275	23063	PASS	A	T	868	0.870968	2147483647	0,0,0,862	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749275	23271	PASS	C	A	1181	0.904318	2147483647	0,0,1181,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749275	23403	PASS	A	G	1183	0.972105	2147483647	0,0,0,1182	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749275	23604	PASS	C	A	904	0.945796	2147483647	0,0,902,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749275	23709	PASS	C	T	904	0.943584	2147483647	0,0,0,904	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749275	24506	PASS	T	G	1614	0.973358	0	1,0,1613,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749275	24914	PASS	G	C	9683	0.962305	0	0,0,4826,4850	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749275	25437	PASS	G	T	6664	0.958583	0	3,0,6656,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	ttG/ttT	L15F	orf3a	0.001128	0.971411	2	2	G>T
ERR5749275	26227	PASS	G	T	2015	0.962779	0	0,0,1028,987	.	.	.	.	.	.	.	0.962779	0.970452	1	1	G>T
ERR5749275	27312	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	1453	0.019959	0	1424,0,29,0	HIGH	NONE	FRAME_SHIFT	ORF6	aat/aaAt	N39K?	orf6	0.000911	0.088458	4	2	T>TA
ERR5749275	27506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	4195	0.006675	129	2739,1428,0,28	HIGH	NONE	FRAME_SHIFT	ORF7a	aca/	T39	orf7a	0.000715	0.985435	4	2	GA>G
ERR5749275	27629	PASS	C	T	2738	0.088751	0	2485,0,249,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	gCc/gTc	A79V	orf7a	0.000786	0.088751	2	1	C>T
ERR5749275	27641	PASS	C	T	2736	0.896564	2147483647	0,0,2730,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	tCa/tTa	S83L	orf7a	0.000983	0.911213	2	2	C>T
ERR5749275	27972	PASS	C	T	197	0.923858	2147483647	0,0,197,0	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749275	28048	PASS	G	T	197	0.913706	0	0,1,0,196	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749275	28111	PASS	A	G	206	0.970874	0	0,0,9,197	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749275	28270	PASS	TA	T	17	1.0	0	0,0,9,8	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749275	28280	PASS	G	C	17	0.941176	0	0,0,9,8	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749275	28281	PASS	A	T	17	0.941176	0	0,0,9,8	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749275	28282	PASS	T	A	17	0.941176	0	0,0,9,8	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749275	28881	PASS	G	A	203	0.669951	0	0,0,99,98	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749275	28882	PASS	G	A	203	0.876847	3	1,0,100,102	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749275	28883	PASS	G	C	203	0.91133	0	0,0,101,102	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749275	28977	PASS	C	T	104	0.961538	2147483647	0,0,0,103	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749275	29543	PASS	G	C	754	0.973475	0	0,0,177,577	.	.	.	.	.	.	.	0.001058	0.973475	3	1	G>C
ERR5749275	29675	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	353	0.036827	0	169,169,7,7	.	.	.	.	.	.	.	0.000624	0.883495	2	1	C>T
ERR5749275	29745	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	177	0.039548	0	0,169,0,8	.	.	.	.	.	.	.	0.039548	0.920898	2	1	G>A
ERR5749276	241	PASS	C	T	1888	0.866525	0	0,1,936,940	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749276	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	5601	0.0025	0	5590,0,14,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749276	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	5601	0.001785	0	5583,0,10,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749276	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	5601	0.001428	0	5583,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749276	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	5599	0.002322	0	5171,0,389,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749276	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	5599	0.003393	0	5580,0,19,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749276	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	14935	0.001473	24	9303,5610,20,2	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749276	913	PASS	C	T	9316	0.916702	0	0,2,0,9302	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749276	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	28358	0.001199	1872	14144,13342,33,767	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749276	3037	PASS	C	T	8614	0.825981	30	0,10,4304,4243	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749276	3267	PASS	C	T	10079	0.970632	0	2,0,10072,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749276	5388	PASS	C	A	2270	0.957709	2147483647	0,0,2270,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749276	5628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	8608	0.001278	0	8597,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acg/	T970	nsp3	0.000561	0.973644	3	2	CG>C
ERR5749276	5986	PASS	C	T	6591	0.97269	2147483647	0,0,6583,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749276	6295	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	11910	0.001427	0	11888,0,18,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atA/atG	I1192M	nsp3	0.001427	0.968532	1	1	A>G
ERR5749276	6813	PASS	C	T	17797	0.952183	0	0,0,11002,6755	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T1365I	nsp3	0.001082	0.95799	2	1	C>T
ERR5749276	6954	PASS	T	C	11001	0.823743	2147483647	0,0,0,10955	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749276	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	11748	8.51E-4	4	10103,1635,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749276	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	17590	0.002331	0	17204,0,41,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749276	11104	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	17585	0.001422	0	17518,0,27,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccT/ccC	P44	nsp6	0.000866	0.675414	2	1	T>C
ERR5749276	11287	PASS	GTCTGGTTTT	G	17584	0.997611	0	0,42,0,17542	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749276	11507	PASS	G	A	12497	0.912139	0	1,1,6273,6197	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Att	V179I	nsp6	0.007744	0.914418	2	2	G>A
ERR5749276	12125	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	17906	0.001061	0	0,17815,0,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y12H	nsp8	0.000847	0.113436	1	1	T>C
ERR5749276	12870	PASS	C	T	5057	0.848527	2147483647	0,0,5032,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T62I	nsp9	0.773252	0.848527	1	1	C>T
ERR5749276	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23590	0.001229	0	11781,11744,16,17	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749276	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	3536	0.003394	0	1766,1760,6,6	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749276	14408	PASS	C	T	3536	0.84276	0	0,0,1756,1741	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749276	14676	PASS	C	T	7179	0.812648	0	1,0,7163,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749276	15279	PASS	C	T	8517	0.893977	0	2,0,8500,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749276	16176	PASS	T	C	11034	0.981149	0	0,1,3997,7030	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749276	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	13354	0.001872	0	13329,0,25,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749276	18357	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	14112	0.001559	0	14058,0,22,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccT/ccC	P106	ExoN	0.001226	0.057597	1	1	T>C
ERR5749276	18897	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	22660	0.001015	0	10,22627,0,23	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/	V287	ExoN	0.00046	0.060685	3	3	TG>T
ERR5749276	19188	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATT	A	12342	0.001458	0	0,12322,0,18	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttttgg/	FW384	ExoN	0.000427	0.06319	2	1	ATT>A
ERR5749276	19401	PASS	T	A	10228	0.913864	0	3,0,10204,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcT/tcA	S454	ExoN	0.913864	0.918286	1	1	T>A
ERR5749276	19763	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19486	0.001386	0	9666,9713,17,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T48I	endoR	0.000987	0.809304	2	1	C>T
ERR5749276	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7114	0.003374	0	7087,0,26,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749276	20320	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAT	C	18786	9.58E-4	0	18770,0,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	atc/	I235	endoR	0.000651	0.916979	2	2	CAT>C
ERR5749276	20445	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	18774	0.001811	0	0,18740,0,34	HIGH	NONE	FRAME_SHIFT	ORF1ab	aac/aaAc	N277K?	endoR	0.000518	0.059736	4	2	T>TA
ERR5749276	21255	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	33554	0.001252	2	17273,16213,27,21	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcG/gcA	A199	MethTr	0.000341	0.917425	4	2	G>A
ERR5749276	21637	PASS	C	T	9376	0.961071	0	0,2,0,9365	LOW	SILENT	SYNONYMOUS_CODING	S	ccC/ccT	P25	S	0.954687	0.96491	1	1	C>T
ERR5749276	21764	PASS	ATACATG	A	8870	0.99752	0	22,0,8848,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749276	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	8870	9.02E-4	0	8862,0,8,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749276	21990	PASS	TTTA	T	8871	0.997858	0	0,19,0,8852	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749276	22019	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	14135	0.001486	0	14109,3,21,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Atg/Gtg	M153V	S	0.001486	0.98035	1	1	A>G
ERR5749276	22717	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAA	T	25327	3.95E-4	0	12674,12644,5,5	HIGH	NONE	FRAME_SHIFT	S	aaa/	K386	S	0.000395	0.918478	3	2	TAA>T
ERR5749276	23031	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	9836	0.001627	0	0,9632,0,31	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tTt/tCt	F490S	S	0.001067	0.92095	2	1	T>C
ERR5749276	23063	PASS	A	T	9873	0.872177	0	0,2,0,9830	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749276	23271	PASS	C	A	12510	0.941487	0	1,0,12495,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749276	23403	PASS	A	G	12502	0.969845	0	0,1,0,12489	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749276	23406	PASS	T	C	12502	0.952568	0	0,7,0,12491	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gTt/gCt	V615A	S	0.949411	0.956636	1	1	T>C
ERR5749276	23426	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTT	G	12512	0.001519	0	0,12493,0,19	HIGH	NONE	FRAME_SHIFT	S	gtt/	V622	S	0.000428	0.916192	4	2	GTT>G
ERR5749276	23604	PASS	C	A	9719	0.936413	0	8,0,9707,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749276	23634	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9716	0.001441	0	9702,0,14,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tTc	S691F	S	0.00071	0.931159	2	2	C>T
ERR5749276	23709	PASS	C	T	9715	0.943284	0	0,2,0,9703	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749276	23766	PASS	C	T	9722	0.163547	0	0,8052,0,1667	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCa/tTa	S735L	S	0.001668	0.163547	1	1	C>T
ERR5749276	23817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	14445	0.001523	8	4714,9701,4,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTt/cCt	L752P	S	0.000646	0.066832	1	1	T>C
ERR5749276	24506	PASS	T	G	10350	0.975749	0	6,0,10343,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749276	24914	PASS	G	C	32211	0.960076	3	1,0,16054,16145	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749276	25207	PASS	C	T	4192	0.797471	0	0,5,0,4178	LOW	SILENT	SYNONYMOUS_CODING	S	taC/taT	Y1215	S	0.004687	0.815232	1	1	C>T
ERR5749276	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	2721	0.006248	287	2669,28,1,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749276	26013	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20195	0.001436	0	20157,0,30,0	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	ttC/ttT	F207	orf3a	0.000839	0.974528	1	1	C>T
ERR5749276	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	20171	7.93E-4	0	0,20155,0,16	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749276	26493	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	7395	0.001082	0	0,7387,0,8	.	.	.	.	.	.	.	0.001082	0.069277	3	1	GT>G
ERR5749276	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	8312	0.001083	0	0,8303,0,9	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749276	27552	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATTTGCACTGACTTGCTTTAGCACTCAATTTGCTTTTGCTTGTCCTGACGGCGTAAAACACGTCTATCAG	A	13017	8.45E-4	0	13006,0,11,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF7a	tttgcactgacttgctttagcactcaatttgcttttgcttgtcctgacggcgtaaaacacgtctatcagtta/tta	FALTCFSTQFAFACPDGVKHVYQL54L	orf7a	0.000563	0.985801	6	1	ATTTGCACTGACTTGCTTTAGCACTCAATTTGCTTTTGCTTGTCCTGACGGCGTAAAACACGTCTATCAG>A
ERR5749276	27604	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	13016	0.001306	0	12984,0,18,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Gta/Ata	V71I	orf7a	0.001008	0.967671	3	2	G>A
ERR5749276	27625	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13014	0.00584	0	12901,0,82,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Cgt/Tgt	R78C	orf7a	0.00584	0.951914	1	1	C>T
ERR5749276	27972	PASS	C	T	3418	0.911937	0	0,0,3396,12	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749276	28048	PASS	G	T	3406	0.916031	0	0,6,0,3398	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749276	28111	PASS	A	G	21802	0.979084	0	3,0,18379,3407	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749276	28147	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	18403	7.06E-4	0	18383,7,13,0	HIGH	NONE	FRAME_SHIFT	ORF8	ttt/	F86	orf8	0.000438	0.981624	4	2	CT>C
ERR5749276	28270	PASS	TA	T	35647	0.995624	386	159,5,18173,17318	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749276	28280	PASS	G	C	35574	0.936246	3	9,5,18196,17297	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749276	28281	PASS	A	T	35574	0.919351	7	26,15,18192,17285	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749276	28282	PASS	T	A	35575	0.908981	1	18,15,18148,17306	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749276	28881	PASS	G	A	5072	0.791009	0	0,0,2503,2497	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749276	28882	PASS	G	A	5072	0.833793	0	1,0,2527,2498	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749276	28883	PASS	G	C	5072	0.943415	0	0,0,2530,2537	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749276	28977	PASS	C	T	2580	0.931008	2147483647	0,0,0,2579	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749276	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	36671	9.82E-4	0	18412,18201,22,21	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749276	29284	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	18468	4.87E-4	0	0,18459,0,9	HIGH	NONE	FRAME_SHIFT	N	aaa/	K338	N	0.000393	0.931014	3	2	CA>C
ERR5749277	241	PASS	C	T	1647	0.871888	0	0,1,817,821	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749277	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	5177	0.003477	0	5158,1,18,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749277	656	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	5191	0.004238	0	0,5167,0,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gct/Cct	A131P	leader	0.001202	0.131429	1	1	G>C
ERR5749277	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	14694	7.49E-4	19	9492,5191,11,0	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749277	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9498	0.002	0	0,9454,0,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749277	913	PASS	C	T	9498	0.910086	0	0,7,0,9469	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749277	1813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	13417	0.009242	0	0,13285,0,124	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggt/Aggt	G339R?	nsp2	0.001022	0.152738	4	2	T>TA
ERR5749277	1820	PASS	G	A	13418	0.949024	0	0,2,0,13320	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggt/Agt	G339S	nsp2	0.001189	0.949024	2	2	G>A
ERR5749277	1820	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GA	13418	0.005291	0	0,13339,0,71	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggt/gAgt	G339E?	nsp2	0.001189	0.949024	2	2	G>GA
ERR5749277	3037	PASS	C	T	9260	0.804212	24	1,11,4625,4540	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749277	3124	PASS	T	C	4662	0.954097	0	0,3,0,4653	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaT/gaC	D135	nsp3	0.950739	0.954097	1	1	T>C
ERR5749277	3267	PASS	C	T	10507	0.970877	0	1,0,10503,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749277	3340	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	20914	0.001243	0	10482,10409,13,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N208	nsp3	0.000712	0.845579	3	2	GA>G
ERR5749277	3365	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20003	0.0014	0	9501,10452,15,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Ttt	L216F	nsp3	0.0014	0.053042	1	1	C>T
ERR5749277	3817	PASS	C	T	10354	0.963879	0	0,0,5318,5028	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D366	nsp3	0.000777	0.972816	2	2	C>T
ERR5749277	5170	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	7113	0.001265	0	0,7104,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T819	nsp3	0.000565	0.894036	2	2	CCA>C
ERR5749277	5388	PASS	C	A	2949	0.953204	2147483647	0,0,2948,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749277	5986	PASS	C	T	7024	0.976082	2147483647	0,0,7017,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749277	6286	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12102	0.001735	0	12066,0,21,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acC/acT	T1189	nsp3	0.000549	0.949782	2	2	C>T
ERR5749277	6336	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12098	0.001405	0	12055,0,20,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCg/tTg	S1206L	nsp3	0.001317	0.951419	1	1	C>T
ERR5749277	6813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17973	0.001614	26	11536,6388,27,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T1365I	nsp3	0.001082	0.95799	2	1	C>T
ERR5749277	6936	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23006	0.001434	2	11364,11287,18,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S1406F	nsp3	0.000553	0.91447	2	2	C>T
ERR5749277	6954	PASS	T	C	11533	0.804648	0	0,3,0,11484	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749277	7564	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	8716	0.001262	0	0,8705,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/	Y1617	nsp3	0.000586	0.056194	4	2	CT>C
ERR5749277	7735	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13396	0.001344	0	13370,0,18,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I1672	nsp3	0.000658	0.954659	3	2	C>T
ERR5749277	7811	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAT	C	13384	9.71E-4	0	13369,2,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H1698	nsp3	0.000971	0.883442	2	2	CAT>C
ERR5749277	7967	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13403	0.002388	0	8,13363,0,32	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cct/Tct	P1750S	nsp3	0.002388	0.949148	1	1	C>T
ERR5749277	8084	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAA	G	9784	0.001124	0	9773,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1790	nsp3	0.000543	0.923413	4	2	GAA>G
ERR5749277	8603	PASS	T	C	6367	0.965918	0	0,3,0,6360	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Ctc	F17L	nsp4	0.002607	0.974959	2	1	T>C
ERR5749277	8697	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	5271	0.001138	0	5265,0,6,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	att/	I49	nsp4	0.000737	0.072165	1	1	CTA>C
ERR5749277	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	12177	8.21E-4	4	10387,1780,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749277	10138	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17269	0.002722	7	13124,4082,41,7	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N28	3Cpro	0.000458	0.983567	3	3	C>T
ERR5749277	10323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	13171	0.001974	0	0,13118,0,28	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749277	10369	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13183	0.001365	0	4,13150,0,20	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	cgC/cgT	R105	3Cpro	0.001225	0.120075	1	1	C>T
ERR5749277	10681	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11995	0.001417	0	4,11968,0,17	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y209	3Cpro	0.000888	0.977192	2	2	C>T
ERR5749277	10783	PASS	A	G	1272	0.922956	2147483647	0,0,1271,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acA/acG	T243	3Cpro	0.882353	0.922956	1	1	A>G
ERR5749277	11082	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	17473	6.87E-4	0	17469,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttAg	L37L?	nsp6	0.000427	0.179468	2	1	T>TA
ERR5749277	11199	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34791	8.34E-4	0	17263,17359,17,19	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCc/gTc	A76V	nsp6	0.000309	0.056758	3	2	C>T
ERR5749277	11287	PASS	GTCTGGTTTT	G	17468	0.996622	0	0,59,0,17409	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749277	11300	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17475	0.001087	0	0,17442,0,20	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L110	nsp6	0.001087	0.873873	1	1	C>T
ERR5749277	11355	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	24020	6.66E-4	20	6539,17465,0,16	HIGH	NONE	FRAME_SHIFT	ORF1ab	aga/	R129	nsp6	0.000455	0.982262	3	2	CA>C
ERR5749277	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	19300	0.001244	25	12731,6528,24,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749277	11761	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	25446	7.86E-4	0	12731,12697,10,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N264	nsp6	0.000786	0.354576	2	2	GA>G
ERR5749277	11782	PASS	A	G	12759	0.05596	0	29,11788,1,805	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaA/aaG	K270	nsp6	0.001073	0.917917	2	2	A>G
ERR5749277	12439	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11673	0.037522	0	4,10960,0,704	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P116	nsp8	0.000666	0.637117	2	2	C>T
ERR5749277	12439	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	11673	9.42E-4	0	4,11658,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L117	nsp8	0.000666	0.637117	2	2	CT>C
ERR5749277	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	11660	0.001715	0	11632,0,20,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749277	12513	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11659	0.00163	0	11634,0,20,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aTg	T141M	nsp8	0.000794	0.984064	2	2	C>T
ERR5749277	12513	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CGT	C	11659	0.001115	0	11646,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tgtgat/	CD142	nsp8	0.000794	0.984064	2	2	CGT>C
ERR5749277	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	12615	7.93E-4	0	12605,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749277	13468	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	10916	7.33E-4	0	10908,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggg/	G10	nsp11	0.000713	0.076498	2	2	CG>C
ERR5749277	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21808	0.001651	0	10888,10857,19,19	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749277	13994	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9709	0.001957	0	9681,0,23,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A185V	RdRp	0.000427	0.114441	3	2	C>T
ERR5749277	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	3419	0.00234	0	1714,1699,4,4	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749277	14408	PASS	C	T	3419	0.849664	1	2,3,1705,1672	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749277	14599	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	6674	0.001948	0	6661,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctatta/	LL387	RdRp	0.000639	0.922766	3	2	CTA>C
ERR5749277	14676	PASS	C	T	6674	0.724303	0	3,0,6635,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749277	15279	PASS	C	T	9197	0.883223	0	1,0,9173,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749277	15493	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	9200	0.001739	0	2,9175,0,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gcc/Ccc	A685P	RdRp	0.001408	0.076816	3	2	G>C
ERR5749277	16176	PASS	T	C	10780	0.982282	0	0,1,4259,6519	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749277	16274	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	4259	0.001644	0	4252,0,7,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tca/	S13	helicase	0.001644	0.135942	2	2	CA>C
ERR5749277	16792	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28740	0.001079	8	13704,14991,11,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgt/Tgt	R186C	helicase	0.000335	0.072562	5	2	C>T
ERR5749277	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	13717	0.002187	0	13677,0,30,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749277	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAA	G	13717	7.29E-4	0	13677,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GAA>G
ERR5749277	17122	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCT	G	21149	7.57E-4	29	7432,13701,0,16	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctctac/	LY297	helicase	0.000476	0.056834	3	2	GCT>G
ERR5749277	17502	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	10199	8.82E-4	0	10190,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N423	helicase	0.000611	0.9865	2	2	CA>C
ERR5749277	17615	PASS	A	G	10188	0.890656	0	0,0,5,10152	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749277	17795	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8511	0.001645	0	8494,0,14,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A520V	helicase	0.00111	0.966723	2	2	C>T
ERR5749277	18658	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	21667	6.92E-4	0	21648,4,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tgt/	C207	ExoN	0.000507	0.115741	3	2	TG>T
ERR5749277	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21663	0.001108	0	21624,0,24,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C216	ExoN	0.000374	0.981963	3	2	C>T
ERR5749277	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	21663	6.46E-4	0	21649,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749277	18747	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	21657	6.46E-4	0	21643,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tataat/	YN237	ExoN	0.000375	0.982946	4	2	CTA>C
ERR5749277	18897	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	21671	0.001061	122	4,21635,5,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttT/ttG	F286L	ExoN	0.00046	0.060685	3	3	T>G
ERR5749277	19011	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	13853	6.5E-4	0	13844,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K325	ExoN	0.000408	0.975746	4	2	CA>C
ERR5749277	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	13843	0.001084	0	6,13822,0,15	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749277	19328	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	10285	8.75E-4	0	10276,0,9,0	HIGH	NONE	FRAME_SHIFT+STOP_GAINED	ORF1ab	gat/Tgat	D432*?	ExoN	0.000459	0.937906	4	2	C>CT
ERR5749277	20148	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8151	0.002208	0	0,8103,0,18	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F176	endoR	0.000513	0.969223	2	2	C>T
ERR5749277	20320	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19891	0.001609	0	19827,0,33,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cat/Tat	H234Y	endoR	0.000651	0.916979	2	2	C>T
ERR5749277	20786	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	10194	0.001864	577	0,10152,20,4	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAt/aTt	N43I	MethTr	0.001392	1	1	1	A>T
ERR5749277	20823	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24986	0.001561	5	14766,10144,27,12	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N55	MethTr	0.001138	0.982544	2	2	C>T
ERR5749277	20844	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	24986	6.4E-4	62	14810,10160,0,16	HIGH	NONE	FRAME_SHIFT	ORF1ab	tataat/	YN63	MethTr	0.000293	0.905571	5	2	CTA>C
ERR5749277	21032	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATC	A	14787	0.001082	0	0,14771,0,16	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctc/	L126	MethTr	0.000568	0.088561	2	2	ATC>A
ERR5749277	21077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	14805	0.001013	0	3,14787,0,15	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K141	MethTr	0.000492	0.955529	4	2	CA>C
ERR5749277	21123	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	35067	6.27E-4	50	20236,14809,22,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F156	MethTr	0.000257	0.90982	5	2	GT>G
ERR5749277	21234	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	20250	0.001185	0	20194,0,43,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcA	A192	MethTr	0.000472	0.857572	5	2	C>A
ERR5749277	21304	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20230	0.001532	0	0,20190,0,33	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgc/Tgc	R216C	MethTr	0.000411	0.605296	3	2	C>T
ERR5749277	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	15576	0.002375	0	7757,7782,18,19	HIGH	NONE	FRAME_SHIFT	S	ctt/Tctt	L5S?	S	0.000394	0.091869	4	1	G>GT
ERR5749277	21595	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7811	0.001664	0	0,7784,0,17	LOW	SILENT	SYNONYMOUS_CODING	S	gtC/gtT	V11	S	0.001296	0.918559	3	2	C>T
ERR5749277	21707	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17862	0.001568	34	10029,7798,7,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Cat/Tat	H49Y	S	0.001048	0.072032	1	1	C>T
ERR5749277	21727	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	10046	8.96E-4	0	10031,6,9,0	HIGH	NONE	FRAME_SHIFT	S	tta/	L56	S	0.000896	0.878141	2	2	CT>C
ERR5749277	21764	PASS	ATACATG	A	10040	0.997908	0	21,0,10019,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749277	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	10039	0.001295	0	10026,0,13,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749277	21786	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	10039	0.001992	0	10001,0,35,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gGt/gTt	G75V	S	0.001992	0.058409	1	1	G>T
ERR5749277	21811	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10039	0.001594	0	10017,0,17,0	LOW	SILENT	SYNONYMOUS_CODING	S	gtC/gtT	V83	S	0.001327	0.179245	1	1	C>T
ERR5749277	21990	PASS	TTTA	T	10047	0.994924	0	0,51,7,9989	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749277	21994	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTAC	T	26113	3.83E-4	41	16074,10029,0,10	MODERATE	NONE	CODON_DELETION	S	tac/	Y145	S	0.000341	0.347498	1	1	TTAC>T
ERR5749277	22290	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	16082	5.6E-4	0	8,16065,0,9	HIGH	NONE	FRAME_SHIFT	S	tta/	L244	S	0.000389	0.578006	2	2	CT>C
ERR5749277	22787	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	13349	5.99E-4	0	0,13341,0,8	HIGH	NONE	FRAME_SHIFT	S	atc/	I410	S	0.000599	0.053914	2	2	CA>C
ERR5749277	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23619	0.001313	2	10235,13333,16,17	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749277	23043	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAT	C	10219	8.81E-4	0	0,10210,0,9	HIGH	NONE	FRAME_SHIFT	S	tat/	Y495	S	0.000881	0.056585	2	2	CAT>C
ERR5749277	23063	PASS	A	T	10235	0.855105	2147483647	0,0,0,10192	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749277	23271	PASS	C	A	12799	0.925229	2147483647	0,0,12777,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749277	23277	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12799	0.001719	0	12749,0,27,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCt/aTt	T572I	S	0.001007	0.74768	1	1	C>T
ERR5749277	23403	PASS	A	G	12791	0.963803	2147483647	0,0,0,12784	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749277	23426	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTGCTA	G	12801	6.25E-4	0	0,12793,0,8	MODERATE	NONE	CODON_DELETION	S	gctatt/	AI623	S	0.000428	0.916192	4	2	GTTGCTA>G
ERR5749277	23604	PASS	C	A	10355	0.945534	0	10,0,10338,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749277	23664	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20527	0.002046	0	10177,10277,23,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCa/gTa	A701V	S	0.000837	0.918	2	2	C>T
ERR5749277	23709	PASS	C	T	10345	0.932914	0	0,1,0,10327	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749277	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	16640	0.002224	9	6272,10331,9,28	HIGH	NONE	FRAME_SHIFT	S	ttg/	L753	S	0.000334	0.080808	2	2	CT>C
ERR5749277	23817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	16640	0.001563	16	6267,10307,4,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTt/cCt	L752P	S	0.000646	0.066832	1	1	T>C
ERR5749277	23855	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6281	0.00207	0	6264,0,14,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Cgt/Tgt	R765C	S	0.000815	0.181818	2	2	C>T
ERR5749277	24320	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	9071	8.82E-4	0	0,9024,0,8	HIGH	NONE	FRAME_SHIFT	S	aaa/	K921	S	0.000763	0.138365	4	2	CAA>C
ERR5749277	24506	PASS	T	G	12294	0.974378	0	2,0,12291,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749277	24899	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29982	0.001167	0	14971,14890,20,20	HIGH	NONSENSE	STOP_GAINED	S	Caa/Taa	Q1113*	S	0.000315	0.09021	5	3	C>T
ERR5749277	24914	PASS	G	C	29876	0.95806	0	0,1,14878,14970	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749277	25437	PASS	G	T	16720	0.971411	0	3,0,16707,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	ttG/ttT	L15F	orf3a	0.001128	0.971411	2	2	G>T
ERR5749277	25572	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	16726	0.001375	0	0,16703,0,23	HIGH	NONE	FRAME_SHIFT	ORF3a	atc/	I62	orf3a	0.000543	0.959687	4	2	CA>C
ERR5749277	25587	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	16729	0.002212	0	0,16682,0,37	HIGH	NONE	FRAME_SHIFT	ORF3a	aag/	K67	orf3a	0.000598	0.813206	6	2	CA>C
ERR5749277	25587	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	16729	5.98E-4	0	0,16682,0,10	HIGH	NONE	FRAME_SHIFT	ORF3a	aag/	K67	orf3a	0.000598	0.813206	6	2	CAA>C
ERR5749277	25626	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTTTG	C	21097	0.001043	18	4362,16709,0,22	HIGH	NONE	FRAME_SHIFT	ORF3a	gtttgc/	VC80	orf3a	0.000403	0.915633	3	2	CTTTG>C
ERR5749277	25782	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4362	0.002751	0	4341,0,12,0	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	tgC/tgT	C130	orf3a	0.000916	0.955348	1	1	C>T
ERR5749277	26044	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25738	0.001166	0	25694,0,32,0	HIGH	NONSENSE	STOP_GAINED	ORF3a	Caa/Taa	Q218*	orf3a	0.000469	0.102679	3	3	C>T
ERR5749277	26208	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25731	0.001205	0	5,25651,0,37	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	agC/agT	S272	orf3a	0.000315	0.922222	2	2	C>T
ERR5749277	26227	PASS	G	T	33200	0.970452	8	0,10,7462,25714	.	.	.	.	.	.	.	0.962779	0.970452	1	1	G>T
ERR5749277	26256	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	33590	9.23E-4	25	7848,25686,1,32	LOW	SILENT	SYNONYMOUS_CODING	E	ttC/ttT	F4	E	0.000748	0.969561	2	2	C>T
ERR5749277	26333	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7850	0.00293	0	7818,0,23,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	aCa/aTa	T30I	E	0.00158	0.943221	1	1	C>T
ERR5749277	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	10914	0.0011	0	5,10897,0,12	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749277	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	10910	0.0011	0	0,10892,0,12	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749277	26895	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26377	0.001175	0	26335,4,32,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Cat/Tat	H125Y	M	0.000874	0.97046	1	1	C>T
ERR5749277	26936	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26373	0.001479	0	26327,0,39,0	LOW	SILENT	SYNONYMOUS_CODING	M	ctC/ctT	L138	M	0.001308	0.968147	2	1	C>T
ERR5749277	27078	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26363	0.001176	0	0,26309,0,34	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Cgt/Tgt	R186C	M	0.000415	0.05783	2	2	C>T
ERR5749277	27389	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17281	0.001157	0	15,17212,0,21	.	.	.	.	.	.	.	0.001157	0.899553	2	1	C>T
ERR5749277	27476	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	35121	0.001082	0	17808,17266,20,19	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	aCa/aTa	T28I	orf7a	0.000547	0.22827	4	2	C>T
ERR5749277	27641	PASS	C	T	17804	0.878286	0	1,0,17732,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	tCa/tTa	S83L	orf7a	0.000983	0.911213	2	2	C>T
ERR5749277	27807	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	17838	5.05E-4	0	4,17825,0,9	HIGH	NONE	FRAME_SHIFT	ORF7b	ctattc/	LF18	orf7b	0.000505	0.965257	2	2	CTA>C
ERR5749277	27972	PASS	C	T	6181	0.906326	0	0,0,6105,56	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749277	28048	PASS	G	T	6129	0.909121	0	0,12,0,6108	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749277	28111	PASS	A	G	22964	0.979315	0	3,1,16816,6135	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749277	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16817	0.001903	0	16741,4,33,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749277	28270	PASS	TA	T	32549	0.994869	330	161,11,16604,15778	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749277	28280	PASS	G	C	32511	0.933776	41	26,4,16648,15751	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749277	28281	PASS	A	T	32511	0.914367	26	25,7,16653,15754	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749277	28282	PASS	T	A	32511	0.908985	67	45,7,16597,15772	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749277	28407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TACCCAATA	T	16840	6.53E-4	0	7,16822,0,11	HIGH	NONE	FRAME_SHIFT	N	cccaataat/	PNN46	N	0.000382	0.179673	1	1	TACCCAATA>T
ERR5749277	28603	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	38795	0.002268	0	19335,19177,49,51	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F110	N	0.000427	0.883357	2	2	C>T
ERR5749277	28881	PASS	G	A	9552	0.720687	18	6,0,4675,4697	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749277	28882	PASS	G	A	9552	0.811872	15	6,0,4765,4669	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749277	28883	PASS	G	C	9552	0.940117	0	1,0,4779,4758	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749277	28977	PASS	C	T	4866	0.929716	2147483647	0,0,0,4857	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749277	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	52901	8.7E-4	1	26570,26244,34,30	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749277	29543	PASS	G	C	14727	0.968833	0	0,1,6596,8107	.	.	.	.	.	.	.	0.001058	0.973475	3	1	G>C
ERR5749277	29555	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	14731	6.11E-4	31	6592,8130,9,0	.	.	.	.	.	.	.	0.000611	0.957048	3	1	CAG>C
ERR5749277	29769	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6599	0.002576	0	0,6573,0,18	.	.	.	.	.	.	.	0.001999	0.945205	1	1	C>T
ERR5749278	71	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	1249	0.008006	0	1237,0,12,0	.	.	.	.	.	.	.	0.002088	0.926791	2	1	C>A
ERR5749278	203	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1168	0.007705	0	1153,2,9,0	.	.	.	.	.	.	.	0.001818	0.942611	1	1	C>T
ERR5749278	241	PASS	C	T	2322	0.867786	0	0,0,1156,1159	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749278	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	7059	0.001842	0	7038,0,13,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749278	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGTT	A	7059	0.001417	0	7038,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	catggtcatgttatggtt/	HGHVMV81	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGTT>A
ERR5749278	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	7058	0.00425	0	7027,0,30,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749278	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	7057	0.002692	0	6577,0,404,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749278	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	7057	0.0017	0	7045,0,12,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749278	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	7057	0.002409	0	7040,0,17,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttatg/gtg	VM84V	leader	0.000554	0.991848	4	1	GTTA>G
ERR5749278	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATGG	T	7061	0.003965	0	7028,4,28,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	atggtt/	MV85	leader	0.000587	0.476744	4	1	TATGG>T
ERR5749278	520	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTT	G	7061	0.001133	0	7049,4,8,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttgag/gag	VE86E	leader	0.000583	0.051154	1	1	GGTT>G
ERR5749278	635	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7075	0.004947	0	0,7031,0,44	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgt/Tgt	R124C	leader	0.00148	0.880435	1	1	C>T
ERR5749278	656	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	7076	0.003816	0	1,7041,0,29	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gct/Cct	A131P	leader	0.001202	0.131429	1	1	G>C
ERR5749278	680	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GATCT	G	13609	6.61E-4	28	6525,7075,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gatcta/	DL139	leader	0.000661	0.166667	3	2	GATCT>G
ERR5749278	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13609	0.005217	59	6464,7045,55,17	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L140	leader	0.000316	0.135802	3	2	C>T
ERR5749278	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	13609	0.001029	9	6524,7071,10,4	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749278	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	6533	0.001684	0	0,6522,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L35	nsp2	0.000551	0.081967	3	2	CT>C
ERR5749278	913	PASS	C	T	6533	0.910455	0	0,2,0,6518	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749278	1594	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8046	0.027343	0	0,7803,0,238	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S263	nsp2	0.0019	0.963177	1	1	C>T
ERR5749278	1782	PASS	G	A	125	0.744	0	0,0,62,61	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tGt/tAt	C326Y	nsp2	0.001356	0.744	2	1	G>A
ERR5749278	2144	PASS	G	T	5192	0.752119	0	0,70,0,5118	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtc/Ttc	V447F	nsp2	0.004278	0.752119	2	1	G>T
ERR5749278	2189	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5196	0.017321	0	1,5099,0,91	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Ttt	L462F	nsp2	0.000491	0.960061	3	2	C>T
ERR5749278	2706	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19105	0.003298	0	9557,9454,41,38	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T634I	nsp2	0.000591	0.821437	1	1	C>T
ERR5749278	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	19115	0.001569	1573	9547,8917,12,578	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749278	3037	PASS	C	T	9397	0.827392	21	0,7,4697,4628	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749278	3096	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4728	0.002961	0	0,4701,0,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCa/tTa	S126L	nsp3	0.001801	0.932094	1	1	C>T
ERR5749278	3177	PASS	C	T	12584	0.886364	4	0,1,7847,4721	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P153L	nsp3	0.000773	0.96008	3	2	C>T
ERR5749278	3267	PASS	C	T	7856	0.969705	0	1,0,7851,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749278	3802	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	10147	0.001478	29	4891,5239,1,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gaT/gaA	D361E	nsp3	0.000554	0.064198	4	2	T>A
ERR5749278	3832	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	4892	0.001635	0	4884,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L373	nsp3	0.000689	0.327273	4	2	CT>C
ERR5749278	3961	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	4877	0.00123	0	4872,0,6,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K415	nsp3	0.000417	0.869983	2	2	CA>C
ERR5749278	4529	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTTTAC	T	5785	0.001556	0	2,5774,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	tacttt/	YF605	nsp3	0.000527	0.402778	3	1	TTTTAC>T
ERR5749278	4668	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12187	0.003036	0	12139,1,39,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S650F	nsp3	0.002266	0.970109	2	1	C>T
ERR5749278	4693	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	12186	0.001477	0	12168,0,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/	V659	nsp3	0.000654	0.078873	1	1	TG>T
ERR5749278	5388	PASS	C	A	3137	0.962703	2147483647	0,0,3136,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749278	5512	PASS	C	T	3137	0.953777	2147483647	0,0,0,3134	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N931	nsp3	0.002299	0.987013	1	1	C>T
ERR5749278	5986	PASS	C	T	7527	0.977946	2147483647	0,0,7525,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749278	6543	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9002	0.001888	0	8978,0,17,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T1275I	nsp3	0.001888	0.955595	1	1	C>T
ERR5749278	6606	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9002	0.005554	0	8944,0,50,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S1296F	nsp3	0.002262	0.945412	1	1	C>T
ERR5749278	6954	PASS	T	C	10003	0.817855	0	0,1,11,9941	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749278	6990	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	10014	0.001897	0	0,9995,0,19	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L1425	nsp3	0.000504	0.101156	4	2	CT>C
ERR5749278	8084	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	10983	0.001548	0	10969,0,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1790	nsp3	0.000543	0.923413	4	2	GA>G
ERR5749278	8917	PASS	C	T	15594	0.201937	3	9547,2779,2542,712	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F121	nsp4	0.004594	0.201937	1	1	C>T
ERR5749278	9430	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1429	0.006998	0	0,1416,0,10	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I292	nsp4	0.001411	0.960894	1	1	C>T
ERR5749278	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	13167	0.004785	27	11674,1430,63,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749278	10263	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	29884	8.03E-4	3	14943,14857,32,38	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A70D	3Cpro	0.000593	0.192529	3	2	C>A
ERR5749278	10595	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	10377	0.001446	0	0,10348,0,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F181L	3Cpro	0.000964	0.076408	1	1	T>C
ERR5749278	10704	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	12951	0.001776	18	2555,10369,0,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aGg/aAg	R217K	3Cpro	0.000771	0.158537	2	1	G>A
ERR5749278	11082	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	17194	0.003141	0	17149,0,54,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000427	0.179468	2	1	TG>T
ERR5749278	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	17194	0.025416	0	16668,0,472,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749278	11104	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	17189	0.001222	0	17116,0,24,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccT/ccC	P44	nsp6	0.000866	0.675414	2	1	T>C
ERR5749278	11264	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	17191	0.001454	0	0,17149,0,28	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Ttg/Ctg	L98	nsp6	0.001454	0.956786	1	1	T>C
ERR5749278	11287	PASS	GTCTGGTTTT	G	17191	0.994648	0	0,92,0,17099	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749278	11575	PASS	C	T	6412	0.921085	33	1,2,0,6398	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F201	nsp6	0.912731	0.921085	1	1	C>T
ERR5749278	11750	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7364	0.004481	1	3733,3571,28,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L260F	nsp6	0.001019	0.70989	2	1	C>T
ERR5749278	12374	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11713	0.001622	0	0,11686,0,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Ttt	L95F	nsp8	0.001063	0.932196	1	1	C>T
ERR5749278	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	15275	0.001309	0	15218,0,20,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749278	13458	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9978	0.003909	0	9930,1,41,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCg/tTg	S6L	nsp11	0.001017	0.058608	4	2	C>T
ERR5749278	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19921	0.001456	0	9945,9917,17,17	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749278	13536	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9965	0.002208	0	0,9930,0,28	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y32	RdRp	0.002208	0.799427	1	1	C>T
ERR5749278	14168	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	10825	9.24E-4	0	0,10815,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	atatta/	IL244	RdRp	0.000479	0.314961	1	1	CTA>C
ERR5749278	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	7149	0.006015	1997	6940,79,6,122	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749278	14408	PASS	C	T	13822	0.841846	1	2,3,6913,6811	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749278	14676	PASS	C	T	6221	0.826234	0	1,0,6209,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749278	15279	PASS	C	T	9709	0.899887	0	1,0,9694,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749278	16176	PASS	T	C	10872	0.982616	3	1,0,4591,6278	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749278	16794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	30073	0.001097	92	15764,14276,33,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gta/	V187	helicase	0.000354	0.077626	2	2	TG>T
ERR5749278	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	15796	0.001456	0	15773,0,23,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749278	17766	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	8574	0.001866	0	8558,0,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F511	helicase	0.000768	0.920632	2	2	CT>C
ERR5749278	18357	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	9060	0.001545	0	9033,0,16,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccT/ccC	P106	ExoN	0.001226	0.057597	1	1	T>C
ERR5749278	18501	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9026	0.001883	0	11,8965,0,17	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y154	ExoN	0.000336	0.857143	4	2	C>T
ERR5749278	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	25413	7.48E-4	0	25394,0,19,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749278	18747	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25406	0.002598	0	25280,0,82,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V236	ExoN	0.000375	0.982946	4	2	C>T
ERR5749278	18761	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	25399	0.001142	0	25357,0,36,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTg/aGg	M241R	ExoN	0.001048	0.251353	3	1	T>G
ERR5749278	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9481	0.004324	0	9432,0,42,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749278	20233	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19341	0.004498	0	19246,0,88,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ccc/Tcc	P205S	endoR	0.000964	0.980008	2	1	C>T
ERR5749278	20235	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	19341	0.001655	0	19309,0,32,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	agg/	R206	endoR	0.000596	0.925795	3	2	CA>C
ERR5749278	21658	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9068	0.002757	51	0,9040,2,23	LOW	SILENT	SYNONYMOUS_CODING	S	ttC/ttT	F32	S	0.001649	0.937508	2	2	C>T
ERR5749278	21707	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20044	0.001048	79	10972,9039,0,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Cat/Tat	H49Y	S	0.001048	0.072032	1	1	C>T
ERR5749278	21764	PASS	ATACATG	A	10975	0.994715	0	58,0,10917,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749278	21990	PASS	TTTA	T	10979	0.998543	0	0,16,1,10962	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749278	22001	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	AC	24949	5.21E-4	30	13959,10977,13,0	HIGH	NONE	FRAME_SHIFT	S	aaa/aCaa	K147T?	S	0.000521	0.32037	2	2	A>AC
ERR5749278	22290	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	13972	5.73E-4	0	0,13964,0,8	HIGH	NONE	FRAME_SHIFT	S	tta/	L244	S	0.000389	0.578006	2	2	CT>C
ERR5749278	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	13589	0.001619	0	0,13561,0,23	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749278	23063	PASS	A	T	11642	0.864542	0	0,1,6,11581	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749278	23271	PASS	C	A	9788	0.922456	2147483647	0,0,9777,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749278	23403	PASS	A	G	9791	0.967215	0	0,2,0,9786	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749278	23604	PASS	C	A	10738	0.933693	0	9,0,10724,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749278	23709	PASS	C	T	10723	0.935093	0	0,7,0,10700	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749278	23758	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10742	0.001489	0	0,10720,0,16	LOW	SILENT	SYNONYMOUS_CODING	S	acC/acT	T732	S	0.001489	0.964055	1	1	C>T
ERR5749278	24506	PASS	T	G	10565	0.976526	0	2,0,10561,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749278	24914	PASS	G	C	39318	0.960705	0	0,0,19599,19702	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749278	25350	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	19759	0.001468	0	19715,1,30,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCa/cAa	P1263Q	S	0.000626	0.97904	4	2	C>A
ERR5749278	25496	PASS	T	C	39361	0.96555	0	0,0,19639,19699	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aTa/aCa	I35T	orf3a	0.000369	0.96555	3	2	T>C
ERR5749278	25555	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	19744	0.001469	0	0,19715,0,29	HIGH	NONE	FRAME_SHIFT	ORF3a	ttt/	F56	orf3a	0.000552	0.900573	5	2	GT>G
ERR5749278	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	3586	0.002231	0	3578,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749278	26151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	23069	0.001214	0	0,23013,0,42	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	tcC/tcA	S253	orf3a	0.000501	0.913698	4	2	C>A
ERR5749278	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	23072	8.67E-4	0	0,23052,0,20	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749278	26526	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	7640	0.001832	0	0,7615,0,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Gca/Cca	A2P	M	0.001224	0.951192	3	1	G>C
ERR5749278	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGT	G	10146	8.87E-4	0	0,10132,0,9	HIGH	NONE	FRAME_SHIFT	M	cttgta/	LV87	M	0.000483	0.053997	3	1	GCTTGT>G
ERR5749278	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	10147	0.002267	0	0,10111,0,23	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749278	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	G	10147	0.001281	0	0,10111,0,13	HIGH	NONE	FRAME_SHIFT	M	cttgtaggcttgatgtggctcagctacttcattgcttctttc/	LVGLMWLSYFIASF87	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT>G
ERR5749278	26895	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26023	0.002306	0	25948,5,62,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Cat/Tat	H125Y	M	0.000874	0.97046	1	1	C>T
ERR5749278	27382	PASS	G	C	18977	0.363914	0	0,11504,0,7448	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF6	Gat/Cat	D61H	orf6	0.001236	0.927964	2	2	G>C
ERR5749278	27383	PASS	A	T	18978	0.360575	0	0,11542,0,7425	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF6	gAt/gTt	D61V	orf6	0.001454	0.928985	1	1	A>T
ERR5749278	27384	PASS	T	C	18978	0.35009	0	0,11505,0,7438	LOW	SILENT	SYNONYMOUS_CODING	ORF6	gaT/gaC	D61	orf6	0.00154	0.931035	3	3	T>C
ERR5749278	27532	PASS	C	T	14187	0.393177	8	8519,4,5655,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Cat/Tat	H47Y	orf7a	0.001165	0.982473	2	1	C>T
ERR5749278	27577	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14183	0.002468	0	14141,0,40,0	HIGH	NONSENSE	STOP_GAINED	ORF7a	Caa/Taa	Q62*	orf7a	0.000614	0.952205	4	2	C>T
ERR5749278	27972	PASS	C	T	4501	0.91002	0	0,0,4458,27	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749278	28048	PASS	G	T	4472	0.933363	0	0,7,0,4458	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749278	28111	PASS	A	G	21991	0.979492	0	5,1,17504,4474	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749278	28239	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTGTTTTAGATT	G	17512	9.71E-4	0	17496,0,17,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF8	gttgttttagatttc/gtc	VVLDF116V	orf8	0.000417	0.984998	9	2	GTTGTTTTAGATT>G
ERR5749278	28253	PASS	C	T	17497	0.050123	0	16498,0,940,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749278	28270	PASS	TA	T	33894	0.995132	431	171,4,17274,16455	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749278	28280	PASS	G	C	33824	0.933538	59	21,0,17302,16441	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749278	28281	PASS	A	T	33824	0.910833	19	23,8,17304,16441	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749278	28282	PASS	T	A	33825	0.912106	12	28,14,17276,16441	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749278	28292	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	34820	7.18E-4	0	17348,17435,12,13	HIGH	NONE	FRAME_SHIFT	N	aat/	N8	N	0.000304	0.055324	4	2	CAA>C
ERR5749278	28406	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTACCCAATA	T	17518	5.14E-4	0	4,17505,0,9	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	N	ttacccaataat/tat	LPNN45Y	N	0.00043	0.921074	3	2	TTACCCAATA>T
ERR5749278	28407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TACCCAATA	T	17518	0.001655	0	4,17485,0,29	HIGH	NONE	FRAME_SHIFT	N	cccaataat/	PNN46	N	0.000382	0.179673	1	1	TACCCAATA>T
ERR5749278	28603	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	36406	0.002829	0	18126,18000,56,56	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F110	N	0.000427	0.883357	2	2	C>T
ERR5749278	28881	PASS	G	A	868	0.786866	0	0,0,432,425	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749278	28882	PASS	G	A	868	0.831797	0	0,0,433,433	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749278	28883	PASS	G	C	868	0.956221	0	0,0,432,433	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749278	28977	PASS	C	T	435	0.926437	2147483647	0,0,0,431	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749278	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	31668	0.001105	0	15911,15712,19,19	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749279	241	PASS	C	T	18701	0.864499	0	1,2,9293,9343	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749279	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	12599	7.94E-4	0	12592,0,10,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749279	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	12599	0.001191	0	12580,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749279	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12592	0.002859	0	11644,1,905,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749279	676	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	37549	7.99E-4	5	24914,12593,18,14	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G137	leader	0.000799	0.919273	2	1	C>T
ERR5749279	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	37552	3.46E-4	21	24924,12611,13,0	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749279	913	PASS	C	T	24918	0.918974	0	0,16,0,24873	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749279	1510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	26073	0.004679	0	0,25734,0,132	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G235	nsp2	0.002159	0.937304	1	1	T>C
ERR5749279	1968	PASS	C	T	60	0.95	0	0,0,59,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T388I	nsp2	0.001009	0.95	2	2	C>T
ERR5749279	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	88161	0.001248	2147483647	43980,41389,94,2460	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749279	3037	PASS	C	T	23420	0.81392	52	1,21,11695,11541	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749279	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	11839	0.001689	533	10,11793,21,5	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749279	3177	PASS	C	T	36678	0.901603	0	5,2,24843,11784	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P153L	nsp3	0.000773	0.96008	3	2	C>T
ERR5749279	3267	PASS	C	T	24871	0.969	0	4,0,24856,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749279	3671	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	28654	9.42E-4	0	14293,14178,17,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E318K	nsp3	0.000351	0.0625	6	2	G>A
ERR5749279	5388	PASS	C	A	6886	0.959773	2147483647	0,0,6884,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749279	5986	PASS	C	T	15543	0.977997	0	1,0,15530,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749279	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14565	0.001785	0	0,14401,0,34	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749279	6954	PASS	T	C	28037	0.828869	0	0,5,2,27892	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749279	7528	PASS	C	T	19296	0.911536	0	0,3,20,19243	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V1603	nsp3	0.002527	0.916131	1	1	C>T
ERR5749279	7564	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	19324	6.21E-4	0	0,19311,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/	Y1617	nsp3	0.000586	0.056194	4	2	CT>C
ERR5749279	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	22006	0.002545	0	21922,0,69,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749279	11287	PASS	GTCTGGTTTT	G	21996	0.998409	0	0,33,0,21961	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749279	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	19747	0.001114	0	19704,0,22,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749279	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	35997	0.001445	0	17972,17933,27,28	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749279	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	13614	0.00404	2147483647	13299,97,9,202	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749279	14408	PASS	C	T	26477	0.839521	4	3,6,13208,13070	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749279	14676	PASS	C	T	16113	0.791535	0	9,0,16052,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749279	15240	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26601	0.001053	0	26527,31,29,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N600	RdRp	0.000934	0.931284	2	2	C>T
ERR5749279	15279	PASS	C	T	26567	0.894719	0	3,0,26519,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749279	16176	PASS	T	C	23043	0.983596	0	0,0,10467,12569	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749279	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	24681	7.29E-4	0	24661,2,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749279	19329	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	22178	0.001217	0	22128,0,29,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcC	A430	ExoN	0.001217	0.228916	1	1	T>C
ERR5749279	19698	PASS	C	T	23863	0.953778	0	3,0,23836,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I26	endoR	0.02305	0.953778	1	1	C>T
ERR5749279	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34431	0.002323	0	34327,0,83,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749279	20544	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34775	8.34E-4	0	34704,7,31,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S308	endoR	0.000834	0.975334	2	1	C>T
ERR5749279	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34761	9.21E-4	0	34679,1,32,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749279	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	41954	0.001025	1	20551,20918,24,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749279	21764	PASS	ATACATG	A	15366	0.997397	0	40,0,15326,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749279	21990	PASS	TTTA	T	15369	0.998308	0	0,26,4,15339	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749279	22450	PASS	C	T	12011	0.803846	0	2,0,11820,63	LOW	SILENT	SYNONYMOUS_CODING	S	ctC/ctT	L296	S	0.00215	0.803846	1	1	C>T
ERR5749279	23063	PASS	A	T	14559	0.866474	2147483647	0,0,0,14501	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749279	23271	PASS	C	A	25563	0.921292	0	4,0,25525,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749279	23403	PASS	A	G	25552	0.972331	0	0,5,0,25537	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749279	23604	PASS	C	A	18416	0.948632	0	12,0,18390,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749279	23709	PASS	C	T	18396	0.945532	0	0,7,5,18360	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749279	24237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13607	0.001323	0	13574,0,18,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gTt	A892V	S	0.001242	0.889739	1	1	C>T
ERR5749279	24506	PASS	T	G	21037	0.975614	0	5,0,21026,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749279	24914	PASS	G	C	38637	0.960789	0	0,0,19227,19388	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749279	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	30161	0.002652	146	20160,9889,95,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749279	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	28148	0.001279	303	28045,16,26,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749279	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	28117	0.001103	0	28086,0,31,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749279	27209	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	21109	0.004453	0	20995,1,99,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF6	cAt/cTt	H3L	orf6	0.00088	0.957103	3	2	A>T
ERR5749279	27425	PASS	C	T	21099	0.856486	0	0,5,0,21042	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	aCa/aTa	T11I	orf7a	0.001016	0.856486	2	1	C>T
ERR5749279	27972	PASS	C	T	13490	0.910897	40	2,2,13404,50	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749279	28048	PASS	G	T	13458	0.916778	0	0,15,4,13430	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749279	28087	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13469	0.001782	0	8,13434,0,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	gCt/gTt	A65V	orf8	0.001718	0.963754	2	1	C>T
ERR5749279	28111	PASS	A	G	34668	0.978914	1	4,4,21197,13452	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749279	28198	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	21206	0.002594	0	21125,1,68,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tGt/tTt	C102F	orf8	0.000718	0.94386	4	2	G>T
ERR5749279	28270	PASS	TA	T	41051	0.994836	509	216,8,20897,19942	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749279	28280	PASS	G	C	40984	0.940099	21	13,2,20960,19926	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749279	28281	PASS	A	T	40984	0.916699	20	22,7,20955,19932	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749279	28282	PASS	T	A	40986	0.914263	6	26,16,20910,19935	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749279	28881	PASS	G	A	22124	0.76573	15	6,0,10939,10884	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749279	28882	PASS	G	A	22124	0.830591	14	8,1,11053,10850	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749279	28883	PASS	G	C	22126	0.944409	0	2,1,11070,11008	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749279	28977	PASS	C	T	11261	0.935263	0	0,1,5,11239	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749279	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	39870	8.78E-4	136	28605,11207,5,34	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749279	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	56794	9.86E-4	0	28512,28198,31,33	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749280	241	PASS	C	T	16785	0.851772	0	0,1,8340,8358	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749280	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	11211	0.001249	0	11198,0,14,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749280	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	11211	0.001873	0	11183,0,21,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749280	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	11201	0.001607	0	10486,1,661,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749280	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	11201	8.93E-4	0	11190,1,10,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749280	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	11197	0.001161	0	11181,1,13,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749280	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	30990	5.81E-4	2	19745,11224,13,5	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749280	913	PASS	C	T	19749	0.912654	0	0,15,0,19708	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749280	3037	PASS	C	T	16579	0.81935	42	2,20,8282,8175	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749280	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	8356	0.002154	502	2,8331,18,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749280	3267	PASS	C	T	18381	0.97122	0	2,0,18367,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749280	4764	PASS	A	G	13158	0.932665	0	2,0,13142,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cAt/cGt	H682R	nsp3	0.000673	0.93404	4	2	A>G
ERR5749280	5388	PASS	C	A	5714	0.957298	2147483647	0,0,5711,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749280	5628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19050	0.008766	0	18867,0,174,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aTg	T970M	nsp3	0.000561	0.973644	3	2	C>T
ERR5749280	5986	PASS	C	T	10116	0.978153	0	2,0,10112,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749280	6954	PASS	T	C	20021	0.815244	0	0,2,1,19910	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749280	7564	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	15123	6.61E-4	0	0,15113,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/	Y1617	nsp3	0.000586	0.056194	4	2	CT>C
ERR5749280	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	30101	0.001096	117	13241,16827,33,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749280	10642	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	15468	0.003297	0	2,15391,0,68	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acG/acT	T196	3Cpro	0.001264	0.951979	3	1	G>T
ERR5749280	11082	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	17227	0.001277	0	17211,0,22,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000427	0.179468	2	1	TG>T
ERR5749280	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	17227	0.015035	0	16910,0,287,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749280	11287	PASS	GTCTGGTTTT	G	17221	0.998084	0	0,33,0,17188	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749280	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	30740	0.001171	10	19288,11393,19,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749280	12809	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15367	0.001562	0	15336,0,27,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Ttt	L42F	nsp9	0.001562	1	1	1	C>T
ERR5749280	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29155	0.001441	0	14557,14525,23,23	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749280	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12118	0.004621	2147483647	11836,87,3,190	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749280	14408	PASS	C	T	23588	0.846193	9	1,5,11779,11671	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749280	14676	PASS	C	T	12545	0.708808	0	5,0,12496,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749280	14724	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12534	0.001995	0	12482,9,29,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F428	RdRp	0.000952	0.789267	3	2	C>T
ERR5749280	15279	PASS	C	T	21914	0.890025	0	4,0,21879,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749280	16176	PASS	T	C	18825	0.978539	0	1,1,8434,10384	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749280	18744	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20101	0.001343	0	20042,0,27,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y235	ExoN	0.000912	0.953624	2	2	C>T
ERR5749280	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24831	0.002014	0	24768,0,52,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749280	21764	PASS	ATACATG	A	10256	0.99415	0	60,0,10196,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749280	21990	PASS	TTTA	T	10258	0.99766	0	0,24,3,10231	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749280	23063	PASS	A	T	10091	0.868497	0	0,3,1,10030	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749280	23271	PASS	C	A	20689	0.925903	0	3,0,20672,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749280	23403	PASS	A	G	20692	0.965832	0	0,6,0,20677	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749280	23604	PASS	C	A	12602	0.943739	0	9,0,12580,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749280	23709	PASS	C	T	12598	0.937689	0	0,2,5,12578	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749280	24506	PASS	T	G	16703	0.970365	0	8,0,16691,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749280	24914	PASS	G	C	29414	0.959781	3	1,0,14640,14752	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749280	25350	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14126	0.002619	0	14083,3,38,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCa/cTa	P1263L	S	0.000626	0.97904	4	2	C>T
ERR5749280	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	23127	0.001297	192	23042,20,23,9	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749280	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	9763	0.001434	0	0,9748,0,14	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749280	27391	PASS	A	C	14652	0.938165	0	0,18,25,14608	.	.	.	.	.	.	.	0.000702	0.938682	3	1	A>C
ERR5749280	27972	PASS	C	T	8637	0.906912	0	1,0,8574,43	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749280	28048	PASS	G	T	8601	0.923614	0	0,13,0,8587	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749280	28111	PASS	A	G	25722	0.978307	2	2,0,17108,8607	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749280	28250	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TCTG	17094	9.36E-4	0	17011,2,16,0	MODERATE	NONE	CODON_INSERTION	ORF8	ttc/CTGttc	F120LF	orf8	0.000494	0.993968	5	3	T>TCTG
ERR5749280	28250	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TG	17094	0.003803	0	17011,2,65,0	HIGH	NONE	FRAME_SHIFT	ORF8	ttc/Gttc	F120V?	orf8	0.000494	0.993968	5	3	T>TG
ERR5749280	28253	PASS	C	T	17069	0.944519	0	101,0,16944,2	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749280	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	17069	0.005624	0	16971,2,96,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749280	28254	PASS	A	C	17069	0.903099	0	55,0,16902,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	Atc/Ctc	I121L	orf8	0.000541	0.914398	3	2	A>C
ERR5749280	28270	PASS	TA	T	33271	0.994019	486	194,5,16856,16216	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749280	28271	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AA	A	33269	9.02E-4	86	17014,16223,30,0	.	.	.	.	.	.	.	0.000482	0.924941	3	2	AA>A
ERR5749280	28280	PASS	G	C	33204	0.936363	27	10,0,16922,16193	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749280	28281	PASS	A	T	33204	0.916456	19	18,5,16914,16197	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749280	28282	PASS	T	A	33206	0.914413	17	25,10,16879,16212	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749280	28881	PASS	G	A	16002	0.755656	24	9,0,7893,7895	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749280	28882	PASS	G	A	15999	0.836177	18	7,0,7997,7871	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749280	28883	PASS	G	C	15998	0.940305	0	1,0,8011,7966	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749280	28977	PASS	C	T	8144	0.935781	0	0,0,1,8128	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749280	29095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20785	0.001155	0	20737,3,26,0	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F274	N	0.000792	0.961279	2	2	C>T
ERR5749280	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	41253	0.001479	0	20709,20455,36,35	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749281	241	PASS	C	T	9911	0.860458	0	1,1,4929,4939	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749281	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	8948	0.002459	0	8930,0,22,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749281	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	8948	8.94E-4	0	8907,0,8,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749281	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	8948	0.002682	0	8907,0,24,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749281	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	8943	0.001454	0	8406,2,457,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749281	656	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	8969	0.001784	0	4,8944,0,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gct/Cct	A131P	leader	0.001202	0.131429	1	1	G>C
ERR5749281	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	21079	0.001091	32	12090,8962,21,2	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749281	913	PASS	C	T	12109	0.920307	0	0,6,0,12088	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749281	1027	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	9991	0.002502	75	9935,10,21,4	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccT/ccC	P74	nsp2	0.001454	0.276316	1	1	T>C
ERR5749281	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	35426	0.001242	2625	17649,16587,35,1032	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749281	3037	PASS	C	T	12456	0.872832	9	0,3,6220,6197	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749281	3267	PASS	C	T	11854	0.968534	2147483647	0,0,11845,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749281	5388	PASS	C	A	4344	0.963168	2147483647	0,0,4344,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749281	5986	PASS	C	T	7784	0.972636	2147483647	0,0,7781,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749281	6954	PASS	T	C	11607	0.822952	0	0,1,0,11531	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749281	8772	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12399	0.001532	0	12340,1,22,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T73I	nsp4	0.001457	0.166667	1	1	C>T
ERR5749281	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	19523	0.001434	68	10934,8561,28,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749281	11287	PASS	GTCTGGTTTT	G	11224	0.996614	0	0,36,0,11186	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749281	12388	PASS	T	C	13471	0.961473	0	0,2,0,13458	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaT/gaC	D99	nsp8	0.001786	0.961473	1	1	T>C
ERR5749281	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	13104	0.00145	0	13067,0,20,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749281	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19024	0.001156	0	9497,9474,13,13	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749281	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	11256	0.005508	2147483647	10994,69,4,181	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749281	14408	PASS	C	T	21910	0.851392	6	1,4,10925,10844	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749281	14676	PASS	C	T	7333	0.712123	0	3,0,7285,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749281	14805	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7337	0.001908	0	0,7315,0,18	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y455	RdRp	0.001051	0.904964	2	2	C>T
ERR5749281	15279	PASS	C	T	12070	0.89594	0	5,0,12047,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749281	15493	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	12072	0.001408	0	0,12046,0,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gcc/Ccc	A685P	RdRp	0.001408	0.076816	3	2	G>C
ERR5749281	16176	PASS	T	C	13028	0.981808	0	0,0,7008,6009	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749281	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAA	G	13483	8.16E-4	0	13461,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GAA>G
ERR5749281	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	17192	6.4E-4	0	17181,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749281	18756	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	17188	7.56E-4	0	17175,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F240	ExoN	0.000392	0.942688	3	2	GT>G
ERR5749281	19962	PASS	G	T	19092	0.971716	0	1,0,19081,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acG/acT	T114	endoR	0.015202	0.971716	1	1	G>T
ERR5749281	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19091	0.001205	0	19057,0,25,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749281	20930	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12139	0.00346	0	12086,1,43,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aTg	T91M	MethTr	0.000902	0.95585	2	2	C>T
ERR5749281	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19019	0.001314	0	9289,9490,14,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749281	21764	PASS	ATACATG	A	8218	0.993794	0	51,0,8167,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749281	21846	PASS	C	T	16331	0.771661	33	1,14,8116,8055	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCt/aTt	T95I	S	0.001104	0.788523	1	1	C>T
ERR5749281	21990	PASS	TTTA	T	8224	0.998176	0	0,15,1,8208	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749281	23040	PASS	A	G	9365	0.933049	0	0,1,2,9347	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cAa/cGa	Q493R	S	0.001893	0.933049	1	1	A>G
ERR5749281	23063	PASS	A	T	9400	0.854574	0	0,2,0,9346	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749281	23271	PASS	C	A	12353	0.921719	0	0,0,12342,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749281	23403	PASS	A	G	12353	0.968591	0	0,4,0,12342	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749281	23604	PASS	C	A	10471	0.941648	0	13,0,10448,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749281	23709	PASS	C	T	10459	0.938426	0	0,5,2,10430	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749281	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	19800	5.56E-4	6	9325,10464,3,8	HIGH	NONE	FRAME_SHIFT	S	ttg/	L753	S	0.000334	0.080808	2	2	CT>C
ERR5749281	24320	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	8457	0.002838	0	0,8429,0,24	HIGH	NONE	FRAME_SHIFT	S	aaa/	K921	S	0.000763	0.138365	4	2	CA>C
ERR5749281	24506	PASS	T	G	9612	0.975759	0	2,0,9608,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749281	24914	PASS	G	C	26172	0.958391	0	0,0,13039,13115	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749281	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	11361	0.001936	236	11263,18,11,11	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749281	26526	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	6716	0.002382	0	1,6694,0,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Gca/Aca	A2T	M	0.001224	0.951192	3	1	G>A
ERR5749281	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	8677	9.22E-4	0	0,8666,0,8	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749281	27972	PASS	C	T	7069	0.905079	0	0,0,7010,37	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749281	28048	PASS	G	T	7035	0.919972	0	0,6,0,7021	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749281	28111	PASS	A	G	18460	0.977519	8	1,3,11416,7034	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749281	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11413	0.00149	0	11370,1,18,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749281	28270	PASS	TA	T	22159	0.994494	288	119,4,11256,10781	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749281	28280	PASS	G	C	22108	0.937308	5	9,4,11282,10772	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749281	28281	PASS	A	T	22108	0.91252	38	20,2,11276,10772	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749281	28282	PASS	T	A	22113	0.906571	8	16,8,11239,10780	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749281	28881	PASS	G	A	11025	0.770975	6	3,0,5457,5452	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749281	28882	PASS	G	A	11025	0.836372	9	4,0,5504,5427	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749281	28883	PASS	G	C	11024	0.947206	3	2,0,5515,5501	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749281	28977	PASS	C	T	5610	0.924777	0	0,1,0,5599	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749281	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	40125	8.47E-4	1	20156,19914,24,21	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749282	241	PASS	C	T	338	0.878698	0	0,0,169,169	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749282	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	924	0.008658	0	906,10,8,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749282	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	924	0.00974	0	905,10,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749282	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	903	0.005537	0	898,0,5,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttatg/gtg	VM84V	leader	0.000554	0.991848	4	1	GTTA>G
ERR5749282	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	2027	0.012827	67	1087,914,26,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749282	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	2029	0.003943	20	1105,916,8,0	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749282	913	PASS	C	T	1113	0.902965	0	0,1,0,1110	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749282	1230	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AGT	A	2640	0.007197	0	0,2621,0,19	HIGH	NONE	FRAME_SHIFT	ORF1ab	tgtgat/	CD143	nsp2	0.00129	0.969658	2	2	AGT>A
ERR5749282	1594	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1540	0.007792	0	9,1516,0,14	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S263	nsp2	0.0019	0.963177	1	1	C>T
ERR5749282	1684	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4383	0.003194	0	4366,0,14,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I293	nsp2	0.000638	0.973136	2	2	C>T
ERR5749282	2084	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1120	0.008929	0	554,555,5,5	HIGH	NONSENSE	STOP_GAINED	ORF1ab	Cag/Tag	Q427*	nsp2	0.001943	0.253112	1	1	C>T
ERR5749282	3037	PASS	C	T	1602	0.810237	3	0,1,800,787	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749282	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	807	0.007435	0	0,799,0,7	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tCg	L142S	nsp3	0.001349	0.761905	2	1	T>C
ERR5749282	3177	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2280	0.005263	24	1458,807,14,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P153L	nsp3	0.000773	0.96008	3	2	C>T
ERR5749282	3267	PASS	C	T	1472	0.96875	2147483647	0,0,1470,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749282	4338	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3401	0.003234	20	1026,2354,0,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S540F	nsp3	0.000366	0.051643	2	2	C>T
ERR5749282	4980	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3833	0.005479	51	1653,2159,0,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T754I	nsp3	0.005479	0.982571	1	1	C>T
ERR5749282	5388	PASS	C	A	466	0.957082	2147483647	0,0,466,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749282	5392	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	466	0.012876	0	460,0,6,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N891	nsp3	0.012876	0.944629	2	2	C>T
ERR5749282	5986	PASS	C	T	1850	0.980541	2147483647	0,0,1850,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749282	6568	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	G	2101	0.008567	0	2081,0,19,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gaC/gaG	D1283E	nsp3	0.000975	0.974638	3	3	C>G
ERR5749282	6954	PASS	T	C	3534	0.826542	0	0,1,0,3510	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749282	6982	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3542	0.008187	0	0,3505,0,32	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C1421	nsp3	0.001915	0.911934	1	1	C>T
ERR5749282	7564	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	1853	0.009174	0	0,1836,0,17	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/tTat	Y1617L?	nsp3	0.000586	0.056194	4	2	C>CT
ERR5749282	7658	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	4871	0.002669	28	3004,1853,14,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Att/Ttt	I1647F	nsp3	0.001526	0.055791	1	1	A>T
ERR5749282	8950	PASS	C	T	3170	0.975079	0	1,0,3069,96	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I132	nsp4	0.002808	0.982604	1	1	C>T
ERR5749282	8964	PASS	C	T	3074	0.970072	2147483647	0,0,3059,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCa/tTa	S137L	nsp4	0.000553	0.981649	4	2	C>T
ERR5749282	9532	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3207	0.004054	0	3071,123,13,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F326	nsp4	0.000899	0.966959	1	1	C>T
ERR5749282	9559	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3084	0.005512	0	3065,0,19,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y335	nsp4	0.001348	0.062899	2	2	C>T
ERR5749282	9661	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5934	0.002528	0	3068,2844,8,8	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F369	nsp4	0.000584	0.920378	2	2	C>T
ERR5749282	10156	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4932	0.004663	0	4906,1,25,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D34	3Cpro	0.001207	0.949463	1	1	C>T
ERR5749282	11173	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6605	0.00212	0	6512,55,21,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ctC/ctT	L67	nsp6	0.00115	0.587518	1	1	C>T
ERR5749282	11235	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTAG	C	6582	0.008052	0	0,6529,0,53	MODERATE	NONE	CODON_DELETION	ORF1ab	agt/	S89	nsp6	0.000512	0.942208	2	2	CTAG>C
ERR5749282	11287	PASS	GTCTGGTTTT	G	6583	0.999544	0	0,3,0,6580	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749282	11344	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7780	0.006041	30	1191,6541,0,48	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I124	nsp6	0.001229	0.964849	1	1	C>T
ERR5749282	11690	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGT	G	2291	0.013968	0	2259,0,32,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/	V241	nsp6	0.000953	0.091324	4	2	GGT>G
ERR5749282	11991	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	8954	0.007483	0	8872,0,69,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gAa/gGa	E50G	nsp7	0.003937	0.05063	1	1	A>G
ERR5749282	12025	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8950	0.004916	0	8879,0,49,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S61	nsp7	0.001295	0.948026	1	1	C>T
ERR5749282	13134	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	5548	0.005047	0	5520,0,28,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	atc/	I38	nsp10	0.000682	0.107576	2	2	CA>C
ERR5749282	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	5548	0.006128	0	5514,0,34,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749282	13356	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7690	0.003381	29	2126,5534,16,12	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T111I	nsp10	0.000806	0.091518	1	1	C>T
ERR5749282	14408	PASS	C	T	540	0.811111	0	0,0,270,263	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749282	14676	PASS	C	T	978	0.795501	2147483647	0,0,975,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749282	14688	PASS	C	T	978	0.964213	2147483647	0,0,978,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N416	RdRp	0.000534	0.979772	2	2	C>T
ERR5749282	14805	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	978	0.00818	0	0,968,0,9	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y455	RdRp	0.001051	0.904964	2	2	C>T
ERR5749282	15279	PASS	C	T	1791	0.890006	2147483647	0,0,1790,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749282	16176	PASS	T	C	1797	0.982749	0	0,0,524,1272	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749282	16508	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	4087	0.007096	0	4058,0,29,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L92	helicase	0.000561	0.074909	2	2	GT>G
ERR5749282	16523	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4087	0.00416	0	4069,0,18,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T96I	helicase	0.001196	0.056848	2	1	C>T
ERR5749282	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	4247	0.001884	0	4239,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749282	17418	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	3955	0.00354	0	3206,729,12,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaG/aaC	K394N	helicase	0.001518	0.108696	2	1	G>C
ERR5749282	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	10200	9.8E-4	0	10190,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749282	18747	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10199	0.003922	0	10153,0,44,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V236	ExoN	0.000375	0.982946	4	2	C>T
ERR5749282	19763	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4633	0.004317	0	2295,2301,13,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T48I	endoR	0.000987	0.809304	2	1	C>T
ERR5749282	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	1077	0.024141	0	1051,0,26,0	HIGH	NONE	FRAME_SHIFT+STOP_GAINED	ORF1ab	gat/Tgat	D124*?	endoR	0.000884	0.981982	5	2	C>CT
ERR5749282	20445	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAA	T	8286	0.005431	0	0,8241,0,45	HIGH	NONE	FRAME_SHIFT	ORF1ab	aac/	N277	endoR	0.000518	0.059736	4	2	TAA>T
ERR5749282	21234	PASS	C	T	5995	0.645038	0	3,0,5895,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A192	MethTr	0.000472	0.857572	5	2	C>T
ERR5749282	21334	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	5996	0.004503	0	0,5961,0,31	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gca/Tca	A226S	MethTr	0.000897	0.077475	3	1	G>T
ERR5749282	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	4607	0.02583	365	2304,2178,0,119	HIGH	NONE	FRAME_SHIFT	S	ctt/Tctt	L5S?	S	0.000394	0.091869	4	1	G>GT
ERR5749282	21575	PASS	C	T	4436	0.861136	0	0,0,2103,2293	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749282	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	4435	0.005637	70	2124,2287,0,25	HIGH	NONE	FRAME_SHIFT	S	gtt/Tgtt	V6C?	S	0.000619	0.877942	3	2	C>CT
ERR5749282	21614	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2318	0.010785	0	0,2288,0,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L18F	S	0.001194	0.949239	2	2	C>T
ERR5749282	21614	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTTACAACCAGAACTCAATTACCCCCTGCATACACTAA	C	2318	0.006903	0	0,2302,0,16	HIGH	NONE	FRAME_SHIFT	S	acaaccagaactcaattaccccctgcatacactaattct/	TTRTQLPPAYTNS19	S	0.001194	0.949239	2	2	CTTACAACCAGAACTCAATTACCCCCTGCATACACTAA>C
ERR5749282	21655	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	2319	0.004743	0	0,2306,0,11	LOW	SILENT	SYNONYMOUS_CODING	S	tcT/tcC	S31	S	0.001481	0.110354	1	1	T>C
ERR5749282	21658	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2319	0.007762	0	0,2299,0,20	LOW	SILENT	SYNONYMOUS_CODING	S	ttC/ttT	F32	S	0.001649	0.937508	2	2	C>T
ERR5749282	21764	PASS	ATACATG	A	3338	0.997004	0	10,0,3328,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749282	21811	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3339	0.003294	0	3326,0,12,0	LOW	SILENT	SYNONYMOUS_CODING	S	gtC/gtT	V83	S	0.001327	0.179245	1	1	C>T
ERR5749282	21817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	3339	0.003893	0	3326,0,13,0	HIGH	NONE	FRAME_SHIFT	S	ttt/	F86	S	0.000689	0.961354	3	2	AT>A
ERR5749282	21990	PASS	TTTA	T	3342	0.998803	0	0,4,0,3338	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749282	22384	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	2870	0.004878	0	2850,0,15,0	LOW	SILENT	SYNONYMOUS_CODING	S	acT/acC	T274	S	0.001609	0.118834	1	1	T>C
ERR5749282	22444	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2866	0.004885	0	2844,0,15,0	LOW	SILENT	SYNONYMOUS_CODING	S	gaC/gaT	D294	S	0.004885	0.182432	1	1	C>T
ERR5749282	23063	PASS	A	T	3149	0.849794	2147483647	0,0,0,3134	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749282	23271	PASS	C	A	1647	0.92714	2147483647	0,0,1646,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749282	23403	PASS	A	G	1646	0.967801	0	0,2,0,1644	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749282	23604	PASS	C	A	2912	0.938874	0	2,0,2907,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749282	23709	PASS	C	T	2907	0.936016	0	0,1,0,2905	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749282	23712	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	2907	0.00172	0	0,2902,0,5	HIGH	NONE	FRAME_SHIFT	S	ttt/	F718	S	0.000679	0.958955	3	2	AT>A
ERR5749282	23817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	3967	0.010587	60	1054,2867,0,46	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTt/cCt	L752P	S	0.000646	0.066832	1	1	T>C
ERR5749282	24010	PASS	A	G	2038	0.926398	0	0,1,986,1050	LOW	SILENT	SYNONYMOUS_CODING	S	tcA/tcG	S816	S	0.000455	0.926398	4	2	A>G
ERR5749282	24506	PASS	T	G	3435	0.975546	2147483647	0,0,3435,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749282	24914	PASS	G	C	12756	0.956099	0	0,0,6345,6404	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749282	25135	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	731	0.008208	0	725,0,6,0	HIGH	NONE	FRAME_SHIFT	S	aat/	N1192	S	0.003281	0.884331	3	2	GA>G
ERR5749282	25391	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTA	T	9649	0.005182	0	9599,0,50,0	HIGH	NONE	FRAME_SHIFT+START_LOST	ORF3a	atg/	M1	orf3a	0.000585	0.191026	1	1	TTA>T
ERR5749282	25469	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9638	0.004254	0	9588,0,43,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	tCa/tTa	S26L	orf3a	0.001214	0.959377	2	2	C>T
ERR5749282	25553	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9639	0.002386	0	0,9609,0,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	gCt/gTt	A54V	orf3a	0.001165	0.868131	3	2	C>T
ERR5749282	25555	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	9640	0.003216	0	0,9609,0,31	HIGH	NONE	FRAME_SHIFT	ORF3a	ttt/	F56	orf3a	0.000552	0.900573	5	2	GT>G
ERR5749282	25587	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	9648	0.00228	0	0,9612,0,36	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	ctC/ctA	L65	orf3a	0.000598	0.813206	6	2	C>A
ERR5749282	25587	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	9648	0.007048	0	0,9580,0,68	HIGH	NONE	FRAME_SHIFT	ORF3a	aag/	K67	orf3a	0.000598	0.813206	6	2	CAA>C
ERR5749282	25681	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	430	0.018605	0	422,0,8,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gtt/Att	V97I	orf3a	0.018605	0.934285	1	1	G>A
ERR5749282	25844	PASS	C	T	430	0.923256	2147483647	0,0,0,429	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aCt/aTt	T151I	orf3a	0.001226	0.938776	1	1	C>T
ERR5749282	26044	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8042	0.003109	0	8008,0,29,0	HIGH	NONSENSE	STOP_GAINED	ORF3a	Caa/Taa	Q218*	orf3a	0.000469	0.102679	3	3	C>T
ERR5749282	26209	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	8037	0.002364	0	0,8014,0,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gtg/Ctg	V273L	orf3a	0.000792	0.234679	3	1	G>C
ERR5749282	26526	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	2217	0.005864	0	0,2201,0,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Gca/Tca	A2S	M	0.001224	0.951192	3	1	G>T
ERR5749282	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	3144	0.00827	0	0,3118,0,26	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749282	26895	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11196	0.002858	0	11160,1,32,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Cat/Tat	H125Y	M	0.000874	0.97046	1	1	C>T
ERR5749282	27312	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	8541	0.002693	0	8518,0,23,0	HIGH	NONE	FRAME_SHIFT	ORF6	aat/aaAt	N39K?	orf6	0.000911	0.088458	4	2	T>TA
ERR5749282	27403	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATT	A	8536	0.003983	0	0,8502,0,34	HIGH	NONE	FRAME_SHIFT	ORF7a	att/	I4	orf7a	0.000512	0.916	3	2	ATT>A
ERR5749282	27461	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	8553	0.002221	0	3,8531,0,19	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	tGt/tTt	C23F	orf7a	0.002221	0.974441	1	1	G>T
ERR5749282	27494	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16636	0.001743	1	8071,8531,13,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	cCt/cTt	P34L	orf7a	0.000672	0.961447	2	2	C>T
ERR5749282	27552	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATT	A	8086	0.002597	0	8065,0,21,0	HIGH	NONE	FRAME_SHIFT	ORF7a	ttt/	F54	orf7a	0.000563	0.985801	6	1	ATT>A
ERR5749282	27577	PASS	C	T	8041	0.808979	0	1,0,8002,0	HIGH	NONSENSE	STOP_GAINED	ORF7a	Caa/Taa	Q62*	orf7a	0.000614	0.952205	4	2	C>T
ERR5749282	27641	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8035	0.001867	0	8012,0,15,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	tCa/tTa	S83L	orf7a	0.000983	0.911213	2	2	C>T
ERR5749282	27741	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8128	0.002953	0	43,8051,0,25	LOW	SILENT	SYNONYMOUS_CODING	ORF7a	ctC/ctT	L116	orf7a	0.000363	0.954278	3	2	C>T
ERR5749282	27754	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	8128	0.00283	0	43,8030,0,54	HIGH	NONSENSE	STOP_GAINED	ORF7a	Gaa/Taa	E121*	orf7a	0.001253	0.928716	1	1	G>T
ERR5749282	27972	PASS	C	T	1332	0.90015	0	0,0,1316,12	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749282	28048	PASS	G	T	1323	0.894936	0	0,2,0,1320	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749282	28111	PASS	A	G	10497	0.979518	0	2,0,9164,1324	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749282	28227	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9170	0.001963	0	9140,0,19,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	Cat/Tat	H112Y	orf8	0.000906	0.951206	2	2	C>T
ERR5749282	28249	PASS	A	G	9166	0.063605	0	8543,1,609,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	gAt/gGt	D119G	orf8	0.000443	0.063605	3	2	A>G
ERR5749282	28249	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	9165	0.00251	0	9142,1,23,0	HIGH	NONE	FRAME_SHIFT	ORF8	ttc/	F120	orf8	0.000443	0.063605	3	2	AT>A
ERR5749282	28270	PASS	TA	T	17637	0.993253	243	116,7,9024,8494	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749282	28280	PASS	G	C	17596	0.937543	6	3,0,9075,8491	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749282	28281	PASS	A	T	17596	0.913048	1	8,6,9067,8477	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749282	28282	PASS	T	A	17600	0.910398	7	10,4,9044,8500	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749282	28378	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	9173	0.003161	0	0,9137,0,30	LOW	SILENT	SYNONYMOUS_CODING	N	gcG/gcA	A35	N	0.001609	0.060482	3	1	G>A
ERR5749282	28603	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23146	0.001987	0	11533,11450,27,27	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F110	N	0.000427	0.883357	2	2	C>T
ERR5749282	28651	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	11598	6.04E-4	0	0,11591,0,7	HIGH	NONE	FRAME_SHIFT	N	aaa/	K127	N	0.000502	0.918117	3	2	CA>C
ERR5749282	28732	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	12154	0.002304	1	549,11577,0,28	HIGH	NONE	FRAME_SHIFT	N	aat/	N154	N	0.000892	0.966905	2	2	CA>C
ERR5749282	28881	PASS	G	A	1082	0.768946	0	1,0,537,526	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749282	28882	PASS	G	A	1082	0.831793	0	0,0,542,530	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749282	28883	PASS	G	C	1082	0.942699	0	0,0,544,538	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749282	28977	PASS	C	T	549	0.925319	2147483647	0,0,0,546	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749282	29091	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTT	C	8779	0.001025	0	8770,0,9,0	HIGH	NONE	FRAME_SHIFT	N	ttc/	F274	N	0.000452	0.073908	3	1	CTT>C
ERR5749282	29095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8779	0.003987	0	8734,0,35,0	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F274	N	0.000792	0.961279	2	2	C>T
ERR5749282	29253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8777	0.002962	0	0,8726,0,28	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCg/tTg	S327L	N	0.000361	0.053998	4	2	C>T
ERR5749282	29272	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8777	0.001709	0	0,8753,0,16	LOW	SILENT	SYNONYMOUS_CODING	N	taC/taT	Y333	N	0.001709	0.892106	1	1	C>T
ERR5749282	29284	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8778	0.001481	0	0,8745,0,13	LOW	SILENT	SYNONYMOUS_CODING	N	atC/atT	I337	N	0.000393	0.931014	3	2	C>T
ERR5749282	29284	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	8778	7.97E-4	0	0,8771,0,7	HIGH	NONE	FRAME_SHIFT	N	aaa/	K338	N	0.000393	0.931014	3	2	CA>C
ERR5749282	29555	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5339	0.003559	13	2335,2981,4,16	.	.	.	.	.	.	.	0.000611	0.957048	3	1	C>T
ERR5749282	29679	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	4657	0.001503	0	2331,2321,4,3	.	.	.	.	.	.	.	0.000443	0.838763	2	1	CT>C
ERR5749282	29781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	2341	0.004699	0	0,2328,0,13	.	.	.	.	.	.	.	0.00173	0.972321	2	1	G>T
ERR5749283	241	PASS	C	T	18325	0.853915	0	0,1,9107,9126	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749283	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	10052	0.001094	0	10035,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749283	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10044	0.002688	0	9229,0,780,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749283	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	27277	6.6E-4	10	17183,10069,15,3	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749283	913	PASS	C	T	17198	0.910862	0	0,11,0,17162	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749283	1510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	18366	0.004628	0	0,18084,0,92	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G235	nsp2	0.002159	0.937304	1	1	T>C
ERR5749283	3037	PASS	C	T	15606	0.810842	33	0,11,7798,7696	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749283	3047	PASS	G	T	8983	0.233775	2147483647	46,6370,1104,1459	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gat/Tat	D110Y	nsp3	0.004044	0.233775	2	1	G>T
ERR5749283	3267	PASS	C	T	16649	0.970148	0	5,0,16634,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749283	4237	PASS	T	C	25715	0.912425	0	0,0,12893,12757	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaT/aaC	N506	nsp3	0.000302	0.918634	2	2	T>C
ERR5749283	4255	PASS	G	A	25763	0.820091	43	19,1,12806,12732	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccG/ccA	P512	nsp3	0.001102	0.871853	2	1	G>A
ERR5749283	5388	PASS	C	A	4220	0.955213	2147483647	0,0,4215,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749283	5575	PASS	C	T	4224	0.946023	94	3,1,0,4219	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y952	nsp3	0.01018	0.961493	1	1	C>T
ERR5749283	5986	PASS	C	T	9784	0.975572	0	2,0,9776,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749283	6954	PASS	T	C	18918	0.808595	0	0,7,0,18799	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749283	11287	PASS	GTCTGGTTTT	G	15509	0.99697	0	0,47,0,15462	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749283	11507	PASS	G	A	22376	0.902172	9	4,0,11183,11126	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Att	V179I	nsp6	0.007744	0.914418	2	2	G>A
ERR5749283	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	9534	0.004405	2894	9274,81,5,168	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749283	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	18448	6.5E-4	0	9260,9196,6,6	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749283	14408	PASS	C	T	18448	0.84459	9	1,5,9209,9106	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749283	14676	PASS	C	T	11055	0.82768	0	5,0,11024,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749283	14829	PASS	G	T	11061	0.220233	0	0,8267,0,2790	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atT	M463I	RdRp	0.220233	0.868726	1	1	G>T
ERR5749283	15279	PASS	C	T	18468	0.895495	0	5,0,18440,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749283	15420	PASS	T	G	18439	0.916753	0	0,35,0,18391	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcG	A660	RdRp	0.908883	0.934773	1	1	T>G
ERR5749283	15438	PASS	G	T	18461	0.054927	0	0,17277,0,1180	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atT	M666I	RdRp	0.054927	0.054927	1	1	G>T
ERR5749283	16176	PASS	T	C	16193	0.980979	0	0,0,7576,8612	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749283	17502	PASS	C	T	11460	0.982635	2147483647	0,0,11448,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F422	helicase	0.000611	0.9865	2	2	C>T
ERR5749283	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	17566	6.26E-4	0	17555,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749283	19011	PASS	C	T	20079	0.975746	0	4,0,20069,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D324	ExoN	0.000408	0.975746	4	2	C>T
ERR5749283	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22452	0.001737	0	22392,0,42,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749283	21764	PASS	ATACATG	A	8987	0.997218	0	25,0,8962,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749283	21990	PASS	TTTA	T	8986	0.996995	0	0,27,1,8958	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749283	23063	PASS	A	T	9714	0.867305	0	0,2,0,9656	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749283	23271	PASS	C	A	17444	0.919915	0	2,0,17425,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749283	23403	PASS	A	G	17437	0.967884	0	0,4,0,17421	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749283	23604	PASS	C	A	11988	0.941275	0	12,0,11969,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749283	23709	PASS	C	T	11966	0.933812	0	0,3,2,11937	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749283	24320	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	8870	0.001917	0	0,8850,0,17	HIGH	NONE	FRAME_SHIFT	S	aaa/	K921	S	0.000763	0.138365	4	2	CA>C
ERR5749283	24506	PASS	T	G	15093	0.974226	0	4,0,15087,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749283	24914	PASS	G	C	26826	0.958697	0	0,0,13351,13458	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749283	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	19107	0.001884	61	12428,6621,46,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749283	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	21099	9.95E-4	0	21078,0,21,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749283	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	21231	0.001554	1320	20936,111,75,83	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749283	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	8649	8.09E-4	0	0,8642,0,7	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749283	27765	PASS	C	T	18286	0.96161	0	0,2,0,18276	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7b	Ctt/Ttt	L4F	orf7b	0.00109	0.970449	1	1	C>T
ERR5749283	27972	PASS	C	T	8124	0.903127	39	2,2,8057,33	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749283	28048	PASS	G	T	8096	0.908473	0	0,11,0,8080	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749283	28111	PASS	A	G	24920	0.978331	9	1,3,16807,8101	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749283	28239	PASS	GTTGTT	G	16781	0.984983	0	258,0,16528,1	HIGH	NONE	FRAME_SHIFT	ORF8	gtttta/	VL117	orf8	0.000417	0.984998	9	2	GTTGTT>G
ERR5749283	28249	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	ATC	16577	0.001086	0	16552,1,18,0	HIGH	NONE	FRAME_SHIFT	ORF8	ttc/CTttc	F120L?	orf8	0.000443	0.063605	3	2	A>ATC
ERR5749283	28250	PASS	T	TCTG	16577	0.992399	0	99,0,16450,1	MODERATE	NONE	CODON_INSERTION	ORF8	ttc/CTGttc	F120LF	orf8	0.000494	0.993968	5	3	T>TCTG
ERR5749283	28250	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TATG	16577	9.65E-4	0	99,0,16,0	MODERATE	NONE	CODON_INSERTION	ORF8	ttc/ATGttc	F120MF	orf8	0.000494	0.993968	5	3	T>TATG
ERR5749283	28253	PASS	CA	C	16577	0.99451	0	91,0,16485,1	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749283	28270	PASS	TA	T	31906	0.996333	163	102,13,16472,15317	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749283	28271	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AA	A	31906	0.001379	125	16530,15331,44,0	.	.	.	.	.	.	.	0.000482	0.924941	3	2	AA>A
ERR5749283	28280	PASS	G	C	31907	0.946438	4	7,3,16532,15310	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749283	28281	PASS	A	T	31907	0.93199	16	15,4,16528,15305	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749283	28282	PASS	T	A	31910	0.905327	4	11,6,16500,15314	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749283	28877	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	14905	0.00161	8	7484,7353,15,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Agt/Tgt	S202C	N	0.000959	0.88894	1	1	A>T
ERR5749283	28878	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	14904	0.001744	1	7505,7354,14,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGt/aCt	S202T	N	0.001	0.909986	3	2	G>C
ERR5749283	28881	PASS	G	A	14819	0.772724	1	5,3,7347,7262	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749283	28882	PASS	G	A	14819	0.821108	2	3,1,7418,7247	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749283	28883	PASS	G	C	14819	0.943653	0	0,0,7433,7374	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749283	28977	PASS	C	T	7537	0.923046	0	0,3,0,7515	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749283	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	36124	0.001024	0	18140,17917,23,24	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749284	241	PASS	C	T	317	0.817035	0	0,0,157,158	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749284	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	4492	0.003117	24	2834,1644,14,0	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749284	913	PASS	C	T	2848	0.935393	2147483647	0,0,0,2845	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749284	1266	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GC	G	8412	0.00107	11	2582,5821,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggc/	G154	nsp2	0.00107	0.98689	2	2	GC>G
ERR5749284	1782	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	11063	0.001356	0	5512,5522,13,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tGt/tTt	C326F	nsp2	0.001356	0.744	2	1	G>T
ERR5749284	2672	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	6051	0.003801	0	6025,0,23,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gca/Aca	A623T	nsp2	0.001351	0.18509	3	1	G>A
ERR5749284	2722	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	12070	0.003728	0	6002,5998,27,25	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcA/gcG	A1	nsp3	0.003728	0.9625	1	1	A>G
ERR5749284	2779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	6050	0.003967	0	0,6017,0,24	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	agT/agC	S20	nsp3	0.003967	0.16	2	2	T>C
ERR5749284	3037	PASS	C	T	3461	0.809304	6	0,2,1730,1700	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749284	3267	PASS	C	T	4389	0.976532	2147483647	0,0,4387,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749284	3335	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	8729	0.002749	0	4367,4304,12,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Caa	E206Q	nsp3	0.001289	0.891976	4	3	G>C
ERR5749284	3671	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	6459	0.002168	0	3218,3180,10,10	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E318K	nsp3	0.000351	0.0625	6	2	G>A
ERR5749284	4668	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	4854	0.002266	0	4838,2,14,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tAt	S650Y	nsp3	0.002266	0.970109	2	1	C>A
ERR5749284	4732	PASS	T	C	4852	0.363768	0	3031,0,1819,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taT/taC	Y671	nsp3	0.363768	0.363768	1	1	T>C
ERR5749284	5388	PASS	C	A	834	0.955635	2147483647	0,0,834,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749284	5986	PASS	C	T	3379	0.97662	2147483647	0,0,3378,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749284	6310	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5131	0.004093	0	5105,0,21,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	agC/agT	S1197	nsp3	0.00099	0.94715	2	2	C>T
ERR5749284	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	3112	0.005463	0	0,3095,0,17	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L1328S?	nsp3	0.000731	0.14377	4	2	C>CT
ERR5749284	6954	PASS	T	C	5313	0.826087	2147483647	0,0,0,5294	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749284	7843	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	16029	0.002495	1	7959,7987,38,43	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaC/aaA	N1708K	nsp3	0.000845	0.916161	2	2	C>A
ERR5749284	10336	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	7722	0.002849	0	0,7700,0,22	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N95	3Cpro	0.002849	0.949353	2	2	CA>C
ERR5749284	10369	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7726	0.002589	0	3,7701,0,20	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	cgC/cgT	R105	3Cpro	0.001225	0.120075	1	1	C>T
ERR5749284	11104	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	8973	0.003901	0	8907,0,37,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccT/ccC	P44	nsp6	0.000866	0.675414	2	1	T>C
ERR5749284	11287	PASS	GTCTGGTTTT	G	8968	0.999219	0	0,6,0,8961	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749284	11355	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	10703	0.003177	23	1728,8941,0,34	HIGH	NONE	FRAME_SHIFT	ORF1ab	aga/	R129	nsp6	0.000455	0.982262	3	2	CA>C
ERR5749284	13033	PASS	T	A	8608	0.965381	0	61,9,7389,1146	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaT/aaA	N3K	nsp10	0.965381	0.965381	1	1	T>A
ERR5749284	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	7449	0.003759	0	7416,0,30,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgT/tgC	C46	nsp10	0.000528	0.198485	2	2	T>C
ERR5749284	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CGGCACA	C	6774	0.002657	0	3383,3373,9,9	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	acaggcact/act	TGT24T	RdRp	0.000536	0.074627	4	2	CGGCACA>C
ERR5749284	14098	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	5548	0.002704	0	5485,44,16,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggt/Agt	G220S	RdRp	0.000806	0.065317	4	2	G>A
ERR5749284	14408	PASS	C	T	2677	0.827792	0	4,3,1337,1313	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749284	14676	PASS	C	T	2335	0.716488	0	1,0,2326,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749284	15237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	2593	0.005013	0	2572,8,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aac/	N600	RdRp	0.001014	0.955128	2	2	CA>C
ERR5749284	15279	PASS	C	T	2585	0.892843	2147483647	0,0,2582,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749284	15542	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8988	0.003227	0	8955,0,29,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aTg	T701M	RdRp	0.00059	0.073325	3	2	C>T
ERR5749284	16176	PASS	T	C	3413	0.980955	0	0,0,794,2619	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749284	16468	PASS	C	T	9289	0.975993	6	2,1,8488,792	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ccc/Tcc	P78S	helicase	0.001077	0.977186	1	1	C>T
ERR5749284	16573	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	8493	0.002355	0	8470,0,21,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gac/Aac	D113N	helicase	0.000597	0.156477	4	2	G>A
ERR5749284	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	6516	0.002455	0	6490,0,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749284	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAA	G	6516	0.001535	0	6490,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GAA>G
ERR5749284	17615	PASS	A	G	5383	0.905071	2147483647	0,0,0,5371	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749284	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	14184	8.46E-4	0	14172,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749284	19011	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8937	0.005595	0	8870,0,51,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D324	ExoN	0.000408	0.975746	4	2	C>T
ERR5749284	19396	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	5011	0.002594	0	4983,0,15,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gag/Cag	E453Q	ExoN	0.002594	0.078431	2	2	G>C
ERR5749284	21077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	7081	0.003389	0	2,7055,0,24	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K141	MethTr	0.000492	0.955529	4	2	CA>C
ERR5749284	21764	PASS	ATACATG	A	5410	0.998521	0	8,0,5402,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749284	21777	PASS	G	T	5410	0.058595	0	5077,0,333,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gGg/gTg	G72V	S	0.039098	0.058595	2	1	G>T
ERR5749284	21990	PASS	TTTA	T	5415	0.995383	0	0,25,5,5385	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749284	21991	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTA	T	5417	0.002769	0	7,5393,0,15	HIGH	NONE	FRAME_SHIFT	S	tat/	Y144	S	0.00078	0.991378	2	1	TTA>T
ERR5749284	22712	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTA	C	22325	0.001254	0	11161,11137,14,14	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	actaaa/aaa	TK385K	S	0.001254	0.842266	2	2	CCTA>C
ERR5749284	22771	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	11202	0.002321	0	0,11149,0,41	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	agA/agT	R403S	S	0.000511	0.112051	3	3	A>T
ERR5749284	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	11210	0.001784	0	0,11180,0,22	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749284	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16597	0.001687	1	5375,11189,8,21	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749284	23063	PASS	A	T	5380	0.867844	2147483647	0,0,0,5360	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749284	23271	PASS	C	A	6266	0.930099	0	2,0,6255,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749284	23403	PASS	A	G	6263	0.970621	0	0,3,0,6259	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749284	23604	PASS	C	A	5228	0.945295	0	2,0,5223,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749284	23709	PASS	C	T	5221	0.923386	2147483647	0,0,0,5213	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749284	24506	PASS	T	G	5112	0.980438	2147483647	0,0,5112,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749284	24914	PASS	G	C	26207	0.959973	0	1,1,13066,13124	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749284	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTG	C	14361	0.002298	15	12536,1792,33,0	MODERATE	NONE	CODON_DELETION	S	tgc/	C1254	S	0.000828	0.956514	4	2	CCTG>C
ERR5749284	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	984	0.010163	132	963,9,2,8	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749284	26270	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14687	0.00143	31	4193,10466,0,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	aCa/aTa	T9I	E	0.000586	0.930791	3	2	C>T
ERR5749284	26319	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	4193	0.002862	0	4168,0,16,0	LOW	SILENT	SYNONYMOUS_CODING	E	gtA/gtT	V25	E	0.001432	0.971582	2	1	A>T
ERR5749284	26416	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	8298	0.002892	29	4084,4143,48,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	Gtt/Ttt	V58F	E	0.000457	0.913418	2	2	G>T
ERR5749284	26526	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	4194	0.003338	0	1,4174,0,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Gca/Tca	A2S	M	0.001224	0.951192	3	1	G>T
ERR5749284	26985	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15273	0.00131	0	15233,0,24,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Cat/Tat	H155Y	M	0.001017	0.889358	1	1	C>T
ERR5749284	27312	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	11335	0.001323	0	11320,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF6	aat/	N39	orf6	0.000911	0.088458	4	2	TA>T
ERR5749284	27476	PASS	C	T	22250	0.22827	74	8457,8449,2439,2898	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	aCa/aTa	T28I	orf7a	0.000547	0.22827	4	2	C>T
ERR5749284	27532	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	10904	0.002109	0	10874,2,27,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Cat/Aat	H47N	orf7a	0.001165	0.982473	2	1	C>A
ERR5749284	27972	PASS	C	T	2889	0.903081	20	1,1,2866,13	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749284	28048	PASS	G	T	2875	0.934609	0	0,4,0,2871	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749284	28111	PASS	A	G	16419	0.97844	0	1,0,13531,2878	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749284	28237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	13538	5.91E-4	0	13530,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF8	gtt/Tgtt	V116C?	orf8	0.000442	0.966707	4	2	G>GT
ERR5749284	28270	PASS	TA	T	26232	0.995349	270	121,6,13355,12755	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749284	28280	PASS	G	C	26186	0.938364	19	10,1,13367,12747	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749284	28281	PASS	A	T	26186	0.918621	25	21,5,13356,12745	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749284	28282	PASS	T	A	26189	0.919012	8	25,15,13338,12751	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749284	28396	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	13549	0.001476	0	8,13490,0,24	LOW	SILENT	SYNONYMOUS_CODING	N	cgG/cgC	R41	N	0.000496	0.946059	5	2	G>C
ERR5749284	28881	PASS	G	A	2445	0.740695	6	2,0,1193,1207	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749284	28882	PASS	G	A	2444	0.836743	0	1,0,1216,1206	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749284	28883	PASS	G	C	2444	0.936579	3	1,0,1218,1225	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749284	28977	PASS	C	T	1258	0.921304	2147483647	0,0,0,1257	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749284	29077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19643	0.001375	0	19603,0,28,0	LOW	SILENT	SYNONYMOUS_CODING	N	taC/taT	Y268	N	0.000408	0.88565	3	2	C>T
ERR5749284	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	39012	0.001589	0	19578,19338,41,39	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749285	241	PASS	C	T	10583	0.85609	6	0,3,5261,5262	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749285	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	11266	0.002485	0	11240,0,28,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749285	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	11268	7.1E-4	0	11211,2,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749285	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	11268	0.00355	0	11211,2,40,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749285	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	11262	0.001953	0	10395,5,762,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749285	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	11262	0.001066	0	11245,5,12,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749285	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	11261	7.1E-4	0	11243,5,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749285	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	11260	7.99E-4	0	11243,5,9,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749285	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	32274	4.34E-4	7	20974,11285,12,2	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749285	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	32274	8.37E-4	9	20959,11283,22,5	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749285	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20972	0.001049	0	0,20930,0,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749285	913	PASS	C	T	20972	0.926283	0	0,9,0,20934	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749285	3037	PASS	C	T	17462	0.814111	54	0,18,8717,8595	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749285	3267	PASS	C	T	19792	0.968422	0	5,0,19772,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749285	4094	PASS	A	G	38976	0.965312	5	12,8,17884,21040	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Act/Gct	T459A	nsp3	0.965312	0.967802	1	1	A>G
ERR5749285	4338	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	32758	3.66E-4	20	14851,17894,1,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	att/	I541	nsp3	0.000366	0.051643	2	2	CTA>C
ERR5749285	5388	PASS	C	A	5903	0.954091	2147483647	0,0,5898,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749285	5986	PASS	C	T	11208	0.973055	2147483647	0,0,11201,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749285	6954	PASS	T	C	21154	0.824619	0	0,9,0,21038	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749285	7058	PASS	G	A	21228	0.887507	36	1,4,0,21173	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggt/Agt	G1447S	nsp3	0.000616	0.910617	2	2	G>A
ERR5749285	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	28456	8.79E-4	69	14952,13478,25,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749285	10323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	16871	0.001897	0	1,16803,0,34	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749285	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21485	0.001443	0	21429,0,36,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749285	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	21474	0.001816	0	21395,0,67,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749285	11287	PASS	GTCTGGTTTT	G	21476	0.997858	0	0,46,0,21430	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749285	12970	PASS	C	T	15430	0.852495	0	0,1,3,15372	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N95	nsp9	0.8352	0.861883	1	1	C>T
ERR5749285	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	36688	0.001172	0	18311,18289,25,25	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749285	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	11261	0.004795	3128	11000,75,5,173	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749285	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	21899	7.31E-4	0	10998,10907,8,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749285	14408	PASS	C	T	21899	0.837892	7	2,6,10937,10790	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749285	14676	PASS	C	T	13630	0.810125	0	4,0,13599,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749285	15279	PASS	C	T	22347	0.883564	0	3,0,22304,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749285	16176	PASS	T	C	20266	0.982631	0	0,0,9266,10991	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749285	18498	PASS	G	T	28085	0.080328	2	10,25278,0,2781	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atT	M153I	ExoN	0.001072	0.080328	3	1	G>T
ERR5749285	18504	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	28106	7.83E-4	0	8,27713,0,344	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K155N	ExoN	0.000518	0.094148	4	3	A>C
ERR5749285	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26023	0.002037	0	25947,0,55,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749285	20987	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	43028	5.81E-4	0	21513,21487,12,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L111	MethTr	0.000276	0.056129	4	2	CT>C
ERR5749285	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30834	0.00107	1	15089,15368,19,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749285	21762	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTATACA	C	11396	0.002194	0	11371,0,25,0	MODERATE	NONE	CODON_DELETION	S	atacat/	IH68	S	0.001297	0.875707	2	2	CTATACA>C
ERR5749285	21764	PASS	ATACATG	A	11396	0.995788	0	48,0,11348,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749285	21990	PASS	TTTA	T	11400	0.997193	0	0,32,2,11366	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749285	22427	PASS	G	A	8344	0.856544	2147483647	0,0,8313,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gta/Ata	V289I	S	0.856544	0.86163	1	1	G>A
ERR5749285	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	15217	0.001314	0	0,15189,0,21	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749285	23063	PASS	A	T	13100	0.860382	0	0,2,0,13029	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749285	23271	PASS	C	A	23008	0.921201	0	3,0,22982,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749285	23403	PASS	A	G	23006	0.967965	0	0,2,0,22984	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749285	23481	PASS	C	T	37143	0.964516	0	1,3,14101,22984	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCt/tTt	S640F	S	0.001098	0.964516	1	1	C>T
ERR5749285	23604	PASS	C	A	14125	0.961345	0	5,0,14116,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749285	23709	PASS	C	T	14115	0.945802	0	0,5,2,14090	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749285	24506	PASS	T	G	17850	0.97423	0	12,0,17834,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749285	24914	PASS	G	C	36336	0.958553	0	0,0,18079,18222	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749285	25660	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	18160	7.16E-4	0	18121,26,13,0	HIGH	NONE	FRAME_SHIFT	ORF3a	tac/	Y91	orf3a	0.000716	0.91928	2	2	GT>G
ERR5749285	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	18159	0.001487	312	18103,13,14,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749285	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	18132	9.93E-4	0	18114,0,18,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749285	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	11780	0.001613	0	1,11757,0,19	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749285	27972	PASS	C	T	9703	0.90405	0	0,0,9642,41	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749285	28048	PASS	G	T	9670	0.920683	0	0,19,0,9643	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749285	28111	PASS	A	G	28534	0.97743	3	6,1,18846,9673	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749285	28270	PASS	TA	T	36374	0.994474	470	199,7,18574,17599	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749285	28280	PASS	G	C	36289	0.935711	14	12,3,18615,17581	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749285	28281	PASS	A	T	36289	0.914933	34	27,6,18605,17582	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749285	28282	PASS	T	A	36292	0.911661	6	19,11,18583,17595	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749285	28881	PASS	G	A	18980	0.760537	18	7,0,9392,9299	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749285	28882	PASS	G	A	18979	0.820328	16	9,1,9494,9292	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749285	28883	PASS	G	C	18979	0.940092	0	1,1,9516,9444	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749285	28977	PASS	C	T	9708	0.919654	0	0,3,0,9689	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749285	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	54616	9.7E-4	0	27461,27075,33,32	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749286	241	PASS	C	T	551	0.85118	0	0,0,274,274	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749286	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	2221	0.004052	0	2111,101,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749286	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	2227	0.005837	0	2107,107,13,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749286	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATGGTTG	T	2227	0.006736	0	2105,107,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	atggttgag/	MVE85	leader	0.000587	0.476744	4	1	TATGGTTG>T
ERR5749286	913	PASS	C	T	4282	0.905885	0	0,4,0,4266	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749286	1021	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	3668	0.003544	0	3648,4,16,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caG/caT	Q72H	nsp2	0.003544	0.054381	1	1	G>T
ERR5749286	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	9414	0.001806	789	4705,4371,10,305	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749286	3037	PASS	C	T	3037	0.824498	12	0,4,1517,1501	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749286	3267	PASS	C	T	4849	0.970097	2147483647	0,0,4848,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749286	3734	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	1418	0.006347	0	0,1406,0,12	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gac/Tac	D339Y	nsp3	0.00428	0.968741	2	1	G>T
ERR5749286	4206	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3789	0.006334	0	3760,0,27,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCg/gTg	A496V	nsp3	0.003069	0.879444	1	1	C>T
ERR5749286	5388	PASS	C	A	611	0.973813	2147483647	0,0,611,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749286	5986	PASS	C	T	1989	0.980895	2147483647	0,0,1987,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749286	6954	PASS	T	C	4241	0.824805	2147483647	0,0,0,4217	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749286	7926	PASS	C	T	2742	0.970095	0	0,1,0,2740	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCa/gTa	A1736V	nsp3	0.000531	0.97019	5	2	C>T
ERR5749286	8208	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4396	0.004777	0	0,4366,0,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T1830I	nsp3	0.001142	0.84438	1	1	C>T
ERR5749286	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	4417	0.004075	6	3934,465,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749286	10323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	6142	0.010583	0	0,6063,0,70	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749286	10533	PASS	G	T	5761	0.891685	0	4,0,5534,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tGt/tTt	C160F	3Cpro	0.000835	0.917216	4	2	G>T
ERR5749286	10789	PASS	C	T	454	0.955947	2147483647	0,0,454,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D245	3Cpro	0.001434	0.956641	1	1	C>T
ERR5749286	11287	PASS	GTCTGGTTTT	G	10532	0.994968	0	0,53,0,10479	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749286	11824	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7717	0.005183	0	0,7667,0,42	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I284	nsp6	0.000465	0.922016	2	2	C>T
ERR5749286	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	5370	0.004469	0	5341,0,24,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749286	12970	PASS	C	T	1300	0.837692	2147483647	0,0,0,1295	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N95	nsp9	0.8352	0.861883	1	1	C>T
ERR5749286	13458	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CGTTTTTA	C	4987	0.006417	0	4955,0,32,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcgttttta/	SFL6	nsp11	0.001017	0.058608	4	2	CGTTTTTA>C
ERR5749286	14168	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	5147	0.002526	0	0,5134,0,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	atatta/	IL244	RdRp	0.000479	0.314961	1	1	CTA>C
ERR5749286	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	3388	0.004723	850	3280,52,1,53	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749286	14408	PASS	C	T	6532	0.839253	1	2,3,3256,3228	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749286	14676	PASS	C	T	3236	0.841162	0	3,0,3228,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749286	14913	PASS	C	T	2149	0.977199	2147483647	0,0,2144,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N491	RdRp	0.011397	0.981624	1	1	C>T
ERR5749286	15279	PASS	C	T	3290	0.882067	2147483647	0,0,3285,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749286	15493	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	3290	0.010334	0	0,3251,0,37	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gcc/Ccc	A685P	RdRp	0.001408	0.076816	3	2	G>C
ERR5749286	15542	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	8153	0.00368	0	8116,1,32,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aAg	T701K	RdRp	0.00059	0.073325	3	2	C>A
ERR5749286	15839	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	8155	0.006744	0	3,8062,0,58	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tGg/tCg	W800S	RdRp	0.001405	0.074516	2	1	G>C
ERR5749286	16176	PASS	T	C	4707	0.983429	0	0,0,807,3899	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749286	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	6070	0.001647	0	6052,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749286	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAA	G	6070	0.001318	0	6052,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GAA>G
ERR5749286	17678	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5122	0.006248	0	0,5088,0,33	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aTg	T481M	helicase	0.001162	0.968704	2	1	C>T
ERR5749286	18232	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1748	0.007437	0	0,1733,0,13	HIGH	NONSENSE	STOP_GAINED	ORF1ab	Caa/Taa	Q65*	ExoN	0.002195	0.056093	1	1	C>T
ERR5749286	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	13166	6.84E-4	0	13157,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749286	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	2476	0.002423	0	0,2470,0,6	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749286	19328	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	4094	0.006351	0	4068,0,26,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F431	ExoN	0.000459	0.937906	4	2	CT>C
ERR5749286	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	1831	0.008192	0	1816,0,15,0	HIGH	NONE	FRAME_SHIFT+STOP_GAINED	ORF1ab	gat/Tgat	D124*?	endoR	0.000884	0.981982	5	2	C>CT
ERR5749286	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1831	0.009831	0	1812,0,18,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749286	21077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	10232	0.004789	0	3,10180,0,49	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K141	MethTr	0.000492	0.955529	4	2	CA>C
ERR5749286	21123	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	15955	0.002444	79	5717,10183,0,42	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggG/ggC	G155	MethTr	0.000257	0.90982	5	2	G>C
ERR5749286	21145	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	15955	0.001379	98	5699,10234,22,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/	L163	MethTr	0.001379	0.921396	3	2	CT>C
ERR5749286	21764	PASS	ATACATG	A	4361	0.994038	0	26,0,4335,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749286	21974	PASS	G	T	4361	0.928915	0	0,4,0,4356	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gat/Tat	D138Y	S	0.001167	0.928915	2	2	G>T
ERR5749286	21990	PASS	TTTA	T	4361	1.0	2147483647	0,0,0,4361	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749286	22225	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	1139	0.006146	0	0,1131,0,8	LOW	SILENT	SYNONYMOUS_CODING	S	tcG/tcT	S221	S	0.001195	0.94526	3	1	G>T
ERR5749286	22280	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ACTTTACTTG	A	1142	0.005254	0	3,1133,0,6	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	cttgctttacat/cat	LALH242H	S	0.00046	0.997799	1	1	ACTTTACTTG>A
ERR5749286	23063	PASS	A	T	4723	0.868728	0	0,1,0,4706	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749286	23271	PASS	C	A	10941	0.917466	0	1,0,10931,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749286	23403	PASS	A	G	10931	0.970634	0	0,2,0,10922	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749286	23522	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTA	G	4205	0.007134	0	4162,1,30,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	gaacatgtcaacaactcatatgagtgtgacatacccattggtgcaggtata/gta	EHVNNSYECDIPIGAGI654V	S	0.00053	0.959726	5	2	GAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTA>G
ERR5749286	23522	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTT	G	4205	0.002854	0	4162,1,12,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	gaacatgtcaacaactcatatgagtgtgacatacccattggtgcaggtatatgcgctagttat/gat	EHVNNSYECDIPIGAGICASY654D	S	0.00053	0.959726	5	2	GAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTT>G
ERR5749286	23604	PASS	C	A	4202	0.925512	0	5,0,4196,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749286	23709	PASS	C	T	4242	0.935644	0	0,5,42,4189	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749286	24506	PASS	T	G	4573	0.973759	0	2,0,4571,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749286	24914	PASS	G	C	26547	0.958978	0	0,0,13195,13341	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749286	25138	PASS	T	C	2390	0.894979	0	3,0,2380,0	LOW	SILENT	SYNONYMOUS_CODING	S	aaT/aaC	N1192	S	0.001865	0.901453	2	2	T>C
ERR5749286	25555	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	12383	0.004603	0	0,12269,0,57	HIGH	NONE	FRAME_SHIFT	ORF3a	ttt/	F56	orf3a	0.000552	0.900573	5	2	GT>G
ERR5749286	25555	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTT	G	12383	0.004603	0	0,12269,0,57	HIGH	NONE	FRAME_SHIFT	ORF3a	ttt/	F56	orf3a	0.000552	0.900573	5	2	GTT>G
ERR5749286	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	638	0.014107	141	616,12,0,9	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749286	26461	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5251	0.00419	0	0,5210,0,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	Ctt/Ttt	L73F	E	0.001401	0.928597	1	1	C>T
ERR5749286	26564	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	9310	0.004941	101	4053,5199,1,47	LOW	SILENT	SYNONYMOUS_CODING	M	aaA/aaG	K14	M	0.003994	0.071529	1	1	A>G
ERR5749286	26730	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	8035	0.001245	0	3997,4034,5,5	HIGH	NONE	FRAME_SHIFT	M	tac/	Y71	M	0.000371	0.919543	3	2	GT>G
ERR5749286	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	4049	0.003458	0	0,4035,0,14	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749286	27312	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	9926	0.002619	0	9900,0,26,0	HIGH	NONE	FRAME_SHIFT	ORF6	aat/aaAt	N39K?	orf6	0.000911	0.088458	4	2	T>TA
ERR5749286	27459	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	9938	0.002616	0	2,9907,0,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	gaG/gaT	E22D	orf7a	0.002024	0.943812	1	1	G>T
ERR5749286	27798	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	7840	0.002041	0	0,7822,0,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7b	Gcc/Ccc	A15P	orf7b	0.002041	0.051256	2	1	G>C
ERR5749286	27915	PASS	G	A	1345	0.956877	2147483647	0,0,1345,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	Gga/Aga	G8R	orf8	0.949134	0.95909	1	1	G>A
ERR5749286	27972	PASS	C	T	1346	0.900446	0	0,0,1339,3	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749286	28048	PASS	G	T	1344	0.915179	0	0,3,0,1340	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749286	28111	PASS	A	G	15291	0.981296	0	0,0,13939,1344	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749286	28209	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	13945	0.005665	0	13855,0,81,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	Gaa/Caa	E106Q	orf8	0.001409	0.963166	2	2	G>C
ERR5749286	28270	PASS	TA	T	26982	0.995923	237	109,6,13764,13108	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749286	28280	PASS	G	C	26930	0.943557	0	4,3,13793,13097	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749286	28281	PASS	A	T	26930	0.912997	6	8,3,13786,13096	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749286	28282	PASS	T	A	26932	0.91007	2	6,8,13749,13105	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749286	28337	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	13933	0.006029	0	0,13834,0,94	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Tat	D22Y	N	0.001279	0.935503	2	1	G>T
ERR5749286	28651	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10394	0.00202	0	0,10367,0,21	LOW	SILENT	SYNONYMOUS_CODING	N	aaC/aaT	N126	N	0.000502	0.918117	3	2	C>T
ERR5749286	28881	PASS	G	A	3761	0.789418	0	0,0,1867,1846	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749286	28882	PASS	G	A	3761	0.851901	0	1,0,1882,1851	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749286	28883	PASS	G	C	3761	0.942568	0	0,0,1883,1872	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749286	28977	PASS	C	T	1908	0.872117	0	0,1,0,1816	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749286	29035	PASS	T	C	8007	0.054952	3079	6090,1441,1,465	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749286	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	12107	0.001404	0	6079,6004,11,11	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749286	29253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6092	0.002134	0	0,6067,0,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCg/tTg	S327L	N	0.000361	0.053998	4	2	C>T
ERR5749287	241	PASS	C	T	13845	0.86645	0	0,1,6898,6907	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749287	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	10512	0.001522	0	10492,1,16,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749287	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	10512	0.001237	0	10453,1,13,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749287	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	10512	0.003425	0	10453,1,36,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749287	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10507	0.002665	0	9575,6,826,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749287	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	10507	8.57E-4	0	10492,6,9,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749287	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTT	G	10507	0.001142	76	10481,3,9,3	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/	V84	leader	0.000554	0.991848	4	1	GTT>G
ERR5749287	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	29683	0.001718	6	19113,10508,37,14	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749287	913	PASS	C	T	19150	0.921671	0	0,16,0,19111	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749287	2110	PASS	C	T	24047	0.81008	0	0,9,0,23872	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N435	nsp2	0.024426	0.811371	1	1	C>T
ERR5749287	2305	PASS	G	T	11703	0.070409	0	10826,0,872,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaG/aaT	K500N	nsp2	0.000443	0.070409	4	3	G>T
ERR5749287	3037	PASS	C	T	13980	0.824177	42	0,14,6985,6902	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749287	3267	PASS	C	T	18691	0.968594	0	6,0,18673,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749287	3575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	10710	7.47E-4	0	10702,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/ttTa	L287F?	nsp3	0.000594	0.059126	3	1	G>GT
ERR5749287	5388	PASS	C	A	4890	0.958691	0	1,0,4887,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749287	5497	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	4884	0.001638	0	0,4876,0,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	aga/	R928	nsp3	0.000964	0.897745	3	2	CA>C
ERR5749287	5986	PASS	C	T	10492	0.966737	0	2,0,10479,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749287	6091	PASS	C	T	10452	0.918485	0	0,0,12,10415	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N1124	nsp3	0.002493	0.918485	2	2	C>T
ERR5749287	6954	PASS	T	C	20043	0.814199	0	0,6,1,19931	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749287	7528	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14453	0.002698	0	43,14350,0,46	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V1603	nsp3	0.002527	0.916131	1	1	C>T
ERR5749287	7984	PASS	T	C	40362	0.986373	0	1,0,22862,17490	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaT/gaC	D1755	nsp3	0.986373	0.986373	1	1	T>C
ERR5749287	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	25038	7.99E-4	55	13015,12002,20,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749287	11287	PASS	GTCTGGTTTT	G	19426	0.997735	0	0,44,0,19382	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749287	11511	PASS	C	T	22628	0.119454	0	9843,9820,1451,1449	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T180I	nsp6	0.001772	0.119454	1	1	C>T
ERR5749287	11876	PASS	G	A	20141	0.924185	215	6,2,0,20102	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtc/Atc	V12I	nsp7	0.001696	0.924185	1	1	G>A
ERR5749287	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29150	0.001818	0	14550,14511,28,29	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749287	14120	PASS	C	T	27872	0.766002	12	2,8,13894,13619	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCa/cTa	P227L	RdRp	0.00121	0.786944	2	2	C>T
ERR5749287	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10917	0.003114	2315	10684,97,3,129	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749287	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	21283	0.00141	0	10665,10598,16,14	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749287	14408	PASS	C	T	21283	0.841282	2	7,9,10612,10487	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749287	14676	PASS	C	T	12391	0.79017	0	6,0,12346,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749287	15279	PASS	C	T	20554	0.888148	0	1,0,20522,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749287	16176	PASS	T	C	18273	0.981995	10	3,0,8100,10167	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749287	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	21454	6.99E-4	0	21439,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749287	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	23437	4.27E-4	0	3,23424,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749287	19390	PASS	C	T	14512	0.960033	2147483647	0,0,14494,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cca/Tca	P451S	ExoN	0.960033	0.960033	1	1	C>T
ERR5749287	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23844	0.001887	0	23781,0,49,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749287	21764	PASS	ATACATG	A	10205	0.99755	0	25,0,10180,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749287	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	10205	7.84E-4	0	10197,0,8,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749287	21990	PASS	TTTA	T	10212	0.998237	0	0,18,7,10187	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749287	23063	PASS	A	T	11575	0.87568	0	0,4,0,11520	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749287	23271	PASS	C	A	21443	0.92641	0	3,0,21417,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749287	23403	PASS	A	G	21441	0.972623	0	0,2,0,21428	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749287	23604	PASS	C	A	12877	0.94595	0	12,0,12857,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749287	23664	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25549	0.00638	0	12612,12732,87,88	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCa/gTa	A701V	S	0.000837	0.918	2	2	C>T
ERR5749287	23709	PASS	C	T	12867	0.947385	0	0,2,1,12853	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749287	24506	PASS	T	G	16696	0.975443	0	11,0,16684,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749287	24914	PASS	G	C	33222	0.960448	3	0,2,16556,16647	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749287	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	22665	0.001191	44	14656,7969,30,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749287	25413	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14735	0.022464	0	14375,0,344,0	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	atC/atT	I7	orf3a	0.00145	0.968329	2	1	C>T
ERR5749287	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	16088	0.001554	211	16026,9,17,9	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749287	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	39035	4.61E-4	0	0,39016,0,18	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749287	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	10263	0.001462	0	0,10248,0,15	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749287	27382	PASS	G	C	15532	0.923513	0	0,1,0,15516	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF6	Gat/Cat	D61H	orf6	0.001236	0.927964	2	2	G>C
ERR5749287	27383	PASS	A	T	15532	0.928985	0	0,14,0,15511	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF6	gAt/gTt	D61V	orf6	0.001454	0.928985	1	1	A>T
ERR5749287	27384	PASS	T	C	15532	0.877929	0	0,1,0,15500	LOW	SILENT	SYNONYMOUS_CODING	ORF6	gaT/gaC	D61	orf6	0.00154	0.931035	3	3	T>C
ERR5749287	27533	PASS	A	G	18311	0.124133	2	15970,7,2329,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	cAt/cGt	H47R	orf7a	0.124133	0.124133	1	1	A>G
ERR5749287	27972	PASS	C	T	8197	0.903135	21	0,1,8112,51	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749287	28048	PASS	G	T	8154	0.928869	0	0,6,0,8137	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749287	28095	PASS	A	T	8163	0.963126	109	3,0,0,8149	HIGH	NONSENSE	STOP_GAINED	ORF8	Aaa/Taa	K68*	orf8	0.002672	0.967672	2	2	A>T
ERR5749287	28111	PASS	A	G	28163	0.978447	0	4,1,19989,8156	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749287	28270	PASS	TA	T	38781	0.995513	394	171,7,19774,18833	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749287	28280	PASS	G	C	38704	0.933909	9	4,0,19809,18812	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749287	28281	PASS	A	T	38704	0.919931	33	18,2,19804,18822	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749287	28282	PASS	T	A	38706	0.910298	3	14,9,19745,18836	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749287	28881	PASS	G	A	14665	0.742039	33	11,0,7205,7220	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749287	28882	PASS	G	A	14665	0.825707	15	6,0,7336,7182	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749287	28883	PASS	G	C	14665	0.942789	3	2,0,7344,7301	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749287	28977	PASS	C	T	7462	0.937014	0	0,4,0,7446	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749287	29077	PASS	C	T	25457	0.88565	0	1,0,25337,3	LOW	SILENT	SYNONYMOUS_CODING	N	taC/taT	Y268	N	0.000408	0.88565	3	2	C>T
ERR5749287	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	50620	0.001008	0	25393,25143,33,31	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749288	241	PASS	C	T	2029	0.887629	0	0,0,1010,1008	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749288	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	2301	0.004781	0	2290,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749288	635	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2306	0.020382	0	0,2254,0,52	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgt/Tgt	R124C	leader	0.00148	0.880435	1	1	C>T
ERR5749288	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12787	0.001486	14	10460,2301,19,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L140	leader	0.000316	0.135802	3	2	C>T
ERR5749288	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	12787	0.00172	7	10460,2305,21,1	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749288	843	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTG	C	20905	8.13E-4	0	10456,10435,9,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctgat/	PD13	nsp2	0.000301	0.050923	4	2	CTG>C
ERR5749288	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10475	0.002482	0	0,10421,0,28	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749288	913	PASS	C	T	10475	0.916754	0	0,9,0,10450	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749288	1636	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAA	G	6371	0.00204	0	6357,1,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K278	nsp2	0.00204	0.963192	2	2	GAA>G
ERR5749288	1912	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	17474	0.001545	63	11071,6370,33,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcA	S369	nsp2	0.000681	0.08802	2	1	C>A
ERR5749288	2305	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTAAATAAATTTTTGGCTTTGTGTGCTGACTCTATCATTATTGGTGGAGCTAAACTTAAAGC	G	4690	0.002132	0	4680,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtaaataaatttttggctttgtgtgctgactctatcattattggtggagctaaacttaaagccttg/	VNKFLALCADSIIIGGAKLKAL502	nsp2	0.000443	0.070409	4	3	GCTTGTAAATAAATTTTTGGCTTTGTGTGCTGACTCTATCATTATTGGTGGAGCTAAACTTAAAGC>G
ERR5749288	3037	PASS	C	T	5272	0.817337	12	0,4,2637,2595	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749288	3267	PASS	C	T	10964	0.970996	2147483647	0,0,10958,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749288	3466	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	10968	0.002918	0	2,10919,0,36	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caT/caC	H249	nsp3	0.000976	0.051008	3	3	T>C
ERR5749288	4002	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	2734	0.003658	0	0,2721,0,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aAt	T428N	nsp3	0.001296	0.806154	2	1	C>A
ERR5749288	4317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	7530	0.002656	0	0,7493,0,29	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aGt/aTt	S533I	nsp3	0.001619	0.118421	2	1	G>T
ERR5749288	4586	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10313	0.001842	0	0,10284,0,20	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L623	nsp3	0.001842	0.935691	2	2	C>T
ERR5749288	5388	PASS	C	A	1287	0.964258	2147483647	0,0,1287,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749288	5784	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	18840	0.001486	161	9298,9482,0,55	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aAt	T1022N	nsp3	0.001294	0.919357	2	1	C>A
ERR5749288	5986	PASS	C	T	3461	0.973707	2147483647	0,0,3456,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749288	6274	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	14354	0.002508	0	14318,0,36,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1186	nsp3	0.000755	0.990148	2	2	TA>T
ERR5749288	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3866	0.004139	0	0,3808,0,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749288	6813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11603	0.003016	0	7696,3866,24,12	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T1365I	nsp3	0.001082	0.95799	2	1	C>T
ERR5749288	6954	PASS	T	C	7700	0.805714	0	0,2,0,7647	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749288	7097	PASS	A	G	998	0.980962	29	0,1,997,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Att/Gtt	I1460V	nsp3	0.980962	0.985062	1	1	A>G
ERR5749288	7735	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9196	0.017834	0	9022,0,169,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I1672	nsp3	0.000658	0.954659	3	2	C>T
ERR5749288	7926	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	9196	0.00174	0	0,9179,0,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCa/gAa	A1736E	nsp3	0.000531	0.97019	5	2	C>A
ERR5749288	7945	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	9196	0.002719	0	0,9166,0,29	HIGH	NONSENSE	STOP_GAINED	ORF1ab	taC/taA	Y1742*	nsp3	0.001244	0.950558	2	2	C>A
ERR5749288	8015	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	9091	0.00385	0	9044,4,36,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gcg/Ccg	A1766P	nsp3	0.00385	0.392265	3	2	G>C
ERR5749288	8084	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	9085	0.001541	0	9061,0,14,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E1789K	nsp3	0.000543	0.923413	4	2	G>A
ERR5749288	8964	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9604	0.003332	0	9565,2,33,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCa/tTa	S137L	nsp4	0.000553	0.981649	4	2	C>T
ERR5749288	9130	PASS	G	T	9594	0.963415	2147483647	0,0,0,9589	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtG/gtT	V192	nsp4	0.001321	0.963415	2	1	G>T
ERR5749288	9430	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1564	0.008951	0	0,1547,0,14	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I292	nsp4	0.001411	0.960894	1	1	C>T
ERR5749288	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	7403	0.003917	26	5804,1570,29,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749288	9559	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5834	0.002571	0	5781,1,17,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y335	nsp4	0.001348	0.062899	2	2	C>T
ERR5749288	9561	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5834	0.005485	0	5761,1,42,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCa/tTa	S336L	nsp4	0.00171	0.161742	2	2	C>T
ERR5749288	10386	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	18609	0.001021	9	10571,8019,7,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	tca/	S113	3Cpro	0.000642	0.160456	4	2	CT>C
ERR5749288	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	16401	0.002439	0	16336,0,61,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749288	11152	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16373	0.002687	0	16277,0,47,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V60	nsp6	0.000678	0.974465	2	2	C>T
ERR5749288	11287	PASS	GTCTGGTTTT	G	16396	0.998963	0	0,17,0,16379	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749288	11761	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	26583	0.00252	17	13241,13183,54,82	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaG/aaT	K263N	nsp6	0.000786	0.354576	2	2	G>T
ERR5749288	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	7585	0.002505	0	7565,0,19,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749288	13458	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9848	0.00264	0	9814,0,26,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCg/tTg	S6L	nsp11	0.001017	0.058608	4	2	C>T
ERR5749288	14098	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	7706	0.002595	0	7618,61,25,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggt/Tgt	G220C	RdRp	0.000806	0.065317	4	2	G>T
ERR5749288	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	5943	0.003534	1317	5758,93,3,83	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749288	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	11488	0.001741	0	5753,5722,10,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749288	14408	PASS	C	T	11488	0.849582	0	1,1,5732,5658	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749288	14676	PASS	C	T	7970	0.766876	0	1,0,7935,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749288	15279	PASS	C	T	6230	0.892456	2147483647	0,0,6224,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749288	15839	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	10676	0.001405	0	7,10612,0,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tGg/tTg	W800L	RdRp	0.001405	0.074516	2	1	G>T
ERR5749288	15905	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AGG	A	7131	0.002103	0	7116,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggt/	G823	RdRp	0.000835	0.057692	2	1	AGG>A
ERR5749288	16117	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	7132	0.001963	0	0,7099,0,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gat/Aat	D893N	RdRp	0.001841	0.244898	3	1	G>A
ERR5749288	16117	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	7132	0.001963	0	0,7099,0,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gat/Cat	D893H	RdRp	0.001841	0.244898	3	1	G>C
ERR5749288	16176	PASS	T	C	8858	0.978325	0	0,0,1726,7132	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749288	16466	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	15935	0.002134	20	14161,1726,47,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCa/cAa	P77Q	helicase	0.002134	0.96252	2	1	C>A
ERR5749288	16523	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	14209	0.001196	0	14177,0,30,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aAa	T96K	helicase	0.001196	0.056848	2	1	C>A
ERR5749288	16689	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	14190	0.00155	0	0,14168,0,22	HIGH	NONE	FRAME_SHIFT	ORF1ab	gct/	A152	helicase	0.00155	0.885448	2	2	TG>T
ERR5749288	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	9476	0.001161	0	9461,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749288	16946	PASS	C	T	9458	0.951893	0	1,0,9442,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCa/gTa	A237V	helicase	0.001418	0.951893	1	1	C>T
ERR5749288	17122	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCT	G	16444	5.47E-4	18	6969,9466,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctctac/	LY297	helicase	0.000476	0.056834	3	2	GCT>G
ERR5749288	17167	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6969	0.003874	0	6930,0,28,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cat/Tat	H311Y	helicase	0.001728	0.238095	1	1	C>T
ERR5749288	17615	PASS	A	G	7207	0.906757	0	0,1,0,7191	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749288	17756	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	5904	0.002033	0	5889,1,12,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aGa/aCa	R507T	helicase	0.000865	0.165644	4	2	G>C
ERR5749288	17964	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	5901	0.002203	0	0,5876,0,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atT	M576I	helicase	0.002203	0.846335	1	1	G>T
ERR5749288	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	15794	6.33E-4	0	15784,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749288	18713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15793	0.00133	0	15759,0,21,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCc/gTc	A225V	ExoN	0.00133	0.982769	1	1	C>T
ERR5749288	18744	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	15790	0.002913	0	15693,0,55,0	HIGH	NONSENSE	STOP_GAINED	ORF1ab	taC/taA	Y235*	ExoN	0.000912	0.953624	2	2	C>A
ERR5749288	18803	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	31526	0.001332	7	15681,15670,69,86	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aGc/aTc	S255I	ExoN	0.000786	0.897116	2	1	G>T
ERR5749288	19079	PASS	A	G	17126	0.963331	0	2,0,17121,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gAa/gGa	E347G	ExoN	0.001121	0.967175	2	1	A>G
ERR5749288	19096	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	17183	0.002037	0	17067,63,37,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gca/Aca	A353T	ExoN	0.000726	0.105058	3	2	G>A
ERR5749288	19343	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTTTTGTTAATTTAAAACAA	C	6759	0.002515	0	6742,0,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tttgttaatttaaaacaatta/	FVNLKQL436	ExoN	0.000519	0.192257	7	2	CTTTTGTTAATTTAAAACAA>C
ERR5749288	19656	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	8083	0.003959	0	8042,0,41,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaG/aaT	K12N	endoR	0.001929	0.189573	1	1	G>T
ERR5749288	19854	PASS	C	T	8085	0.964626	91	3,5,0,8048	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D78	endoR	0.950322	0.965654	1	1	C>T
ERR5749288	20420	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATT	A	15787	0.002914	0	0,15741,0,46	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F268	endoR	0.000383	0.069626	2	1	ATT>A
ERR5749288	21123	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	24471	0.001471	57	8139,16277,3,51	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggG/ggT	G155	MethTr	0.000257	0.90982	5	2	G>T
ERR5749288	21733	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	5728	0.00227	0	5701,6,19,0	LOW	SILENT	SYNONYMOUS_CODING	S	ccT/ccG	P57	S	0.001662	0.065814	2	1	T>G
ERR5749288	21764	PASS	ATACATG	A	5722	0.993883	0	35,0,5687,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749288	21987	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	5727	0.00227	0	5,5708,0,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gGt/gCt	G142A	S	0.000998	0.922156	5	2	G>C
ERR5749288	21990	PASS	TTTA	T	5727	0.999127	0	0,5,5,5717	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749288	22014	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	12467	0.006658	0	12363,3,97,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aGt/aTt	S151I	S	0.001357	0.20398	2	1	G>T
ERR5749288	22225	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	12457	0.002649	0	0,12415,0,34	LOW	SILENT	SYNONYMOUS_CODING	S	tcG/tcC	S221	S	0.001195	0.94526	3	1	G>C
ERR5749288	22295	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16490	0.001516	86	4005,12455,21,5	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Cat/Tat	H245Y	S	0.000662	0.930915	2	2	C>T
ERR5749288	22690	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	11886	0.00143	0	11703,1,18,0	LOW	SILENT	SYNONYMOUS_CODING	S	acT/acC	T376	S	0.000815	0.051311	2	1	T>C
ERR5749288	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	11913	0.003022	0	0,11853,0,46	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggT	G413	S	0.001101	0.887758	3	2	G>T
ERR5749288	22927	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	5967	0.001173	0	5960,0,7,0	HIGH	NONE	FRAME_SHIFT	S	ttt/	F456	S	0.000791	0.909717	4	3	GT>G
ERR5749288	23063	PASS	A	T	5951	0.879516	2147483647	0,0,0,5924	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749288	23271	PASS	C	A	19932	0.92364	0	2,0,19912,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749288	23294	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	19953	0.001754	0	19842,23,37,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gat/Cat	D578H	S	0.001754	0.102649	2	1	G>C
ERR5749288	23311	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	19934	0.001555	0	19824,23,34,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gaG/gaC	E583D	S	0.001115	0.705903	2	1	G>C
ERR5749288	23311	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	19934	0.001505	0	19824,23,51,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gaG/gaT	E583D	S	0.001115	0.705903	2	1	G>T
ERR5749288	23403	PASS	A	G	19930	0.966583	2147483647	0,0,0,19915	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749288	23604	PASS	C	A	5625	0.950222	0	6,0,5615,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749288	23709	PASS	C	T	5617	0.935019	0	0,5,0,5609	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749288	24506	PASS	T	G	8495	0.97422	2147483647	0,0,8495,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749288	24914	PASS	G	C	27329	0.955798	6	0,3,13617,13690	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749288	25395	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	12375	0.001616	0	12311,0,22,0	HIGH	MISSENSE	START_LOST	ORF3a	atG/atA	M1I	orf3a	0.001616	0.079175	2	1	G>A
ERR5749288	25395	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	12375	0.002424	0	12311,0,41,0	HIGH	MISSENSE	START_LOST	ORF3a	atG/atT	M1I	orf3a	0.001616	0.079175	2	1	G>T
ERR5749288	25469	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	12361	0.002184	0	12332,2,27,0	HIGH	NONE	FRAME_SHIFT	ORF3a	gat/	D27	orf3a	0.001214	0.959377	2	2	CAG>C
ERR5749288	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	2030	0.008374	290	1994,18,1,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749288	25710	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1996	0.004509	0	1984,0,11,0	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	ctC/ctT	L106	orf3a	0.002127	0.789778	2	2	C>T
ERR5749288	25904	PASS	C	T	1996	0.826152	32	1,0,0,1986	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	tCa/tTa	S171L	orf3a	0.000757	0.83473	1	1	C>T
ERR5749288	26091	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	11176	0.001611	0	11159,0,18,0	HIGH	NONE	FRAME_SHIFT	ORF3a	aat/	N234	orf3a	0.000569	0.128212	4	2	CA>C
ERR5749288	26158	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	11179	0.001342	0	0,11140,0,38	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gtt/Ttt	V256F	orf3a	0.000297	0.905181	6	2	G>T
ERR5749288	26159	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTAATCCAG	T	11179	0.001789	0	0,11159,0,20	HIGH	NONE	FRAME_SHIFT	ORF3a	ccagtaatg/	PVM258	orf3a	0.000311	0.053032	2	2	TTAATCCAG>T
ERR5749288	26208	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	11194	0.003037	0	3,11157,0,34	HIGH	NONE	FRAME_SHIFT	ORF3a	gtg/	V273	orf3a	0.000315	0.922222	2	2	CG>C
ERR5749288	26333	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6791	0.003681	0	6753,0,29,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	aCa/aTa	T30I	E	0.00158	0.943221	1	1	C>T
ERR5749288	26493	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	6791	0.002062	0	0,6757,0,18	.	.	.	.	.	.	.	0.001082	0.069277	3	1	G>A
ERR5749288	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	5601	0.001964	0	0,5590,0,11	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749288	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	5603	0.001249	0	0,5596,0,7	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749288	26958	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19491	0.001847	0	19451,0,36,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Cgt/Tgt	R146C	M	0.00096	0.122326	1	1	C>T
ERR5749288	27145	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	19500	0.00159	0	6,19463,0,31	HIGH	NONE	FRAME_SHIFT	M	gac/	D209	M	0.000476	0.863895	2	2	CAG>C
ERR5749288	27312	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	10525	0.001615	0	10499,0,21,0	LOW	SILENT	SYNONYMOUS_CODING	ORF6	atT/atA	I37	orf6	0.000911	0.088458	4	2	T>A
ERR5749288	27312	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	10524	0.001615	0	10508,0,17,0	HIGH	NONE	FRAME_SHIFT	ORF6	aat/aaAt	N39K?	orf6	0.000911	0.088458	4	2	T>TA
ERR5749288	27389	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10512	0.004566	0	0,10438,0,54	.	.	.	.	.	.	.	0.001157	0.899553	2	1	C>T
ERR5749288	27513	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	12724	0.002515	0	12682,1,38,0	HIGH	NONSENSE	STOP_GAINED	ORF7a	taC/taA	Y40*	orf7a	0.001863	0.982462	2	2	C>A
ERR5749288	27552	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATTTGCACTGACTTGCTTTAGCACTCAATTTGCTTTTGCTTGTCCTGACGGCGTAAAACACGTCTATCAG	A	12723	7.86E-4	0	12713,0,10,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF7a	tttgcactgacttgctttagcactcaatttgcttttgcttgtcctgacggcgtaaaacacgtctatcagtta/tta	FALTCFSTQFAFACPDGVKHVYQL54L	orf7a	0.000563	0.985801	6	1	ATTTGCACTGACTTGCTTTAGCACTCAATTTGCTTTTGCTTGTCCTGACGGCGTAAAACACGTCTATCAG>A
ERR5749288	27567	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTTTAGCACTCAATTTGCTT	C	12723	0.001886	0	12698,0,24,0	HIGH	NONE	FRAME_SHIFT	ORF7a	tttagcactcaatttgctttt/	FSTQFAF59	orf7a	0.000449	0.998291	4	1	CTTTAGCACTCAATTTGCTT>C
ERR5749288	27577	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAATTTGCTTTTGCTTGTCCTGACGGCGTAAAACACGTCTATCAGTT	C	12723	0.002672	0	12689,0,34,0	HIGH	NONE	FRAME_SHIFT	ORF7a	caatttgcttttgcttgtcctgacggcgtaaaacacgtctatcagtta/	QFAFACPDGVKHVYQL62	orf7a	0.000614	0.952205	4	2	CAATTTGCTTTTGCTTGTCCTGACGGCGTAAAACACGTCTATCAGTT>C
ERR5749288	27598	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GACGGCGTAAAACACGTCTA	G	12722	8.65E-4	0	12712,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF7a	gacggcgtaaaacacgtctat/	DGVKHVY69	orf7a	0.000699	0.958994	6	2	GACGGCGTAAAACACGTCTA>G
ERR5749288	27643	PASS	C	T	12693	0.717561	0	2,0,12561,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Cct/Tct	P84S	orf7a	0.00166	0.858006	2	1	C>T
ERR5749288	27672	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TCA	T	12741	0.00102	0	79,12649,0,13	HIGH	NONE	FRAME_SHIFT	ORF7a	caa/	Q94	orf7a	0.00102	0.999439	2	1	TCA>T
ERR5749288	27925	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	2782	0.014738	0	2739,0,43,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aCa/aAa	T11K	orf8	0.002789	0.084533	2	1	C>A
ERR5749288	27972	PASS	C	T	2807	0.914499	0	1,0,2772,27	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749288	28048	PASS	G	T	2782	0.94069	0	0,2,0,2779	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749288	28111	PASS	A	G	22653	0.97987	0	1,0,19859,2782	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749288	28198	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	19868	0.001913	0	19797,0,53,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tGt/tTt	C102F	orf8	0.000718	0.94386	4	2	G>T
ERR5749288	28209	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	19868	0.001409	0	19832,0,35,0	HIGH	NONSENSE	STOP_GAINED	ORF8	Gaa/Taa	E106*	orf8	0.001409	0.963166	2	2	G>T
ERR5749288	28227	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CATG	C	19867	9.06E-4	0	19849,0,18,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF8	catgac/cac	HD112H	orf8	0.000906	0.951206	2	2	CATG>C
ERR5749288	28250	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TG	19854	0.001209	0	19833,1,24,0	HIGH	NONE	FRAME_SHIFT	ORF8	ttc/Gttc	F120V?	orf8	0.000494	0.993968	5	3	T>TG
ERR5749288	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19853	0.010124	0	19578,1,214,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749288	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	19845	0.001209	0	19828,1,24,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749288	28270	PASS	TA	T	38576	0.994945	466	200,8,19593,18788	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749288	28271	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AA	A	38568	5.7E-4	62	19757,18796,22,0	.	.	.	.	.	.	.	0.000482	0.924941	3	2	AA>A
ERR5749288	28280	PASS	G	C	38507	0.939258	11	12,4,19651,18773	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749288	28281	PASS	A	T	38507	0.913211	40	23,3,19631,18780	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749288	28282	PASS	T	A	38509	0.913553	28	18,3,19608,18791	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749288	28287	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	39497	0.001975	0	19600,19740,45,43	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gGa/gAa	G5E	N	0.000961	0.079824	2	1	G>A
ERR5749288	28292	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	39515	5.82E-4	0	19696,19796,11,12	HIGH	NONE	FRAME_SHIFT	N	aat/	N8	N	0.000304	0.055324	4	2	CA>C
ERR5749288	28302	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	20076	0.001793	105	19666,19792,0,36	HIGH	NONE	FRAME_SHIFT	N	aat/	N11	N	0.001527	0.953728	4	2	GA>G
ERR5749288	28321	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	19861	8.06E-4	0	1,19844,0,16	HIGH	NONE	FRAME_SHIFT	N	ttt/	F17	N	0.00045	0.947809	3	2	GT>G
ERR5749288	28406	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTACCCAATA	T	19877	8.55E-4	0	7,19853,0,17	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	N	ttacccaataat/tat	LPNN45Y	N	0.00043	0.921074	3	2	TTACCCAATA>T
ERR5749288	28512	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13591	0.001398	0	13569,1,19,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	cCa/cTa	P80L	N	0.000621	0.172671	3	2	C>T
ERR5749288	28732	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17912	0.001117	18	4311,13572,10,10	LOW	SILENT	SYNONYMOUS_CODING	N	aaC/aaT	N153	N	0.000892	0.966905	2	2	C>T
ERR5749288	28881	PASS	G	A	8472	0.779273	9	4,0,4207,4162	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749288	28882	PASS	G	A	8472	0.826959	0	0,0,4247,4156	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749288	28883	PASS	G	C	8472	0.94771	0	1,0,4249,4219	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749288	28957	PASS	C	T	4319	0.950683	0	0,1,0,4313	LOW	SILENT	SYNONYMOUS_CODING	N	aaC/aaT	N228	N	0.01097	0.950683	1	1	C>T
ERR5749288	28977	PASS	C	T	4321	0.937746	2147483647	0,0,0,4315	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749288	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	39122	0.001457	0	19645,19392,34,33	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749288	29253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	19705	6.09E-4	0	0,19693,0,12	HIGH	NONE	FRAME_SHIFT	N	gga/	G328	N	0.000361	0.053998	4	2	CG>C
ERR5749289	219	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	12397	0.002823	3	6125,6222,19,25	.	.	.	.	.	.	.	0.001608	0.789851	2	1	G>T
ERR5749289	241	PASS	C	T	12368	0.854544	3	0,2,6099,6207	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749289	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	12580	0.001272	0	12569,0,16,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749289	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	12580	0.001669	0	12527,0,21,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749289	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	12580	0.001828	0	12527,0,23,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749289	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12570	0.001114	0	12022,1,462,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749289	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	12570	6.36E-4	0	12561,1,8,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749289	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	12568	6.37E-4	0	12555,3,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749289	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	33210	0.001054	18	20570,12594,29,6	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749289	913	PASS	C	T	20594	0.912256	0	0,8,0,20563	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749289	2305	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTAAATAAATTTTTGGCTTTGTGTGCTGACTCTATCATTATTGGTGGAGCTAAACTTAAAGC	G	17558	5.7E-4	0	17548,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtaaataaatttttggctttgtgtgctgactctatcattattggtggagctaaacttaaagccttg/	VNKFLALCADSIIIGGAKLKAL502	nsp2	0.000443	0.070409	4	3	GCTTGTAAATAAATTTTTGGCTTTGTGTGCTGACTCTATCATTATTGGTGGAGCTAAACTTAAAGC>G
ERR5749289	3037	PASS	C	T	22647	0.811189	42	2,20,11311,11140	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749289	3267	PASS	C	T	19376	0.971821	0	2,0,19366,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749289	3743	PASS	C	T	13806	0.893235	0	0,2,0,13755	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cat/Tat	H342Y	nsp3	0.00405	0.893235	1	1	C>T
ERR5749289	5388	PASS	C	A	7604	0.957785	0	1,0,7598,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749289	5672	PASS	C	A	19814	0.974866	0	9,0,19801,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cct/Act	P985T	nsp3	0.004226	0.977953	2	1	C>A
ERR5749289	5986	PASS	C	T	13438	0.973731	2147483647	0,0,13429,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749289	6954	PASS	T	C	20588	0.820381	0	0,5,3,20480	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749289	7764	PASS	C	T	21326	0.960471	0	2,0,21305,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCc/tTc	S1682F	nsp3	0.001052	0.964731	1	1	C>T
ERR5749289	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	34162	0.001288	133	16919,17199,44,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749289	11287	PASS	GTCTGGTTTT	G	17858	0.997536	0	0,44,0,17814	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749289	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29408	9.18E-4	0	14692,14655,15,15	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749289	13623	PASS	A	G	14726	0.931889	0	0,2,0,14697	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaA/gaG	E61	RdRp	0.00237	0.931889	2	2	A>G
ERR5749289	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	17674	0.00464	2147483647	17241,129,9,284	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749289	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	34310	5.83E-4	0	17219,17091,11,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749289	14408	PASS	C	T	34310	0.850277	14	2,9,17137,16905	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749289	14676	PASS	C	T	12930	0.729466	0	4,0,12872,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749289	15279	PASS	C	T	22261	0.885719	0	1,0,22217,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749289	16176	PASS	T	C	20716	0.981126	0	1,0,10880,9825	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749289	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	32282	0.002478	0	32173,0,82,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749289	21764	PASS	ATACATG	A	13312	0.995267	0	63,0,13249,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749289	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	13311	6.76E-4	0	13302,0,9,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749289	21990	PASS	TTTA	T	13314	0.998423	0	0,21,2,13291	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749289	23063	PASS	A	T	11895	0.862043	0	0,0,1,11829	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749289	23271	PASS	C	A	20934	0.913108	0	1,0,20916,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749289	23403	PASS	A	G	20932	0.966702	0	0,6,1,20910	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749289	23604	PASS	C	A	16328	0.94194	0	16,0,16307,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749289	23709	PASS	C	T	16317	0.940859	0	0,7,4,16289	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749289	24506	PASS	T	G	17805	0.97321	0	5,0,17799,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749289	24914	PASS	G	C	34909	0.960297	0	0,0,17390,17495	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749289	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	24704	0.001012	303	24606,12,15,12	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749289	25782	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24666	9.32E-4	0	24570,1,25,0	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	tgC/tgT	C130	orf3a	0.000916	0.955348	1	1	C>T
ERR5749289	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	24908	0.001245	1291	24455,185,139,97	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749289	25915	PASS	A	G	24690	0.972661	335	12,33,0,24625	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Aca/Gca	T175A	orf3a	0.967777	0.972774	1	1	A>G
ERR5749289	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	11198	0.001518	0	5,11174,0,17	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749289	26927	PASS	A	G	29494	0.979284	0	4,0,29478,0	LOW	SILENT	SYNONYMOUS_CODING	M	gaA/gaG	E135	M	0.001168	0.979284	1	1	A>G
ERR5749289	27972	PASS	C	T	10607	0.901857	58	3,3,10519,43	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749289	28048	PASS	G	T	10576	0.922561	0	0,11,0,10562	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749289	28111	PASS	A	G	26319	0.978913	1	3,1,15718,10588	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749289	28270	PASS	TA	T	30539	0.994663	415	169,5,15512,14864	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749289	28280	PASS	G	C	30468	0.937705	19	16,4,15540,14849	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749289	28281	PASS	A	T	30468	0.908199	22	21,6,15544,14855	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749289	28282	PASS	T	A	30469	0.89573	10	19,9,15470,14855	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749289	28881	PASS	G	A	16964	0.674664	161	75,0,9833,6456	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749289	28881	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	16964	0.001592	39	75,0,489,72	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aCg	R203T	N	0.000709	0.947368	4	2	G>C
ERR5749289	28882	PASS	G	A	16960	0.755837	118	63,1,10204,6432	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749289	28883	PASS	G	C	16961	0.916927	12	10,1,10403,6533	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749289	28977	PASS	C	T	6701	0.930458	0	0,0,12,6672	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749289	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	42204	0.001185	1	22764,19355,32,30	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749290	241	PASS	C	T	3122	0.875721	0	1,1,1555,1555	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749290	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	9180	0.001198	0	9165,0,11,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749290	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGTT	A	9180	8.71E-4	0	9165,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	catggtcatgttatggtt/	HGHVMV81	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGTT>A
ERR5749290	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	9180	0.001961	0	9150,0,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749290	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	9172	0.002399	0	8395,0,710,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749290	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	9171	8.72E-4	0	9163,0,8,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749290	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	22848	4.38E-4	12	13638,9192,9,1	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749290	913	PASS	C	T	13647	0.911189	0	0,6,0,13605	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749290	1368	PASS	T	C	14929	0.925045	0	4,0,14899,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTt/aCt	I188T	nsp2	0.925045	0.945837	1	1	T>C
ERR5749290	2706	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	41237	0.00114	0	20688,20472,32,30	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T634I	nsp2	0.000591	0.821437	1	1	C>T
ERR5749290	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	41272	0.002011	2147483647	20605,19128,39,1386	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749290	2862	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	29226	5.47E-4	22	8467,20743,0,16	HIGH	NONE	FRAME_SHIFT	ORF1ab	gaa/	E49	nsp3	0.000547	0.850688	4	2	CAG>C
ERR5749290	3037	PASS	C	T	16811	0.816549	18	0,6,8396,8289	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749290	3267	PASS	C	T	14365	0.969788	2147483647	0,0,14359,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749290	3802	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	19689	7.62E-4	5	8738,10936,9,6	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N363	nsp3	0.000554	0.064198	4	2	TA>T
ERR5749290	5388	PASS	C	A	5195	0.964966	0	1,0,5192,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749290	5497	PASS	C	T	5186	0.88951	0	0,3,0,5172	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C926	nsp3	0.000964	0.897745	3	2	C>T
ERR5749290	5784	PASS	C	T	25557	0.919357	15	0,6,12607,12902	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T1022I	nsp3	0.001294	0.919357	2	1	C>T
ERR5749290	5849	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13010	0.00146	0	3,12955,0,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cct/Tct	P1044S	nsp3	0.00146	0.830206	2	1	C>T
ERR5749290	5986	PASS	C	T	12508	0.975775	2147483647	0,0,12501,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749290	6205	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	30211	4.63E-4	31	17687,12510,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1163	nsp3	0.000463	0.134216	1	1	GA>G
ERR5749290	6954	PASS	T	C	15146	0.810247	0	0,2,1,15061	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749290	7936	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	18597	0.001237	0	0,18566,0,31	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcG/gcT	A1739	nsp3	0.001237	0.911187	1	1	G>T
ERR5749290	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	19381	0.00356	54	15957,3355,69,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749290	9661	PASS	C	T	30956	0.91714	25	1,11,15962,14885	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F369	nsp4	0.000584	0.920378	2	2	C>T
ERR5749290	10138	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	26208	4.58E-4	8	20808,5388,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggt/	G29	3Cpro	0.000458	0.983567	3	3	CG>C
ERR5749290	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	20259	0.002271	0	19723,1,46,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749290	11287	PASS	GTCTGGTTTT	G	20244	0.998864	0	0,23,0,20221	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749290	11355	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	30802	4.55E-4	0	10540,20248,5,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	aga/	R129	nsp6	0.000455	0.982262	3	2	CA>C
ERR5749290	11690	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGT	G	17598	9.66E-4	0	17572,9,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/	V241	nsp6	0.000953	0.091324	4	2	GGT>G
ERR5749290	11750	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34318	0.001166	1	17501,16717,29,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L260F	nsp6	0.001019	0.70989	2	1	C>T
ERR5749290	12459	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	35815	9.77E-4	7	20326,15441,16,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T123I	nsp8	0.000658	0.986093	1	1	C>T
ERR5749290	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	17366	6.33E-4	0	17355,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749290	13208	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAT	A	34624	6.35E-4	0	17317,17287,11,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	atg/	M63	nsp10	0.000407	0.953357	4	2	AAT>A
ERR5749290	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23886	0.001214	0	11937,11889,15,16	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749290	13665	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8798	0.002046	0	8778,0,18,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H75	RdRp	0.002046	0.977554	1	1	C>T
ERR5749290	14168	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	13372	9.72E-4	0	0,13359,0,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	atatta/	IL244	RdRp	0.000479	0.314961	1	1	CTA>C
ERR5749290	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12658	0.004108	2147483647	12351,108,4,191	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749290	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	24588	8.54E-4	0	12327,12245,11,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749290	14408	PASS	C	T	24588	0.837238	9	0,3,12281,12109	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749290	14676	PASS	C	T	9684	0.775712	0	6,0,9634,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749290	15246	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	12916	0.001703	678	12871,8,0,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttA/ttT	L602F	RdRp	0.001432	0.633333	1	1	A>T
ERR5749290	15279	PASS	C	T	12883	0.892028	0	2,0,12866,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749290	15905	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AG	A	8433	0.002134	0	8415,0,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggt/	G823	RdRp	0.000835	0.057692	2	1	AG>A
ERR5749290	16176	PASS	T	C	15110	0.979285	0	0,1,6673,8431	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749290	18403	PASS	A	G	20890	0.978459	0	12,0,20829,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Aca/Gca	T122A	ExoN	0.975463	0.978459	1	1	A>G
ERR5749290	18636	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	51407	6.61E-4	9	30481,20880,25,9	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtG/gtA	V199	ExoN	0.00055	0.963467	3	2	G>A
ERR5749290	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	30512	0.001409	0	30469,0,43,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749290	18756	PASS	G	T	30497	0.936354	0	35,0,30408,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccG/ccT	P239	ExoN	0.000392	0.942688	3	2	G>T
ERR5749290	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18271	0.002737	0	18207,0,53,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749290	20091	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	18234	5.48E-4	0	0,18224,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	caa/Acaa	Q159T?	endoR	0.000368	0.051583	1	1	C>CA
ERR5749290	20233	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	23865	9.64E-4	0	23823,3,35,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ccc/Acc	P205T	endoR	0.000964	0.980008	2	1	C>A
ERR5749290	21094	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGAGGGTT	A	18286	0.001312	0	3,18259,0,24	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	aaagagggtttt/att	KEGF146I	MethTr	0.000554	0.211111	5	2	AAAGAGGGTT>A
ERR5749290	21255	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	53585	0.001026	2	27783,25727,35,28	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcG/gcA	A199	MethTr	0.000341	0.917425	4	2	G>A
ERR5749290	21304	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	27806	0.001223	0	3,27728,0,57	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgc/Agc	R216S	MethTr	0.000411	0.605296	3	2	C>A
ERR5749290	21305	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	27806	0.001726	0	3,27710,0,56	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cGc/cAc	R216H	MethTr	0.000727	0.703943	1	1	G>A
ERR5749290	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	21967	0.035872	2461	10968,10028,0,788	HIGH	NONE	FRAME_SHIFT	S	ctt/Tctt	L5S?	S	0.000394	0.091869	4	1	G>GT
ERR5749290	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GTT	21967	0.006146	431	10968,10028,0,135	HIGH	NONE	FRAME_SHIFT	S	ctt/TTctt	L5F?	S	0.000394	0.091869	4	1	G>GTT
ERR5749290	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GTTT	21967	0.001184	83	10968,10028,0,26	MODERATE	NONE	CODON_INSERTION	S	ctt/TTTctt	L5FL	S	0.000394	0.091869	4	1	G>GTTT
ERR5749290	21575	PASS	C	T	20808	0.85025	0	1,1,9531,10799	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749290	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	20798	0.004568	263	9783,10877,0,95	HIGH	NONE	FRAME_SHIFT	S	gtt/Tgtt	V6C?	S	0.000619	0.877942	3	2	C>CT
ERR5749290	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	20798	0.001971	112	9783,10877,0,41	HIGH	NONE	FRAME_SHIFT	S	gtt/TTgtt	V6L?	S	0.000619	0.877942	3	2	C>CTT
ERR5749290	21764	PASS	ATACATG	A	14975	0.996461	0	53,0,14922,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749290	21990	PASS	TTTA	T	14982	0.997797	0	0,33,7,14942	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749290	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	15114	0.001257	0	0,15070,0,20	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749290	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	31547	0.001078	15	16386,15099,25,10	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749290	23063	PASS	A	T	16402	0.854286	0	0,5,9,16294	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749290	23271	PASS	C	A	16835	0.921414	2147483647	0,0,16820,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749290	23403	PASS	A	G	16829	0.968269	0	0,1,0,16815	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749290	23604	PASS	C	A	16088	0.929015	0	14,0,16062,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749290	23709	PASS	C	T	16071	0.930869	0	0,3,0,16048	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749290	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	24772	9.69E-4	10	8674,16074,4,20	HIGH	NONE	FRAME_SHIFT	S	ttg/	L753	S	0.000334	0.080808	2	2	CT>C
ERR5749290	24320	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	13516	0.001184	0	0,13463,0,16	HIGH	NONE	FRAME_SHIFT	S	aaa/	K921	S	0.000763	0.138365	4	2	CAA>C
ERR5749290	24382	PASS	C	T	13550	0.907823	0	0,8,0,13505	LOW	SILENT	SYNONYMOUS_CODING	S	tcC/tcT	S940	S	0.002118	0.920404	2	1	C>T
ERR5749290	24506	PASS	T	G	14282	0.974373	0	2,0,14279,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749290	24914	PASS	G	C	48318	0.958318	3	1,0,24076,24216	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749290	25531	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATTGTTGGCGTTGCACTTCTTGCTGT	A	23917	5.02E-4	0	1,23904,0,12	HIGH	NONE	FRAME_SHIFT	ORF3a	gttggcgttgcacttcttgctgttttt/	VGVALLAVF48	orf3a	0.000473	0.975891	5	2	ATTGTTGGCGTTGCACTTCTTGCTGT>A
ERR5749290	25572	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	23946	5.43E-4	0	0,23933,0,13	HIGH	NONE	FRAME_SHIFT	ORF3a	atc/	I62	orf3a	0.000543	0.959687	4	2	CA>C
ERR5749290	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	8280	0.002657	481	8216,26,1,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749290	25685	PASS	C	T	8233	0.959674	0	5,0,8227,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	gCt/gTt	A98V	orf3a	0.002048	0.964351	1	1	C>T
ERR5749290	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	39237	3.31E-4	0	0,39224,0,13	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749290	26493	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	9299	0.002473	0	0,9276,0,23	.	.	.	.	.	.	.	0.001082	0.069277	3	1	GT>G
ERR5749290	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	15318	6.53E-4	0	0,15302,0,10	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749290	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	15320	7.18E-4	0	0,15309,0,11	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749290	27972	PASS	C	T	10647	0.903447	18	1,1,10530,73	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749290	28048	PASS	G	T	10571	0.919118	0	0,14,0,10551	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749290	28111	PASS	A	G	29136	0.9757	1	8,3,18538,10578	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749290	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18527	0.002051	0	18440,2,39,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749290	28270	PASS	TA	T	35856	0.995203	373	167,8,18303,17381	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749290	28280	PASS	G	C	35788	0.936655	16	13,3,18344,17356	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749290	28281	PASS	A	T	35788	0.915083	41	26,4,18331,17358	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749290	28282	PASS	T	A	35790	0.907572	2	23,17,18299,17369	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749290	28881	PASS	G	A	11893	0.772135	15	6,0,5896,5843	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749290	28882	PASS	G	A	11892	0.822822	2	3,1,5946,5821	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749290	28883	PASS	G	C	11892	0.943744	3	2,0,5956,5923	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749290	28977	PASS	C	T	6073	0.92442	2147483647	0,0,0,6061	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749290	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	42315	8.74E-4	290	36204,6029,3,39	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749290	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	71859	0.0016	0	36095,35578,72,67	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749291	239	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTC	T	20197	4.95E-4	0	10060,10127,5,5	.	.	.	.	.	.	.	0.000495	0.25	4	1	TTC>T
ERR5749291	241	PASS	C	T	20193	0.853959	0	2,2,10030,10064	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749291	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	15274	0.001309	0	15257,5,20,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749291	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	15274	6.55E-4	0	15216,5,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749291	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	15274	6.55E-4	0	15216,5,10,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749291	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	15274	0.001964	0	15216,5,30,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749291	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	15264	0.002293	0	13943,5,1222,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749291	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	15264	0.001114	0	15242,5,17,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749291	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	15262	6.55E-4	0	15245,5,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749291	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	35535	0.001182	28	20188,15300,34,8	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749291	913	PASS	C	T	20220	0.922997	0	0,9,0,20184	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749291	1027	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	15821	0.001454	222	15764,18,13,10	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccT/ccC	P74	nsp2	0.001454	0.276316	1	1	T>C
ERR5749291	1461	PASS	A	G	37897	0.90899	9	10,4,18637,19162	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K219R	nsp2	0.000518	0.90899	2	2	A>G
ERR5749291	1599	PASS	G	T	39618	0.961507	43	0,14,20237,19350	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGt/gTt	G265V	nsp2	0.001427	0.96468	2	1	G>T
ERR5749291	3037	PASS	C	T	21425	0.826091	38	1,16,10707,10557	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749291	3267	PASS	C	T	18807	0.968629	0	1,0,18796,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749291	3335	PASS	G	A	36660	0.891789	33	18,2,18707,17817	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E206K	nsp3	0.001289	0.891976	4	3	G>A
ERR5749291	4999	PASS	C	T	11099	0.935129	129	4,4,11085,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N760	nsp3	0.001692	0.947468	1	1	C>T
ERR5749291	5388	PASS	C	A	6552	0.955586	2147483647	0,0,6549,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749291	5986	PASS	C	T	10149	0.976057	2147483647	0,0,10141,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749291	6954	PASS	T	C	18174	0.823154	0	0,3,1,18068	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749291	7239	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	46462	6.46E-4	0	23011,23198,17,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCa/gTa	A1507V	nsp3	0.000568	0.901952	2	2	C>T
ERR5749291	8084	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	23131	8.65E-4	0	23116,0,20,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1790	nsp3	0.000543	0.923413	4	2	GA>G
ERR5749291	9541	PASS	C	T	38056	0.95412	0	3,4,18860,19153	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ctC/ctT	L329	nsp4	0.000346	0.955771	2	2	C>T
ERR5749291	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	38056	6.04E-4	70	18862,19169,23,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749291	10165	PASS	C	T	18482	0.967915	226	7,7,18427,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y37	3Cpro	0.000632	0.976163	2	2	C>T
ERR5749291	11104	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	19172	0.001356	0	19062,0,27,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccT/ccC	P44	nsp6	0.000866	0.675414	2	1	T>C
ERR5749291	11287	PASS	GTCTGGTTTT	G	19164	0.998382	27	1,31,0,19133	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749291	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	36339	9.36E-4	4	19802,16469,16,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749291	12125	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	18298	0.001366	0	4,18221,0,29	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y12H	nsp8	0.000847	0.113436	1	1	T>C
ERR5749291	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	21104	0.002417	0	21020,0,52,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749291	12884	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	17520	0.001655	0	17471,0,32,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Aca/Gca	T67A	nsp9	0.001655	0.08541	1	1	A>G
ERR5749291	12961	PASS	A	G	17511	0.923934	0	0,6,0,17487	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaA/aaG	K92	nsp9	0.00128	0.923934	1	1	A>G
ERR5749291	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	13906	8.63E-4	0	13894,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749291	13208	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAT	A	27705	4.69E-4	0	13851,13846,7,6	HIGH	NONE	FRAME_SHIFT	ORF1ab	atg/	M63	nsp10	0.000407	0.953357	4	2	AAT>A
ERR5749291	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	31360	0.001148	0	15657,15634,19,20	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749291	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	18453	0.003631	2147483647	18073,115,3,251	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749291	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	36027	4.16E-4	0	18061,17973,8,7	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749291	14408	PASS	C	T	36027	0.846282	6	1,4,17980,17803	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749291	14676	PASS	C	T	12948	0.793095	0	6,0,12911,3	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749291	15279	PASS	C	T	23455	0.88706	0	8,0,23412,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749291	15983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	10761	0.001022	0	10750,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T850	RdRp	0.000701	0.338235	2	1	TA>T
ERR5749291	16176	PASS	T	C	22945	0.984136	0	0,0,12157,10781	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749291	17615	PASS	A	G	17328	0.92111	0	0,1,9,17274	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749291	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27144	8.84E-4	0	27101,3,24,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749291	21077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	19324	5.69E-4	0	11,19302,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K141	MethTr	0.000492	0.955529	4	2	CA>C
ERR5749291	21302	PASS	C	T	29650	0.843069	0	0,25,3,29497	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCa/cTa	P215L	MethTr	0.001031	0.843069	1	1	C>T
ERR5749291	21304	PASS	C	A	29650	0.584486	0	0,1087,3,28546	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgc/Agc	R216S	MethTr	0.000411	0.605296	3	2	C>A
ERR5749291	21305	PASS	G	A	29650	0.680438	0	0,7,3,29056	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cGc/cAc	R216H	MethTr	0.000727	0.703943	1	1	G>A
ERR5749291	21375	PASS	G	A	29755	0.856898	0	0,2,7,29669	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttG/ttA	L239	MethTr	0.002365	0.858793	2	2	G>A
ERR5749291	21727	PASS	C	T	12457	0.878141	0	2,0,12434,0	LOW	SILENT	SYNONYMOUS_CODING	S	ttC/ttT	F55	S	0.000896	0.878141	2	2	C>T
ERR5749291	21764	PASS	ATACATG	A	12457	0.996869	0	39,0,12418,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749291	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	12458	9.63E-4	0	12446,0,12,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749291	21990	PASS	TTTA	T	12466	0.998315	0	0,21,5,12440	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749291	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	13971	0.001432	0	0,13945,0,21	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749291	23063	PASS	A	T	522	0.858238	2147483647	0,0,0,521	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749291	23122	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	535	0.016822	179	1,523,9,0	LOW	SILENT	SYNONYMOUS_CODING	S	gcA/gcC	A520	S	0.002483	0.155172	2	1	A>C
ERR5749291	23191	PASS	C	T	22135	0.963226	0	1,0,22111,1	LOW	SILENT	SYNONYMOUS_CODING	S	ttC/ttT	F543	S	0.000538	0.973337	2	2	C>T
ERR5749291	23271	PASS	C	A	22128	0.910656	0	3,0,22092,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749291	23403	PASS	A	G	22116	0.975222	0	0,2,0,22097	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749291	23604	PASS	C	A	16601	0.93404	0	12,0,16576,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749291	23709	PASS	C	T	16580	0.942159	0	0,4,4,16547	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749291	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	33158	4.52E-4	5	16549,16594,5,10	HIGH	NONE	FRAME_SHIFT	S	ttg/	L753	S	0.000334	0.080808	2	2	CT>C
ERR5749291	23817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	33158	0.001176	7	16524,16573,25,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTt/cCt	L752P	S	0.000646	0.066832	1	1	T>C
ERR5749291	24506	PASS	T	G	19003	0.973425	0	5,0,18994,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749291	24914	PASS	G	C	41698	0.960742	6	2,0,20763,20899	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749291	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	23318	0.001758	352	23204,20,27,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749291	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	23443	0.001109	967	23070,152,115,71	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749291	26270	PASS	C	T	66572	0.926996	0	1,8,10890,55608	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	aCa/aTa	T9I	E	0.000586	0.930791	3	2	C>T
ERR5749291	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	14045	0.001068	0	1,14027,0,15	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749291	27643	PASS	C	T	20414	0.763692	0	4,0,20232,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Cct/Tct	P84S	orf7a	0.00166	0.858006	2	1	C>T
ERR5749291	27881	PASS	C	T	11967	0.965238	0	131,0,11833,0	LOW	SILENT	SYNONYMOUS_CODING	ORF7b	caC/caT	H42	orf7b	0.001798	0.979167	2	2	C>T
ERR5749291	27972	PASS	C	T	12021	0.903918	72	3,4,11881,72	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749291	28048	PASS	G	T	11953	0.923952	0	0,20,0,11923	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749291	28111	PASS	A	G	30907	0.979228	0	3,2,18925,11962	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749291	28270	PASS	TA	T	36916	0.994582	447	188,7,18676,18040	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749291	28280	PASS	G	C	36835	0.938238	21	8,0,18713,18031	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749291	28281	PASS	A	T	36835	0.916275	28	28,8,18706,18031	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749291	28282	PASS	T	A	36836	0.909002	20	28,11,18669,18037	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749291	28881	PASS	G	A	16923	0.722331	39	13,0,8253,8351	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749291	28882	PASS	G	A	16921	0.819869	30	11,0,8417,8325	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749291	28883	PASS	G	C	16921	0.940134	0	0,0,8447,8454	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749291	28977	PASS	C	T	8620	0.936775	0	0,2,0,8604	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749291	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	57068	8.59E-4	1	28650,28335,27,29	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749292	179	PASS	T	G	5018	0.857912	0	7,0,5006,0	.	.	.	.	.	.	.	0.850195	0.857981	1	1	T>G
ERR5749292	241	PASS	C	T	9996	0.871349	0	0,0,4972,4982	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749292	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	5685	0.004046	0	5662,0,23,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749292	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	5685	0.001231	0	5655,0,7,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749292	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	5685	0.003342	0	5655,0,19,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749292	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	5681	0.001232	0	5666,2,7,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749292	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	27390	5.11E-4	10	21685,5692,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749292	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	27390	0.001716	6	21643,5682,41,6	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749292	913	PASS	C	T	21684	0.918004	0	0,14,0,21643	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749292	1813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	12292	0.00179	0	2,12253,0,26	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcA	A336	nsp2	0.001022	0.152738	4	2	T>A
ERR5749292	2445	PASS	C	T	8147	0.697189	0	0,8,0,8038	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T547I	nsp2	0.001663	0.815808	1	1	C>T
ERR5749292	3037	PASS	C	T	9812	0.814717	33	0,11,4902,4824	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749292	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	4969	0.004629	573	5,4936,24,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749292	3267	PASS	C	T	19469	0.968257	0	4,0,19457,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749292	4136	PASS	G	T	28651	0.972776	0	1,3,11167,17462	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Ttt	V473F	nsp3	0.00075	0.974623	4	2	G>T
ERR5749292	5388	PASS	C	A	3071	0.965484	2147483647	0,0,3071,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749292	5986	PASS	C	T	6754	0.974978	2147483647	0,0,6751,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749292	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6608	0.001967	0	5,6534,0,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749292	6954	PASS	T	C	18461	0.821461	0	0,5,0,18360	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749292	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	22733	0.002243	0	22121,1,51,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749292	11082	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	22727	5.28E-4	0	22720,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000427	0.179468	2	1	TG>T
ERR5749292	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	22727	0.003124	0	22618,0,91,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749292	11287	PASS	GTCTGGTTTT	G	22720	0.997667	0	0,53,0,22667	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749292	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	41050	0.001364	0	20487,20442,30,31	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749292	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	3321	0.004818	855	3231,36,2,51	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749292	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	6431	0.001088	0	3227,3200,4,3	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749292	14408	PASS	C	T	6431	0.858964	3	0,1,3216,3175	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749292	14676	PASS	C	T	15143	0.734003	0	3,0,15073,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749292	15279	PASS	C	T	22331	0.879719	0	5,0,22292,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749292	16176	PASS	T	C	16401	0.982135	2	2,2,4809,11581	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749292	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15439	0.001231	0	15409,0,20,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749292	20420	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATT	A	24146	4.97E-4	0	30,24102,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F268	endoR	0.000383	0.069626	2	1	ATT>A
ERR5749292	21034	PASS	C	T	21283	0.908941	0	0,9,0,21226	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L126F	MethTr	0.001871	0.915185	1	1	C>T
ERR5749292	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	21300	6.1E-4	0	0,21286,0,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TA>T
ERR5749292	21764	PASS	ATACATG	A	7243	0.997239	0	20,0,7223,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749292	21990	PASS	TTTA	T	7248	0.997517	0	0,18,4,7226	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749292	22927	PASS	G	T	8629	0.908912	0	17,0,8601,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	ttG/ttT	L455F	S	0.000791	0.909717	4	3	G>T
ERR5749292	23063	PASS	A	T	8613	0.848601	2147483647	0,0,0,8572	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749292	23271	PASS	C	A	25078	0.921605	0	3,0,25049,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749292	23403	PASS	A	G	25069	0.972955	0	0,7,0,25046	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749292	23604	PASS	C	A	8991	0.944055	0	5,0,8976,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749292	23709	PASS	C	T	8985	0.941458	0	0,1,0,8976	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749292	24127	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	22131	4.52E-4	10	7338,14793,6,4	HIGH	NONE	FRAME_SHIFT	S	aac/	N856	S	0.000324	0.111888	4	1	TA>T
ERR5749292	24506	PASS	T	G	19770	0.974912	0	7,0,19761,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749292	24914	PASS	G	C	25137	0.958308	0	0,0,12529,12591	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749292	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	20027	0.001198	65	11572,8417,33,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749292	25429	PASS	G	T	11680	0.906678	0	14,0,11647,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gta/Tta	V13L	orf3a	0.00064	0.906678	5	2	G>T
ERR5749292	25954	PASS	G	T	40640	0.983612	2	2,0,25337,15289	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Ggt/Tgt	G188C	orf3a	0.983612	0.984476	1	1	G>T
ERR5749292	26510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	12952	0.001235	0	0,12922,0,16	.	.	.	.	.	.	.	0.001235	0.933642	2	1	T>C
ERR5749292	26526	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	12955	0.001312	0	1,12920,0,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Gca/Aca	A2T	M	0.001224	0.951192	3	1	G>A
ERR5749292	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	7037	9.95E-4	0	0,7030,0,7	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749292	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	7039	0.002841	0	0,7019,0,20	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749292	27972	PASS	C	T	5210	0.891171	0	1,0,5171,19	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749292	28005	PASS	C	T	9901	0.778911	10	704,713,4003,4474	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	Cct/Tct	P38S	orf8	0.007524	0.778911	1	1	C>T
ERR5749292	28048	PASS	G	T	5198	0.921124	0	0,10,0,5187	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749292	28111	PASS	A	G	26541	0.98037	1	9,3,21321,5199	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749292	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	21310	4.69E-4	0	21307,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749292	28270	PASS	TA	T	41288	0.994115	637	250,5,21000,20045	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749292	28280	PASS	G	C	41198	0.937376	41	15,0,21063,20020	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749292	28281	PASS	A	T	41198	0.913685	36	35,9,21042,20018	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749292	28282	PASS	T	A	41201	0.910463	8	30,18,21022,20033	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749292	28881	PASS	G	A	11917	0.728707	14	7,1,5784,5905	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749292	28882	PASS	G	A	11915	0.82501	15	6,0,5900,5866	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749292	28883	PASS	G	C	11915	0.942006	3	1,0,5913,5973	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749292	28977	PASS	C	T	5994	0.942276	0	0,4,0,5984	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749292	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	39664	0.001412	0	19917,19658,34,35	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749293	241	PASS	C	T	20693	0.858841	2	1,3,10242,10346	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749293	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	12341	0.001215	0	12332,0,15,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749293	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	12341	0.001134	0	12323,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749293	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12329	0.001947	0	11349,0,937,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749293	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	36080	4.71E-4	3	23696,12358,13,4	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749293	823	PASS	C	T	23678	0.870513	0	1,0,23615,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V6	nsp2	0.001213	0.901722	1	1	C>T
ERR5749293	913	PASS	C	T	23707	0.91551	0	0,9,0,23669	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749293	3037	PASS	C	T	18279	0.820942	38	1,16,9123,9020	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749293	3267	PASS	C	T	18993	0.972095	0	4,0,18981,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749293	3743	PASS	C	T	9295	0.882733	0	0,2,0,9259	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cat/Tat	H342Y	nsp3	0.00405	0.893235	1	1	C>T
ERR5749293	5388	PASS	C	A	5273	0.963019	2147483647	0,0,5272,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749293	5672	PASS	C	A	22634	0.977953	0	2,0,22632,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cct/Act	P985T	nsp3	0.004226	0.977953	2	1	C>A
ERR5749293	5986	PASS	C	T	9958	0.974895	0	0,0,9948,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749293	6954	PASS	T	C	23911	0.811091	0	0,4,1,23779	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749293	7764	PASS	C	T	16192	0.950593	0	3,0,16176,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCc/tTc	S1682F	nsp3	0.001052	0.964731	1	1	C>T
ERR5749293	8043	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27078	0.001071	0	27005,0,32,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A1775V	nsp3	0.001071	0.946827	1	1	C>T
ERR5749293	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	29782	9.74E-4	132	10417,19334,29,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749293	11287	PASS	GTCTGGTTTT	G	15844	0.99798	0	0,32,0,15812	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749293	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	36334	0.001349	0	18146,18103,25,25	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749293	13623	PASS	A	G	18196	0.930534	0	0,1,0,18160	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaA/gaG	E61	RdRp	0.00237	0.931889	2	2	A>G
ERR5749293	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	13221	0.003328	2593	13001,73,4,134	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749293	14408	PASS	C	T	25891	0.853154	24	0,8,12940,12776	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749293	14676	PASS	C	T	14446	0.754534	0	8,0,14380,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749293	15279	PASS	C	T	24544	0.905639	0	1,0,24515,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749293	16176	PASS	T	C	18397	0.978855	0	0,0,6834,11558	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749293	19160	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23387	0.002223	0	2,23322,0,56	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S374F	ExoN	0.001215	0.871076	1	1	C>T
ERR5749293	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20071	0.003388	0	19990,0,73,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749293	21575	PASS	C	T	30857	0.352853	14	8969,9156,5979,6408	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749293	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	30847	8.75E-4	77	15179,15647,0,27	HIGH	NONE	FRAME_SHIFT	S	gtt/Tgtt	V6C?	S	0.000619	0.877942	3	2	C>CT
ERR5749293	21764	PASS	ATACATG	A	11899	0.99563	0	52,0,11847,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749293	21990	PASS	TTTA	T	11907	0.997984	0	0,24,6,11877	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749293	23063	PASS	A	T	7989	0.866316	0	0,1,0,7948	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749293	23271	PASS	C	A	22515	0.925561	0	3,0,22495,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749293	23403	PASS	A	G	22497	0.968351	0	0,3,0,22477	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749293	23604	PASS	C	A	11803	0.959078	30	10,1,11787,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749293	23709	PASS	C	T	11786	0.944341	0	0,4,0,11768	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749293	24506	PASS	T	G	19503	0.974363	0	9,0,19492,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749293	24914	PASS	G	C	20678	0.957249	0	0,0,10304,10368	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749293	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	26748	0.001047	208	26677,6,20,8	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749293	25915	PASS	A	G	26739	0.972774	206	7,26,0,26688	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Aca/Gca	T175A	orf3a	0.967777	0.972774	1	1	A>G
ERR5749293	26907	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34717	9.51E-4	0	34667,5,35,0	LOW	SILENT	SYNONYMOUS_CODING	M	Ctg/Ttg	L129	M	0.000817	0.976032	1	1	C>T
ERR5749293	26927	PASS	A	G	34710	0.977211	0	2,0,34696,0	LOW	SILENT	SYNONYMOUS_CODING	M	gaA/gaG	E135	M	0.001168	0.979284	1	1	A>G
ERR5749293	27972	PASS	C	T	6614	0.90006	21	1,1,6566,20	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749293	28048	PASS	G	T	6604	0.930497	0	0,1,0,6601	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749293	28111	PASS	A	G	22701	0.978283	6	7,0,16079,6607	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749293	28270	PASS	TA	T	31220	0.995356	323	140,6,15889,15186	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749293	28280	PASS	G	C	31160	0.93973	6	5,1,15923,15167	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749293	28281	PASS	A	T	31160	0.908793	32	28,7,15902,15169	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749293	28282	PASS	T	A	31161	0.914252	8	19,10,15895,15184	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749293	28881	PASS	G	A	11550	0.716277	39	13,0,5637,5688	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749293	28882	PASS	G	A	11550	0.814719	9	6,1,5760,5684	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749293	28883	PASS	G	C	11550	0.940952	2	1,2,5772,5763	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749293	28977	PASS	C	T	5894	0.931116	0	0,2,3,5881	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749293	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	31176	8.34E-4	0	15657,15474,17,16	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749294	241	PASS	C	T	15858	0.872367	3	0,2,7879,7919	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749294	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	12327	0.001379	0	12315,0,17,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749294	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	12328	8.92E-4	0	12271,1,11,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749294	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	12328	0.002839	0	12271,1,35,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749294	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12320	0.001299	0	11584,1,631,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749294	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	12320	0.001867	0	12296,1,23,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749294	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTT	G	12316	6.5E-4	0	12290,1,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/	V84	leader	0.000554	0.991848	4	1	GTT>G
ERR5749294	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	12316	0.001137	0	12290,1,14,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttatg/gtg	VM84V	leader	0.000554	0.991848	4	1	GTTA>G
ERR5749294	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	12318	0.002598	0	12271,3,32,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749294	635	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12344	0.001539	0	0,12320,0,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgt/Tgt	R124C	leader	0.00148	0.880435	1	1	C>T
ERR5749294	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	29960	4.01E-4	26	17600,12345,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749294	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	29960	0.001135	0	17591,12325,20,14	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749294	913	PASS	C	T	17607	0.915602	0	0,10,0,17573	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749294	3037	PASS	C	T	18256	0.812281	22	1,10,9122,9013	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749294	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	9220	0.002169	536	3,9186,20,4	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749294	3267	PASS	C	T	17613	0.970533	0	5,0,17602,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749294	3638	PASS	G	T	10599	0.882064	0	7,0,10571,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggt/Tgt	G307C	nsp3	0.003698	0.896828	1	1	G>T
ERR5749294	5077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	10494	0.003335	0	10425,0,37,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtT/gtC	V786	nsp3	0.001393	0.168205	1	1	T>C
ERR5749294	5388	PASS	C	A	5092	0.956402	2147483647	0,0,5088,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749294	5986	PASS	C	T	10948	0.976982	0	1,0,10937,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749294	6954	PASS	T	C	17779	0.802239	0	0,5,0,17668	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749294	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	29015	0.001034	86	14876,14109,30,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749294	10323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	16089	0.001367	0	0,16032,0,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749294	10507	PASS	C	T	14788	0.842913	0	1,0,14732,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N151	3Cpro	0.00123	0.842913	2	2	C>T
ERR5749294	10789	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18826	0.001434	0	18789,0,28,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D245	3Cpro	0.001434	0.956641	1	1	C>T
ERR5749294	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	16964	0.00171	0	16909,0,49,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749294	11287	PASS	GTCTGGTTTT	G	16958	0.996993	0	0,51,0,16907	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749294	12854	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13761	0.028995	0	13332,1,411,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cct/Tct	P57S	nsp9	0.028995	0.95209	1	1	C>T
ERR5749294	13059	PASS	C	T	24942	0.855104	2	0,2,11150,13754	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T12I	nsp10	0.000448	0.855104	3	2	C>T
ERR5749294	13115	PASS	C	T	11177	0.909099	0	2,0,11163,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L31	nsp10	0.001806	0.922167	1	1	C>T
ERR5749294	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28497	8.42E-4	0	14242,14202,14,13	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749294	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	13927	0.004595	2147483647	13627,91,4,202	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749294	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	27149	7.0E-4	0	13608,13538,10,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749294	14408	PASS	C	T	27149	0.849608	8	3,8,13535,13399	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749294	14646	PASS	T	A	11526	0.970154	2147483647	0,0,11515,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acA	T402	RdRp	0.00675	0.970154	2	1	T>A
ERR5749294	14676	PASS	C	T	11523	0.735659	0	6,0,11469,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749294	14724	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11518	0.003733	0	11415,17,60,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F428	RdRp	0.000952	0.789267	3	2	C>T
ERR5749294	15279	PASS	C	T	19490	0.883735	0	1,0,19462,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749294	16176	PASS	T	C	19145	0.983129	6	3,0,9696,9439	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749294	18504	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	23969	9.6E-4	0	9,23590,0,343	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K155N	ExoN	0.000518	0.094148	4	3	A>C
ERR5749294	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	21630	9.25E-4	0	21610,0,20,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749294	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25207	0.001468	0	25164,0,37,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749294	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28631	0.001677	2	14037,14197,26,31	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749294	21622	PASS	C	A	14354	0.861363	0	0,60,0,14284	LOW	SILENT	SYNONYMOUS_CODING	S	acC/acA	T20	S	0.000846	0.946634	3	2	C>A
ERR5749294	21764	PASS	ATACATG	A	11298	0.995751	0	48,0,11250,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749294	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	11298	7.08E-4	0	11290,0,8,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749294	21990	PASS	TTTA	T	11304	0.998319	0	0,19,5,11280	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749294	23063	PASS	A	T	11920	0.868792	0	0,1,0,11860	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749294	23271	PASS	C	A	18714	0.916533	2147483647	0,0,18697,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749294	23403	PASS	A	G	18718	0.96677	0	0,2,1,18701	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749294	23604	PASS	C	A	13976	0.937822	0	11,0,13961,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749294	23709	PASS	C	T	13967	0.943868	0	0,5,3,13938	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749294	24506	PASS	T	G	15403	0.973447	0	6,0,15397,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749294	24914	PASS	G	C	32461	0.9614	0	1,1,16178,16258	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749294	25495	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	31495	0.00127	3	15700,15683,27,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Ata/Gta	I35V	orf3a	0.000735	0.911134	2	1	A>G
ERR5749294	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	11323	0.002826	0	0,11288,0,32	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749294	26927	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	28261	0.001168	0	28224,0,34,0	LOW	SILENT	SYNONYMOUS_CODING	M	gaA/gaG	E135	M	0.001168	0.979284	1	1	A>G
ERR5749294	27972	PASS	C	T	9869	0.902928	76	3,4,9781,48	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749294	28048	PASS	G	T	9836	0.927511	0	0,9,0,9824	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749294	28111	PASS	A	G	26709	0.978472	2	2,0,16854,9838	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749294	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16845	0.003799	0	16727,1,73,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749294	28270	PASS	TA	T	32727	0.994439	423	180,7,16607,15938	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749294	28280	PASS	G	C	32656	0.93551	15	14,4,16649,15917	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749294	28281	PASS	A	T	32656	0.913707	11	17,7,16638,15917	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749294	28282	PASS	T	A	32659	0.907958	7	27,17,16602,15926	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749294	28690	PASS	G	C	14351	0.963138	0	0,2,0,14333	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	ttG/ttC	L139F	N	0.963138	0.963138	1	1	G>C
ERR5749294	28881	PASS	G	A	11259	0.761169	11	6,1,5536,5556	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749294	28882	PASS	G	A	11258	0.829366	1	4,2,5623,5532	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749294	28883	PASS	G	C	11258	0.944484	0	1,0,5636,5616	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749294	28977	PASS	C	T	5741	0.932416	2147483647	0,0,0,5729	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749294	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	30512	8.85E-4	155	24733,5706,3,26	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749294	29095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24765	0.001171	0	24718,0,30,0	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F274	N	0.000792	0.961279	2	2	C>T
ERR5749294	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	49179	0.001017	0	24703,24395,31,31	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749294	29679	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	16253	6.15E-4	0	8132,8111,5,5	.	.	.	.	.	.	.	0.000443	0.838763	2	1	CT>C
ERR5749295	241	PASS	C	T	2535	0.85641	0	0,1,1258,1264	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749295	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	6211	0.001771	0	6195,6,11,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749295	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	6211	0.001288	0	6160,6,8,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749295	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	6211	0.004669	0	6160,6,29,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749295	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	6214	0.00177	2	5664,13,466,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749295	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	6214	0.001287	0	6193,13,8,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749295	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	6212	0.002254	0	6177,13,14,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749295	657	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6217	0.002413	0	0,6199,0,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A131V	leader	0.001202	0.365979	3	1	C>T
ERR5749295	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	13769	0.002324	11	7534,6202,23,9	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749295	913	PASS	C	T	7557	0.910679	0	0,4,0,7542	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749295	2185	PASS	G	A	9155	0.958056	39	1,0,0,9143	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaG/gaA	E460	nsp2	0.000441	0.963529	4	3	G>A
ERR5749295	2509	PASS	C	T	4093	0.928903	130	4,0,0,4086	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P568	nsp2	0.001408	0.949382	1	1	C>T
ERR5749295	2702	PASS	T	G	21	0.333333	16	4,5,0,12	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F633V	nsp2	0.000632	0.333333	1	1	T>G
ERR5749295	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	5161	0.001938	0	4,4820,0,335	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749295	3037	PASS	C	T	9269	0.79836	42	0,14,4633,4535	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749295	3267	PASS	C	T	7964	0.966474	2147483647	0,0,7962,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749295	4693	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	9085	0.001211	0	9074,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/	V659	nsp3	0.000654	0.078873	1	1	TG>T
ERR5749295	5192	PASS	C	T	4339	0.912192	2147483647	0,0,0,4322	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Ctg/Ttg	L825	nsp3	0.003789	0.912192	1	1	C>T
ERR5749295	5388	PASS	C	A	3548	0.956595	0	1,0,3546,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749295	5986	PASS	C	T	6576	0.974605	0	1,0,6570,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749295	6954	PASS	T	C	8077	0.832487	0	0,5,0,8029	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749295	8084	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	8930	0.001456	0	8912,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1790	nsp3	0.000543	0.923413	4	2	GA>G
ERR5749295	8639	PASS	C	T	7166	0.962183	2147483647	0,0,7164,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cct/Tct	P29S	nsp4	0.962183	0.962789	1	1	C>T
ERR5749295	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	13284	0.002559	49	9321,3928,34,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749295	9962	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2825	0.003186	0	2813,1,9,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cat/Tat	H470Y	nsp4	0.003186	0.114523	1	1	C>T
ERR5749295	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	9193	0.002502	0	9136,2,37,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749295	11287	PASS	GTCTGGTTTT	G	9186	0.99521	0	0,44,3,9139	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749295	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14949	0.002007	0	7457,7439,16,16	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749295	13994	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	6164	0.001136	0	6157,0,7,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L186	RdRp	0.000427	0.114441	3	2	CT>C
ERR5749295	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	5714	0.0042	1285	5575,59,3,75	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749295	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	11109	0.00225	1	5560,5531,14,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749295	14408	PASS	C	T	11109	0.855253	2	1,2,5530,5468	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749295	14676	PASS	C	T	5105	0.766112	0	2,0,5080,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749295	15026	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAT	C	9405	8.51E-4	0	9399,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tataca/	YT530	RdRp	0.000503	0.869455	2	2	CAT>C
ERR5749295	15279	PASS	C	T	7896	0.885132	0	1,0,7889,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749295	16176	PASS	T	C	9532	0.983214	0	0,0,5235,4293	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749295	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	14584	6.86E-4	0	14574,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749295	19343	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTTTTGTTAAT	C	9303	8.6E-4	0	9291,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tttgttaattta/	FVNL436	ExoN	0.000519	0.192257	7	2	CTTTTGTTAAT>C
ERR5749295	19955	PASS	C	T	12195	0.926855	0	2,0,12175,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T112I	endoR	0.0084	0.934633	1	1	C>T
ERR5749295	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12193	0.003937	0	12131,0,53,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749295	21764	PASS	ATACATG	A	7203	0.995141	0	35,0,7168,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749295	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	7203	0.001111	0	7195,0,8,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749295	21990	PASS	TTTA	T	7206	0.996947	0	0,22,3,7181	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749295	22323	PASS	C	T	14532	0.970548	0	0,1,5981,8546	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCt/tTt	S254F	S	0.000812	0.978946	3	2	C>T
ERR5749295	22981	PASS	T	C	8538	0.843055	0	8,0,8482,1	LOW	SILENT	SYNONYMOUS_CODING	S	taT/taC	Y473	S	0.001557	0.861194	3	2	T>C
ERR5749295	23063	PASS	A	T	8542	0.859635	0	0,3,2,8508	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749295	23271	PASS	C	A	9259	0.920942	2147483647	0,0,9250,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749295	23403	PASS	A	G	9261	0.966202	0	0,1,0,9251	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749295	23604	PASS	C	A	8888	0.941719	0	14,0,8865,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749295	23709	PASS	C	T	8878	0.936697	0	0,2,7,8858	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749295	24506	PASS	T	G	7612	0.975565	0	1,0,7610,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749295	24914	PASS	G	C	23303	0.962451	0	0,0,11614,11675	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749295	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	6211	0.001127	0	6204,0,7,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749295	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	7863	8.9E-4	0	0,7853,0,7	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749295	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	7865	0.002543	0	0,7842,0,20	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749295	27972	PASS	C	T	6513	0.910026	0	0,0,6442,48	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749295	28048	PASS	G	T	6472	0.919963	0	0,6,1,6460	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749295	28095	PASS	A	T	6477	0.959549	138	4,0,0,6457	HIGH	NONSENSE	STOP_GAINED	ORF8	Aaa/Taa	K68*	orf8	0.002672	0.967672	2	2	A>T
ERR5749295	28111	PASS	A	G	13456	0.97607	3	2,0,6977,6472	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749295	28270	PASS	TA	T	13537	0.995568	118	57,4,6904,6573	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749295	28280	PASS	G	C	13511	0.941455	0	2,1,6907,6570	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749295	28281	PASS	A	T	13511	0.918659	24	12,1,6902,6574	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749295	28282	PASS	T	A	13513	0.909051	12	11,3,6892,6575	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749295	28292	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	13896	7.2E-4	0	6927,6957,5,5	HIGH	NONE	FRAME_SHIFT	N	aat/	N8	N	0.000304	0.055324	4	2	CA>C
ERR5749295	28881	PASS	G	A	7755	0.779626	0	1,0,3853,3810	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749295	28882	PASS	G	A	7755	0.842037	0	1,0,3887,3795	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749295	28883	PASS	G	C	7755	0.948549	0	0,0,3890,3857	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749295	28977	PASS	C	T	3952	0.930415	0	0,2,0,3938	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749295	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	35303	8.5E-4	0	17726,17522,19,17	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749296	241	PASS	C	T	93	0.806452	0	0,0,45,46	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749296	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	520	0.009615	0	515,0,5,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749296	656	PASS	G	C	525	0.131429	0	0,455,0,70	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gct/Cct	A131P	leader	0.001202	0.131429	1	1	G>C
ERR5749296	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	2335	0.005567	13	1797,525,13,0	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749296	913	PASS	C	T	1807	0.924184	2147483647	0,0,0,1806	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749296	2779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	3152	0.005711	0	0,3130,0,19	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	agT/agA	S20R	nsp3	0.003967	0.16	2	2	T>A
ERR5749296	3037	PASS	C	T	692	0.833815	0	0,0,346,337	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749296	3267	PASS	C	T	2843	0.969047	2147483647	0,0,2843,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749296	5388	PASS	C	A	211	0.943128	2147483647	0,0,210,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749296	5986	PASS	C	T	895	0.963129	2147483647	0,0,894,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749296	6274	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	1571	0.019096	0	1541,0,30,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1186	nsp3	0.000755	0.990148	2	2	TA>T
ERR5749296	6843	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	G	3162	0.007906	126	2123,1010,0,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tGt	S1375C	nsp3	0.000753	0.922467	2	1	C>G
ERR5749296	6954	PASS	T	C	2115	0.813239	2147483647	0,0,0,2101	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749296	6990	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTT	C	2120	0.022642	0	0,2072,0,48	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L1425	nsp3	0.000504	0.101156	4	2	CTT>C
ERR5749296	8106	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1498	0.014686	0	1475,0,22,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCa/gTa	A1796V	nsp3	0.014686	0.89772	1	1	C>T
ERR5749296	8950	PASS	C	T	3609	0.979219	0	0,0,3127,480	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I132	nsp4	0.002808	0.982604	1	1	C>T
ERR5749296	10138	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3233	0.004021	102	2702,517,0,13	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N28	3Cpro	0.000458	0.983567	3	3	C>T
ERR5749296	10702	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2582	0.03873	2	26,2442,0,114	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D216	3Cpro	0.000396	0.098214	2	2	C>T
ERR5749296	10704	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	2583	0.01897	0	26,2508,0,49	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aGg/aTg	R217M	3Cpro	0.000771	0.158537	2	1	G>T
ERR5749296	11287	PASS	GTCTGGTTTT	G	5571	0.999282	0	0,4,0,5567	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749296	11339	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5992	0.020694	38	416,5446,0,129	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L123	nsp6	0.002071	0.968425	1	1	C>T
ERR5749296	11671	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2809	0.024564	0	2737,0,72,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	cgC/cgT	R233	nsp6	0.024564	0.94436	1	1	C>T
ERR5749296	14408	PASS	C	T	114	0.859649	0	0,0,58,56	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749296	14676	PASS	C	T	993	0.738167	2147483647	0,0,991,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749296	15279	PASS	C	T	1390	0.898561	2147483647	0,0,1387,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749296	15652	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	3709	0.006471	0	3680,0,29,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gac/Tac	D738Y	RdRp	0.000691	0.935936	2	2	G>T
ERR5749296	16176	PASS	T	C	599	0.973289	0	0,0,93,506	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749296	17502	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1895	0.015303	0	1866,0,29,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F422	helicase	0.000611	0.9865	2	2	C>T
ERR5749296	17502	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	1895	0.012665	0	1871,0,24,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N423	helicase	0.000611	0.9865	2	2	CA>C
ERR5749296	17795	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1234	0.013776	0	1215,0,18,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A520V	helicase	0.00111	0.966723	2	2	C>T
ERR5749296	18032	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	2016	0.004464	37	773,1234,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L600	helicase	0.000604	0.973948	2	2	CT>C
ERR5749296	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	9235	0.001191	0	9224,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749296	19029	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4267	0.021561	0	4162,0,105,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H330	ExoN	0.003777	0.923016	1	1	C>T
ERR5749296	20930	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3598	0.018899	0	3526,0,70,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aTg	T91M	MethTr	0.000902	0.95585	2	2	C>T
ERR5749296	21004	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	7171	0.015061	1	3519,3511,59,63	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gca/Cca	A116P	MethTr	0.000749	0.857814	3	1	G>C
ERR5749296	21234	PASS	C	T	3872	0.567665	0	1,0,3787,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A192	MethTr	0.000472	0.857572	5	2	C>T
ERR5749296	21304	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3872	0.006715	0	0,3841,0,28	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgc/Tgc	R216C	MethTr	0.000411	0.605296	3	2	C>T
ERR5749296	21438	PASS	G	T	972	0.053498	0	919,1,52,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atT	M260I	MethTr	0.053498	0.053498	1	1	G>T
ERR5749296	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	1928	0.04305	254	962,881,0,83	HIGH	NONE	FRAME_SHIFT	S	ctt/Tctt	L5S?	S	0.000394	0.091869	4	1	G>GT
ERR5749296	21575	PASS	C	T	1827	0.877942	0	0,0,852,963	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749296	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	1826	0.007667	38	860,953,0,14	HIGH	NONE	FRAME_SHIFT	S	gtt/Tgtt	V6C?	S	0.000619	0.877942	3	2	C>CT
ERR5749296	21764	PASS	ATACATG	A	1425	0.997895	0	3,0,1422,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749296	21990	PASS	TTTA	T	1426	0.995091	0	0,7,1,1418	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749296	22483	PASS	T	C	2859	0.905212	0	2,2,1400,1448	LOW	SILENT	SYNONYMOUS_CODING	S	acT/acC	T307	S	0.001987	0.921102	2	2	T>C
ERR5749296	23063	PASS	A	T	1306	0.858346	2147483647	0,0,0,1301	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749296	23170	PASS	C	T	3951	0.975449	2	1,1,2637,1311	LOW	SILENT	SYNONYMOUS_CODING	S	aaC/aaT	N536	S	0.000408	0.975449	3	2	C>T
ERR5749296	23271	PASS	C	A	2639	0.937855	2147483647	0,0,2639,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749296	23403	PASS	A	G	2636	0.971548	2147483647	0,0,0,2635	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749296	23604	PASS	C	A	1422	0.945851	0	2,0,1419,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749296	23664	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	1416	0.007062	27	1407,1406,0,10	HIGH	NONE	FRAME_SHIFT	S	gaa/	E702	S	0.000837	0.918	2	2	CAG>C
ERR5749296	23683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1416	0.009887	0	0,1397,0,18	LOW	SILENT	SYNONYMOUS_CODING	S	taC/taT	Y707	S	0.000704	0.467521	2	2	C>T
ERR5749296	23709	PASS	C	T	1418	0.940762	2147483647	0,0,0,1415	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749296	23817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	1798	0.00723	71	364,1421,12,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTt/cCt	L752P	S	0.000646	0.066832	1	1	T>C
ERR5749296	24320	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1448	0.027624	0	0,1403,0,44	HIGH	NONSENSE	STOP_GAINED	S	Caa/Taa	Q920*	S	0.000763	0.138365	4	2	C>T
ERR5749296	24506	PASS	T	G	1887	0.979332	2147483647	0,0,1887,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749296	24914	PASS	G	C	9979	0.961018	0	0,0,4975,4997	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749296	25844	PASS	C	T	56	0.892857	2147483647	0,0,0,55	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aCt/aTt	T151I	orf3a	0.001226	0.938776	1	1	C>T
ERR5749296	26257	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	5513	0.004535	105	2078,3410,25,0	HIGH	NONE	FRAME_SHIFT	E	tcg/	S6	E	0.000247	0.948926	4	2	GT>G
ERR5749296	26461	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2100	0.011429	0	0,2069,0,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	Ctt/Ttt	L73F	E	0.001401	0.928597	1	1	C>T
ERR5749296	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	1520	0.017105	0	0,1488,0,32	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	atG/atT	M84I	M	0.000483	0.943732	7	2	G>T
ERR5749296	27145	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7246	0.009384	0	2,7166,0,75	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	aCa/aTa	T208I	M	0.000476	0.863895	2	2	C>T
ERR5749296	27312	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAA	T	4268	0.011715	0	4217,0,50,0	HIGH	NONE	FRAME_SHIFT	ORF6	aat/	N39	orf6	0.000911	0.088458	4	2	TAA>T
ERR5749296	27371	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4262	0.005631	0	0,4228,0,28	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF6	cCa/cTa	P57L	orf6	0.00148	0.066731	2	2	C>T
ERR5749296	27389	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	4266	0.009845	0	0,4224,0,42	.	.	.	.	.	.	.	0.001157	0.899553	2	1	CG>C
ERR5749296	27476	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9446	0.005293	183	5171,4221,0,53	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	aCa/aTa	T28I	orf7a	0.000547	0.22827	4	2	C>T
ERR5749296	27509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9447	0.002329	82	5171,4250,0,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	aCa/aTa	T39I	orf7a	0.000843	0.067888	1	1	C>T
ERR5749296	27577	PASS	C	T	5172	0.793503	0	1,0,5059,0	HIGH	NONSENSE	STOP_GAINED	ORF7a	Caa/Taa	Q62*	orf7a	0.000614	0.952205	4	2	C>T
ERR5749296	27625	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5171	0.010636	0	5114,0,56,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Cgt/Tgt	R78C	orf7a	0.00584	0.951914	1	1	C>T
ERR5749296	27676	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	5234	0.006114	1	84,5073,0,74	HIGH	NONSENSE	STOP_GAINED	ORF7a	Gaa/Taa	E95*	orf7a	0.000609	0.877803	2	2	G>T
ERR5749296	27972	PASS	C	T	581	0.898451	0	0,0,573,6	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749296	28048	PASS	G	T	576	0.927083	0	0,2,0,573	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749296	28111	PASS	A	G	8978	0.981288	9	1,1,8399,575	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749296	28200	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TC	T	8402	0.013092	0	8292,0,110,0	HIGH	NONE	FRAME_SHIFT	ORF8	tcg/	S103	orf8	0.000751	0.981434	2	2	TC>T
ERR5749296	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8393	0.005481	0	8323,0,47,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749296	28270	PASS	TA	T	16103	0.989878	472	172,1,8192,7748	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749296	28280	PASS	G	C	16008	0.935782	12	5,0,8199,7738	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749296	28281	PASS	A	T	16008	0.891929	86	38,2,8184,7741	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749296	28282	PASS	T	A	16008	0.851699	53	31,4,8115,7742	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749296	28290	PASS	C	T	16560	0.943901	1	3,5,8244,8290	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	cCc/cTc	P6L	N	0.001339	0.943901	2	1	C>T
ERR5749296	28881	PASS	G	A	719	0.748261	3	1,0,353,357	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749296	28882	PASS	G	A	719	0.821975	0	0,0,360,352	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749296	28883	PASS	G	C	719	0.938804	0	0,0,360,359	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749296	28977	PASS	C	T	365	0.942466	0	0,1,0,364	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749296	29095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5759	0.004341	0	5728,0,26,0	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F274	N	0.000792	0.961279	2	2	C>T
ERR5749296	29386	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	1398	0.004292	0	1392,0,6,0	HIGH	NONE	FRAME_SHIFT	N	aag/	K373	N	0.000887	0.899197	4	2	CA>C
ERR5749297	241	PASS	C	T	3780	0.869312	0	1,1,1885,1885	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749297	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	6513	0.001842	84	6494,8,8,4	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749297	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	6513	0.002457	0	6471,12,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749297	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	6517	0.002915	88	6484,14,14,5	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749297	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	19171	0.001095	17	12638,6503,19,2	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749297	913	PASS	C	T	12661	0.913909	0	0,8,0,12632	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749297	3037	PASS	C	T	8687	0.815702	9	0,3,4344,4279	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749297	3177	PASS	C	T	17026	0.898038	2	3,0,12625,4367	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P153L	nsp3	0.000773	0.96008	3	2	C>T
ERR5749297	3267	PASS	C	T	12649	0.970511	0	2,0,12642,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749297	5388	PASS	C	A	2998	0.962308	2147483647	0,0,2998,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749297	5986	PASS	C	T	7104	0.976633	2147483647	0,0,7097,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749297	6954	PASS	T	C	13494	0.824811	0	0,2,0,13409	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749297	7070	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	20989	0.003097	297	7384,13532,66,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggc/Agc	G1451S	nsp3	0.000698	0.101434	3	1	G>A
ERR5749297	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	14127	6.37E-4	14	9141,4977,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749297	11095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14710	0.00136	0	14658,0,21,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A41	nsp6	0.000515	0.887707	7	2	C>T
ERR5749297	11287	PASS	GTCTGGTTTT	G	14717	0.998573	0	0,21,0,14696	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749297	12493	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	11921	6.71E-4	0	11913,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tataac/	YN135	nsp8	0.000671	0.855797	2	2	CTA>C
ERR5749297	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24694	0.001255	0	12337,12294,17,17	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749297	14408	PASS	C	T	5289	0.840045	2	1,2,2638,2607	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749297	14676	PASS	C	T	8471	0.751269	0	4,0,8437,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749297	15279	PASS	C	T	12876	0.892979	2147483647	0,0,12859,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749297	16176	PASS	T	C	12470	0.980112	0	0,0,4744,7719	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749297	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	17105	0.001111	0	17086,0,19,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749297	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13558	0.001991	0	13522,0,29,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749297	21234	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	18253	4.93E-4	0	18244,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/Tgtt	V194C?	MethTr	0.000472	0.857572	5	2	C>CT
ERR5749297	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GTT	17503	0.002	109	8743,8268,0,35	HIGH	NONE	FRAME_SHIFT	S	ctt/TTctt	L5F?	S	0.000394	0.091869	4	1	G>GTT
ERR5749297	21575	PASS	C	T	16904	0.86654	6	0,3,8013,8685	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749297	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	16897	0.002841	136	8124,8720,0,48	HIGH	NONE	FRAME_SHIFT	S	gtt/Tgtt	V6C?	S	0.000619	0.877942	3	2	C>CT
ERR5749297	21660	PASS	C	T	8812	0.932251	132	4,2,0,8789	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T33I	S	0.008721	0.937304	1	1	C>T
ERR5749297	21764	PASS	ATACATG	A	7717	0.998575	0	11,0,7706,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749297	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	7716	0.001296	0	7706,0,10,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749297	21990	PASS	TTTA	T	7722	0.99728	0	0,21,3,7698	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749297	23063	PASS	A	T	8792	0.863512	0	0,2,0,8748	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749297	23271	PASS	C	A	14898	0.925762	2147483647	0,0,14885,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749297	23403	PASS	A	G	14895	0.96811	0	0,2,0,14883	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749297	23604	PASS	C	A	9486	0.942758	0	6,0,9472,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749297	23709	PASS	C	T	9475	0.946069	0	0,2,0,9463	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749297	24506	PASS	T	G	11544	0.976958	0	2,0,11541,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749297	24914	PASS	G	C	26170	0.958693	0	0,0,13039,13107	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749297	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	17827	0.001739	48	12136,5652,37,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749297	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	6767	0.003103	349	6701,24,5,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749297	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	7822	8.95E-4	0	0,7815,0,7	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749297	27972	PASS	C	T	5447	0.903433	22	1,1,5408,15	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749297	28048	PASS	G	T	5433	0.923247	0	0,7,0,5424	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749297	28111	PASS	A	G	19082	0.978252	0	0,0,13640,5434	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749297	28270	PASS	TA	T	26401	0.995568	263	115,5,13493,12791	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749297	28280	PASS	G	C	26351	0.937118	15	6,0,13517,12782	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749297	28281	PASS	A	T	26351	0.917043	18	12,2,13503,12773	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749297	28282	PASS	T	A	26351	0.905886	0	8,8,13484,12792	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749297	28881	PASS	G	A	9738	0.785377	0	1,0,4843,4784	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749297	28882	PASS	G	A	9737	0.823868	3	2,0,4870,4778	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749297	28883	PASS	G	C	9737	0.942898	0	0,0,4877,4852	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749297	28977	PASS	C	T	4954	0.929552	2147483647	0,0,0,4943	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749297	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	40263	0.001018	0	20221,19980,25,23	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749298	241	PASS	C	T	13082	0.855145	0	1,2,6455,6563	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749298	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	9791	0.00286	0	9767,1,28,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749298	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	9791	0.00143	0	9736,1,14,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749298	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	9791	0.003166	0	9736,1,31,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749298	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	9788	0.003167	0	8943,4,737,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749298	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	9788	0.00143	0	9770,4,14,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749298	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	9790	8.17E-4	0	9764,7,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749298	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	9789	0.00143	0	9761,7,14,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749298	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	27881	5.38E-4	2	18031,9786,11,4	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749298	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	27881	0.001686	9	18031,9786,25,22	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749298	913	PASS	C	T	18049	0.903153	0	0,10,0,18018	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749298	2185	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	22245	4.5E-4	0	3,22232,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L462S?	nsp2	0.000441	0.963529	4	3	G>GT
ERR5749298	3037	PASS	C	T	15096	0.820615	34	2,17,7550,7416	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749298	3267	PASS	C	T	16928	0.968277	0	2,0,16917,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749298	5388	PASS	C	A	4118	0.958475	2147483647	0,0,4118,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749298	5986	PASS	C	T	9681	0.976449	0	1,0,9675,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749298	6954	PASS	T	C	20116	0.814476	0	0,3,0,20002	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749298	7926	PASS	C	T	15780	0.964956	0	0,4,0,15770	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCa/gTa	A1736V	nsp3	0.000531	0.97019	5	2	C>T
ERR5749298	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	26059	8.83E-4	84	11116,14920,23,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749298	10533	PASS	G	T	13203	0.917216	0	10,0,13005,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tGt/tTt	C160F	3Cpro	0.000835	0.917216	4	2	G>T
ERR5749298	10533	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	13203	0.004014	0	13136,0,53,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tac/tTac	Y161L?	3Cpro	0.000835	0.917216	4	2	G>GT
ERR5749298	10789	PASS	C	T	14991	0.956641	2147483647	0,0,14974,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D245	3Cpro	0.001434	0.956641	1	1	C>T
ERR5749298	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	14747	0.003051	0	14671,0,65,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749298	11287	PASS	GTCTGGTTTT	G	14740	0.997015	0	0,43,1,14695	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749298	12970	PASS	C	T	12517	0.850443	0	0,0,1,12458	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N95	nsp9	0.8352	0.861883	1	1	C>T
ERR5749298	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28006	8.93E-4	0	13985,13944,14,14	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749298	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	9744	0.007594	2147483647	9497,47,1,197	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749298	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	18905	6.35E-4	1	9483,9423,7,5	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749298	14408	PASS	C	T	18905	0.835652	6	1,4,9437,9297	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749298	14676	PASS	C	T	11040	0.818659	0	3,0,11015,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749298	14913	PASS	C	T	15405	0.981045	41	0,1,15376,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N491	RdRp	0.011397	0.981624	1	1	C>T
ERR5749298	15279	PASS	C	T	18969	0.879698	0	3,0,18934,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749298	16176	PASS	T	C	15946	0.977486	10	3,0,7251,8683	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749298	16946	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13683	0.002046	0	13637,1,30,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCa/gTa	A237V	helicase	0.001418	0.951893	1	1	C>T
ERR5749298	17334	PASS	G	T	12131	0.181271	4	1,9566,1,2561	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acG/acT	T366	helicase	0.181271	0.181271	1	1	G>T
ERR5749298	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22018	0.001862	0	21964,0,42,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749298	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	24130	5.8E-4	1	12036,12091,6,8	HIGH	NONE	FRAME_SHIFT	S	ctt/Tctt	L5S?	S	0.000394	0.091869	4	1	G>GT
ERR5749298	21764	PASS	ATACATG	A	9637	0.996887	0	30,0,9606,1	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749298	21974	PASS	G	T	9647	0.91842	248	9,6,2,9623	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gat/Tat	D138Y	S	0.001167	0.928915	2	2	G>T
ERR5749298	21990	PASS	TTTA	T	9646	0.99689	0	0,30,10,9606	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749298	23063	PASS	A	T	7850	0.857962	0	0,1,0,7807	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749298	23271	PASS	C	A	17708	0.923424	0	4,0,17677,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749298	23403	PASS	A	G	17696	0.963099	0	0,2,1,17676	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749298	23604	PASS	C	A	11437	0.930751	0	16,0,11413,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749298	23709	PASS	C	T	11412	0.92911	0	0,5,1,11382	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749298	24506	PASS	T	G	14609	0.973852	0	6,0,14600,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749298	24914	PASS	G	C	23425	0.955646	0	0,0,11663,11736	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749298	25138	PASS	T	C	6058	0.901453	2147483647	0,0,6048,0	LOW	SILENT	SYNONYMOUS_CODING	S	aaT/aaC	N1192	S	0.001865	0.901453	2	2	T>C
ERR5749298	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	22555	0.001286	1404	22212,134,88,92	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749298	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	39264	3.82E-4	0	0,39249,0,15	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749298	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	7628	0.00118	0	2,7610,0,9	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749298	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	7628	0.002622	0	0,7606,0,20	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749298	27915	PASS	G	A	7451	0.949134	0	3,0,7442,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	Gga/Aga	G8R	orf8	0.949134	0.95909	1	1	G>A
ERR5749298	27972	PASS	C	T	7486	0.896874	0	0,0,7418,41	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749298	28048	PASS	G	T	7447	0.898885	0	0,16,0,7427	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749298	28111	PASS	A	G	21401	0.977197	4	0,1,13943,7448	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749298	28270	PASS	TA	T	26813	0.994816	311	134,5,13754,12920	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749298	28280	PASS	G	C	26756	0.935229	11	12,4,13786,12901	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749298	28281	PASS	A	T	26756	0.906787	17	17,5,13775,12902	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749298	28282	PASS	T	A	26756	0.904246	3	15,10,13752,12908	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749298	28881	PASS	G	A	11969	0.743504	4	4,1,5955,5821	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749298	28882	PASS	G	A	11968	0.797711	12	5,0,6001,5804	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749298	28883	PASS	G	C	11968	0.94126	0	0,0,6019,5943	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749298	28977	PASS	C	T	6103	0.914141	0	0,0,1,6078	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749298	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	29427	9.18E-4	0	14795,14589,18,17	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749299	186	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4051	0.002962	0	4038,0,12,0	.	.	.	.	.	.	.	0.002255	0.966959	1	1	C>T
ERR5749299	241	PASS	C	T	8058	0.868578	0	0,0,4010,4022	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749299	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	9348	0.001605	0	9336,2,15,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749299	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	9348	0.001391	0	9321,2,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749299	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	9339	0.002142	0	8695,3,583,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749299	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	9339	0.001392	0	9323,3,13,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749299	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	9339	9.64E-4	0	9324,3,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749299	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	9339	0.001178	0	9323,3,11,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749299	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	22687	0.001014	0	13298,9364,13,10	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749299	913	PASS	C	T	13306	0.918458	0	0,5,0,13286	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749299	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	41174	0.001457	2147483647	20560,19121,31,1349	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749299	3037	PASS	C	T	15060	0.809363	45	0,15,7525,7414	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749299	3267	PASS	C	T	13875	0.972829	2147483647	0,0,13868,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749299	4255	PASS	G	A	30734	0.802889	33	30,8,15253,15178	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccG/ccA	P512	nsp3	0.001102	0.871853	2	1	G>A
ERR5749299	4529	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTTTAC	T	9509	8.41E-4	0	1,9500,0,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	tacttt/	YF605	nsp3	0.000527	0.402778	3	1	TTTTAC>T
ERR5749299	5388	PASS	C	A	4865	0.961151	0	4,0,4861,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749299	5986	PASS	C	T	9936	0.977355	0	2,0,9927,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749299	6954	PASS	T	C	14170	0.810445	0	0,6,1,14087	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749299	7070	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	28447	0.001336	104	14131,14199,39,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggc/Agc	G1451S	nsp3	0.000698	0.101434	3	1	G>A
ERR5749299	7070	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	28447	0.002355	87	14131,14199,64,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggc/Tgc	G1451C	nsp3	0.000698	0.101434	3	1	G>T
ERR5749299	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	19724	0.001166	41	12691,7009,23,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749299	10138	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19599	0.001123	8	15125,4442,21,2	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N28	3Cpro	0.000458	0.983567	3	3	C>T
ERR5749299	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	13535	0.001625	0	13496,0,35,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749299	11287	PASS	GTCTGGTTTT	G	13535	0.997784	0	0,28,0,13505	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749299	11507	PASS	G	A	22027	0.903618	6	5,1,11014,10931	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Att	V179I	nsp6	0.007744	0.914418	2	2	G>A
ERR5749299	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18624	0.001611	0	9299,9269,16,16	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749299	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	6279	0.002867	1136	6163,51,1,61	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749299	14408	PASS	C	T	12263	0.847346	6	0,2,6125,6055	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749299	14676	PASS	C	T	8276	0.782262	0	1,0,8246,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749299	15279	PASS	C	T	13002	0.883556	0	2,0,12978,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749299	16176	PASS	T	C	14080	0.981818	3	0,1,7313,6757	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749299	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	16442	0.001034	0	16425,0,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749299	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	17000	9.41E-4	0	0,16984,0,16	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749299	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22472	0.002714	0	22399,0,65,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749299	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	23994	6.25E-4	0	11976,12003,7,8	HIGH	NONE	FRAME_SHIFT	S	ctt/Tctt	L5S?	S	0.000394	0.091869	4	1	G>GT
ERR5749299	21764	PASS	ATACATG	A	10259	0.996491	0	36,0,10223,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749299	21990	PASS	TTTA	T	10262	0.997954	0	0,21,3,10238	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749299	23063	PASS	A	T	11633	0.863578	0	0,7,0,11577	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749299	23271	PASS	C	A	14526	0.920487	0	1,0,14503,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749299	23403	PASS	A	G	14526	0.966818	0	0,1,0,14512	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749299	23604	PASS	C	A	12605	0.939786	0	6,0,12591,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749299	23709	PASS	C	T	12585	0.939531	0	0,7,1,12560	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749299	24506	PASS	T	G	10661	0.973642	0	6,0,10655,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749299	24914	PASS	G	C	31129	0.960326	0	0,1,15517,15595	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749299	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	10301	0.001165	0	0,10289,0,12	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749299	27879	PASS	C	T	8278	0.983329	0	1,0,8269,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7b	Cac/Tac	H42Y	orf7b	0.038895	0.983329	1	1	C>T
ERR5749299	27972	PASS	C	T	8309	0.90408	39	1,2,8233,49	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749299	28001	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	16490	0.001334	0	8223,8225,12,12	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ccG/ccA	P36	orf8	0.00085	0.830607	2	1	G>A
ERR5749299	28048	PASS	G	T	8267	0.92331	0	0,16,0,8242	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749299	28111	PASS	A	G	22774	0.977255	2	3,0,14487,8275	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749299	28250	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TCTG	14487	6.21E-4	0	14476,3,9,0	MODERATE	NONE	CODON_INSERTION	ORF8	ttc/CTGttc	F120LF	orf8	0.000494	0.993968	5	3	T>TCTG
ERR5749299	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	14482	7.6E-4	0	14469,7,11,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749299	28270	PASS	TA	T	28066	0.994762	355	144,4,14290,13629	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749299	28280	PASS	G	C	28012	0.937919	15	6,0,14329,13617	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749299	28281	PASS	A	T	28012	0.917357	8	15,7,14315,13612	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749299	28282	PASS	T	A	28012	0.91111	8	15,7,14281,13627	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749299	28881	PASS	G	A	10861	0.767885	9	4,0,5376,5327	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749299	28882	PASS	G	A	10861	0.830863	3	5,2,5440,5313	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749299	28883	PASS	G	C	10861	0.942178	0	1,1,5449,5404	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749299	28977	PASS	C	T	5534	0.928262	2147483647	0,0,0,5527	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749299	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	30778	0.001397	226	25209,5467,7,40	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749299	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	50043	0.001079	0	25163,24795,32,31	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749299	29311	PASS	C	T	25234	0.790798	0	0,4,0,25221	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F346	N	0.000335	0.790798	3	2	C>T
ERR5749299	29445	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTG	C	410	0.009756	0	406,0,4,0	HIGH	NONE	FRAME_SHIFT	N	gtg/	V392	N	0.000907	0.853797	2	2	CTG>C
ERR5749300	241	PASS	C	T	16820	0.870273	0	0,0,8200,8568	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749300	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	10520	0.002471	0	10493,0,26,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749300	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	10518	0.001236	0	10464,0,13,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749300	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	10518	0.003233	0	10464,0,34,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749300	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10513	0.001046	0	9727,5,675,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749300	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	10513	9.51E-4	0	10498,5,10,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749300	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	10512	9.51E-4	0	10495,5,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749300	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	32275	0.001394	34	21695,10528,41,4	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749300	913	PASS	C	T	21737	0.911625	0	0,13,0,21690	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749300	1027	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	11453	0.002096	196	11405,10,16,9	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccT/ccC	P74	nsp2	0.001454	0.276316	1	1	T>C
ERR5749300	2062	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26960	0.013539	3	26418,32,462,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A419	nsp2	0.001265	0.822961	2	1	C>T
ERR5749300	3037	PASS	C	T	14883	0.823221	27	1,12,7428,7334	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749300	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	7513	0.002396	503	2,7492,18,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749300	3267	PASS	C	T	20423	0.973119	0	3,0,20410,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749300	4255	PASS	G	A	28182	0.833901	28	20,4,14005,13996	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccG/ccA	P512	nsp3	0.001102	0.871853	2	1	G>A
ERR5749300	5388	PASS	C	A	5226	0.960199	2147483647	0,0,5224,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749300	5986	PASS	C	T	10776	0.975037	0	1,0,10760,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749300	6954	PASS	T	C	22267	0.812503	0	0,3,2,22120	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749300	8964	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	13168	7.59E-4	0	13153,5,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K138	nsp4	0.000553	0.981649	4	2	CA>C
ERR5749300	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	31157	0.001476	165	13579,17532,46,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749300	9891	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6412	0.002963	0	6387,0,19,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A446V	nsp4	0.002963	0.958011	1	1	C>T
ERR5749300	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	18627	0.001181	0	18566,0,42,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749300	11287	PASS	GTCTGGTTTT	G	18623	0.997852	26	1,38,0,18583	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749300	11507	PASS	G	A	23010	0.910517	6	3,0,11495,11444	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Att	V179I	nsp6	0.007744	0.914418	2	2	G>A
ERR5749300	12269	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	24412	6.14E-4	0	24398,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aag/	K61	nsp8	0.000434	0.213333	2	1	GA>G
ERR5749300	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	15188	0.001712	0	15150,0,26,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749300	12513	PASS	C	T	15186	0.984064	0	1,0,15175,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aTg	T141M	nsp8	0.000794	0.984064	2	2	C>T
ERR5749300	12756	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	33801	0.00145	12	18568,15162,37,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T24I	nsp9	0.000889	0.877514	1	1	C>T
ERR5749300	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29915	8.69E-4	0	14947,14902,14,14	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749300	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12779	0.004382	2921	12526,92,2,157	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749300	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	24957	5.61E-4	0	12512,12443,7,7	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749300	14408	PASS	C	T	24957	0.847137	3	2,4,12453,12343	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749300	14676	PASS	C	T	13279	0.787861	0	11,0,13219,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749300	15279	PASS	C	T	22144	0.896992	0	7,0,22107,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749300	16176	PASS	T	C	19099	0.981989	3	1,0,8601,10493	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749300	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26544	0.002373	0	26465,0,67,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749300	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30857	9.72E-4	2	15094,15393,14,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749300	21764	PASS	ATACATG	A	10823	0.995288	46	49,2,10772,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749300	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	10821	0.001017	0	10810,0,11,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749300	21990	PASS	TTTA	T	10826	0.997598	0	0,26,4,10796	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749300	23063	PASS	A	T	10299	0.859501	0	0,2,2,10240	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749300	23271	PASS	C	A	22418	0.92622	2147483647	0,0,22403,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749300	23401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	22410	0.025346	0	0,21718,0,687	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	caG/caT	Q613H	S	0.000491	0.839283	2	2	G>T
ERR5749300	23403	PASS	A	G	22410	0.968273	2147483647	0,0,0,22387	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749300	23604	PASS	C	A	13300	0.944962	0	8,0,13284,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749300	23709	PASS	C	T	13292	0.948465	0	0,6,6,13269	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749300	24506	PASS	T	G	17641	0.976759	0	6,0,17635,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749300	24914	PASS	G	C	30652	0.961862	0	0,0,15282,15356	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749300	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	25337	0.001145	466	25228,27,10,19	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749300	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	25290	6.72E-4	0	25272,1,17,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749300	25782	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25271	0.001068	0	25159,1,30,0	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	tgC/tgT	C130	orf3a	0.000916	0.955348	1	1	C>T
ERR5749300	26526	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	11398	0.001579	0	2,11364,0,19	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Gca/Aca	A2T	M	0.001224	0.951192	3	1	G>A
ERR5749300	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	9698	0.001031	0	0,9684,0,10	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749300	26936	PASS	C	T	29851	0.907239	0	8,0,29804,0	LOW	SILENT	SYNONYMOUS_CODING	M	ctC/ctT	L138	M	0.001308	0.968147	2	1	C>T
ERR5749300	27972	PASS	C	T	9518	0.916474	25	0,1,9460,29	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749300	28048	PASS	G	T	9490	0.929083	0	0,15,0,9467	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749300	28111	PASS	A	G	28882	0.977979	7	5,0,19366,9499	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749300	28270	PASS	TA	T	37637	0.995244	417	178,7,19128,18330	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749300	28280	PASS	G	C	37563	0.936134	8	9,3,19161,18298	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749300	28281	PASS	A	T	37563	0.91891	51	22,1,19162,18300	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749300	28282	PASS	T	A	37568	0.90971	2	21,17,19111,18317	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749300	28881	PASS	G	A	17222	0.784229	4	8,4,8530,8487	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749300	28882	PASS	G	A	17219	0.831581	4	4,1,8592,8442	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749300	28883	PASS	G	C	17219	0.946396	0	1,0,8611,8587	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749300	28977	PASS	C	T	8732	0.933692	0	0,1,0,8717	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749300	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	29429	0.001155	99	20674,8695,6,29	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749300	29077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20702	0.001691	0	20636,3,38,0	LOW	SILENT	SYNONYMOUS_CODING	N	taC/taT	Y268	N	0.000408	0.88565	3	2	C>T
ERR5749300	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	41088	0.00129	0	20623,20388,30,30	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749300	29688	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	15449	0.002589	0	7679,7683,40,40	.	.	.	.	.	.	.	0.002374	0.664502	2	1	G>T
ERR5749301	241	PASS	C	T	56	0.821429	0	0,0,28,28	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749301	913	PASS	C	T	2988	0.920348	0	0,1,0,2980	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749301	929	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	2991	0.018388	0	0,2921,0,66	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Att/Ttt	I42F	nsp2	0.000823	0.987013	3	2	A>T
ERR5749301	1426	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2362	0.032176	0	2276,0,85,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y207	nsp2	0.002931	0.892537	1	1	C>T
ERR5749301	1813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	1900	0.014737	0	0,1872,0,28	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K338	nsp2	0.001022	0.152738	4	2	TA>T
ERR5749301	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	9191	0.001414	594	4588,4333,10,240	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749301	3037	PASS	C	T	746	0.808311	3	0,1,374,361	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749301	3096	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	377	0.013263	0	0,368,0,6	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCa/tTa	S126L	nsp3	0.001801	0.932094	1	1	C>T
ERR5749301	3267	PASS	C	T	3668	0.974373	2147483647	0,0,3667,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749301	4206	PASS	C	T	1294	0.879444	2147483647	0,0,1289,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCg/gTg	A496V	nsp3	0.003069	0.879444	1	1	C>T
ERR5749301	4423	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3759	0.018356	0	3682,1,73,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	cgC/cgT	R568	nsp3	0.00063	0.953796	2	2	C>T
ERR5749301	4832	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3025	0.019504	0	1474,1468,38,39	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L705	nsp3	0.000542	0.727166	3	2	C>T
ERR5749301	5388	PASS	C	A	187	0.967914	2147483647	0,0,187,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749301	5986	PASS	C	T	1186	0.975548	2147483647	0,0,1186,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749301	6954	PASS	T	C	3097	0.81143	2147483647	0,0,0,3084	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749301	8603	PASS	T	C	614	0.970684	2147483647	0,0,0,613	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Ctc	F17L	nsp4	0.002607	0.974959	2	1	T>C
ERR5749301	8664	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	487	0.030801	0	472,0,15,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T37I	nsp4	0.003182	0.985915	1	1	C>T
ERR5749301	11073	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TC	T	6637	0.002109	0	6623,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttc/	F34	nsp6	0.000385	0.092251	6	2	TC>T
ERR5749301	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6637	0.022149	0	6450,0,161,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749301	11287	PASS	GTCTGGTTTT	G	6628	0.998491	0	0,10,0,6618	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749301	11767	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7188	0.012521	0	3529,3529,55,55	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	agC/agT	S265	nsp6	0.000949	0.854102	1	1	C>T
ERR5749301	11824	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	3600	0.016667	0	0,3540,0,60	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K285	nsp6	0.000465	0.922016	2	2	CA>C
ERR5749301	12459	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3295	0.003035	49	2245,1040,0,10	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T123I	nsp8	0.000658	0.986093	1	1	C>T
ERR5749301	12534	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2245	0.004454	0	2232,0,11,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T148I	nsp8	0.004454	0.90073	1	1	C>T
ERR5749301	12676	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	2245	0.010245	0	0,2222,0,23	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K196	nsp8	0.000716	0.87302	3	2	CA>C
ERR5749301	13329	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3716	0.007535	0	1,3682,0,32	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T102I	nsp10	0.000676	0.882106	2	2	C>T
ERR5749301	13667	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	261	0.02682	0	253,1,7,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T76I	RdRp	0.02682	0.116606	2	1	C>T
ERR5749301	14408	PASS	C	T	71	0.929577	0	0,0,36,35	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749301	14676	PASS	C	T	2067	0.8418	0	3,0,2059,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749301	15279	PASS	C	T	1308	0.889144	2147483647	0,0,1305,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749301	15654	PASS	C	T	4682	0.060658	0	4367,0,314,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D738	RdRp	0.001856	0.060658	2	2	C>T
ERR5749301	16092	PASS	C	T	2415	0.906832	0	0,1,0,2407	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y884	RdRp	0.002941	0.906832	1	1	C>T
ERR5749301	16176	PASS	T	C	2572	0.984448	0	0,0,155,2416	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749301	16260	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	155	0.045161	0	148,0,7,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N9	helicase	0.045161	0.961661	2	2	CA>C
ERR5749301	16468	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4587	0.017441	9	4347,155,84,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ccc/Tcc	P78S	helicase	0.001077	0.977186	1	1	C>T
ERR5749301	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAA	G	1762	0.030079	0	1705,0,53,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GAA>G
ERR5749301	17615	PASS	A	G	2485	0.910262	2147483647	0,0,0,2477	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749301	20825	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8237	0.014204	271	4569,3548,118,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T56I	MethTr	0.001237	0.202489	2	1	C>T
ERR5749301	21764	PASS	ATACATG	A	2648	0.999245	0	2,0,2646,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749301	21990	PASS	TTTA	T	2648	0.981495	0	0,49,0,2599	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749301	23063	PASS	A	T	1906	0.864113	2147483647	0,0,0,1895	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749301	23271	PASS	C	A	6638	0.93025	0	1,0,6632,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749301	23311	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	6636	0.012206	0	6548,0,85,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gaG/gaC	E583D	S	0.001115	0.705903	2	1	G>C
ERR5749301	23403	PASS	A	G	6634	0.968948	0	0,2,0,6626	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749301	23604	PASS	C	A	1875	0.946133	0	1,0,1872,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749301	23709	PASS	C	T	1875	0.951467	0	0,1,0,1873	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749301	24506	PASS	T	G	3371	0.973302	0	3,0,3367,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749301	24914	PASS	G	C	21180	0.960718	0	0,1,10549,10613	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749301	25437	PASS	G	T	9214	0.963642	0	2,0,9207,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	ttG/ttT	L15F	orf3a	0.001128	0.971411	2	2	G>T
ERR5749301	25531	PASS	A	G	9208	0.975891	2147483647	0,0,0,9200	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Att/Gtt	I47V	orf3a	0.000473	0.975891	5	2	A>G
ERR5749301	25572	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	9215	0.013131	0	0,9094,0,121	HIGH	NONE	FRAME_SHIFT	ORF3a	atc/	I62	orf3a	0.000543	0.959687	4	2	CA>C
ERR5749301	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	207	0.048309	115	188,9,0,10	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749301	26156	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	4430	0.003386	0	0,4408,0,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	gTt/gCt	V255A	orf3a	0.001058	0.924104	2	2	T>C
ERR5749301	26256	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8126	0.0032	33	3688,4409,3,23	LOW	SILENT	SYNONYMOUS_CODING	E	ttC/ttT	F4	E	0.000748	0.969561	2	2	C>T
ERR5749301	26257	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	8126	0.003446	73	3691,4407,0,28	HIGH	NONE	FRAME_SHIFT	E	tcg/tTcg	S6F?	E	0.000247	0.948926	4	2	G>GT
ERR5749301	26461	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3685	0.004885	0	0,3655,0,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	Ctt/Ttt	L73F	E	0.001401	0.928597	1	1	C>T
ERR5749301	26681	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2652	0.00641	0	2633,0,18,0	LOW	SILENT	SYNONYMOUS_CODING	M	ttC/ttT	F53	M	0.001297	0.074505	1	1	C>T
ERR5749301	26801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	2651	0.004904	0	0,2637,0,14	LOW	SILENT	SYNONYMOUS_CODING	M	ctC/ctA	L93	M	0.002753	0.954545	3	1	C>A
ERR5749301	26803	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	2651	0.010562	0	0,2621,0,29	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	aGc/aCc	S94T	M	0.010562	0.090909	1	1	G>C
ERR5749301	26985	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11720	0.008703	0	11592,0,121,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Cat/Tat	H155Y	M	0.001017	0.889358	1	1	C>T
ERR5749301	27297	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6669	0.004498	0	6629,0,32,0	LOW	SILENT	SYNONYMOUS_CODING	ORF6	atC/atT	I32	orf6	0.000978	0.91266	1	1	C>T
ERR5749301	27391	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	6718	0.006252	0	53,6605,0,42	.	.	.	.	.	.	.	0.000702	0.938682	3	1	A>G
ERR5749301	27406	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	6668	0.003149	0	0,6647,0,21	HIGH	NONE	FRAME_SHIFT	ORF7a	ttc/	F6	orf7a	0.00059	0.998683	2	1	CT>C
ERR5749301	27476	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14995	0.002267	84	8280,6667,38,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	aCa/aTa	T28I	orf7a	0.000547	0.22827	4	2	C>T
ERR5749301	27532	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8326	0.003483	0	8292,3,29,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Cat/Tat	H47Y	orf7a	0.001165	0.982473	2	1	C>T
ERR5749301	27654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15831	0.003411	136	8245,7513,54,1	LOW	SILENT	SYNONYMOUS_CODING	ORF7a	ttC/ttT	F87	orf7a	0.000906	0.947433	2	2	C>T
ERR5749301	27972	PASS	C	T	966	0.905797	0	0,0,945,17	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749301	28048	PASS	G	T	948	0.906118	2147483647	0,0,0,948	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749301	28111	PASS	A	G	14294	0.985169	0	3,0,13335,949	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749301	28250	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	13329	0.004126	0	13263,0,59,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	gaT/gaA	D119E	orf8	0.000494	0.993968	5	3	T>A
ERR5749301	28270	PASS	TA	T	25824	0.996515	220	91,3,13197,12537	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749301	28280	PASS	G	C	25779	0.930021	3	5,2,13064,12392	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749301	28281	PASS	A	T	25779	0.908297	11	12,4,13105,12427	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749301	28282	PASS	T	A	25780	0.899884	2	106,109,13075,12428	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749301	28282	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TTA	25780	0.00768	3	13133,12439,96,102	HIGH	NONE	FRAME_SHIFT+STOP_GAINED	N	aat/TAaat	N4*?	N	0.001009	0.957283	3	2	T>TTA
ERR5749301	28732	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8537	0.003631	9	745,7756,0,33	LOW	SILENT	SYNONYMOUS_CODING	N	aaC/aaT	N153	N	0.000892	0.966905	2	2	C>T
ERR5749301	28881	PASS	G	A	1466	0.786494	0	0,0,726,725	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749301	28882	PASS	G	A	1466	0.834243	0	0,0,732,717	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749301	28883	PASS	G	C	1466	0.949522	0	0,0,732,729	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749301	28887	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1475	0.011525	0	724,728,10,10	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aCt/aTt	T205I	N	0.002174	0.814997	2	2	C>T
ERR5749301	28977	PASS	C	T	745	0.926175	2147483647	0,0,0,744	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749301	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	22003	9.54E-4	0	11054,10924,11,11	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749301	29311	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11075	0.00316	0	0,11018,0,43	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F346	N	0.000335	0.790798	3	2	C>T
ERR5749301	29421	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2881	0.008678	0	2852,0,25,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	cCg/cTg	P383L	N	0.002705	0.052892	2	2	C>T
ERR5749301	29451	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2880	0.007986	0	2848,0,30,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aCt/aTt	T393I	N	0.007675	0.757685	2	2	C>T
ERR5749301	29555	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4067	0.002459	53	1180,2871,10,0	.	.	.	.	.	.	.	0.000611	0.957048	3	1	C>T
ERR5749302	241	PASS	C	T	4368	0.854396	3	0,1,2177,2174	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749302	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10261	0.001364	0	9548,0,695,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749302	913	PASS	C	T	15039	0.914888	0	0,9,0,14999	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749302	1813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	18724	0.001175	0	0,18680,0,26	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcA	A336	nsp2	0.001022	0.152738	4	2	T>A
ERR5749302	3037	PASS	C	T	15532	0.83138	16	1,8,7759,7681	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749302	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	7821	0.002046	421	1,7802,15,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749302	3267	PASS	C	T	16620	0.971901	2147483647	0,0,16615,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749302	4237	PASS	T	C	30580	0.912884	3	0,1,15297,15200	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaT/aaC	N506	nsp3	0.000302	0.918634	2	2	T>C
ERR5749302	4255	PASS	G	A	30618	0.849533	63	22,0,15222,15204	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccG/ccA	P512	nsp3	0.001102	0.871853	2	1	G>A
ERR5749302	5388	PASS	C	A	4197	0.961878	2147483647	0,0,4190,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749302	5575	PASS	C	T	4200	0.951905	100	3,0,0,4197	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y952	nsp3	0.01018	0.961493	1	1	C>T
ERR5749302	5986	PASS	C	T	10934	0.975032	0	1,0,10925,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749302	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10379	0.00212	0	0,10251,0,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749302	6954	PASS	T	C	19795	0.823743	0	0,4,0,19686	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749302	7070	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	29875	0.003749	543	9893,19861,114,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggc/Cgc	G1451R	nsp3	0.000698	0.101434	3	1	G>C
ERR5749302	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	21124	0.002746	0	20577,0,58,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749302	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	21115	0.001468	0	21048,0,52,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749302	11287	PASS	GTCTGGTTTT	G	21110	0.998721	0	0,27,0,21083	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749302	11507	PASS	G	A	21967	0.895707	2	3,1,11032,10873	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Att	V179I	nsp6	0.007744	0.914418	2	2	G>A
ERR5749302	12754	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27141	0.001216	6	9385,17717,15,18	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C23	nsp9	0.001216	0.947969	1	1	C>T
ERR5749302	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24294	0.001235	0	12139,12103,16,16	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749302	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	3269	0.006118	928	3181,32,1,54	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749302	14408	PASS	C	T	6327	0.828355	9	0,3,3160,3113	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749302	14676	PASS	C	T	8746	0.78333	0	7,0,8719,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749302	15279	PASS	C	T	14981	0.887457	2147483647	0,0,14967,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749302	15420	PASS	T	G	14961	0.922666	0	0,29,0,14921	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcG	A660	RdRp	0.908883	0.934773	1	1	T>G
ERR5749302	16176	PASS	T	C	15986	0.979232	0	0,1,6969,9008	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749302	17502	PASS	C	T	14433	0.968059	0	2,0,14415,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F422	helicase	0.000611	0.9865	2	2	C>T
ERR5749302	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	25513	5.49E-4	0	25499,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749302	18756	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	25507	3.92E-4	0	25497,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F240	ExoN	0.000392	0.942688	3	2	GT>G
ERR5749302	19011	PASS	C	T	22348	0.971675	0	3,0,22338,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D324	ExoN	0.000408	0.975746	4	2	C>T
ERR5749302	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	22323	4.48E-4	0	0,22313,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749302	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17136	0.003035	0	17073,0,53,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749302	21764	PASS	ATACATG	A	11963	0.998161	0	22,0,11941,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749302	21990	PASS	TTTA	T	11970	0.997744	0	0,27,6,11937	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749302	23063	PASS	A	T	12909	0.865055	0	0,6,0,12852	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749302	23271	PASS	C	A	17287	0.923179	2147483647	0,0,17276,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749302	23403	PASS	A	G	17283	0.968466	0	0,4,0,17256	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749302	23604	PASS	C	A	13962	0.942845	0	9,0,13942,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749302	23690	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	13938	0.014995	0	0,13623,0,229	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aac/Gac	N710D	S	0.002413	0.929812	1	1	A>G
ERR5749302	23709	PASS	C	T	13951	0.935704	0	0,2,0,13931	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749302	24506	PASS	T	G	16232	0.977021	0	10,0,16219,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749302	24899	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	38060	3.15E-4	0	19040,19010,6,6	HIGH	NONE	FRAME_SHIFT	S	atc/	I1114	S	0.000315	0.09021	5	3	CA>C
ERR5749302	24914	PASS	G	C	37916	0.961283	0	1,1,18877,19001	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749302	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	24490	9.8E-4	15	18449,6006,27,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749302	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	7504	0.004131	547	7437,20,7,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749302	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	7458	0.002145	0	7442,0,16,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749302	26509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	11571	0.001037	0	0,11559,0,12	.	.	.	.	.	.	.	0.000852	0.946613	3	1	CT>C
ERR5749302	27765	PASS	C	T	19716	0.968351	0	0,2,0,19700	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7b	Ctt/Ttt	L4F	orf7b	0.00109	0.970449	1	1	C>T
ERR5749302	27972	PASS	C	T	7232	0.900857	14	5,1,7149,45	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749302	28048	PASS	G	T	7193	0.929098	0	0,8,0,7182	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749302	28111	PASS	A	G	30305	0.979376	2	4,0,23099,7194	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749302	28239	PASS	GTTGTT	G	23064	0.984001	0	373,0,22695,0	HIGH	NONE	FRAME_SHIFT	ORF8	gtttta/	VL117	orf8	0.000417	0.984998	9	2	GTTGTT>G
ERR5749302	28249	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	ATC	22794	0.001053	0	22767,0,24,0	HIGH	NONE	FRAME_SHIFT	ORF8	ttc/CTttc	F120L?	orf8	0.000443	0.063605	3	2	A>ATC
ERR5749302	28250	PASS	T	TCTG	22794	0.99241	0	149,0,22621,0	MODERATE	NONE	CODON_INSERTION	ORF8	ttc/CTGttc	F120LF	orf8	0.000494	0.993968	5	3	T>TCTG
ERR5749302	28253	PASS	CA	C	22794	0.993595	0	146,0,22648,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749302	28270	PASS	TA	T	44050	0.996481	305	146,9,22648,21247	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749302	28271	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AA	A	44049	0.001589	198	22722,21256,70,0	.	.	.	.	.	.	.	0.000482	0.924941	3	2	AA>A
ERR5749302	28280	PASS	G	C	44049	0.943268	13	8,1,22734,21224	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749302	28281	PASS	A	T	44049	0.937728	19	24,8,22725,21226	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749302	28282	PASS	T	A	44050	0.905675	9	27,15,22686,21232	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749302	28512	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	19314	6.21E-4	0	19302,0,12,0	HIGH	NONE	FRAME_SHIFT	N	gat/	D81	N	0.000621	0.172671	3	2	CAG>C
ERR5749302	28881	PASS	G	A	11328	0.76227	3	2,0,5604,5561	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749302	28882	PASS	G	A	11328	0.837924	3	2,0,5668,5560	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749302	28883	PASS	G	C	11328	0.94209	6	0,2,5681,5641	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749302	28977	PASS	C	T	5745	0.930722	0	0,2,0,5740	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749302	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	52912	0.001191	0	26576,26237,42,40	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749303	61	PASS	G	T	1082	0.974122	2147483647	0,0,1080,0	.	.	.	.	.	.	.	0.974122	0.974122	1	1	G>T
ERR5749303	71	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1077	0.012999	0	1059,0,15,0	.	.	.	.	.	.	.	0.002088	0.926791	2	1	C>T
ERR5749303	241	PASS	C	T	1499	0.865911	0	0,0,749,745	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749303	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	3624	0.001932	0	3618,0,7,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749303	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	3624	0.004691	0	3604,0,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749303	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	3624	0.002208	0	3346,0,241,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749303	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	3624	0.001656	0	3618,0,6,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749303	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	3621	0.002486	0	3612,0,9,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749303	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	16873	8.89E-4	1	13232,3626,13,2	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749303	850	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26397	9.47E-4	0	13171,13135,16,17	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G15	nsp2	0.000947	0.076956	2	1	C>T
ERR5749303	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13238	0.002342	0	0,13188,0,34	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749303	913	PASS	C	T	13238	0.913658	0	0,8,0,13219	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749303	1492	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	11525	8.68E-4	0	0,11515,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtg/	V230	nsp2	0.000868	0.321508	3	3	TG>T
ERR5749303	2185	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	16263	9.22E-4	0	2,16246,0,15	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L462S?	nsp2	0.000441	0.963529	4	3	G>GT
ERR5749303	2232	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	23266	5.16E-4	16	7003,16251,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	tgt/	C477	nsp2	0.000499	0.381237	2	2	CT>C
ERR5749303	3037	PASS	C	T	7995	0.813884	15	0,5,3992,3934	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749303	3250	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	14510	0.001378	0	14469,0,27,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gaG/gaT	E177D	nsp3	0.001378	0.921255	2	2	G>T
ERR5749303	3267	PASS	C	T	14510	0.970572	2147483647	0,0,14501,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749303	3575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	4738	0.001688	0	4724,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L287	nsp3	0.000594	0.059126	3	1	GT>G
ERR5749303	3575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTT	G	4738	0.001266	0	4724,0,6,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L287	nsp3	0.000594	0.059126	3	1	GTT>G
ERR5749303	4578	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTAACGATC	T	10922	0.001099	0	0,10910,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	aacgatctaaat/	NDLN621	nsp3	0.000519	0.082979	2	2	TTAACGATC>T
ERR5749303	5388	PASS	C	A	1855	0.962264	2147483647	0,0,1855,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749303	5986	PASS	C	T	6239	0.973553	2147483647	0,0,6233,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749303	6582	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	5569	0.001257	0	5562,0,7,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	att/	I1289	nsp3	0.001257	0.973714	2	2	CTA>C
ERR5749303	6936	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24370	9.44E-4	0	12037,11984,13,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S1406F	nsp3	0.000553	0.91447	2	2	C>T
ERR5749303	6954	PASS	T	C	12228	0.803157	2147483647	0,0,0,12143	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749303	7674	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	13194	6.82E-4	0	13178,7,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gcg/	A1652	nsp3	0.000682	0.109264	3	2	CG>C
ERR5749303	8653	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	7618	0.001969	0	7597,0,20,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atT	M33I	nsp4	0.001328	0.132353	2	2	G>T
ERR5749303	10263	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGG	C	23599	5.93E-4	0	11816,11769,7,7	MODERATE	NONE	CODON_DELETION	ORF1ab	ggt/	G71	3Cpro	0.000593	0.192529	3	2	CTGG>C
ERR5749303	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	17735	0.002312	0	17333,1,41,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749303	11082	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	17727	0.001015	0	17716,0,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000427	0.179468	2	1	TG>T
ERR5749303	11104	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	17723	0.001128	0	17642,0,21,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccT/ccC	P44	nsp6	0.000866	0.675414	2	1	T>C
ERR5749303	11152	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	17703	6.78E-4	0	17694,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K61	nsp6	0.000678	0.974465	2	2	CA>C
ERR5749303	11287	PASS	GTCTGGTTTT	G	17724	0.996445	0	0,63,0,17661	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749303	11690	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	15972	0.001252	0	15917,0,21,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggt/Agt	G240S	nsp6	0.000953	0.091324	4	2	G>A
ERR5749303	14220	PASS	C	T	10002	0.965807	0	0,3,0,9995	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D260	RdRp	0.965807	0.965807	1	1	C>T
ERR5749303	14408	PASS	C	T	174	0.867816	0	0,0,87,86	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749303	14676	PASS	C	T	9570	0.820585	0	5,0,9546,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749303	15279	PASS	C	T	9969	0.893971	2147483647	0,0,9957,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749303	15289	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	9969	0.001003	0	9959,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gat/	D618	RdRp	0.000698	0.157576	2	1	TG>T
ERR5749303	15708	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	12097	0.001488	0	0,12053,0,37	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atT	M756I	RdRp	0.001488	0.095967	1	1	G>T
ERR5749303	16176	PASS	T	C	11033	0.979335	0	0,0,2805,8224	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749303	19113	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	40739	0.001006	44	20333,20289,33,77	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gaC/gaA	D358E	ExoN	0.000461	0.125	4	3	C>A
ERR5749303	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	20425	4.41E-4	0	0,20416,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749303	19524	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9102	0.011866	0	0,8980,0,112	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ctC/ctT	L495	ExoN	0.000745	0.953697	2	2	C>T
ERR5749303	20262	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	19971	0.001252	0	19941,0,28,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttA/ttG	L214	endoR	0.000483	0.963481	2	2	A>G
ERR5749303	20320	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAT	C	19963	6.51E-4	0	19950,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	atc/	I235	endoR	0.000651	0.916979	2	2	CAT>C
ERR5749303	20930	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	17542	9.12E-4	0	17526,0,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggt/	G92	MethTr	0.000902	0.95585	2	2	CG>C
ERR5749303	21077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	17542	0.00114	0	3,17519,0,20	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K141	MethTr	0.000492	0.955529	4	2	CA>C
ERR5749303	21123	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	32289	6.19E-4	0	14738,17531,9,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	ata/Tata	I157Y?	MethTr	0.000257	0.90982	5	2	G>GT
ERR5749303	21762	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTATACA	C	7640	0.002356	0	7622,0,18,0	MODERATE	NONE	CODON_DELETION	S	atacat/	IH68	S	0.001297	0.875707	2	2	CTATACA>C
ERR5749303	21764	PASS	ATACATG	A	7640	0.996859	0	24,0,7616,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749303	21913	PASS	A	G	7634	0.904899	0	0,2,0,7599	LOW	SILENT	SYNONYMOUS_CODING	S	ctA/ctG	L117	S	0.003104	0.904899	1	1	A>G
ERR5749303	21990	PASS	TTTA	T	7645	0.997384	0	0,20,4,7621	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749303	22662	PASS	T	C	12498	0.837094	0	3,0,12462,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gTc/gCc	V367A	S	0.837094	0.837094	1	1	T>C
ERR5749303	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	12502	0.00168	0	0,12473,0,21	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749303	23012	PASS	G	A	16284	0.909912	20	8,0,8446,7806	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gaa/Aaa	E484K	S	0.001756	0.909912	2	1	G>A
ERR5749303	23063	PASS	A	T	8523	0.861668	2147483647	0,0,0,8481	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749303	23271	PASS	C	A	18341	0.931192	0	1,0,18319,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749303	23311	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	18318	0.001692	0	18267,1,47,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gaG/gaT	E583D	S	0.001115	0.705903	2	1	G>T
ERR5749303	23323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	35513	8.45E-4	0	18287,17198,15,15	HIGH	NONE	FRAME_SHIFT	S	aca/	T588	S	0.000758	0.951252	2	2	TA>T
ERR5749303	23401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	18336	0.001145	0	0,18298,0,35	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	caG/caT	Q613H	S	0.000491	0.839283	2	2	G>T
ERR5749303	23403	PASS	A	G	18336	0.976222	0	0,3,0,18310	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749303	23604	PASS	C	A	8557	0.95232	0	5,0,8548,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749303	23709	PASS	C	T	8546	0.93611	0	0,22,0,8507	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749303	24506	PASS	T	G	11801	0.972799	0	3,0,11795,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749303	24914	PASS	G	C	31378	0.960546	0	1,1,15637,15720	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749303	25430	PASS	T	C	13994	0.935115	0	1,0,13970,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	gTa/gCa	V13A	orf3a	0.935115	0.935115	1	1	T>C
ERR5749303	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	3709	0.003505	231	3677,14,2,11	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749303	25726	PASS	G	T	3684	0.982899	2147483647	0,0,3683,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gtc/Ttc	V112F	orf3a	0.000948	0.982899	1	1	G>T
ERR5749303	26526	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	8653	0.001734	0	3,8622,0,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Gca/Tca	A2S	M	0.001224	0.951192	3	1	G>T
ERR5749303	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	8112	9.86E-4	0	0,8104,0,8	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749303	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	8112	0.001972	0	0,8095,0,16	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749303	27752	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	14720	8.15E-4	0	0,14708,0,12	HIGH	NONE	FRAME_SHIFT	ORF7a	gaa/	E121	orf7a	0.000582	0.943806	2	2	CAG>C
ERR5749303	27881	PASS	C	T	4291	0.979026	0	1,0,4289,0	LOW	SILENT	SYNONYMOUS_CODING	ORF7b	caC/caT	H42	orf7b	0.001798	0.979167	2	2	C>T
ERR5749303	27972	PASS	C	T	4310	0.904872	0	0,0,4263,32	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749303	28048	PASS	G	T	4285	0.912719	0	0,8,0,4276	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749303	28111	PASS	A	G	20372	0.97958	0	3,0,16067,4289	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749303	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	16059	9.96E-4	0	16044,1,16,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749303	28270	PASS	TA	T	31114	0.99534	327	142,6,15876,15093	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749303	28280	PASS	G	C	31052	0.940165	6	12,6,15909,15077	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749303	28281	PASS	A	T	31052	0.91453	30	27,7,15895,15079	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749303	28282	PASS	T	A	31054	0.908675	7	18,10,15865,15086	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749303	28321	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	16070	0.006098	0	0,15963,0,105	LOW	SILENT	SYNONYMOUS_CODING	N	acG/acT	T16	N	0.00045	0.947809	3	2	G>T
ERR5749303	28881	PASS	G	A	10041	0.768649	3	2,0,4978,4908	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749303	28882	PASS	G	A	10041	0.822727	9	6,1,5019,4906	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749303	28883	PASS	G	C	10041	0.94642	0	0,0,5026,5004	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749303	28977	PASS	C	T	5113	0.926658	2147483647	0,0,0,5101	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749303	29077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22653	0.001192	0	22600,1,28,0	LOW	SILENT	SYNONYMOUS_CODING	N	taC/taT	Y268	N	0.000408	0.88565	3	2	C>T
ERR5749303	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	44957	0.001401	1	22562,22283,37,33	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749304	241	PASS	C	T	94	0.840426	0	0,0,47,47	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749304	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTTGACTT	A	3008	0.001995	0	2829,172,6,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcatttgactta/	KSFDL141	leader	0.000303	0.999303	4	1	AAAGTCATTTGACTT>A
ERR5749304	714	PASS	G	T	2835	0.975309	2147483647	0,0,2834,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGc/gTc	G150V	leader	0.001941	0.984148	2	1	G>T
ERR5749304	913	PASS	C	T	2831	0.907453	2147483647	0,0,0,2831	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749304	1813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	2820	0.002837	0	0,2812,0,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K338	nsp2	0.001022	0.152738	4	2	TA>T
ERR5749304	1912	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	4602	0.007605	149	1741,2825,36,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcA	S369	nsp2	0.000681	0.08802	2	1	C>A
ERR5749304	3037	PASS	C	T	1044	0.820881	6	0,2,522,515	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749304	3267	PASS	C	T	2207	0.969189	2147483647	0,0,2206,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749304	3310	PASS	A	G	2206	0.938803	2147483647	0,0,2205,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaA/gaG	E197	nsp3	0.938803	0.952297	1	1	A>G
ERR5749304	5388	PASS	C	A	300	0.956667	2147483647	0,0,300,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749304	5849	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1890	0.01164	0	0,1863,0,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cct/Tct	P1044S	nsp3	0.00146	0.830206	2	1	C>T
ERR5749304	5986	PASS	C	T	1260	0.975397	2147483647	0,0,1260,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749304	6414	PASS	A	G	2118	0.915486	2147483647	0,0,0,2117	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gAa/gGa	E1232G	nsp3	0.000549	0.930413	2	2	A>G
ERR5749304	6954	PASS	T	C	2947	0.81812	2147483647	0,0,0,2931	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749304	10193	PASS	G	A	3966	0.860313	0	1,0,3961,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E47K	3Cpro	0.000774	0.869819	2	2	G>A
ERR5749304	10195	PASS	A	T	3966	0.963944	0	1,0,3963,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gaA/gaT	E47D	3Cpro	0.951998	0.969772	1	1	A>T
ERR5749304	11287	PASS	GTCTGGTTTT	G	7014	0.998574	0	0,10,0,7004	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749304	14408	PASS	C	T	108	0.888889	0	0,0,54,54	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749304	14676	PASS	C	T	1200	0.775833	0	1,0,1195,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749304	15246	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	1624	0.008005	41	1609,0,12,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttA/ttT	L602F	RdRp	0.001432	0.633333	1	1	A>T
ERR5749304	15279	PASS	C	T	1622	0.88471	2147483647	0,0,1620,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749304	16176	PASS	T	C	1909	0.982713	0	0,0,133,1776	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749304	17615	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	2972	0.004374	0	0,2953,0,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aTg	K460M	helicase	0.001492	0.938608	2	1	A>T
ERR5749304	19328	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	2774	0.002163	0	2768,0,6,0	HIGH	NONE	FRAME_SHIFT+STOP_GAINED	ORF1ab	gat/Tgat	D432*?	ExoN	0.000459	0.937906	4	2	C>CT
ERR5749304	19329	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	2774	0.007931	0	2750,0,23,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcC	A430	ExoN	0.001217	0.228916	1	1	T>C
ERR5749304	19698	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2603	0.02305	0	2538,0,62,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I26	endoR	0.02305	0.953778	1	1	C>T
ERR5749304	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	4325	0.001618	0	0,4318,0,7	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TA>T
ERR5749304	21101	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	4326	0.013176	0	0,4269,0,57	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttc/ttTc	F150F?	MethTr	0.001498	0.083467	2	2	G>GT
ERR5749304	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2798	0.021801	0	1338,1365,34,34	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749304	21764	PASS	ATACATG	A	2372	0.99747	0	6,0,2366,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749304	21990	PASS	TTTA	T	2374	0.995366	0	0,11,2,2361	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749304	23063	PASS	A	T	1864	0.881438	2147483647	0,0,0,1859	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749304	23271	PASS	C	A	3602	0.92754	0	1,0,3599,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749304	23403	PASS	A	G	3603	0.965862	0	0,1,0,3602	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749304	23424	PASS	C	A	3603	0.067721	0	0,3344,0,258	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P621H	S	0.004085	0.067721	2	1	C>A
ERR5749304	23604	PASS	C	A	1951	0.942081	0	2,0,1948,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749304	23709	PASS	C	T	1949	0.937404	0	0,1,0,1944	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749304	24506	PASS	T	G	2157	0.972647	2147483647	0,0,2156,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749304	24914	PASS	G	C	17386	0.960025	0	0,0,8662,8720	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749304	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	9375	0.00224	7	8413,939,23,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749304	25563	PASS	G	C	8441	0.123208	0	0,7382,0,1054	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	caG/caC	Q57H	orf3a	0.001456	0.886549	2	1	G>C
ERR5749304	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	251	0.039841	106	233,8,1,9	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749304	25699	PASS	G	C	234	0.059829	0	219,0,15,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gcc/Ccc	A103P	orf3a	0.000359	0.059829	2	2	G>C
ERR5749304	26208	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	3453	0.004344	0	2,3436,0,15	HIGH	NONE	FRAME_SHIFT	ORF3a	gtg/	V273	orf3a	0.000315	0.922222	2	2	CG>C
ERR5749304	26228	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	5401	0.015923	178	1876,3435,73,17	.	.	.	.	.	.	.	0.000649	0.94873	2	1	C>A
ERR5749304	27506	PASS	G	A	9051	0.982764	0	2,1,4761,4284	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	gGa/gAa	G38E	orf7a	0.000715	0.985435	4	2	G>A
ERR5749304	27972	PASS	C	T	530	0.909434	0	0,0,508,20	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749304	28048	PASS	G	T	510	0.933333	0	0,1,0,509	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749304	28111	PASS	A	G	7842	0.979342	0	1,0,7324,510	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749304	28270	PASS	TA	T	14263	0.995583	171	64,1,7241,6959	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749304	28280	PASS	G	C	14232	0.940275	9	4,0,7248,6954	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749304	28281	PASS	A	T	14232	0.919056	14	8,1,7249,6951	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749304	28282	PASS	T	A	14233	0.912106	1	5,6,7232,6954	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749304	28292	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	14585	0.001097	0	7263,7306,8,8	HIGH	NONE	FRAME_SHIFT	N	aat/	N8	N	0.000304	0.055324	4	2	CA>C
ERR5749304	28321	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	7328	0.008461	0	0,7266,0,62	HIGH	NONE	FRAME_SHIFT	N	ttt/	F17	N	0.00045	0.947809	3	2	GT>G
ERR5749304	28406	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTACCCAATA	T	7333	0.006409	0	1,7285,0,47	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	N	ttacccaataat/tat	LPNN45Y	N	0.00043	0.921074	3	2	TTACCCAATA>T
ERR5749304	28881	PASS	G	A	582	0.728522	0	0,0,285,288	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749304	28882	PASS	G	A	582	0.824742	0	0,0,291,288	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749304	28883	PASS	G	C	582	0.939863	0	0,0,291,291	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749304	28977	PASS	C	T	297	0.939394	2147483647	0,0,0,297	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749304	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	6389	0.001878	0	6074,297,12,0	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcA	A254	N	0.000601	0.054952	4	2	T>A
ERR5749304	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	12075	0.001242	0	6068,5980,13,11	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749304	29253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6088	0.004763	0	0,6046,0,32	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCg/tTg	S327L	N	0.000361	0.053998	4	2	C>T
ERR5749304	29779	PASS	G	T	767	0.975228	2147483647	0,0,0,766	.	.	.	.	.	.	.	0.001489	0.975228	1	1	G>T
ERR5749305	241	PASS	C	T	2400	0.847917	0	0,0,1194,1194	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749305	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	6648	0.002708	0	6631,0,18,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749305	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	6648	0.001354	0	6610,0,9,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749305	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	6648	0.00346	0	6610,0,23,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749305	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	6643	0.002559	0	6033,0,551,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749305	657	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6654	0.002254	0	1,6633,0,19	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A131V	leader	0.001202	0.365979	3	1	C>T
ERR5749305	673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	14335	0.001046	50	7681,6639,0,15	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggc/	G137	leader	0.000454	0.602236	3	2	CG>C
ERR5749305	676	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14335	0.001325	47	7679,6634,2,20	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G137	leader	0.000799	0.919273	2	1	C>T
ERR5749305	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	14335	0.002093	28	7664,6629,7,23	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749305	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTTG	A	14335	8.37E-4	13	7664,6629,10,2	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcatttgac/	KSFD141	leader	0.000303	0.999303	4	1	AAAGTCATTTG>A
ERR5749305	758	PASS	C	T	7681	0.970056	0	2,0,7670,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cat/Tat	H165Y	leader	0.970056	0.970056	1	1	C>T
ERR5749305	913	PASS	C	T	7680	0.917708	0	0,3,0,7670	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749305	1694	PASS	T	C	15380	0.974382	0	9,0,15362,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Ttg/Ctg	L297	nsp2	0.001643	0.974382	1	1	T>C
ERR5749305	1862	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	15384	5.85E-4	0	0,15375,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/	Y354	nsp2	0.000585	0.936867	4	2	CT>C
ERR5749305	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	33147	0.001207	2519	16531,15502,35,995	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749305	3037	PASS	C	T	10560	0.806629	30	0,10,5264,5211	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749305	3267	PASS	C	T	9611	0.968161	0	6,0,9603,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749305	3802	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	12854	9.34E-4	6	6731,6107,4,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N363	nsp3	0.000554	0.064198	4	2	TA>T
ERR5749305	5170	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	7463	0.001206	0	0,7454,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T819	nsp3	0.000565	0.894036	2	2	CCA>C
ERR5749305	5388	PASS	C	A	3047	0.955694	2147483647	0,0,3046,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749305	5784	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16813	0.001606	0	8273,8478,14,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T1022I	nsp3	0.001294	0.919357	2	1	C>T
ERR5749305	5986	PASS	C	T	8339	0.972778	2147483647	0,0,8337,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749305	6031	PASS	C	T	8331	0.908294	2147483647	0,0,8321,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N1104	nsp3	0.00356	0.908294	1	1	C>T
ERR5749305	6706	PASS	C	T	7539	0.882876	0	0,3,0,7513	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N1329	nsp3	0.000687	0.883999	2	2	C>T
ERR5749305	6954	PASS	T	C	14810	0.822282	0	0,9,0,14735	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749305	7735	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11944	0.001507	0	11913,0,18,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I1672	nsp3	0.000658	0.954659	3	2	C>T
ERR5749305	8669	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	5462	0.002197	0	5445,0,12,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F39L	nsp4	0.000973	0.22449	1	1	T>C
ERR5749305	8964	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	13236	9.07E-4	0	13224,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K138	nsp4	0.000553	0.981649	4	2	CAA>C
ERR5749305	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	13094	0.00252	13	11651,1410,33,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749305	10138	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20051	0.001247	0	15717,4304,21,5	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N28	3Cpro	0.000458	0.983567	3	3	C>T
ERR5749305	10156	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15743	0.001207	0	15716,1,24,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D34	3Cpro	0.001207	0.949463	1	1	C>T
ERR5749305	10323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	15727	0.006549	0	0,15589,0,107	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749305	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17613	0.002668	0	17549,0,49,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749305	11082	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	17607	0.001022	0	17595,0,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000427	0.179468	2	1	TG>T
ERR5749305	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	17607	0.003237	0	17501,0,78,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749305	11095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTT	C	17601	7.95E-4	0	17580,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L43	nsp6	0.000515	0.887707	7	2	CTT>C
ERR5749305	11235	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTAG	C	17595	5.12E-4	0	0,17586,0,9	MODERATE	NONE	CODON_DELETION	ORF1ab	agt/	S89	nsp6	0.000512	0.942208	2	2	CTAG>C
ERR5749305	11287	PASS	GTCTGGTTTT	G	17605	0.997046	0	0,52,0,17553	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749305	11455	PASS	C	T	7188	0.968698	0	1,0,7182,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A161	nsp6	0.00147	0.968698	1	1	C>T
ERR5749305	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	19619	0.001325	22	12404,7174,11,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749305	11824	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	12419	0.001047	0	0,12406,0,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K285	nsp6	0.000465	0.922016	2	2	CA>C
ERR5749305	12079	PASS	G	A	35857	0.937056	12	10,3,17837,17967	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	agG/agA	R79	nsp7	0.000984	0.937056	1	1	G>A
ERR5749305	12162	PASS	A	G	29034	0.967727	4	1,0,10991,18024	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cAg/cGg	Q24R	nsp8	0.000894	0.982497	1	1	A>G
ERR5749305	12357	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	11003	9.09E-4	0	0,10993,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	atg/	M90	nsp8	0.000909	0.956941	3	2	CA>C
ERR5749305	12459	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25410	0.001063	34	14379,10999,25,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T123I	nsp8	0.000658	0.986093	1	1	C>T
ERR5749305	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	14406	0.001249	0	14369,0,18,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749305	13459	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTT	G	10060	9.94E-4	0	10049,0,10,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ttttta/tta	FL7L	nsp11	0.000691	0.060726	5	2	GTTT>G
ERR5749305	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20086	0.002191	0	10019,9992,24,24	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749305	13994	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	11843	7.6E-4	0	11832,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L186	RdRp	0.000427	0.114441	3	2	CT>C
ERR5749305	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	4412	0.005666	1166	4299,40,3,68	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749305	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	8561	9.34E-4	0	4295,4264,4,4	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749305	14408	PASS	C	T	8561	0.833547	0	0,0,4267,4228	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749305	14676	PASS	C	T	6120	0.692647	0	3,0,6074,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749305	15240	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9305	0.002902	0	9267,6,28,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N600	RdRp	0.000934	0.931284	2	2	C>T
ERR5749305	15279	PASS	C	T	9298	0.883523	0	13,0,9276,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749305	15289	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	9298	8.6E-4	0	9290,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gat/	D618	RdRp	0.000698	0.157576	2	1	TG>T
ERR5749305	16176	PASS	T	C	10508	0.98011	0	0,1,4523,5973	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749305	16508	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	16038	5.61E-4	0	16027,2,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L92	helicase	0.000561	0.074909	2	2	GT>G
ERR5749305	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAA	G	16652	0.001141	0	16590,0,19,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GAA>G
ERR5749305	17615	PASS	A	G	11776	0.904212	2147483647	0,0,0,11740	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749305	17747	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTG	C	9579	9.4E-4	0	9567,1,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctgct/	PA504	helicase	0.000839	0.968462	2	2	CTG>C
ERR5749305	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	24122	8.29E-4	0	24102,0,20,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749305	18744	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24118	9.12E-4	0	24033,0,22,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y235	ExoN	0.000912	0.953624	2	2	C>T
ERR5749305	18756	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	24116	4.15E-4	0	24107,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F240	ExoN	0.000392	0.942688	3	2	GT>G
ERR5749305	19186	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	15504	7.09E-4	0	0,15493,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L383	ExoN	0.000709	0.96164	4	3	CT>C
ERR5749305	19888	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AG	A	22160	5.87E-4	36	9198,12949,12,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	aga/	R90	endoR	0.000587	0.083187	2	2	AG>A
ERR5749305	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9206	0.001847	0	9185,0,18,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749305	20844	PASS	C	T	25596	0.905571	1	13,8,14044,11488	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P62	MethTr	0.000293	0.905571	5	2	C>T
ERR5749305	20987	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	28106	7.47E-4	0	14054,14035,11,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L111	MethTr	0.000276	0.056129	4	2	CT>C
ERR5749305	21032	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATC	A	14085	5.68E-4	0	0,14077,0,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctc/	L126	MethTr	0.000568	0.088561	2	2	ATC>A
ERR5749305	21736	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10287	0.002527	0	10248,5,27,0	LOW	SILENT	SYNONYMOUS_CODING	S	ttC/ttT	F58	S	0.001596	0.804427	3	2	C>T
ERR5749305	21764	PASS	ATACATG	A	10281	0.997277	0	23,0,10253,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749305	21974	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GATCCATTTTTGGGTGTTTATT	G	10284	0.001167	0	3,10269,0,12	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	gatccatttttgggtgtttattac/gac	DPFLGVYY138D	S	0.001167	0.928915	2	2	GATCCATTTTTGGGTGTTTATT>G
ERR5749305	21987	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	10285	0.001653	0	3,10246,0,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gGt/gTt	G142V	S	0.000998	0.922156	5	2	G>T
ERR5749305	21990	PASS	TTTA	T	10284	0.995527	0	0,46,3,10235	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749305	21991	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTA	T	10294	9.71E-4	0	13,10269,0,10	HIGH	NONE	FRAME_SHIFT	S	tat/	Y144	S	0.00078	0.991378	2	1	TTA>T
ERR5749305	22001	PASS	A	G	27103	0.32037	78	11538,6708,5263,3557	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aaa/Gaa	K147E	S	0.000521	0.32037	2	2	A>G
ERR5749305	22290	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16826	0.001545	0	2,16783,0,29	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gTt	A243V	S	0.000389	0.578006	2	2	C>T
ERR5749305	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	15424	0.001362	0	0,15396,0,21	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749305	22927	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	11377	7.91E-4	0	11368,0,9,0	HIGH	NONE	FRAME_SHIFT	S	ttt/	F456	S	0.000791	0.909717	4	3	GT>G
ERR5749305	22995	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	11345	8.81E-4	0	11339,0,10,0	HIGH	NONE	FRAME_SHIFT	S	aca/	T478	S	0.000881	0.67268	2	2	CA>C
ERR5749305	23063	PASS	A	T	11360	0.866109	0	0,1,0,11314	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749305	23271	PASS	C	A	9955	0.918734	0	1,0,9944,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749305	23403	PASS	A	G	9952	0.970358	2147483647	0,0,0,9945	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749305	23604	PASS	C	A	11397	0.932438	0	4,0,11382,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749305	23709	PASS	C	T	11408	0.940831	0	0,3,23,11371	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749305	23712	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	11410	7.89E-4	0	22,11379,0,9	HIGH	NONE	FRAME_SHIFT	S	ttt/	F718	S	0.000679	0.958955	3	2	AT>A
ERR5749305	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	18123	0.001048	6	6715,11389,10,9	HIGH	NONE	FRAME_SHIFT	S	ttg/	L753	S	0.000334	0.080808	2	2	CT>C
ERR5749305	24506	PASS	T	G	12876	0.972973	0	5,0,12866,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749305	24512	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12876	0.001476	0	12856,0,19,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L984F	S	0.001476	0.154545	1	1	C>T
ERR5749305	24914	PASS	G	C	34962	0.955723	0	0,0,17415,17526	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749305	25422	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGGAACTG	T	17786	6.75E-4	0	17756,5,12,0	HIGH	NONE	FRAME_SHIFT	ORF3a	ggaactgta/	GTV11	orf3a	0.000545	0.213989	6	1	TGGAACTG>T
ERR5749305	25422	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGGAACTGTAACTTTG	T	17786	6.18E-4	0	17756,5,11,0	MODERATE	NONE	CODON_DELETION	ORF3a	ggaactgtaactttg/	GTVTL11	orf3a	0.000545	0.213989	6	1	TGGAACTGTAACTTTG>T
ERR5749305	25587	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	17782	6.19E-4	0	0,17765,0,11	HIGH	NONE	FRAME_SHIFT	ORF3a	aag/	K67	orf3a	0.000598	0.813206	6	2	CA>C
ERR5749305	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	4612	0.003252	291	4566,20,2,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749305	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	4578	0.001529	0	4571,0,7,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749305	26208	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27350	8.78E-4	0	1,27307,0,26	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	agC/agT	S272	orf3a	0.000315	0.922222	2	2	C>T
ERR5749305	26270	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34705	8.36E-4	14	7345,27316,2,31	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	aCa/aTa	T9I	E	0.000586	0.930791	3	2	C>T
ERR5749305	26333	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7349	0.001905	0	7322,0,17,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	aCa/aTa	T30I	E	0.00158	0.943221	1	1	C>T
ERR5749305	26907	PASS	C	T	25200	0.976032	0	14,0,25168,0	LOW	SILENT	SYNONYMOUS_CODING	M	Ctg/Ttg	L129	M	0.000817	0.976032	1	1	C>T
ERR5749305	27476	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34274	0.00178	55	16966,17234,13,50	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	aCa/aTa	T28I	orf7a	0.000547	0.22827	4	2	C>T
ERR5749305	27654	PASS	C	T	17159	0.947433	44	3,3,16906,200	LOW	SILENT	SYNONYMOUS_CODING	ORF7a	ttC/ttT	F87	orf7a	0.000906	0.947433	2	2	C>T
ERR5749305	27684	PASS	C	T	16936	0.90411	0	0,6,23,16844	LOW	SILENT	SYNONYMOUS_CODING	ORF7a	taC/taT	Y97	orf7a	0.000478	0.90411	2	2	C>T
ERR5749305	27816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	22154	5.87E-4	13	5162,16979,0,13	HIGH	NONE	FRAME_SHIFT	ORF7b	tta/	L22	orf7b	0.000423	0.053007	1	1	GT>G
ERR5749305	27972	PASS	C	T	5186	0.895488	0	0,0,5146,21	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749305	28048	PASS	G	T	5160	0.913178	0	0,9,0,5150	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749305	28111	PASS	A	G	23460	0.97971	0	3,1,18289,5160	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749305	28270	PASS	TA	T	35286	0.994049	527	216,6,18004,17072	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749305	28280	PASS	G	C	35218	0.939917	60	25,1,18048,17050	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749305	28281	PASS	A	T	35218	0.909563	61	40,6,18052,17056	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749305	28282	PASS	T	A	35222	0.90963	24	38,15,17991,17066	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749305	28292	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	36386	4.4E-4	0	18117,18224,8,8	HIGH	NONE	FRAME_SHIFT	N	aat/	N8	N	0.000304	0.055324	4	2	CAA>C
ERR5749305	28651	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	18494	7.03E-4	0	0,18481,0,13	HIGH	NONE	FRAME_SHIFT	N	aaa/	K127	N	0.000502	0.918117	3	2	CA>C
ERR5749305	28881	PASS	G	A	4446	0.710976	9	3,0,2165,2195	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749305	28882	PASS	G	A	4446	0.822537	0	0,0,2219,2186	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749305	28883	PASS	G	C	4446	0.947143	0	0,1,2222,2221	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749305	28977	PASS	C	T	2266	0.930274	2147483647	0,0,0,2261	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749305	29095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22155	0.001986	0	22095,0,44,0	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F274	N	0.000792	0.961279	2	2	C>T
ERR5749305	29158	PASS	A	C	22145	0.962655	0	21,0,22103,4	LOW	SILENT	SYNONYMOUS_CODING	N	ggA/ggC	G295	N	0.962655	0.962655	1	1	A>C
ERR5749305	29311	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	22158	4.51E-4	0	5,22143,0,10	HIGH	NONE	FRAME_SHIFT	N	aaa/	K347	N	0.000335	0.790798	3	2	CA>C
ERR5749306	71	PASS	C	T	1149	0.066144	0	1066,0,82,0	.	.	.	.	.	.	.	0.002088	0.926791	2	1	C>T
ERR5749306	241	PASS	C	T	1608	0.845149	0	0,0,800,795	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749306	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	5826	0.001202	0	5818,0,7,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749306	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	5822	0.002233	0	5433,0,376,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749306	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	5822	0.001202	0	5815,0,7,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749306	657	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	G	5836	0.003084	0	3,5812,0,19	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gGt	A131G	leader	0.001202	0.365979	3	1	C>G
ERR5749306	673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25825	0.002633	434	19986,5758,3,74	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y136	leader	0.000454	0.602236	3	2	C>T
ERR5749306	843	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGA	C	39892	3.01E-4	0	19960,19922,6,6	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gatggc/ggc	DG14G	nsp2	0.000301	0.050923	4	2	CTGA>C
ERR5749306	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19979	0.001201	0	0,19926,0,28	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749306	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	19979	5.51E-4	0	0,19968,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L35	nsp2	0.000551	0.081967	3	2	CT>C
ERR5749306	913	PASS	C	T	19980	0.910611	0	0,13,0,19925	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749306	932	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAC	G	19988	6.5E-4	0	0,19975,0,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T44	nsp2	0.00048	0.184416	2	2	GAC>G
ERR5749306	1247	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	12080	0.001076	0	0,12067,0,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T149	nsp2	0.001076	0.098425	2	2	GA>G
ERR5749306	1813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	13480	0.003264	0	0,13409,0,50	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcA	A336	nsp2	0.001022	0.152738	4	2	T>A
ERR5749306	2185	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	22679	4.41E-4	0	5,22664,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L462S?	nsp2	0.000441	0.963529	4	3	G>GT
ERR5749306	2453	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTCATGCCTCT	C	8158	0.00429	0	0,8123,0,35	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctcatgcctcta/	LMPL550	nsp2	0.00429	0.842201	2	2	CTCATGCCTCT>C
ERR5749306	3037	PASS	C	T	8513	0.820157	27	0,9,4249,4188	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749306	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	4311	0.004639	510	3,4286,20,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749306	3267	PASS	C	T	17753	0.969864	2147483647	0,0,17745,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749306	3671	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	14632	0.002119	0	7276,7208,19,19	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E318K	nsp3	0.000351	0.0625	6	2	G>A
ERR5749306	4133	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	16859	7.71E-4	22	10828,6019,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/	V472	nsp3	0.000771	0.155556	2	1	GT>G
ERR5749306	4234	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	21605	0.001296	0	10810,10768,14,14	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N506	nsp3	0.00099	0.714088	3	3	CA>C
ERR5749306	4551	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAACT	C	12969	0.002622	0	0,12935,0,34	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaact/	TT611	nsp3	0.001721	0.897919	3	2	CAACT>C
ERR5749306	5388	PASS	C	A	2656	0.955572	2147483647	0,0,2652,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749306	5986	PASS	C	T	7374	0.977895	2147483647	0,0,7370,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749306	6310	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18057	0.00144	0	17997,0,27,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	agC/agT	S1197	nsp3	0.00099	0.94715	2	2	C>T
ERR5749306	6472	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	18062	8.3E-4	0	4,18043,0,15	HIGH	NONE	FRAME_SHIFT	ORF1ab	gaa/	E1252	nsp3	0.00083	0.966307	2	2	CG>C
ERR5749306	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	6993	0.017732	0	0,6869,0,124	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L1328S?	nsp3	0.000731	0.14377	4	2	C>CT
ERR5749306	6869	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ACTG	A	15077	9.29E-4	0	15061,3,14,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	actgtt/att	TV1384I	nsp3	0.000929	0.168901	2	2	ACTG>A
ERR5749306	6954	PASS	T	C	15050	0.807774	0	0,1,0,14945	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749306	7740	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	15812	0.001265	0	15788,0,23,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gAt/gGt	D1674G	nsp3	0.000834	0.078818	3	2	A>G
ERR5749306	8123	PASS	C	T	17068	0.776482	0	1,0,16848,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Ttt	L1802F	nsp3	0.001144	0.778589	1	1	C>T
ERR5749306	9072	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	25434	0.001927	5	12746,12597,40,50	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCc/aAc	T173N	nsp4	0.001037	0.930675	2	1	C>A
ERR5749306	11075	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TC	21374	0.001029	0	21350,0,22,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/tCtt	F35S?	nsp6	0.000555	0.885796	4	2	T>TC
ERR5749306	11095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTT	C	21367	5.15E-4	0	21336,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L43	nsp6	0.000515	0.887707	7	2	CTT>C
ERR5749306	11199	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	42565	9.16E-4	36	21118,21217,117,67	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCc/gAc	A76D	nsp6	0.000309	0.056758	3	2	C>A
ERR5749306	11199	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	42565	7.99E-4	0	21118,21217,17,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCc/gTc	A76V	nsp6	0.000309	0.056758	3	2	C>T
ERR5749306	11287	PASS	GTCTGGTTTT	G	21364	0.994992	0	0,107,0,21257	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749306	11674	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	18977	5.8E-4	0	18966,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F235	nsp6	0.00054	0.985782	3	2	CT>C
ERR5749306	11830	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	18970	0.001792	0	0,18931,0,34	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtA/gtG	V286	nsp6	0.001792	0.969936	1	1	A>G
ERR5749306	12273	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AG	A	11572	7.78E-4	0	11564,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aag/	K61	nsp8	0.000778	0.2	3	2	AG>A
ERR5749306	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	12237	8.17E-4	0	12227,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749306	13458	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13070	0.001607	0	13040,0,22,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCg/tTg	S6L	nsp11	0.001017	0.058608	4	2	C>T
ERR5749306	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26107	9.96E-4	0	13042,13008,15,16	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749306	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	26107	5.36E-4	0	13041,13028,7,7	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggc/	G23	RdRp	0.000536	0.074627	4	2	CG>C
ERR5749306	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CGG	C	26107	9.19E-4	0	13041,13028,12,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggc/	G23	RdRp	0.000536	0.074627	4	2	CGG>C
ERR5749306	13994	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11626	0.00172	0	11598,0,21,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A185V	RdRp	0.000427	0.114441	3	2	C>T
ERR5749306	14408	PASS	C	T	1705	0.838123	0	0,0,858,835	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749306	14676	PASS	C	T	11507	0.798992	0	4,0,11471,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749306	15279	PASS	C	T	14389	0.914171	2147483647	0,0,14372,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749306	15905	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AG	A	10780	8.35E-4	0	10771,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggt/	G823	RdRp	0.000835	0.057692	2	1	AG>A
ERR5749306	16176	PASS	T	C	14189	0.978504	3	1,1,3403,10776	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749306	17615	PASS	A	G	10988	0.901438	2147483647	0,0,0,10958	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749306	17626	PASS	C	T	10990	0.934304	0	0,1,0,10972	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cat/Tat	H464Y	helicase	0.001039	0.946125	2	2	C>T
ERR5749306	18498	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	28910	0.001072	0	0,28739,0,146	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atT	M153I	ExoN	0.001072	0.080328	3	1	G>T
ERR5749306	18504	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AG	A	28932	5.18E-4	0	0,28917,0,15	HIGH	NONE	FRAME_SHIFT	ORF1ab	gga/	G156	ExoN	0.000518	0.094148	4	3	AG>A
ERR5749306	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	23351	0.001285	0	23321,0,30,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749306	18744	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23346	0.003213	0	23225,0,80,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y235	ExoN	0.000912	0.953624	2	2	C>T
ERR5749306	18984	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTT	G	23330	7.72E-4	0	23312,0,18,0	MODERATE	NONE	CODON_DELETION	ORF1ab	gtt/	V317	ExoN	0.000419	0.950929	5	2	GGTT>G
ERR5749306	19011	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	23329	8.14E-4	0	23310,0,19,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K325	ExoN	0.000408	0.975746	4	2	CA>C
ERR5749306	19296	PASS	G	A	11922	0.977017	78	0,2,11918,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttG/ttA	L419	ExoN	0.000586	0.977017	2	2	G>A
ERR5749306	19328	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	11919	0.001007	0	11907,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F431	ExoN	0.000459	0.937906	4	2	CT>C
ERR5749306	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9092	0.00198	0	9069,0,18,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749306	20719	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	14969	8.02E-4	0	0,14957,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctatta/	LL21	MethTr	0.000341	0.209091	2	2	CTA>C
ERR5749306	20951	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	21091	7.11E-4	0	21075,1,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gat/	D99	MethTr	0.000431	0.138667	3	3	CAG>C
ERR5749306	20987	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	42061	0.002116	0	20947,20880,52,53	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T110I	MethTr	0.000276	0.056129	4	2	C>T
ERR5749306	20987	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	42059	3.8E-4	0	21044,21001,8,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L111	MethTr	0.000276	0.056129	4	2	CT>C
ERR5749306	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	19773	0.002579	1	9847,9879,24,27	HIGH	NONE	FRAME_SHIFT	S	ctt/Tctt	L5S?	S	0.000394	0.091869	4	1	G>GT
ERR5749306	21618	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	9932	0.001611	0	0,9916,0,16	HIGH	NONE	FRAME_SHIFT	S	acc/	T20	S	0.001611	0.955482	3	2	CA>C
ERR5749306	21764	PASS	ATACATG	A	9905	0.998486	0	15,0,9890,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749306	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	9905	7.07E-4	0	9898,0,7,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749306	21817	PASS	A	G	9902	0.959301	0	1,0,9893,0	LOW	SILENT	SYNONYMOUS_CODING	S	ccA/ccG	P85	S	0.000689	0.961354	3	2	A>G
ERR5749306	21990	PASS	TTTA	T	9911	0.997175	0	0,28,5,9878	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749306	23063	PASS	A	T	10079	0.868241	2147483647	0,0,0,10033	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749306	23271	PASS	C	A	22831	0.921028	0	2,0,22805,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749306	23403	PASS	A	G	22825	0.966966	0	0,1,0,22807	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749306	23604	PASS	C	A	10220	0.931018	0	5,0,10209,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749306	23709	PASS	C	T	10214	0.94018	0	0,14,0,10191	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749306	24320	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	8951	0.002905	0	0,8922,0,26	HIGH	NONE	FRAME_SHIFT	S	aaa/	K921	S	0.000763	0.138365	4	2	CA>C
ERR5749306	24506	PASS	T	G	14600	0.97637	0	4,0,14593,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749306	24914	PASS	G	C	33689	0.958532	0	1,1,16774,16888	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749306	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	24521	0.001917	52	16914,7546,52,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749306	25429	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTAACTT	G	17034	7.04E-4	0	17023,0,12,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF3a	gtaactttg/gtg	VTL13V	orf3a	0.00064	0.906678	5	2	GTAACTT>G
ERR5749306	25603	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17038	0.006691	0	0,16915,0,120	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	Cta/Tta	L71	orf3a	0.001967	0.924436	1	1	C>T
ERR5749306	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	3762	0.009569	456	3696,22,11,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749306	25690	PASS	G	T	3713	0.974145	2147483647	0,0,3711,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Ggc/Tgc	G100C	orf3a	0.971091	0.979849	1	1	G>T
ERR5749306	26257	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	34303	4.66E-4	22	10038,24249,0,16	HIGH	NONE	FRAME_SHIFT	E	tcg/tTcg	S6F?	E	0.000247	0.948926	4	2	G>GT
ERR5749306	26509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	10034	0.001196	0	0,10022,0,12	.	.	.	.	.	.	.	0.000852	0.946613	3	1	CT>C
ERR5749306	26532	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	10035	0.002192	0	0,10002,0,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Tcc/Ccc	S4P	M	0.001836	0.05891	2	2	T>C
ERR5749306	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	G	9548	0.001362	0	0,9532,0,13	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/	ACLVGLMWLSYFIASF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT>G
ERR5749306	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	9549	0.002304	0	0,9524,0,22	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749306	27078	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CGT	C	28975	5.52E-4	0	1,28958,0,16	HIGH	NONE	FRAME_SHIFT	M	gta/	V187	M	0.000415	0.05783	2	2	CGT>C
ERR5749306	27513	PASS	C	T	18132	0.982462	2147483647	0,0,18122,0	LOW	SILENT	SYNONYMOUS_CODING	ORF7a	taC/taT	Y40	orf7a	0.001863	0.982462	2	2	C>T
ERR5749306	27972	PASS	C	T	5199	0.903058	0	0,0,5166,22	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749306	28048	PASS	G	T	5182	0.920687	0	0,5,0,5174	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749306	28111	PASS	A	G	27049	0.980295	2	5,2,21853,5179	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749306	28270	PASS	TA	T	42190	0.994548	469	218,12,21560,20400	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749306	28270	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAA	T	42190	3.32E-4	48	218,12,7,7	.	.	.	.	.	.	.	0.000322	1	2	1	TAA>T
ERR5749306	28280	PASS	G	C	42114	0.934345	20	15,3,21613,20384	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749306	28281	PASS	A	T	42114	0.904189	14	37,19,21583,20369	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749306	28282	PASS	T	A	42116	0.909274	7	30,19,21582,20396	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749306	28287	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	43461	0.001035	1	21609,21738,25,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gGa/gAa	G5E	N	0.000961	0.079824	2	1	G>A
ERR5749306	28881	PASS	G	A	9352	0.751604	0	3,2,4615,4587	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749306	28882	PASS	G	A	9351	0.819591	4	4,1,4681,4579	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749306	28883	PASS	G	C	9351	0.94129	3	0,1,4688,4657	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749306	28960	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	4748	0.043808	0	0,4510,0,235	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	caG/caT	Q229H	N	0.00273	0.921139	2	2	G>T
ERR5749306	28977	PASS	C	T	4748	0.925232	0	0,2,0,4740	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749306	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	47960	9.59E-4	0	24094,23791,32,29	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749306	29686	PASS	C	T	10846	0.782593	15	0,5,5410,5248	.	.	.	.	.	.	.	0.001045	0.802514	2	1	C>T
ERR5749307	241	PASS	C	T	1034	0.87234	0	0,1,513,515	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749307	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	3386	0.002363	0	3379,0,8,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749307	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	3386	0.001772	0	3373,0,6,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749307	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	3382	0.001774	0	3373,0,6,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttatg/gtg	VM84V	leader	0.000554	0.991848	4	1	GTTA>G
ERR5749307	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATGGTTG	T	3382	0.001774	0	3371,0,6,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	atggttgag/	MVE85	leader	0.000587	0.476744	4	1	TATGGTTG>T
ERR5749307	625	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	3389	0.004721	0	0,3366,0,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaG/aaC	K120N	leader	0.004721	0.298809	2	1	G>C
ERR5749307	635	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3389	0.008557	0	0,3355,0,32	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgt/Tgt	R124C	leader	0.00148	0.880435	1	1	C>T
ERR5749307	680	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	16737	0.001852	22	13307,3386,34,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gat/Tat	D139Y	leader	0.000661	0.166667	3	2	G>T
ERR5749307	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	16737	0.002031	20	13300,3389,33,1	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749307	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTTG	A	16737	8.36E-4	10	13300,3389,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcatttgac/	KSFD141	leader	0.000303	0.999303	4	1	AAAGTCATTTG>A
ERR5749307	913	PASS	C	T	13337	0.893004	0	0,9,0,13300	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749307	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	38268	0.002143	2147483647	19139,17522,39,1478	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749307	3037	PASS	C	T	7285	0.797117	36	0,12,3651,3566	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749307	3247	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	13319	0.001502	0	13284,0,27,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	agT/agG	S176R	nsp3	0.001502	0.200222	2	2	T>G
ERR5749307	3267	PASS	C	T	13317	0.972667	0	1,0,13303,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749307	3671	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GAA	9664	0.00207	0	4831,4816,10,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/aaAAt	N319K?	nsp3	0.000351	0.0625	6	2	G>GAA
ERR5749307	4529	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTTTACTTTTACACCAGTAAAACAAC	T	10483	0.002289	0	0,10459,0,24	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttttacttttacaccagtaaaacaact/	FYFYTSKTT604	nsp3	0.000527	0.402778	3	1	TTTTACTTTTACACCAGTAAAACAAC>T
ERR5749307	4832	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTAGGTA	C	14555	6.18E-4	0	7292,7255,5,4	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtatagaa/gaa	GIE706E	nsp3	0.000542	0.727166	3	2	CTAGGTA>C
ERR5749307	5077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	6441	0.003105	0	6402,0,21,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtT/gtC	V786	nsp3	0.001393	0.168205	1	1	T>C
ERR5749307	5388	PASS	C	A	1985	0.954156	2147483647	0,0,1985,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749307	5986	PASS	C	T	6447	0.977354	0	1,0,6444,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749307	6311	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AC	A	12687	0.002365	0	12657,0,30,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T1198	nsp3	0.002365	0.973136	2	2	AC>A
ERR5749307	6516	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	18773	0.001225	112	6064,12686,23,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	att/aAtt	I1268N?	nsp3	0.000479	0.186047	4	2	T>TA
ERR5749307	6579	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	6085	0.003451	0	6057,0,25,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cTt/cGt	L1287R	nsp3	0.003451	0.968477	2	1	T>G
ERR5749307	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	6073	0.004117	0	0,6048,0,25	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L1328S?	nsp3	0.000731	0.14377	4	2	C>CT
ERR5749307	6706	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	6075	0.001152	0	0,6068,0,7	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1330	nsp3	0.000687	0.883999	2	2	CA>C
ERR5749307	6813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18008	0.001166	3	11899,6078,16,5	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T1365I	nsp3	0.001082	0.95799	2	1	C>T
ERR5749307	6954	PASS	T	C	11874	0.800657	0	0,2,0,11784	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749307	8084	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	11826	0.001268	0	11811,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1790	nsp3	0.000543	0.923413	4	2	GA>G
ERR5749307	9561	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7639	0.005629	0	7589,0,49,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCa/tTa	S336L	nsp4	0.00171	0.161742	2	2	C>T
ERR5749307	10138	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	15973	0.002003	41	12256,3674,39,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaC/aaA	N28K	3Cpro	0.000458	0.983567	3	3	C>A
ERR5749307	10228	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAT	C	12296	9.76E-4	0	12284,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	att/	I59	3Cpro	0.000533	0.961998	2	2	CAT>C
ERR5749307	10386	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	25620	0.001093	79	13276,12288,28,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tca/tTTca	S113F?	3Cpro	0.000642	0.160456	4	2	C>CTT
ERR5749307	10386	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25620	0.001054	92	13320,12263,0,29	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T111I	3Cpro	0.000642	0.160456	4	2	C>T
ERR5749307	10507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	13318	0.002027	0	13253,0,63,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaC/aaA	N151K	3Cpro	0.00123	0.842913	2	2	C>A
ERR5749307	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	17483	0.002231	0	17416,0,59,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749307	11287	PASS	GTCTGGTTTT	G	17474	0.997825	0	0,38,0,17436	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749307	11767	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	32660	9.49E-4	0	16304,16250,20,19	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	agC/agT	S265	nsp6	0.000949	0.854102	1	1	C>T
ERR5749307	11824	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	16372	5.5E-4	0	0,16363,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K285	nsp6	0.000465	0.922016	2	2	CA>C
ERR5749307	12125	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	15946	0.001254	0	0,15845,0,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y12H	nsp8	0.000847	0.113436	1	1	T>C
ERR5749307	12318	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15557	0.003407	0	7733,7730,31,31	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S76F	nsp8	0.003407	0.097044	1	1	C>T
ERR5749307	12676	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	11169	7.16E-4	0	0,11161,0,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K196	nsp8	0.000716	0.87302	3	2	CA>C
ERR5749307	13459	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	9284	9.69E-4	0	9275,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/ttTa	L8F?	nsp11	0.000691	0.060726	5	2	G>GT
ERR5749307	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18544	0.001672	0	9264,9233,16,16	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749307	13623	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	9284	0.00237	0	0,9248,0,32	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gaA/gaT	E61D	RdRp	0.00237	0.931889	2	2	A>T
ERR5749307	13995	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTTG	T	9119	8.77E-4	0	9111,0,8,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ttgtta/tta	LL186L	RdRp	0.000877	0.050235	2	2	TTTG>T
ERR5749307	14168	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	9108	0.003513	0	0,9076,0,32	HIGH	NONE	FRAME_SHIFT	ORF1ab	atatta/	IL244	RdRp	0.000479	0.314961	1	1	CTA>C
ERR5749307	14408	PASS	C	T	1417	0.819337	3	0,1,704,690	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749307	14676	PASS	C	T	8242	0.742538	0	1,0,8205,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749307	15279	PASS	C	T	8238	0.940155	2147483647	0,0,8230,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749307	16176	PASS	T	C	10563	0.971978	0	0,0,2426,8132	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749307	17615	PASS	A	G	9326	0.882157	2147483647	0,0,0,9301	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749307	17678	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	9340	0.001499	0	1,9318,0,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aAg	T481K	helicase	0.001162	0.968704	2	1	C>A
ERR5749307	18232	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5467	0.002195	0	0,5451,0,12	HIGH	NONSENSE	STOP_GAINED	ORF1ab	Caa/Taa	Q65*	ExoN	0.002195	0.056093	1	1	C>T
ERR5749307	18498	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	22848	0.001094	0	0,22704,0,128	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atT	M153I	ExoN	0.001072	0.080328	3	1	G>T
ERR5749307	18636	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	45960	8.7E-4	93	22955,22937,2,40	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtG/gtA	V199	ExoN	0.00055	0.963467	3	2	G>A
ERR5749307	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	22967	0.001306	0	22937,0,30,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749307	18788	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	45836	0.002269	27	22808,22807,123,78	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aAa	T250K	ExoN	0.000792	0.51652	2	1	C>A
ERR5749307	18984	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	20785	0.001443	0	20751,0,31,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atC	M315I	ExoN	0.000419	0.950929	5	2	G>C
ERR5749307	19011	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	20785	0.001058	0	20763,0,22,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K325	ExoN	0.000408	0.975746	4	2	CA>C
ERR5749307	19096	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	20807	0.001586	0	20696,48,36,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gca/Aca	A353T	ExoN	0.000726	0.105058	3	2	G>A
ERR5749307	19328	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	9996	0.0011	0	9985,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F431	ExoN	0.000459	0.937906	4	2	CT>C
ERR5749307	19343	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTTTTGTTAATTTAAAACAA	C	9996	0.001601	0	9980,0,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tttgttaatttaaaacaatta/	FVNLKQL436	ExoN	0.000519	0.192257	7	2	CTTTTGTTAATTTAAAACAA>C
ERR5749307	21077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	16241	0.001478	0	11,16206,0,24	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K141	MethTr	0.000492	0.955529	4	2	CA>C
ERR5749307	21658	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8063	0.001984	54	0,8042,2,14	LOW	SILENT	SYNONYMOUS_CODING	S	ttC/ttT	F32	S	0.001649	0.937508	2	2	C>T
ERR5749307	21733	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	8188	0.002076	0	8155,7,19,0	LOW	SILENT	SYNONYMOUS_CODING	S	ccT/ccC	P57	S	0.001662	0.065814	2	1	T>C
ERR5749307	21764	PASS	ATACATG	A	8181	0.996455	0	29,0,8152,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749307	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	8181	0.001467	0	8169,0,12,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749307	21990	PASS	TTTA	T	8184	0.994746	0	0,43,4,8137	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749307	22227	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	13791	0.002828	0	0,13752,0,39	HIGH	NONE	FRAME_SHIFT	S	tta/	L223	S	0.000419	0.824305	2	2	CT>C
ERR5749307	22280	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ACTTTACTTG	A	13800	5.8E-4	0	3,13789,0,8	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	cttgctttacat/cat	LALH242H	S	0.00046	0.997799	1	1	ACTTTACTTG>A
ERR5749307	23063	PASS	A	T	8277	0.853087	0	0,2,0,8224	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749307	23271	PASS	C	A	17527	0.914589	2147483647	0,0,17515,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749307	23403	PASS	A	G	17520	0.951027	0	0,1,0,17500	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749307	23541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGAGTGTGACATACCCATT	A	8337	0.002159	0	8319,0,18,0	HIGH	NONE	FRAME_SHIFT	S	tatgagtgtgacatacccatt/	YECDIPI660	S	0.000911	0.950734	4	2	ATGAGTGTGACATACCCATT>A
ERR5749307	23604	PASS	C	A	8336	0.942538	0	5,0,8325,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749307	23606	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8336	0.001919	0	8318,0,17,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Cgg/Tgg	R682W	S	0.001401	0.064309	2	2	C>T
ERR5749307	23635	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8333	0.00252	0	8305,2,22,0	LOW	SILENT	SYNONYMOUS_CODING	S	tcC/tcT	S691	S	0.002385	0.958978	1	1	C>T
ERR5749307	23709	PASS	C	T	8331	0.931581	0	0,4,0,8312	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749307	24127	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	12159	0.001069	6	7798,4334,6,7	HIGH	NONE	FRAME_SHIFT	S	aac/	N856	S	0.000324	0.111888	4	1	TA>T
ERR5749307	24127	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAACGGCCTTACTG	T	12159	0.001151	24	7798,4334,14,0	HIGH	NONE	FRAME_SHIFT	S	aacggccttactgtt/	NGLTV856	S	0.000324	0.111888	4	1	TAACGGCCTTACTG>T
ERR5749307	24506	PASS	T	G	10268	0.975166	0	2,0,10263,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749307	24914	PASS	G	C	34513	0.958161	0	0,0,17210,17286	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749307	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	2116	0.006144	175	2085,16,3,10	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749307	26159	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTAATCCAG	T	17268	9.27E-4	0	0,17252,0,16	HIGH	NONE	FRAME_SHIFT	ORF3a	ccagtaatg/	PVM258	orf3a	0.000311	0.053032	2	2	TTAATCCAG>T
ERR5749307	26209	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	17306	0.004276	0	2,17179,0,113	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gtg/Ttg	V273L	orf3a	0.000792	0.234679	3	1	G>T
ERR5749307	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	7712	0.00402	0	0,7681,0,31	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749307	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	7714	0.006093	0	0,7652,0,47	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749307	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	G	7714	0.001945	0	0,7652,0,15	HIGH	NONE	FRAME_SHIFT	M	cttgtaggcttgatgtggctcagctacttcattgcttctttc/	LVGLMWLSYFIASF87	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT>G
ERR5749307	26907	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20259	0.001481	0	20220,2,30,0	LOW	SILENT	SYNONYMOUS_CODING	M	Ctg/Ttg	L129	M	0.000817	0.976032	1	1	C>T
ERR5749307	26927	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	20257	0.002024	0	20215,0,41,0	LOW	SILENT	SYNONYMOUS_CODING	M	gaA/gaG	E135	M	0.001168	0.979284	1	1	A>G
ERR5749307	27312	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAA	T	14174	0.001129	0	14159,0,16,0	HIGH	NONE	FRAME_SHIFT	ORF6	aat/	N39	orf6	0.000911	0.088458	4	2	TAA>T
ERR5749307	28394	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	G	9	0.888889	9	0,1,8,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Cgg/Ggg	R41G	N	0.001221	0.917026	3	2	C>G
ERR5749307	28651	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	14813	7.43E-4	0	0,14801,0,11	HIGH	NONE	FRAME_SHIFT	N	aaa/	K127	N	0.000502	0.918117	3	2	CAA>C
ERR5749307	28881	PASS	G	A	6562	0.728284	9	4,0,3271,3193	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749307	28882	PASS	G	A	6560	0.810366	2	3,1,3312,3155	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749307	28883	PASS	G	C	6560	0.942531	0	1,1,3320,3233	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749307	28977	PASS	C	T	3373	0.919953	0	0,4,0,3358	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749307	29095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21491	0.00107	0	21464,0,23,0	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F274	N	0.000792	0.961279	2	2	C>T
ERR5749307	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	42628	0.001032	0	21434,21126,26,26	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749308	241	PASS	C	T	20	0.75	0	0,0,10,10	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749308	913	PASS	C	T	592	0.932432	2147483647	0,0,0,592	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749308	1426	PASS	C	T	444	0.876126	2147483647	0,0,442,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y207	nsp2	0.002931	0.892537	1	1	C>T
ERR5749308	1813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	1081	0.008326	0	0,1072,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K338	nsp2	0.001022	0.152738	4	2	TA>T
ERR5749308	1846	PASS	A	G	1082	0.945471	2147483647	0,0,0,1080	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaA/aaG	K347	nsp2	0.001438	0.945471	2	2	A>G
ERR5749308	3037	PASS	C	T	480	0.833333	0	0,0,241,236	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749308	3122	PASS	G	C	242	0.053719	0	0,229,0,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gat/Cat	D135H	nsp3	0.045455	0.053719	1	1	G>C
ERR5749308	3267	PASS	C	T	541	0.977819	2147483647	0,0,541,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749308	3575	PASS	G	GT	389	0.059126	0	366,0,23,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/ttTa	L287F?	nsp3	0.000594	0.059126	3	1	G>GT
ERR5749308	3877	PASS	T	C	176	0.960227	2147483647	0,0,175,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcC	A386	nsp3	0.000588	0.960227	2	1	T>C
ERR5749308	5388	PASS	C	A	145	0.951724	2147483647	0,0,145,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749308	5986	PASS	C	T	400	0.9725	2147483647	0,0,400,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749308	6954	PASS	T	C	1124	0.847865	2147483647	0,0,0,1121	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749308	9198	PASS	C	T	2239	0.91782	2147483647	0,0,0,2235	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T215I	nsp4	0.000543	0.93476	4	2	C>T
ERR5749308	10193	PASS	G	A	1465	0.864164	2147483647	0,0,1464,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E47K	3Cpro	0.000774	0.869819	2	2	G>A
ERR5749308	10195	PASS	A	T	1465	0.952901	2147483647	0,0,1465,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gaA/gaT	E47D	3Cpro	0.951998	0.969772	1	1	A>T
ERR5749308	10642	PASS	G	T	945	0.058201	0	0,889,0,56	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acG/acT	T196	3Cpro	0.001264	0.951979	3	1	G>T
ERR5749308	11074	PASS	C	CT	3457	0.052358	0	3271,0,181,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CT
ERR5749308	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	3457	0.030952	0	3350,0,107,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000965	0.945355	5	2	CT>C
ERR5749308	11287	PASS	GTCTGGTTTT	G	3454	0.999421	0	0,2,0,3452	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749308	13274	PASS	C	T	2831	0.94207	2147483647	0,0,0,2829	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cca/Tca	P84S	nsp10	0.94207	0.943631	1	1	C>T
ERR5749308	14408	PASS	C	T	655	0.854962	0	0,0,328,324	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749308	14676	PASS	C	T	246	0.731707	2147483647	0,0,244,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749308	15071	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	979	0.015322	1	477,480,11,8	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cTt/cAt	L544H	RdRp	0.000813	0.0625	2	2	T>A
ERR5749308	15279	PASS	C	T	639	0.874804	2147483647	0,0,637,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749308	15839	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	2451	0.019992	0	0,2400,0,49	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tGg/tCg	W800S	RdRp	0.001405	0.074516	2	1	G>C
ERR5749308	16176	PASS	T	C	428	0.974299	0	0,0,110,318	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749308	20420	PASS	AT	A	3289	0.069626	0	0,3060,0,229	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F268	endoR	0.000383	0.069626	2	1	AT>A
ERR5749308	21304	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	2511	0.017523	0	0,2444,0,66	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgc/Agc	R216S	MethTr	0.000411	0.605296	3	2	C>A
ERR5749308	21305	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	2511	0.0227	0	0,2444,0,64	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cGc/cAc	R216H	MethTr	0.000727	0.703943	1	1	G>A
ERR5749308	21764	PASS	ATACATG	A	1191	0.963896	0	43,0,1148,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749308	21990	PASS	TTTA	T	1193	0.998324	27	1,1,0,1191	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749308	22858	PASS	C	T	3120	0.967308	0	0,0,839,2279	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749308	23063	PASS	A	T	839	0.876043	2147483647	0,0,0,837	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749308	23271	PASS	C	A	782	0.915601	2147483647	0,0,781,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749308	23294	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	782	0.028133	0	757,0,25,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gat/Tat	D578Y	S	0.001754	0.102649	2	1	G>T
ERR5749308	23403	PASS	A	G	783	0.961686	2147483647	0,0,0,783	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749308	23604	PASS	C	A	843	0.937129	2147483647	0,0,843,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749308	23634	PASS	C	T	841	0.931035	2147483647	0,0,840,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tTc	S691F	S	0.00071	0.931159	2	2	C>T
ERR5749308	23709	PASS	C	T	842	0.933492	0	0,2,0,838	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749308	24506	PASS	T	G	839	0.973778	2147483647	0,0,839,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749308	24914	PASS	G	C	8252	0.960131	0	0,0,4116,4130	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749308	25437	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	5804	0.03377	0	5596,0,208,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	ttG/ttT	L15F	orf3a	0.001128	0.971411	2	2	G>T
ERR5749308	27641	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1939	0.017019	0	1903,0,34,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	tCa/tTa	S83L	orf7a	0.000983	0.911213	2	2	C>T
ERR5749308	27972	PASS	C	T	161	0.89441	33	2,2,156,0	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749308	28048	PASS	G	T	159	0.943396	0	0,1,0,158	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749308	28111	PASS	A	G	3868	0.981386	0	2,0,3704,159	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749308	28270	PASS	TA	T	7185	0.996521	80	28,0,3664,3496	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749308	28280	PASS	G	C	7172	0.936559	3	0,1,3670,3495	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749308	28281	PASS	A	T	7172	0.905884	6	3,0,3665,3490	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749308	28282	PASS	T	A	7172	0.904769	0	4,3,3656,3493	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749308	28881	PASS	G	A	152	0.664474	0	0,0,77,69	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749308	28882	PASS	G	A	152	0.809211	0	0,0,81,69	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749308	28883	PASS	G	C	152	0.960526	0	0,0,81,71	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749308	28977	PASS	C	T	82	0.939024	2147483647	0,0,0,82	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749309	241	PASS	C	T	22085	0.866652	0	1,2,10973,11019	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749309	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	13154	0.003193	0	13113,1,42,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749309	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	13154	9.12E-4	0	13078,1,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749309	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	13154	0.001596	0	13078,1,21,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749309	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	13154	0.003117	0	13078,1,41,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749309	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	13145	0.001978	0	12115,1,890,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749309	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	13145	0.002739	0	13108,1,36,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749309	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	13145	8.37E-4	0	13124,1,11,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttatg/gtg	VM84V	leader	0.000554	0.991848	4	1	GTTA>G
ERR5749309	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	13146	0.001978	0	13109,2,26,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749309	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	34445	5.81E-4	40	21248,13173,20,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749309	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	34444	0.002119	21	21209,13154,56,17	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749309	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21260	0.001129	0	0,21211,0,29	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749309	913	PASS	C	T	21261	0.911199	0	0,11,0,21222	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749309	3037	PASS	C	T	23667	0.82296	36	0,12,11826,11676	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749309	3267	PASS	C	T	20051	0.969627	2147483647	0,0,20039,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749309	3741	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	13880	6.48E-4	0	0,13871,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H342	nsp3	0.000648	0.968922	2	2	TAC>T
ERR5749309	3743	PASS	C	T	13880	0.87745	0	0,5,0,13830	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cat/Tat	H342Y	nsp3	0.00405	0.893235	1	1	C>T
ERR5749309	5077	PASS	T	C	13002	0.168205	0	10714,0,2259,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtT/gtC	V786	nsp3	0.001393	0.168205	1	1	T>C
ERR5749309	5388	PASS	C	A	7735	0.95863	2147483647	0,0,7726,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749309	5672	PASS	C	A	21349	0.975315	2147483647	0,0,21349,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cct/Act	P985T	nsp3	0.004226	0.977953	2	1	C>A
ERR5749309	5986	PASS	C	T	14783	0.976054	0	1,0,14773,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749309	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13962	0.001289	0	1,13789,0,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749309	6954	PASS	T	C	23428	0.806556	0	0,3,1,23278	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749309	7764	PASS	C	T	23311	0.959418	0	2,0,23292,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCc/tTc	S1682F	nsp3	0.001052	0.964731	1	1	C>T
ERR5749309	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	33881	3.54E-4	36	16706,17163,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749309	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	16588	0.001387	0	16541,0,42,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749309	11287	PASS	GTCTGGTTTT	G	16579	0.997346	0	0,44,0,16535	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749309	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	16074	0.001369	0	16027,1,23,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749309	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	38293	0.001384	0	19113,19070,32,32	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749309	13623	PASS	A	G	19184	0.893401	0	0,2,0,19141	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaA/gaG	E61	RdRp	0.00237	0.931889	2	2	A>G
ERR5749309	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	15999	0.003125	2147483647	15676,121,7,191	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749309	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	31196	6.73E-4	0	15659,15530,10,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749309	14408	PASS	C	T	31196	0.85402	9	0,3,15602,15362	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749309	14676	PASS	C	T	13629	0.732409	0	1,0,13571,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749309	15279	PASS	C	T	23169	0.889335	0	3,0,23133,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749309	16176	PASS	T	C	20926	0.981028	3	1,0,10329,10583	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749309	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	25670	6.62E-4	0	25653,0,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749309	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	23976	4.59E-4	0	2,23963,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749309	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	31787	0.001982	0	31710,0,64,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749309	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	33084	0.001481	1	16219,16477,29,33	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749309	21764	PASS	ATACATG	A	14643	0.9972	0	41,0,14602,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749309	21990	PASS	TTTA	T	14647	0.996313	0	0,54,2,14591	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749309	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	14986	0.001268	0	0,14958,0,21	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749309	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27050	9.61E-4	2	12041,14963,11,18	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749309	23063	PASS	A	T	12041	0.870692	0	0,1,1,11988	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749309	23271	PASS	C	A	21388	0.925145	0	2,0,21367,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749309	23403	PASS	A	G	21377	0.965945	0	0,5,0,21358	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749309	23522	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAACATGTCAACAACTCATA	G	16982	5.3E-4	0	16968,2,9,0	HIGH	NONE	FRAME_SHIFT	S	gaacatgtcaacaactcatat/	EHVNNSY654	S	0.00053	0.959726	5	2	GAACATGTCAACAACTCATA>G
ERR5749309	23604	PASS	C	A	16973	0.951334	0	6,0,16948,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749309	23624	PASS	G	T	16959	0.958606	0	5,0,16947,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gct/Tct	A688S	S	0.003694	0.958606	2	1	G>T
ERR5749309	23709	PASS	C	T	16952	0.939417	0	0,3,3,16920	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749309	24506	PASS	T	G	18739	0.974919	0	8,0,18726,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749309	24914	PASS	G	C	33579	0.960481	0	0,0,16715,16838	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749309	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	21778	0.00124	62	13595,8145,31,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749309	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	26460	7.18E-4	0	26439,2,19,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749309	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	26648	0.001576	1351	26215,169,138,97	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749309	25915	PASS	A	G	26472	0.967777	354	13,28,2,26411	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Aca/Gca	T175A	orf3a	0.967777	0.972774	1	1	A>G
ERR5749309	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	12647	0.003005	0	1,12607,0,38	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749309	26927	PASS	A	G	31067	0.977178	0	4,0,31052,3	LOW	SILENT	SYNONYMOUS_CODING	M	gaA/gaG	E135	M	0.001168	0.979284	1	1	A>G
ERR5749309	27972	PASS	C	T	12333	0.911619	0	0,0,12243,60	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749309	28048	PASS	G	T	12275	0.922525	0	0,13,0,12256	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749309	28111	PASS	A	G	32532	0.977868	8	0,2,20238,12278	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749309	28250	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TCTG	20229	4.94E-4	0	20220,2,10,0	MODERATE	NONE	CODON_INSERTION	ORF8	ttc/CTGttc	F120LF	orf8	0.000494	0.993968	5	3	T>TCTG
ERR5749309	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	20226	0.002472	0	20175,5,50,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749309	28270	PASS	TA	T	39268	0.995824	378	164,7,20019,19085	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749309	28280	PASS	G	C	39199	0.936325	19	10,1,20055,19076	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749309	28281	PASS	A	T	39199	0.919207	18	24,9,20050,19076	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749309	28282	PASS	T	A	39200	0.913469	0	10,8,20015,19087	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749309	28881	PASS	G	A	15786	0.771823	11	9,2,7827,7719	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749309	28882	PASS	G	A	15785	0.827494	9	4,0,7913,7714	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749309	28883	PASS	G	C	15785	0.942287	0	1,1,7915,7839	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749309	28977	PASS	C	T	8032	0.932146	2147483647	0,0,0,8020	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749309	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	48616	0.001604	0	24432,24082,42,41	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749309	29192	PASS	T	C	48742	0.940667	0	3,3,24452,24241	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Ttt/Ctt	F307L	N	0.000391	0.940667	2	2	T>C
ERR5749310	241	PASS	C	T	4928	0.857143	0	0,0,2453,2458	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749310	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	11695	0.001454	0	11682,0,17,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749310	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	11695	0.002223	0	11661,0,26,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749310	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	11695	0.003078	0	10703,11,915,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749310	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	11695	7.7E-4	0	11674,12,9,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749310	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	29813	4.03E-4	0	18084,11710,7,5	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749310	823	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18086	0.001493	0	18044,2,32,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V6	nsp2	0.001213	0.901722	1	1	C>T
ERR5749310	913	PASS	C	T	18089	0.927691	0	0,11,0,18064	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749310	1440	PASS	G	T	19841	0.899148	0	74,0,19753,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGc/gTc	G212V	nsp2	0.004949	0.899148	2	1	G>T
ERR5749310	3037	PASS	C	T	24169	0.817328	64	1,25,12071,11924	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749310	3267	PASS	C	T	21549	0.969511	0	3,0,21529,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749310	3575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	13860	7.22E-4	0	13850,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/ttTa	L287F?	nsp3	0.000594	0.059126	3	1	G>GT
ERR5749310	4237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTA	T	44414	3.15E-4	0	22223,22177,7,7	HIGH	NONE	FRAME_SHIFT	ORF1ab	ata/	I508	nsp3	0.000302	0.918634	2	2	TTA>T
ERR5749310	5388	PASS	C	A	7151	0.954412	2147483647	0,0,7151,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749310	5986	PASS	C	T	16116	0.971829	0	1,0,16106,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749310	6843	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	42479	7.53E-4	0	26325,16072,24,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S1375F	nsp3	0.000753	0.922467	2	1	C>T
ERR5749310	6954	PASS	T	C	26303	0.828347	0	0,27,0,26141	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749310	9532	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25575	8.99E-4	10	19039,6502,21,2	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F326	nsp4	0.000899	0.966959	1	1	C>T
ERR5749310	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	25575	0.001408	42	19029,6510,36,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749310	10138	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	32522	8.3E-4	0	23419,9063,21,7	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N28	3Cpro	0.000458	0.983567	3	3	C>T
ERR5749310	10323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	23442	0.002048	0	1,23345,0,54	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749310	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28529	0.001998	0	28439,2,60,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749310	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	28518	0.001683	0	28435,0,72,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749310	11287	PASS	GTCTGGTTTT	G	28515	0.999018	0	0,28,0,28487	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749310	11782	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	23886	0.001926	0	11,23638,0,49	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaA/aaG	K270	nsp6	0.001073	0.917917	2	2	A>G
ERR5749310	12269	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	28775	4.87E-4	0	28761,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aag/	K61	nsp8	0.000434	0.213333	2	1	GA>G
ERR5749310	12459	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	52466	0.00101	10	23651,28755,30,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T123I	nsp8	0.000658	0.986093	1	1	C>T
ERR5749310	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	23683	9.71E-4	0	23623,0,25,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749310	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	18584	7.0E-4	0	18571,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749310	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	36652	0.001446	0	18297,18247,29,29	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749310	13554	PASS	C	T	18333	0.920199	0	0,2,0,18269	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y38	RdRp	0.000637	0.920199	2	2	C>T
ERR5749310	13994	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20823	0.001297	0	20784,0,27,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A185V	RdRp	0.000427	0.114441	3	2	C>T
ERR5749310	14408	PASS	C	T	12316	0.844755	0	3,3,6148,6089	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749310	14676	PASS	C	T	13801	0.696906	0	3,0,13712,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749310	15279	PASS	C	T	21639	0.901936	0	2,0,21603,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749310	15652	PASS	G	T	24316	0.933912	0	16,0,24294,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gac/Tac	D738Y	RdRp	0.000691	0.935936	2	2	G>T
ERR5749310	16176	PASS	T	C	22532	0.982336	0	0,0,9970,12546	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749310	16508	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	28729	0.002019	0	28625,6,96,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGt/gTt	G91V	helicase	0.000561	0.074909	2	2	G>T
ERR5749310	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	26488	0.001095	0	26458,0,29,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749310	17615	PASS	A	G	20343	0.915303	0	0,1,2,20291	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749310	18366	PASS	A	G	30237	0.982174	0	3,0,30208,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ctA/ctG	L109	ExoN	0.000756	0.984275	2	2	A>G
ERR5749310	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	30191	7.29E-4	0	30160,1,22,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749310	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25822	0.00182	0	25762,0,48,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749310	20844	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	54555	2.93E-4	4	26658,27881,10,6	HIGH	NONE	FRAME_SHIFT	ORF1ab	tataat/	YN63	MethTr	0.000293	0.905571	5	2	CTA>C
ERR5749310	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	26662	8.25E-4	0	0,26630,0,22	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TA>T
ERR5749310	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	37247	6.17E-4	0	18574,18659,11,12	HIGH	NONE	FRAME_SHIFT	S	ctt/Tctt	L5S?	S	0.000394	0.091869	4	1	G>GT
ERR5749310	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	37210	0.001129	1	18203,18579,22,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749310	21764	PASS	ATACATG	A	18728	0.997117	0	54,0,18674,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749310	21990	PASS	TTTA	T	18735	0.997972	0	0,38,6,18691	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749310	23063	PASS	A	T	115	0.834783	2147483647	0,0,0,115	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749310	23271	PASS	C	A	22329	0.918312	0	1,0,22298,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749310	23403	PASS	A	G	22323	0.973749	0	0,1,0,22306	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749310	23604	PASS	C	A	20734	0.934938	0	20,0,20700,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749310	23709	PASS	C	T	20719	0.944785	0	0,3,0,20693	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749310	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	38746	5.42E-4	7	17993,20732,13,8	HIGH	NONE	FRAME_SHIFT	S	ttg/	L753	S	0.000334	0.080808	2	2	CT>C
ERR5749310	24010	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATTTATTGAAGATCTAC	A	18128	4.96E-4	0	154,17970,0,9	HIGH	NONE	FRAME_SHIFT	S	attgaagatctacttttc/	IEDLLF818	S	0.000455	0.926398	4	2	ATTTATTGAAGATCTAC>A
ERR5749310	24506	PASS	T	G	23133	0.973285	0	9,0,23112,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749310	24914	PASS	G	C	48810	0.956956	0	0,0,24299,24474	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749310	25350	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25740	0.001243	0	25702,2,33,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCa/cTa	P1263L	S	0.000626	0.97904	4	2	C>T
ERR5749310	25496	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	51333	5.84E-4	249	25023,25374,607,298	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aTa/aGa	I35R	orf3a	0.000369	0.96555	3	2	T>G
ERR5749310	25624	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	42643	9.38E-4	14	16883,25711,23,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Cac/Tac	H78Y	orf3a	0.00089	0.983312	1	1	C>T
ERR5749310	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	16965	0.002535	716	16862,21,14,31	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749310	26461	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14271	0.001401	0	12,14202,0,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	Ctt/Ttt	L73F	E	0.001401	0.928597	1	1	C>T
ERR5749310	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	18887	7.41E-4	0	6,18866,0,14	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749310	27676	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	31133	0.001221	0	29,30827,0,260	HIGH	NONSENSE	STOP_GAINED	ORF7a	Gaa/Taa	E95*	orf7a	0.000609	0.877803	2	2	G>T
ERR5749310	27765	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	31202	0.00109	0	0,31125,0,34	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7b	Ctt/Ttt	L4F	orf7b	0.00109	0.970449	1	1	C>T
ERR5749310	27972	PASS	C	T	15047	0.896989	36	3,2,14918,72	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749310	28048	PASS	G	T	14989	0.92321	0	0,14,0,14965	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749310	28111	PASS	A	G	40872	0.978861	6	5,6,25852,14997	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749310	28270	PASS	TA	T	50410	0.994783	611	263,11,25515,24632	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749310	28280	PASS	G	C	50312	0.938623	2	14,10,25580,24603	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749310	28281	PASS	A	T	50312	0.916084	21	29,11,25574,24604	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749310	28282	PASS	T	A	50314	0.907958	12	27,14,25477,24624	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749310	28881	PASS	G	A	22404	0.720943	73	24,0,10862,11079	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749310	28882	PASS	G	A	22403	0.825202	35	21,3,11136,11062	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749310	28883	PASS	G	C	22402	0.945005	3	0,2,11183,11201	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749310	28977	PASS	C	T	11424	0.936362	0	0,1,0,11403	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749310	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	81929	8.3E-4	0	41144,40672,46,43	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749311	241	PASS	C	T	12191	0.852268	0	0,0,6051,6094	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749311	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	14776	8.8E-4	0	14764,1,13,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749311	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	14777	0.001489	0	14744,2,22,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749311	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	14766	0.002032	0	13708,5,998,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749311	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	34236	5.26E-4	6	19420,14792,13,5	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749311	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19430	0.001081	0	0,19393,0,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749311	913	PASS	C	T	19430	0.915697	0	0,11,0,19398	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749311	3037	PASS	C	T	22874	0.810746	64	1,25,11424,11247	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749311	3267	PASS	C	T	19690	0.971864	0	4,0,19678,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749311	5144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23206	0.001163	0	11592,11407,17,18	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L809	nsp3	0.000909	0.822022	1	1	C>T
ERR5749311	5388	PASS	C	A	7573	0.961706	2147483647	0,0,7570,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749311	5986	PASS	C	T	14577	0.977362	0	1,0,14568,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749311	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13904	0.001726	0	3,13725,0,28	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749311	6954	PASS	T	C	22131	0.814785	0	0,3,0,22008	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749311	8950	PASS	C	T	41586	0.975112	3	2,6,17786,23778	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I132	nsp4	0.002808	0.982604	1	1	C>T
ERR5749311	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	32745	0.001313	105	18487,14215,43,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749311	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	18312	0.001147	0	18271,0,37,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749311	11287	PASS	GTCTGGTTTT	G	18310	0.998635	0	0,25,0,18285	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749311	12513	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20841	0.001152	0	20810,0,25,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aTg	T141M	nsp8	0.000794	0.984064	2	2	C>T
ERR5749311	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29858	0.001541	0	14904,14866,27,27	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749311	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	15875	0.005102	2147483647	15540,97,4,228	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749311	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	30940	6.14E-4	0	15524,15423,9,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749311	14408	PASS	C	T	30940	0.834454	7	2,6,15455,15244	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749311	14676	PASS	C	T	12710	0.763808	0	3,0,12662,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749311	15279	PASS	C	T	21377	0.881181	0	3,0,21339,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749311	16176	PASS	T	C	22406	0.980853	11	5,0,12047,10345	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749311	17181	PASS	T	C	14516	0.987738	0	9,0,14504,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaT/gaC	D315	helicase	0.986595	0.991193	1	1	T>C
ERR5749311	18504	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	27180	8.46E-4	0	3,26791,0,342	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K155N	ExoN	0.000518	0.094148	4	3	A>C
ERR5749311	18576	PASS	C	T	27282	0.867898	0	0,9,0,27187	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D179	ExoN	0.005404	0.876866	2	2	C>T
ERR5749311	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	32071	0.002089	0	31967,2,70,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749311	21234	PASS	C	T	32573	0.650631	0	22,0,32084,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A192	MethTr	0.000472	0.857572	5	2	C>T
ERR5749311	21764	PASS	ATACATG	A	14504	0.996828	0	45,0,14458,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749311	21990	PASS	TTTA	T	14513	0.998966	0	0,15,6,14492	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749311	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	15519	0.00116	0	0,15494,0,18	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749311	23063	PASS	A	T	14872	0.868747	2147483647	0,0,0,14805	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749311	23271	PASS	C	A	20579	0.924243	0	3,0,20563,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749311	23403	PASS	A	G	20576	0.967924	0	0,1,0,20564	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749311	23604	PASS	C	A	17775	0.945148	0	9,0,17756,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749311	23709	PASS	C	T	17758	0.941773	0	0,4,3,17727	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749311	24506	PASS	T	G	17219	0.975086	0	5,0,17212,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749311	24914	PASS	G	C	39261	0.960877	0	2,2,19562,19671	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749311	25496	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	38851	6.69E-4	1	19137,19165,269,260	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aTa/aGa	I35R	orf3a	0.000369	0.96555	3	2	T>G
ERR5749311	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	22917	6.98E-4	0	22901,0,16,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749311	25844	PASS	C	T	22887	0.921396	0	0,4,7,22841	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aCt/aTt	T151I	orf3a	0.001226	0.938776	1	1	C>T
ERR5749311	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	13623	0.002055	0	1,13592,0,28	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749311	27577	PASS	C	T	39367	0.863871	0	2,2,21347,17874	HIGH	NONSENSE	STOP_GAINED	ORF7a	Caa/Taa	Q62*	orf7a	0.000614	0.952205	4	2	C>T
ERR5749311	27672	PASS	TCAAGAACTTTACTCTCCAATTTTTCTTATTGTTGCGGCAATAGTGTTTATAACACTTTGCTTCACACTCAAAAGAAAG	T	21022	0.999191	137	8,410,0,21005	MODERATE	NONE	CODON_DELETION	ORF7a	caagaactttactctccaatttttcttattgttgcggcaatagtgtttataacactttgcttcacactcaaaagaaag/	QELYSPIFLIVAAIVFITLCFTLKRK94	orf7a	0.00102	0.999439	2	1	TCAAGAACTTTACTCTCCAATTTTTCTTATTGTTGCGGCAATAGTGTTTATAACACTTTGCTTCACACTCAAAAGAAAG>T
ERR5749311	27972	PASS	C	T	12354	0.902542	23	0,1,12262,55	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749311	28048	PASS	G	T	12307	0.92744	0	0,11,0,12294	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749311	28111	PASS	A	G	30399	0.978552	1	4,4,18075,12309	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749311	28270	PASS	TA	T	35089	0.995212	348	161,9,17857,17064	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749311	28280	PASS	G	C	35018	0.933177	16	9,1,17895,17052	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749311	28281	PASS	A	T	35018	0.918442	9	17,8,17899,17046	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749311	28282	PASS	T	A	35022	0.907287	2	17,13,17847,17063	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749311	28292	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	35971	6.95E-4	0	17931,18017,12,13	HIGH	NONE	FRAME_SHIFT	N	aat/	N8	N	0.000304	0.055324	4	2	CA>C
ERR5749311	28881	PASS	G	A	16126	0.758279	9	4,0,7952,7937	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749311	28882	PASS	G	A	16126	0.826119	19	10,1,8054,7899	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749311	28883	PASS	G	C	16125	0.943504	3	0,1,8073,8034	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749311	28977	PASS	C	T	8238	0.927167	0	0,2,1,8220	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749311	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	53432	0.001029	0	26855,26488,34,33	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749312	147	PASS	C	T	6969	0.952934	2147483647	0,0,6964,0	.	.	.	.	.	.	.	0.952934	0.952934	1	1	C>T
ERR5749312	186	PASS	C	T	6961	0.966959	0	1,0,6954,0	.	.	.	.	.	.	.	0.002255	0.966959	1	1	C>T
ERR5749312	241	PASS	C	T	13866	0.842132	2	1,2,6910,6880	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749312	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	11763	0.00204	0	11730,9,24,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749312	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	11761	7.65E-4	0	11698,9,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749312	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	11761	6.8E-4	0	11698,9,8,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749312	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	11761	0.002976	0	11698,9,35,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749312	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	11750	0.002723	0	10635,9,994,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749312	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	11750	0.001702	0	11721,9,20,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749312	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	11748	6.81E-4	0	11726,9,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749312	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	11749	7.66E-4	0	11719,10,9,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749312	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	35562	9.28E-4	2	23762,11762,24,9	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749312	913	PASS	C	T	23768	0.914801	0	0,12,0,23725	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749312	3037	PASS	C	T	19461	0.806022	60	0,20,9729,9563	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749312	3267	PASS	C	T	23218	0.970885	0	2,0,23207,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749312	5388	PASS	C	A	5166	0.9518	2147483647	0,0,5161,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749312	5628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21012	0.009852	0	20795,0,209,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aTg	T970M	nsp3	0.000561	0.973644	3	2	C>T
ERR5749312	5986	PASS	C	T	13152	0.974072	0	1,0,13144,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749312	6196	PASS	C	T	13154	0.945644	0	0,3,0,13147	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P1159	nsp3	0.004402	0.945644	1	1	C>T
ERR5749312	6954	PASS	T	C	24558	0.825393	0	0,8,1,24403	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749312	7936	PASS	G	T	21945	0.911187	0	0,31,1,21908	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcG/gcT	A1739	nsp3	0.001237	0.911187	1	1	G>T
ERR5749312	7967	PASS	C	T	21946	0.949148	0	0,7,1,21931	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cct/Tct	P1750S	nsp3	0.002388	0.949148	1	1	C>T
ERR5749312	8603	PASS	T	C	12758	0.972018	138	4,2,0,12745	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Ctc	F17L	nsp4	0.002607	0.974959	2	1	T>C
ERR5749312	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	31082	5.47E-4	46	16409,14655,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749312	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	22258	0.001842	0	22188,0,65,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749312	11287	PASS	GTCTGGTTTT	G	22244	0.997887	0	0,46,0,22197	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749312	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	39699	0.001134	7	25173,14459,24,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749312	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	19982	0.001151	0	19929,0,26,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749312	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	13683	6.58E-4	0	13674,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749312	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34147	0.001933	0	17041,16997,36,36	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749312	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	9717	0.005454	2732	9466,85,5,158	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749312	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	18848	7.96E-4	0	9450,9396,8,7	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749312	14408	PASS	C	T	18848	0.8316	1	3,4,9402,9291	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749312	14676	PASS	C	T	14683	0.832664	0	8,0,14644,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749312	15279	PASS	C	T	23342	0.878202	0	3,0,23316,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749312	15960	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12176	0.003039	0	12131,0,42,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A840	RdRp	0.001581	0.81574	1	1	C>T
ERR5749312	16176	PASS	T	C	21967	0.981882	0	0,0,9772,12179	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749312	17615	PASS	A	G	16424	0.916525	0	0,1,2,16373	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749312	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	24114	8.29E-4	0	24094,0,20,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749312	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29568	0.001522	0	29494,0,47,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749312	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	31289	8.63E-4	0	31232,0,27,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749312	21077	PASS	C	T	24488	0.955529	387	11,2,0,24457	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T140I	MethTr	0.000492	0.955529	4	2	C>T
ERR5749312	21302	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27155	0.001584	0	2,27087,0,53	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCa/cTa	P215L	MethTr	0.001031	0.843069	1	1	C>T
ERR5749312	21304	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	27155	0.001105	0	1,27082,0,59	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgc/Agc	R216S	MethTr	0.000411	0.605296	3	2	C>A
ERR5749312	21305	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	27155	0.001473	0	1,27052,0,54	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cGc/cAc	R216H	MethTr	0.000727	0.703943	1	1	G>A
ERR5749312	21764	PASS	ATACATG	A	13527	0.99756	0	33,0,13494,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749312	21990	PASS	TTTA	T	13535	0.997784	0	0,30,7,13498	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749312	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	17844	0.001905	0	1,17801,0,34	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749312	23063	PASS	A	T	14487	0.855457	0	0,4,0,14389	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749312	23271	PASS	C	A	25417	0.921273	0	5,0,25377,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749312	23277	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25417	0.016603	0	24796,1,573,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCt/aTt	T572I	S	0.001007	0.74768	1	1	C>T
ERR5749312	23403	PASS	A	G	25410	0.96954	0	0,6,0,25388	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749312	23604	PASS	C	A	16210	0.935657	0	16,0,16188,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749312	23709	PASS	C	T	16194	0.939175	0	0,2,1,16173	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749312	24506	PASS	T	G	19183	0.9743	0	4,0,19174,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749312	24914	PASS	G	C	39393	0.960374	0	0,0,19623,19748	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749312	25681	PASS	G	A	20254	0.934285	0	1,0,20247,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gtt/Att	V97I	orf3a	0.018605	0.934285	1	1	G>A
ERR5749312	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	20396	0.001226	1200	20122,118,65,76	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749312	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	13389	8.22E-4	0	0,13377,0,11	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749312	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	13390	0.001643	0	0,13366,0,22	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749312	27972	PASS	C	T	11117	0.907979	0	0,0,11025,50	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749312	28048	PASS	G	T	11076	0.911159	0	0,17,0,11048	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749312	28111	PASS	A	G	34963	0.978234	1	3,2,23862,11083	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749312	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	23839	5.45E-4	0	23833,1,13,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749312	28270	PASS	TA	T	46008	0.995501	404	197,13,23573,22228	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749312	28280	PASS	G	C	45923	0.935914	4	7,3,23619,22208	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749312	28281	PASS	A	T	45923	0.915641	30	27,7,23609,22210	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749312	28282	PASS	T	A	45924	0.912616	13	18,7,23571,22235	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749312	28881	PASS	G	A	19857	0.769452	30	11,0,9819,9757	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749312	28882	PASS	G	A	19857	0.824999	0	1,0,9931,9717	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749312	28883	PASS	G	C	19858	0.943398	0	2,1,9939,9895	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749312	28977	PASS	C	T	10101	0.92872	0	0,2,0,10091	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749312	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	62569	0.001343	0	31420,31029,50,49	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749312	29745	PASS	G	T	9080	0.918062	0	0,13,0,9057	.	.	.	.	.	.	.	0.039548	0.920898	2	1	G>T
ERR5749312	29769	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9084	0.002422	0	0,9044,0,23	.	.	.	.	.	.	.	0.001999	0.945205	1	1	C>T
ERR5749313	239	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTC	T	12391	6.46E-4	0	6157,6226,4,4	.	.	.	.	.	.	.	0.000495	0.25	4	1	TTC>T
ERR5749313	241	PASS	C	T	12392	0.866123	3	0,2,6144,6191	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749313	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	11430	0.001925	0	11405,6,22,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749313	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	11429	0.001662	0	11282,9,19,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749313	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	11429	0.001487	0	11282,9,17,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749313	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	11429	0.008487	0	11282,9,97,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749313	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	11417	0.002715	0	10612,8,599,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749313	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	11417	0.002628	37	11381,6,28,2	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749313	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	11414	0.001314	0	11380,9,15,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749313	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	29053	9.98E-4	49	17577,11447,28,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749313	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	29051	0.00327	5	17528,11409,63,32	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749313	913	PASS	C	T	17599	0.909483	0	0,13,0,17561	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749313	3037	PASS	C	T	17586	0.84772	24	0,8,8791,8690	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749313	3177	PASS	C	T	25787	0.888781	19	3,8,16925,8818	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P153L	nsp3	0.000773	0.96008	3	2	C>T
ERR5749313	3250	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	16937	0.003424	0	16866,0,60,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaG/gaA	E177	nsp3	0.001378	0.921255	2	2	G>A
ERR5749313	3267	PASS	C	T	16937	0.969121	0	3,0,16921,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749313	5388	PASS	C	A	6169	0.957205	2147483647	0,0,6167,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749313	5986	PASS	C	T	11179	0.973074	2147483647	0,0,11161,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749313	6954	PASS	T	C	17834	0.819726	0	0,1,1,17750	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749313	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	28699	0.00108	81	15533,13135,31,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749313	9559	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15579	0.001348	0	15493,16,21,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y335	nsp4	0.001348	0.062899	2	2	C>T
ERR5749313	11287	PASS	GTCTGGTTTT	G	16058	0.996637	0	0,54,0,16004	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749313	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	32224	8.07E-4	0	18537,13623,16,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749313	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	18116	0.001214	0	18059,0,22,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749313	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24531	0.001223	0	12251,12219,16,17	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749313	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	15239	0.004331	2147483647	14870,159,10,193	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749313	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	29617	0.002026	0	14834,14743,31,29	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749313	14408	PASS	C	T	29617	0.845629	2	3,5,14758,14579	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749313	14676	PASS	C	T	10862	0.800405	0	3,0,10820,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749313	15279	PASS	C	T	17905	0.890589	0	2,0,17883,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749313	16176	PASS	T	C	18050	0.98133	2	2,0,9681,8362	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749313	18681	PASS	C	T	23660	0.886771	0	4,0,23641,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A214	ExoN	0.028796	0.923661	1	1	C>T
ERR5749313	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	23662	9.3E-4	0	23640,0,22,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749313	19328	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	16116	8.07E-4	0	16094,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F431	ExoN	0.000459	0.937906	4	2	CT>C
ERR5749313	19687	PASS	C	A	16522	0.889118	0	919,0,15595,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cca/Aca	P23T	endoR	0.001245	0.889118	2	1	C>A
ERR5749313	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26877	0.002716	0	26780,0,75,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749313	20987	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	34895	4.87E-4	0	17465,17416,9,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L111	MethTr	0.000276	0.056129	4	2	CT>C
ERR5749313	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26795	7.84E-4	0	13119,13385,12,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749313	21764	PASS	ATACATG	A	11451	0.995721	0	48,0,11402,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749313	21990	PASS	TTTA	T	11455	0.99677	0	0,37,4,11414	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749313	22185	PASS	C	T	32994	0.919834	4	1,4,15799,17167	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCg/aTg	T208M	S	0.001725	0.919834	1	1	C>T
ERR5749313	22227	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	17233	5.22E-4	0	0,17223,0,9	HIGH	NONE	FRAME_SHIFT	S	tta/	L223	S	0.000419	0.824305	2	2	CT>C
ERR5749313	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	12619	0.001664	0	0,12593,0,21	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749313	23063	PASS	A	T	13136	0.868453	0	0,2,0,13065	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749313	23271	PASS	C	A	17567	0.921899	0	6,0,17547,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749313	23403	PASS	A	G	17561	0.96777	0	0,5,0,17540	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749313	23604	PASS	C	A	14292	0.949762	0	9,0,14280,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749313	23709	PASS	C	T	14287	0.937986	0	0,19,4,14241	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749313	24010	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATTTATTGAAGATCTAC	A	14065	9.24E-4	0	139,13921,0,13	HIGH	NONE	FRAME_SHIFT	S	attgaagatctacttttc/	IEDLLF818	S	0.000455	0.926398	4	2	ATTTATTGAAGATCTAC>A
ERR5749313	24506	PASS	T	G	14249	0.975226	0	7,0,14240,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749313	24914	PASS	G	C	35745	0.958652	0	2,2,17810,17906	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749313	25572	PASS	C	T	16578	0.935758	0	0,14,1,16551	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	tcC/tcT	S60	orf3a	0.000543	0.959687	4	2	C>T
ERR5749313	25573	PASS	A	C	16578	0.94927	0	0,12,1,16553	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Aaa/Caa	K61Q	orf3a	0.001796	0.954465	3	2	A>C
ERR5749313	25574	PASS	A	T	16578	0.899143	0	0,3,1,16543	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aAa/aTa	K61I	orf3a	0.899143	0.932074	1	1	A>T
ERR5749313	25626	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	34728	4.03E-4	2	18134,16577,6,8	HIGH	NONE	FRAME_SHIFT	ORF3a	ttt/	F79	orf3a	0.000403	0.915633	3	2	CT>C
ERR5749313	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	18173	0.002036	294	18086,11,25,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749313	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	18342	0.001636	921	17983,173,88,71	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749313	26156	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTG	T	44410	0.001058	0	1,44350,0,47	HIGH	NONE	FRAME_SHIFT	ORF3a	gtt/	V256	orf3a	0.001058	0.924104	2	2	TTG>T
ERR5749313	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	44411	0.00313	0	1,44175,0,139	HIGH	NONE	FRAME_SHIFT	ORF3a	gtt/	V256	orf3a	0.000249	0.122153	5	2	TG>T
ERR5749313	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	44411	0.001576	0	1,44175,0,70	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749313	26158	PASS	G	T	44411	0.905181	0	0,121,1,43921	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gtt/Ttt	V256F	orf3a	0.000297	0.905181	6	2	G>T
ERR5749313	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	G	11890	6.73E-4	0	5,11853,0,8	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/	ACLVGLMWLSYFIASF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT>G
ERR5749313	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	11890	0.00143	0	5,11853,0,17	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749313	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	11890	8.41E-4	0	5,11875,0,10	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749313	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	11886	0.002524	0	1,11849,0,30	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749313	27240	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAT	G	17278	5.21E-4	0	17269,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF6	atatta/	IL14	orf6	0.000521	0.117458	2	2	GAT>G
ERR5749313	27972	PASS	C	T	10705	0.905558	19	1,1,10595,63	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749313	28001	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	21250	0.001035	0	10605,10604,14,14	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ccG/ccA	P36	orf8	0.00085	0.830607	2	1	G>A
ERR5749313	28048	PASS	G	T	10650	0.921127	0	0,19,0,10620	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749313	28111	PASS	A	G	25785	0.97549	18	9,0,15110,10664	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749313	28270	PASS	TA	T	29227	0.994491	379	162,6,14909,14157	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749313	28280	PASS	G	C	29161	0.936388	8	6,1,14952,14144	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749313	28281	PASS	A	T	29161	0.909091	25	19,4,14939,14137	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749313	28282	PASS	T	A	29162	0.910569	5	17,10,14900,14148	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749313	28406	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTACCCAATA	T	15131	5.95E-4	0	11,15110,0,9	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	N	ttacccaataat/tat	LPNN45Y	N	0.00043	0.921074	3	2	TTACCCAATA>T
ERR5749313	28881	PASS	G	A	18611	0.788136	0	2,2,9269,9129	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749313	28882	PASS	G	A	18611	0.827683	3	2,0,9332,9105	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749313	28883	PASS	G	C	18611	0.942507	3	0,1,9346,9247	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749313	28977	PASS	C	T	9480	0.921624	0	0,2,0,9449	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749313	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	34656	0.001096	166	25145,9432,5,39	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749313	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	49951	0.001361	0	25090,24762,42,40	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749313	29675	PASS	C	T	16968	0.87553	14	2,9,8496,8393	.	.	.	.	.	.	.	0.000624	0.883495	2	1	C>T
ERR5749314	241	PASS	C	T	17337	0.863183	1	2,4,8625,8629	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749314	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	8189	0.001465	0	7761,4,404,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749314	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	30437	3.94E-4	2	22217,8208,10,2	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749314	913	PASS	C	T	22211	0.918149	0	0,11,0,22167	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749314	3037	PASS	C	T	18148	0.79557	58	0,19,9078,8875	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749314	3177	PASS	C	T	31006	0.911372	12	3,5,21822,9129	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P153L	nsp3	0.000773	0.96008	3	2	C>T
ERR5749314	3267	PASS	C	T	21849	0.970845	2147483647	0,0,21834,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749314	4675	PASS	A	G	14636	0.967819	0	3,0,14619,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaA/aaG	K652	nsp3	0.015625	0.967819	2	2	A>G
ERR5749314	5388	PASS	C	A	5634	0.956159	2147483647	0,0,5632,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749314	5986	PASS	C	T	12748	0.975447	0	2,0,12738,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749314	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12051	0.00166	0	2,11892,0,35	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749314	6954	PASS	T	C	23917	0.805034	0	0,4,2,23761	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749314	7528	PASS	C	T	16368	0.897788	0	0,6,18,16315	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V1603	nsp3	0.002527	0.916131	1	1	C>T
ERR5749314	8480	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11725	0.003497	0	0,11556,0,54	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cct/Tct	P1921S	nsp3	0.003497	0.88186	1	1	C>T
ERR5749314	11287	PASS	GTCTGGTTTT	G	19641	0.998218	0	0,35,0,19606	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749314	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	10953	9.13E-4	0	10944,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749314	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29998	0.001633	0	14973,14929,28,28	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749314	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	9661	0.004761	2949	9395,88,3,171	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749314	14408	PASS	C	T	18685	0.84806	15	0,5,9341,9206	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749314	14676	PASS	C	T	13487	0.700675	0	5,0,13412,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749314	15279	PASS	C	T	22121	0.935898	0	3,0,22102,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749314	16176	PASS	T	C	18097	0.979941	0	0,0,7714,10368	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749314	18788	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	42491	0.002824	0	21103,21139,77,74	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T250I	ExoN	0.000792	0.51652	2	1	C>T
ERR5749314	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29669	0.002427	0	29582,0,74,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749314	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30375	9.55E-4	0	30293,0,33,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749314	21764	PASS	ATACATG	A	12641	0.997548	0	31,0,12610,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749314	21994	PASS	TTAC	T	36334	0.347498	2147483647	23684,22,4,12622	MODERATE	NONE	CODON_DELETION	S	tac/	Y145	S	0.000341	0.347498	1	1	TTAC>T
ERR5749314	22450	PASS	C	T	9420	0.790234	0	2,0,9267,51	LOW	SILENT	SYNONYMOUS_CODING	S	ctC/ctT	L296	S	0.00215	0.803846	1	1	C>T
ERR5749314	23063	PASS	A	T	12596	0.857891	0	0,4,0,12535	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749314	23271	PASS	C	A	22699	0.92753	0	1,0,22677,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749314	23403	PASS	A	G	22691	0.966286	0	0,9,0,22665	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749314	23604	PASS	C	A	15069	0.957861	0	2,0,15058,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749314	23709	PASS	C	T	15049	0.938667	0	0,3,0,15017	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749314	23817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	33234	0.001023	0	18128,15048,21,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTt/cCt	L752P	S	0.000646	0.066832	1	1	T>C
ERR5749314	24506	PASS	T	G	17266	0.973126	0	8,0,17255,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749314	24794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	16214	0.021525	0	15837,0,372,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gct/Tct	A1078S	S	0.001791	0.957884	1	1	G>T
ERR5749314	24914	PASS	G	C	32214	0.956044	0	0,0,16050,16147	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749314	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	24131	0.001699	57	16976,7105,47,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749314	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	24137	0.001243	375	24062,13,16,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749314	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	24108	7.05E-4	0	24091,0,17,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749314	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	24304	0.00144	1133	23896,161,141,85	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749314	27128	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29113	0.001546	0	0,29048,0,48	LOW	SILENT	SYNONYMOUS_CODING	M	ggC/ggT	G202	M	0.000719	0.147659	1	1	C>T
ERR5749314	27972	PASS	C	T	11177	0.908562	21	1,1,11097,43	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749314	28048	PASS	G	T	11148	0.926803	0	0,12,0,11135	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749314	28111	PASS	A	G	31188	0.978838	9	2,5,20013,11154	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749314	28270	PASS	TA	T	38733	0.995869	399	164,5,19761,18812	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749314	28280	PASS	G	C	38676	0.934352	31	17,2,19804,18792	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749314	28281	PASS	A	T	38676	0.891173	26	25,7,19757,18801	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749314	28282	PASS	T	A	38676	0.918735	40	34,8,19759,18806	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749314	28881	PASS	G	A	19354	0.788106	9	6,1,9609,9495	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749314	28882	PASS	G	A	19354	0.825669	19	10,1,9683,9443	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749314	28883	PASS	G	C	19354	0.942234	0	1,1,9702,9624	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749314	28977	PASS	C	T	9846	0.930124	0	0,3,2,9822	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749314	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	36336	8.53E-4	80	26460,9814,9,26	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749314	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	52595	9.13E-4	0	26411,26098,30,30	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749314	29386	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	10077	8.93E-4	0	10067,1,9,0	HIGH	NONE	FRAME_SHIFT	N	aag/aaAg	K373K?	N	0.000887	0.899197	4	2	C>CA
ERR5749315	241	PASS	C	T	18766	0.860972	3	0,2,9299,9388	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749315	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	11976	0.002088	19	11947,4,24,1	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749315	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	11976	0.00167	0	11905,5,20,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749315	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	11976	0.003257	0	11905,5,39,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749315	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	11973	0.001336	0	11101,8,748,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749315	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	11973	0.001754	0	11943,9,21,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749315	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	11973	6.68E-4	0	11944,7,8,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttatg/gtg	VM84V	leader	0.000554	0.991848	4	1	GTTA>G
ERR5749315	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	11973	0.00167	0	11938,9,20,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749315	569	PASS	G	A	11974	0.874395	0	0,3,3,11926	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gag/Aag	E102K	leader	0.874395	0.874395	1	1	G>A
ERR5749315	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	31353	4.78E-4	30	19359,11978,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749315	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	31354	0.002328	9	19312,11954,52,21	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749315	1191	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	11351	0.002291	0	0,11314,0,34	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCa/cAa	P129Q	nsp2	0.000749	0.916048	3	2	C>A
ERR5749315	2841	PASS	C	T	67	0.985075	18	1,0,0,66	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCc/gTc	A41V	nsp3	0.985075	0.985075	1	1	C>T
ERR5749315	3037	PASS	C	T	14328	0.829285	21	3,14,7153,7089	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749315	3671	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	24386	0.001025	0	12155,12053,14,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E318K	nsp3	0.000351	0.0625	6	2	G>A
ERR5749315	4002	PASS	C	T	23854	0.806154	0	0,24,0,23726	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T428I	nsp3	0.001296	0.806154	2	1	C>T
ERR5749315	5180	PASS	G	A	11665	0.911187	0	0,2,0,11634	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gat/Aat	D821N	nsp3	0.001806	0.911187	2	2	G>A
ERR5749315	6574	PASS	T	C	11196	0.959718	0	1,0,11185,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcT/tcC	S1285	nsp3	0.959718	0.959718	1	1	T>C
ERR5749315	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11165	0.001612	0	3,11042,0,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749315	7124	PASS	C	T	21535	0.953007	0	5,0,21511,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cct/Tct	P1469S	nsp3	0.953007	0.953007	1	1	C>T
ERR5749315	9203	PASS	G	A	13527	0.964515	0	0,2,0,13509	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gat/Aat	D217N	nsp4	0.931507	0.964515	2	1	G>A
ERR5749315	9929	PASS	G	A	5962	0.918819	2147483647	0,0,5960,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gat/Aat	D459N	nsp4	0.918819	0.918819	1	1	G>A
ERR5749315	10097	PASS	G	A	5975	0.955146	55	2,0,9,5959	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggt/Agt	G15S	3Cpro	0.006523	0.955146	1	1	G>A
ERR5749315	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	14935	0.002946	0	14866,0,56,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749315	11325	PASS	C	T	14942	0.892049	0	0,3,0,14936	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCa/tTa	S118L	nsp6	0.001283	0.892049	2	2	C>T
ERR5749315	11337	PASS	T	C	14942	0.987619	0	0,2,0,14934	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTa/tCa	L122S	nsp6	0.00626	0.987619	1	1	T>C
ERR5749315	11572	PASS	C	T	14	0.642857	23	4,0,1,9	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F200	nsp6	0.005575	0.918642	2	2	C>T
ERR5749315	11824	PASS	C	T	15221	0.922016	0	0,4,0,15181	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I284	nsp6	0.000465	0.922016	2	2	C>T
ERR5749315	12534	PASS	C	T	14788	0.90073	0	1,0,14772,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T148I	nsp8	0.004454	0.90073	1	1	C>T
ERR5749315	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28610	0.001084	0	14290,14252,17,18	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749315	13536	PASS	C	T	14304	0.799427	0	0,4,0,14217	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y32	RdRp	0.002208	0.799427	1	1	C>T
ERR5749315	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	11601	0.004224	2767	11349,87,7,155	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749315	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	22597	0.001505	0	11323,11253,18,16	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749315	14408	PASS	C	T	22597	0.845378	3	0,1,11272,11155	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749315	16293	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9100	0.001538	0	9080,1,15,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C19	helicase	0.001538	0.968351	1	1	C>T
ERR5749315	16549	PASS	G	T	19362	0.875736	0	46,0,19280,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gac/Tac	D105Y	helicase	0.875736	0.875736	1	1	G>T
ERR5749315	17678	PASS	C	T	12973	0.968704	79	2,0,0,12967	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aTg	T481M	helicase	0.001162	0.968704	2	1	C>T
ERR5749315	17766	PASS	C	T	10571	0.920632	2147483647	0,0,10558,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V510	helicase	0.000768	0.920632	2	2	C>T
ERR5749315	18713	PASS	C	T	19848	0.982769	0	8,0,19829,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCc/gTc	A225V	ExoN	0.00133	0.982769	1	1	C>T
ERR5749315	19262	PASS	A	G	40024	0.951729	1	2,4,17272,22703	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAc/aGc	N408S	ExoN	0.951729	0.951729	1	1	A>G
ERR5749315	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27777	0.001944	0	27690,3,59,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749315	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23887	9.63E-4	0	23828,0,25,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749315	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30672	9.45E-4	1	14941,15312,15,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749315	21597	PASS	C	T	15425	0.897569	0	0,4,0,15401	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCt/tTt	S12F	S	0.00218	0.901607	2	1	C>T
ERR5749315	21764	PASS	ATACATG	A	1277	0.997651	0	3,0,1274,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749315	22016	PASS	T	A	19406	0.94646	0	3,0,19392,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tgg/Agg	W152R	S	0.000941	0.94646	2	2	T>A
ERR5749315	22600	PASS	A	C	19249	0.963998	1	8,2,13341,5891	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	agA/agC	R346S	S	0.000471	0.963998	3	3	A>C
ERR5749315	22803	PASS	A	G	13349	0.9788	2147483647	0,0,0,13337	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cAa/cGa	Q414R	S	0.002015	0.9788	2	1	A>G
ERR5749315	22917	PASS	T	G	4910	0.975153	0	2,0,4908,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTg/cGg	L452R	S	0.005552	0.975153	2	1	T>G
ERR5749315	23403	PASS	A	G	19969	0.969052	0	0,6,0,19949	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749315	23593	PASS	G	T	14581	0.924148	0	10,0,14562,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	caG/caT	Q677H	S	0.021779	0.924148	3	2	G>T
ERR5749315	23731	PASS	C	T	14581	0.932378	0	0,3,0,14561	LOW	SILENT	SYNONYMOUS_CODING	S	acC/acT	T723	S	0.932378	0.932378	1	1	C>T
ERR5749315	24237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10570	0.004636	0	10500,0,54,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gTt	A892V	S	0.001242	0.889739	1	1	C>T
ERR5749315	24257	PASS	G	T	10559	0.956056	2147483647	0,0,10549,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gct/Tct	A899S	S	0.005048	0.956056	2	2	G>T
ERR5749315	24998	PASS	G	A	14934	0.846993	34	1,4,0,14890	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Aac	D1146N	S	0.001186	0.846993	3	1	G>A
ERR5749315	25317	PASS	C	T	21133	0.956514	5	0,1,15127,5984	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tTc	S1252F	S	0.000828	0.956514	4	2	C>T
ERR5749315	25687	PASS	G	A	24896	0.944569	0	5,0,24883,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gct/Act	A99T	orf3a	0.000967	0.944569	1	1	G>A
ERR5749315	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	24896	6.03E-4	0	24880,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749315	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	47647	3.36E-4	0	1,47630,0,16	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749315	26767	PASS	T	C	9856	0.957792	0	0,7,24,9821	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	aTc/aCc	I82T	M	0.954318	0.968313	2	1	T>C
ERR5749315	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	9844	0.001422	0	1,9828,0,14	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749315	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	9845	0.002438	0	0,9817,0,24	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749315	27603	PASS	C	T	20882	0.959582	0	1,0,20858,0	LOW	SILENT	SYNONYMOUS_CODING	ORF7a	ggC/ggT	G70	orf7a	0.002411	0.959582	1	1	C>T
ERR5749315	27739	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20969	0.001001	0	1,20926,0,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Ctc/Ttc	L116F	orf7a	0.001001	0.957506	1	1	C>T
ERR5749315	27882	PASS	G	T	9796	0.972438	0	1,0,9785,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7b	Gcc/Tcc	A43S	orf7b	0.972438	0.972438	1	1	G>T
ERR5749315	28270	PASS	TA	T	35033	0.990067	224	85,264,17525,17160	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749315	28273	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AA	A	35062	0.003166	218	17597,17358,8,103	HIGH	NONE	FRAME_SHIFT+START_LOST	N	atg/	M1	N	0.000399	0.842333	4	1	AA>A
ERR5749315	28881	PASS	G	A	14772	0.79231	3	2,0,7418,7219	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749315	28882	PASS	G	A	14771	0.842597	6	3,0,7465,7196	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749315	28883	PASS	G	C	14771	0.946381	6	0,2,7471,7278	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749315	28908	PASS	G	T	7396	0.904543	0	0,4,0,7378	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gGc/gTc	G212V	N	0.904543	0.904543	1	1	G>T
ERR5749315	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	38364	0.001017	0	19259,19045,25,25	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749315	29311	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19313	0.002278	0	8,19224,0,59	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F346	N	0.000335	0.790798	3	2	C>T
ERR5749315	29451	PASS	C	T	8023	0.352861	0	4511,0,3478,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aCt/aTt	T393I	N	0.007675	0.757685	2	2	C>T
ERR5749316	241	PASS	C	T	12461	0.853944	3	0,1,6216,6154	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749316	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	11857	0.001012	0	11846,0,12,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749316	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	11857	0.001349	0	11835,0,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749316	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	11853	0.001772	0	11084,0,726,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749316	913	PASS	C	T	21786	0.891857	0	0,16,0,21698	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749316	1510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	21211	0.003017	0	0,20713,0,77	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G235	nsp2	0.002159	0.937304	1	1	T>C
ERR5749316	1813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	20129	0.001192	0	0,20065,0,34	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcA	A336	nsp2	0.001022	0.152738	4	2	T>A
ERR5749316	3037	PASS	C	T	22961	0.787858	138	0,45,11517,11127	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749316	3267	PASS	C	T	21197	0.972072	0	4,0,21184,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749316	3340	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	42155	7.12E-4	710	21147,20625,27,341	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtG/gtT	V207	nsp3	0.000712	0.845579	3	2	G>T
ERR5749316	5388	PASS	C	A	7089	0.958386	2147483647	0,0,7085,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749316	5986	PASS	C	T	15207	0.976655	0	1,0,15195,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749316	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14129	0.001345	0	3,13923,0,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749316	6954	PASS	T	C	23317	0.79174	0	0,2,1,23151	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749316	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	32937	4.55E-4	40	17519,15403,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749316	10077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	6718	0.002531	377	11,6658,16,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTc/tCc	F8S	3Cpro	0.001833	0.454545	1	1	T>C
ERR5749316	11082	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	19251	6.23E-4	0	19248,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000427	0.179468	2	1	TG>T
ERR5749316	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	19251	0.001662	0	19185,0,50,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749316	11287	PASS	GTCTGGTTTT	G	19250	0.99787	0	0,40,0,19209	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749316	11507	PASS	G	A	32894	0.885906	4	4,1,16499,16246	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Att	V179I	nsp6	0.007744	0.914418	2	2	G>A
ERR5749316	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28368	0.001586	0	14162,14101,25,25	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749316	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	11435	0.007258	2147483647	11082,104,4,245	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749316	14408	PASS	C	T	22028	0.829808	15	0,5,11026,10821	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749316	14676	PASS	C	T	12811	0.824526	0	5,0,12788,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749316	15279	PASS	C	T	21424	0.838125	0	4,0,21370,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749316	16176	PASS	T	C	20486	0.971737	6	0,2,10377,10094	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749316	18504	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	30831	9.73E-4	0	4,30051,0,685	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K155N	ExoN	0.000518	0.094148	4	3	A>C
ERR5749316	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	25482	4.71E-4	0	0,25470,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749316	19962	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	34995	0.015202	0	34425,0,567,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acG/acT	T114	endoR	0.015202	0.971716	1	1	G>T
ERR5749316	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34994	0.001857	0	34897,0,66,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749316	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	36275	7.44E-4	0	36196,0,28,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749316	21764	PASS	ATACATG	A	14874	0.99684	0	46,0,14827,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749316	21990	PASS	TTTA	T	14879	0.997715	0	0,34,4,14841	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749316	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	31017	8.38E-4	1	15079,15900,14,12	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749316	23031	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	14998	0.001067	0	3,14535,0,410	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tTt/tGt	F490C	S	0.001067	0.92095	2	1	T>G
ERR5749316	23063	PASS	A	T	15059	0.822233	0	0,5,0,14936	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749316	23271	PASS	C	A	22123	0.92492	0	5,0,22100,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749316	23403	PASS	A	G	22108	0.955717	0	0,3,0,22073	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749316	23604	PASS	C	A	18052	0.953302	0	5,0,18041,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749316	23709	PASS	C	T	18012	0.907839	0	0,4,1,17954	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749316	24506	PASS	T	G	16911	0.970729	0	9,0,16898,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749316	24914	PASS	G	C	41214	0.953293	6	0,3,20560,20617	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749316	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	27198	0.001618	57	20262,6876,56,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749316	25496	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	40861	8.32E-4	293	20264,19935,174,452	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aTa/aGa	I35R	orf3a	0.000369	0.96555	3	2	T>G
ERR5749316	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	24046	0.00104	290	23962,19,13,12	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749316	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	24015	8.33E-4	0	23995,0,20,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749316	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	24216	0.001569	1683	23854,126,103,108	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749316	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	14079	6.39E-4	0	1,14069,0,9	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749316	27128	PASS	C	T	28471	0.147659	0	0,24053,0,4398	LOW	SILENT	SYNONYMOUS_CODING	M	ggC/ggT	G202	M	0.000719	0.147659	1	1	C>T
ERR5749316	27972	PASS	C	T	12990	0.906543	75	4,4,12883,55	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749316	28048	PASS	G	T	12922	0.89514	0	0,24,0,12888	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749316	28111	PASS	A	G	32447	0.973742	6	2,4,19500,12923	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749316	28270	PASS	TA	T	37265	0.994177	371	200,17,19251,17797	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749316	28280	PASS	G	C	37191	0.929983	14	14,4,19302,17777	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749316	28281	PASS	A	T	37191	0.910005	24	32,11,19296,17781	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749316	28282	PASS	T	A	37194	0.900199	4	30,20,19254,17796	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749316	28651	PASS	C	T	17834	0.896546	0	0,6,2,17777	LOW	SILENT	SYNONYMOUS_CODING	N	aaC/aaT	N126	N	0.000502	0.918117	3	2	C>T
ERR5749316	28881	PASS	G	A	19753	0.745608	9	4,0,9885,9557	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749316	28882	PASS	G	A	19753	0.803726	1	4,2,9977,9494	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749316	28883	PASS	G	C	19754	0.932115	0	2,2,9987,9739	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749316	28977	PASS	C	T	10112	0.894482	0	0,3,0,10073	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749316	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	41444	7.0E-4	77	31296,10079,10,24	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749316	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	62085	0.001305	0	31243,30718,49,47	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749316	29738	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11023	0.001905	0	0,10987,0,26	.	.	.	.	.	.	.	0.001703	0.890671	2	1	C>T
ERR5749317	241	PASS	C	T	7344	0.886029	0	1,1,3663,3654	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749317	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	11111	0.00144	0	11097,0,16,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749317	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	11111	9.9E-4	0	10806,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749317	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	11111	0.02223	0	10806,0,247,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749317	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	11111	0.00396	0	10806,0,44,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749317	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	11112	0.00207	0	9978,8,789,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749317	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	11112	0.00135	0	11089,8,15,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749317	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	29717	4.71E-4	27	18557,11143,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749317	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	29717	0.001211	12	18534,11134,28,8	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749317	913	PASS	C	T	18564	0.908964	0	0,9,0,18534	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749317	2453	PASS	C	T	15029	0.720208	0	0,11,0,14791	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L550F	nsp2	0.00429	0.842201	2	2	C>T
ERR5749317	3037	PASS	C	T	20162	0.811626	47	2,22,10082,9892	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749317	3267	PASS	C	T	20099	0.968357	0	2,0,20087,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749317	3671	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GA	25537	4.7E-4	0	12784,12751,6,6	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/aaAt	N319K?	nsp3	0.000351	0.0625	6	2	G>GA
ERR5749317	3832	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	18630	9.13E-4	0	18609,4,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L373	nsp3	0.000689	0.327273	4	2	CT>C
ERR5749317	5388	PASS	C	A	5661	0.963257	2147483647	0,0,5657,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749317	5512	PASS	C	T	5658	0.948745	0	0,1,0,5653	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N931	nsp3	0.002299	0.987013	1	1	C>T
ERR5749317	5986	PASS	C	T	13723	0.977337	0	1,0,13709,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749317	6606	PASS	C	T	13263	0.945412	2147483647	0,0,13241,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S1296F	nsp3	0.002262	0.945412	1	1	C>T
ERR5749317	6954	PASS	T	C	24770	0.818813	0	0,7,3,24625	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749317	7067	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	41931	5.25E-4	85	17048,24861,22,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gaa/	E1450	nsp3	0.000274	0.059217	5	3	GA>G
ERR5749317	7070	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	41931	0.001884	282	16970,24849,80,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggc/Agc	G1451S	nsp3	0.000698	0.101434	3	1	G>A
ERR5749317	7764	PASS	C	T	23510	0.962654	0	2,0,23485,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCc/tTc	S1682F	nsp3	0.001052	0.964731	1	1	C>T
ERR5749317	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	24672	7.3E-4	30	16400,8253,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749317	10296	PASS	C	T	41074	0.925159	0	2,2,20177,20823	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S81F	3Cpro	0.002839	0.925159	1	1	C>T
ERR5749317	10323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	20882	0.00182	0	0,20795,0,40	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749317	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	23920	0.001714	0	23836,1,72,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749317	11287	PASS	GTCTGGTTTT	G	23910	0.997114	0	0,69,0,23841	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749317	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	38286	9.93E-4	14	22875,15331,32,10	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749317	12459	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	46322	8.2E-4	14	21776,24497,25,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T123I	nsp8	0.000658	0.986093	1	1	C>T
ERR5749317	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	21800	0.001239	0	21752,0,28,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749317	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	32507	0.001292	0	16229,16179,25,25	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749317	13665	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18101	0.003425	0	18025,3,65,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H75	RdRp	0.002046	0.977554	1	1	C>T
ERR5749317	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	5590	0.005546	1652	5439,52,2,96	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749317	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	10835	7.38E-4	0	5433,5402,4,4	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749317	14408	PASS	C	T	10835	0.821597	0	1,1,5409,5351	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749317	14676	PASS	C	T	12628	0.83006	0	5,0,12590,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749317	15279	PASS	C	T	20842	0.85985	0	5,0,20783,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749317	16176	PASS	T	C	19872	0.979821	3	1,0,9212,10650	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749317	18131	PASS	C	T	12076	0.848211	0	0,0,12032,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T31I	ExoN	0.0025	0.853992	1	1	C>T
ERR5749317	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	26853	0.001415	0	26814,0,38,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749317	19188	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	27600	5.07E-4	0	0,27586,0,14	HIGH	NONE	FRAME_SHIFT	ORF1ab	tgg/	W385	ExoN	0.000427	0.06319	2	1	AT>A
ERR5749317	19269	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	47874	7.73E-4	4	20250,27571,13,26	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N410	ExoN	0.000773	0.954777	2	2	C>T
ERR5749317	19983	PASS	C	T	28006	0.857888	0	2,0,27420,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749317	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	28006	0.012497	0	27580,0,350,0	HIGH	NONE	FRAME_SHIFT+STOP_GAINED	ORF1ab	gat/Tgat	D124*?	endoR	0.000884	0.981982	5	2	C>CT
ERR5749317	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	28006	0.002321	0	27580,0,65,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gat/TTgat	D124L?	endoR	0.000884	0.981982	5	2	C>CTT
ERR5749317	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	31214	0.001153	0	31136,0,39,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749317	21764	PASS	ATACATG	A	14045	0.997081	0	41,0,14004,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749317	21990	PASS	TTTA	T	14044	0.998362	0	0,23,1,14020	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749317	22690	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	19167	9.91E-4	0	18863,5,22,0	LOW	SILENT	SYNONYMOUS_CODING	S	acT/acC	T376	S	0.000815	0.051311	2	1	T>C
ERR5749317	23063	PASS	A	T	15826	0.85726	0	0,3,0,15754	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749317	23271	PASS	C	A	20256	0.912026	0	3,0,20228,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749317	23277	PASS	C	T	20256	0.74768	2147483647	0,0,20030,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCt/aTt	T572I	S	0.001007	0.74768	1	1	C>T
ERR5749317	23403	PASS	A	G	20253	0.971659	0	0,4,0,20229	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749317	23604	PASS	C	A	17348	0.952041	0	10,0,17334,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749317	23709	PASS	C	T	17323	0.935288	0	0,7,7,17277	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749317	24506	PASS	T	G	19048	0.975273	0	10,0,19034,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749317	24914	PASS	G	C	43290	0.959413	0	0,0,21575,21678	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749317	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	28025	0.00132	53	20957,7015,44,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749317	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	15928	0.002511	613	15834,17,18,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749317	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	15884	7.55E-4	0	15872,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749317	25904	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15906	0.001697	0	23,15845,0,35	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	tCa/tTa	S171L	orf3a	0.000757	0.83473	1	1	C>T
ERR5749317	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	14146	7.78E-4	0	6,14129,0,11	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749317	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	14147	0.001343	0	5,14119,0,19	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749317	27384	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	22601	0.006504	0	35,22335,0,170	LOW	SILENT	SYNONYMOUS_CODING	ORF6	gaT/gaC	D61	orf6	0.00154	0.931035	3	3	T>C
ERR5749317	27425	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	22638	0.001016	0	45,22551,0,40	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	aCa/aAa	T11K	orf7a	0.001016	0.856486	2	1	C>A
ERR5749317	27476	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	47369	0.014186	25	24432,22213,330,377	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	aCa/aTa	T28I	orf7a	0.000547	0.22827	4	2	C>T
ERR5749317	27972	PASS	C	T	11258	0.907621	17	2,1,11160,62	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749317	28048	PASS	G	T	11209	0.915247	0	0,17,0,11184	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749317	28111	PASS	A	G	34431	0.97964	7	5,6,23194,11210	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749317	28117	PASS	A	G	34431	0.982196	3	7,1,23190,11219	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	gAt/gGt	D75G	orf8	0.982196	0.982196	1	1	A>G
ERR5749317	28270	PASS	TA	T	44838	0.992975	726	308,11,22801,21722	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749317	28271	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AA	A	44834	0.001338	172	23039,21736,60,0	.	.	.	.	.	.	.	0.000482	0.924941	3	2	AA>A
ERR5749317	28280	PASS	G	C	44733	0.934545	21	13,2,22930,21696	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749317	28281	PASS	A	T	44733	0.908367	30	29,8,22913,21708	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749317	28282	PASS	T	A	44735	0.911054	5	24,15,22879,21716	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749317	28406	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTACCCAATA	T	23233	4.3E-4	0	26,23197,0,10	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	N	ttacccaataat/tat	LPNN45Y	N	0.00043	0.921074	3	2	TTACCCAATA>T
ERR5749317	28881	PASS	G	A	13709	0.757313	1	4,2,6787,6697	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749317	28882	PASS	G	A	13709	0.812824	4	4,1,6861,6692	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749317	28883	PASS	G	C	13709	0.941717	0	0,0,6872,6823	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749317	28977	PASS	C	T	6969	0.928828	0	0,1,0,6950	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749317	29095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34667	8.08E-4	0	34611,6,29,0	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F274	N	0.000792	0.961279	2	2	C>T
ERR5749317	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	68789	9.3E-4	0	34570,34111,42,40	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749317	29635	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21183	0.001133	3	9988,11140,10,16	LOW	SILENT	SYNONYMOUS_CODING	ORF10	taC/taT	Y26	orf10	0.001133	0.928275	1	1	C>T
ERR5749318	241	PASS	C	T	3227	0.872017	0	1,2,1603,1610	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749318	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	6599	0.002273	0	6585,0,15,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749318	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	6599	0.001515	0	6542,0,10,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749318	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	6599	0.005758	0	6542,0,38,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749318	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	6597	0.001971	0	6584,0,13,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749318	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	6596	0.002577	0	6574,0,17,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749318	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	28434	0.001196	18	21798,6600,32,2	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749318	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21817	0.001742	0	0,21764,0,40	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749318	913	PASS	C	T	21818	0.908745	0	0,12,0,21771	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749318	1862	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTTTATGCA	C	18289	6.01E-4	0	0,18276,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	tatgcattt/	YAF354	nsp2	0.000585	0.936867	4	2	CTTTATGCA>C
ERR5749318	2151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATTGGC	A	24022	4.16E-4	0	0,24012,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	tggcttgaa/	WLE450	nsp2	0.000402	0.971954	3	2	ATTGGC>A
ERR5749318	3037	PASS	C	T	14442	0.801413	24	0,8,7213,7089	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749318	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	7313	0.003966	729	5,7272,29,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749318	3177	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30115	9.63E-4	34	22785,7272,30,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P153L	nsp3	0.000773	0.96008	3	2	C>T
ERR5749318	3267	PASS	C	T	22839	0.970533	0	5,0,22819,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749318	3961	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	11364	7.92E-4	0	11354,1,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K415	nsp3	0.000417	0.869983	2	2	CA>C
ERR5749318	4578	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTAACGATC	T	16250	6.77E-4	0	0,16239,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	aacgatctaaat/	NDLN621	nsp3	0.000519	0.082979	2	2	TTAACGATC>T
ERR5749318	5388	PASS	C	A	3898	0.957927	2147483647	0,0,3898,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749318	5986	PASS	C	T	11404	0.977026	0	3,0,11393,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749318	6954	PASS	T	C	21750	0.815448	0	0,5,0,21605	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749318	8084	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	24160	0.001076	0	24114,0,29,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E1789K	nsp3	0.000543	0.923413	4	2	G>A
ERR5749318	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	16203	7.41E-4	16	11247,4944,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749318	9727	PASS	T	C	11254	0.968722	0	0,0,12,11233	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taT/taC	Y391	nsp4	0.015758	0.973696	1	1	T>C
ERR5749318	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24446	0.001514	0	24369,6,40,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749318	11082	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	24435	8.18E-4	0	24420,0,20,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000427	0.179468	2	1	TG>T
ERR5749318	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	24435	0.002906	0	24305,0,104,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749318	11152	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24409	0.002294	0	24300,0,57,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V60	nsp6	0.000678	0.974465	2	2	C>T
ERR5749318	11287	PASS	GTCTGGTTTT	G	24428	0.997748	0	0,55,0,24373	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749318	12741	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26568	0.001468	8	9428,17085,10,32	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T19I	nsp9	0.000486	0.962552	2	2	C>T
ERR5749318	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29533	0.001456	0	14741,14693,25,25	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749318	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	5692	0.003514	1421	5537,70,0,83	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749318	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	11039	0.001721	0	5526,5500,10,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749318	14408	PASS	C	T	11039	0.838572	2	1,2,5500,5438	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749318	14676	PASS	C	T	13318	0.808079	0	11,0,13276,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749318	15279	PASS	C	T	17858	0.889741	0	6,0,17826,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749318	16176	PASS	T	C	16085	0.973391	0	0,0,4365,11712	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749318	16468	PASS	C	T	32166	0.973917	1	8,2,27776,4365	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ccc/Tcc	P78S	helicase	0.001077	0.977186	1	1	C>T
ERR5749318	17615	PASS	A	G	14932	0.911532	0	0,0,3,14892	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749318	17642	PASS	C	T	14939	0.949863	0	0,3,0,14930	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A469V	helicase	0.949863	0.955	1	1	C>T
ERR5749318	18501	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	35666	3.36E-4	0	0,35654,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K155	ExoN	0.000336	0.857143	4	2	CA>C
ERR5749318	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	23577	5.51E-4	0	23564,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749318	19113	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	60079	6.49E-4	123	30006,29925,27,110	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gaC/gaA	D358E	ExoN	0.000461	0.125	4	3	C>A
ERR5749318	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	30108	3.99E-4	0	3,30093,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749318	19404	PASS	T	C	17307	0.697695	0	4844,0,12418,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caT/caC	H455	ExoN	0.00084	0.697695	2	2	T>C
ERR5749318	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18342	0.002781	0	18278,0,52,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749318	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	13462	0.001114	0	4,13443,0,15	HIGH	NONE	FRAME_SHIFT	S	ctt/Tctt	L5S?	S	0.000394	0.091869	4	1	G>GT
ERR5749318	21732	PASS	C	CT	12118	0.076745	0	11023,7,930,0	HIGH	NONE	FRAME_SHIFT	S	ttc/ttTc	F58F?	S	0.000576	0.076745	4	2	C>CT
ERR5749318	21732	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	12118	0.011305	0	11023,7,137,0	HIGH	NONE	FRAME_SHIFT	S	ttc/ttTTc	F58F?	S	0.000576	0.076745	4	2	C>CTT
ERR5749318	21736	PASS	C	T	12108	0.804427	57	1789,7,9920,0	LOW	SILENT	SYNONYMOUS_CODING	S	ttC/ttT	F58	S	0.001596	0.804427	3	2	C>T
ERR5749318	21736	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	12108	0.005451	0	12023,7,66,0	HIGH	NONE	FRAME_SHIFT	S	tcc/tTcc	S60F?	S	0.001596	0.804427	3	2	C>CT
ERR5749318	21764	PASS	ATACATG	A	12098	0.996528	0	43,0,12056,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749318	21990	PASS	TTTA	T	12119	0.996947	0	0,37,7,12075	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749318	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	33146	0.001659	0	13638,19432,23,35	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749318	23063	PASS	A	T	13657	0.848283	0	0,5,0,13571	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749318	23271	PASS	C	A	25682	0.928861	0	2,0,25655,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749318	23403	PASS	A	G	25674	0.963192	0	0,3,2,25658	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749318	23604	PASS	C	A	14008	0.944889	0	11,0,13990,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749318	23709	PASS	C	T	13998	0.93249	0	0,2,2,13976	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749318	24320	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	11278	0.001951	0	0,11256,0,22	HIGH	NONE	FRAME_SHIFT	S	aaa/	K921	S	0.000763	0.138365	4	2	CA>C
ERR5749318	24410	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	11299	0.001947	0	11,11260,0,28	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gat/Tat	D950Y	S	0.001947	0.846282	2	1	G>T
ERR5749318	24506	PASS	T	G	17063	0.973275	0	9,0,17053,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749318	24914	PASS	G	C	37102	0.954719	0	0,1,18483,18590	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749318	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	26773	0.001531	64	19548,7169,50,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749318	25510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	19758	0.001771	23	110,19562,3,53	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Tca/Aca	S40T	orf3a	0.001771	0.96355	3	1	T>A
ERR5749318	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	8468	0.002244	341	8420,14,6,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749318	25916	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8603	0.015692	0	10,8448,0,141	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aCa/aTa	T175I	orf3a	0.001191	0.964713	2	2	C>T
ERR5749318	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	34937	3.72E-4	0	0,34924,0,13	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749318	26158	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	34937	3.43E-4	0	0,34925,0,12	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF3a	gttaat/gat	VN256D	orf3a	0.000297	0.905181	6	2	GTTA>G
ERR5749318	26208	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34991	8.0E-4	0	6,34921,0,34	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	agC/agT	S272	orf3a	0.000315	0.922222	2	2	C>T
ERR5749318	26257	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	47945	4.38E-4	26	12949,34975,0,21	HIGH	NONE	FRAME_SHIFT	E	tcg/tTcg	S6F?	E	0.000247	0.948926	4	2	G>GT
ERR5749318	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	11568	7.78E-4	0	2,11557,0,9	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749318	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	11569	0.003112	0	2,11530,0,36	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749318	27552	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATTTGCACTGACTTGCTTTAGCACTCAATTTGCTTTTGCTTGTCCTGACGGCGTAAAACACGTCTATCAGTTACGTGCCAGATCAG	A	22220	5.85E-4	0	22205,2,13,0	HIGH	NONE	FRAME_SHIFT	ORF7a	gcactgacttgctttagcactcaatttgcttttgcttgtcctgacggcgtaaaacacgtctatcagttacgtgccagatcagtttca/	ALTCFSTQFAFACPDGVKHVYQLRARSVS55	orf7a	0.000563	0.985801	6	1	ATTTGCACTGACTTGCTTTAGCACTCAATTTGCTTTTGCTTGTCCTGACGGCGTAAAACACGTCTATCAGTTACGTGCCAGATCAG>A
ERR5749318	27972	PASS	C	T	8938	0.913292	19	1,1,8863,48	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749318	28048	PASS	G	T	8914	0.920126	0	0,17,1,8892	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749318	28111	PASS	A	G	34779	0.977946	4	5,0,25841,8913	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749318	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25838	0.001742	0	25735,3,50,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749318	28270	PASS	TA	T	50049	0.995584	467	213,11,25546,24282	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749318	28280	PASS	G	C	49952	0.932335	8	15,7,25578,24237	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749318	28281	PASS	A	T	49952	0.927911	36	30,7,25575,24260	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749318	28282	PASS	T	A	49954	0.906454	5	30,20,25514,24265	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749318	28310	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25860	0.001817	0	16,25776,0,53	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Ccc/Tcc	P13S	N	0.00095	0.92832	2	1	C>T
ERR5749318	28603	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	40193	0.001567	0	20036,19905,38,40	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F110	N	0.000427	0.883357	2	2	C>T
ERR5749318	28881	PASS	G	A	14489	0.762026	4	4,1,7163,7121	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749318	28882	PASS	G	A	14489	0.821865	6	5,1,7247,7101	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749318	28883	PASS	G	C	14489	0.944855	2	3,1,7255,7221	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749318	28977	PASS	C	T	7385	0.925796	0	0,1,3,7363	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749318	28977	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGGTAAAGGCCAACAACAACAAGGCCAAACTGTCACTA	C	7385	0.001219	0	3,7373,0,9	HIGH	NONE	FRAME_SHIFT	N	tctggtaaaggccaacaacaacaaggccaaactgtcactaag/	SGKGQQQQGQTVTK235	N	0.001219	1	3	2	CTGGTAAAGGCCAACAACAACAAGGCCAAACTGTCACTA>C
ERR5749318	29095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	32093	0.002493	0	31997,0,83,0	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F274	N	0.000792	0.961279	2	2	C>T
ERR5749318	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	63720	0.001601	0	31986,31584,65,62	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749319	71	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1616	0.006188	0	1603,0,11,0	.	.	.	.	.	.	.	0.002088	0.926791	2	1	C>T
ERR5749319	222	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2122	0.006598	0	1051,1052,7,7	.	.	.	.	.	.	.	0.002134	0.864859	1	1	C>T
ERR5749319	241	PASS	C	T	2120	0.884434	0	0,1,1054,1059	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749319	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	6300	0.003492	0	6281,0,22,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749319	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	6300	0.003968	0	6266,0,25,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749319	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	6316	0.0019	0	6287,18,12,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749319	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	6318	0.002532	0	6279,20,16,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttatg/gtg	VM84V	leader	0.000554	0.991848	4	1	GTTA>G
ERR5749319	556	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6327	0.002213	0	27,6277,0,18	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y97	leader	0.001497	0.173414	1	1	C>T
ERR5749319	657	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6316	0.002217	0	4,6296,0,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A131V	leader	0.001202	0.365979	3	1	C>T
ERR5749319	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	19871	0.002315	40	13508,6309,43,3	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749319	913	PASS	C	T	13552	0.897285	0	0,10,0,13515	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749319	3037	PASS	C	T	12699	0.81723	42	0,14,6349,6237	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749319	3267	PASS	C	T	15393	0.971156	0	1,0,15377,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749319	3877	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	7636	0.00131	0	7228,0,12,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcC	A386	nsp3	0.000588	0.960227	2	1	T>C
ERR5749319	3877	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	7636	0.001179	0	7228,0,395,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcG	A386	nsp3	0.000588	0.960227	2	1	T>G
ERR5749319	5388	PASS	C	A	3856	0.955913	2147483647	0,0,3856,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749319	5986	PASS	C	T	9862	0.974549	0	1,0,9858,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749319	6954	PASS	T	C	17033	0.81254	2147483647	0,0,0,16931	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749319	6990	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17101	9.36E-4	0	0,16816,0,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S1424F	nsp3	0.000504	0.101156	4	2	C>T
ERR5749319	8151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	30985	7.42E-4	679	15210,15504,252,5	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gTc/gGc	V1811G	nsp3	0.00055	0.34	2	1	T>G
ERR5749319	8240	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15613	0.001345	0	0,15583,0,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cat/Tat	H1841Y	nsp3	0.001345	0.104353	1	1	C>T
ERR5749319	9198	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	14651	7.51E-4	0	0,14640,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F216	nsp4	0.000543	0.93476	4	2	CT>C
ERR5749319	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	14984	8.01E-4	8	12075,2897,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749319	9699	PASS	T	C	12064	0.898956	0	0,1,76,11958	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTc/aCc	I382T	nsp4	0.898956	0.898956	1	1	T>C
ERR5749319	10681	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CGCT	C	14640	8.88E-4	0	10,14617,0,13	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gctgtt/gtt	AV211V	3Cpro	0.000888	0.977192	2	2	CGCT>C
ERR5749319	10692	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	17777	9.56E-4	12	3146,14614,0,17	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N214	3Cpro	0.000956	0.982968	4	2	TA>T
ERR5749319	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	20975	0.002002	0	20906,0,65,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749319	11110	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	20966	4.77E-4	0	20956,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	atg/	M47	nsp6	0.000477	0.803913	2	2	TA>T
ERR5749319	11199	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	41790	0.001029	0	20753,20830,23,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCc/gTc	A76V	nsp6	0.000309	0.056758	3	2	C>T
ERR5749319	11287	PASS	GTCTGGTTTT	G	20960	0.997424	0	0,54,0,20906	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749319	12125	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	18750	0.00144	0	1,18664,0,30	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y12H	nsp8	0.000847	0.113436	1	1	T>C
ERR5749319	12162	PASS	A	G	31200	0.967532	2	0,2,12430,18752	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cAg/cGg	Q24R	nsp8	0.000894	0.982497	1	1	A>G
ERR5749319	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	16049	0.001308	0	16013,0,21,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749319	12781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6923	0.005489	0	6883,0,38,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y32	nsp9	0.001869	0.974683	2	2	C>T
ERR5749319	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	13823	0.001013	0	13810,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749319	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24025	0.001623	1	11994,11942,23,25	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749319	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	4493	0.004451	1260	4377,38,3,73	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749319	14408	PASS	C	T	8719	0.84184	0	1,1,4359,4290	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749319	14676	PASS	C	T	9436	0.764519	0	4,0,9410,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749319	14724	PASS	C	T	9410	0.789267	0	1,0,9283,6	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F428	RdRp	0.000952	0.789267	3	2	C>T
ERR5749319	14724	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	9410	0.028055	0	9135,6,264,0	HIGH	NONE	FRAME_SHIFT+STOP_GAINED	ORF1ab	aag/Taag	K430*?	RdRp	0.000952	0.789267	3	2	C>CT
ERR5749319	15023	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TCGCA	T	11797	0.001017	0	11785,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttcgca/	FA528	RdRp	0.001017	0.073446	2	2	TCGCA>T
ERR5749319	15025	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCA	G	11789	9.33E-4	0	11786,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gca/	A529	RdRp	0.000933	0.946354	3	2	GCA>G
ERR5749319	15026	PASS	C	T	11789	0.869455	0	1,0,11732,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCa/gTa	A529V	RdRp	0.000503	0.869455	2	2	C>T
ERR5749319	15279	PASS	C	T	13033	0.889051	0	2,0,13016,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749319	15983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	8464	0.001181	0	8451,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T850	RdRp	0.000701	0.338235	2	1	TA>T
ERR5749319	16176	PASS	T	C	13575	0.978637	0	0,1,5099,8472	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749319	16559	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	21730	6.44E-4	0	21716,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	att/	I109	helicase	0.000644	0.051993	3	2	CA>C
ERR5749319	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	17836	0.001626	0	17793,0,29,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749319	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAA	G	17836	7.85E-4	0	17793,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GAA>G
ERR5749319	16939	PASS	T	C	17813	0.955257	0	3,0,17786,12	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Tta/Cta	L235	helicase	0.000959	0.959205	2	2	T>C
ERR5749319	17615	PASS	A	G	13373	0.887983	2147483647	0,0,0,13325	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749319	17756	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	10020	9.98E-4	0	10010,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K508	helicase	0.000865	0.165644	4	2	GA>G
ERR5749319	18457	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22338	0.001253	0	22262,0,29,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cca/Tca	P140S	ExoN	0.001253	0.951352	2	1	C>T
ERR5749319	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24450	0.001145	0	24407,0,28,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C216	ExoN	0.000374	0.981963	3	2	C>T
ERR5749319	19011	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	21122	0.001468	0	21090,0,31,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K325	ExoN	0.000408	0.975746	4	2	CAA>C
ERR5749319	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	21139	5.2E-4	0	35,21093,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749319	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15882	0.001196	0	15851,0,20,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749319	20987	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	39538	3.54E-4	0	19784,19742,7,7	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L111	MethTr	0.000276	0.056129	4	2	CT>C
ERR5749319	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	19823	0.001463	0	0,19794,0,29	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TA>T
ERR5749319	21516	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	12477	0.001122	0	12462,1,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	agagtt/	RV287	MethTr	0.000412	0.905456	2	2	CAG>C
ERR5749319	21764	PASS	ATACATG	A	11430	0.99755	0	28,0,11402,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749319	21990	PASS	TTTA	T	11438	0.997552	0	0,28,4,11406	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749319	22280	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ACTTTACTTG	A	19556	4.6E-4	0	1,19546,0,9	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	cttgctttacat/cat	LALH242H	S	0.00046	0.997799	1	1	ACTTTACTTG>A
ERR5749319	22432	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8449	0.002959	0	8401,0,37,0	LOW	SILENT	SYNONYMOUS_CODING	S	gaC/gaT	D290	S	0.002959	0.755028	1	1	C>T
ERR5749319	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30052	8.98E-4	19	13088,16910,19,9	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749319	23063	PASS	A	T	13098	0.875477	0	0,3,0,13042	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749319	23271	PASS	C	A	17822	0.925878	0	2,0,17805,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749319	23403	PASS	A	G	17818	0.961163	2147483647	0,0,0,17792	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749319	23522	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTA	G	12711	8.65E-4	0	12698,2,11,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	gaacatgtcaacaactcatatgagtgtgacatacccattggtgcaggtata/gta	EHVNNSYECDIPIGAGI654V	S	0.00053	0.959726	5	2	GAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTA>G
ERR5749319	23604	PASS	C	A	12704	0.941829	0	8,0,12687,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749319	23709	PASS	C	T	12695	0.941237	0	0,4,10,12657	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749319	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	21854	0.001419	71	9146,12677,0,31	HIGH	NONE	FRAME_SHIFT	S	ttg/	L753	S	0.000334	0.080808	2	2	CT>C
ERR5749319	24237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10594	0.001416	0	10570,0,18,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gTt	A892V	S	0.001242	0.889739	1	1	C>T
ERR5749319	24506	PASS	T	G	15162	0.975465	0	4,0,15154,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749319	24914	PASS	G	C	38722	0.958318	0	0,0,19290,19406	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749319	25571	PASS	C	T	18599	0.893113	0	0,11,0,18545	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	tCc/tTc	S60F	orf3a	0.001558	0.922217	1	1	C>T
ERR5749319	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	6890	0.002758	319	6841,19,5,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749319	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	32002	8.44E-4	0	9,31966,0,27	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749319	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	12112	0.001073	0	0,12093,0,13	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749319	27972	PASS	C	T	8949	0.907476	23	0,1,8886,36	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749319	28048	PASS	G	T	8920	0.916816	0	0,13,0,8902	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749319	28111	PASS	A	G	29386	0.978391	5	8,1,20437,8926	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749319	28270	PASS	TA	T	39505	0.994937	449	183,5,20186,19119	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749319	28270	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAA	T	39505	3.8E-4	57	183,5,8,7	.	.	.	.	.	.	.	0.000322	1	2	1	TAA>T
ERR5749319	28280	PASS	G	C	39429	0.935479	18	14,3,20237,19104	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749319	28281	PASS	A	T	39429	0.920262	25	29,9,20228,19111	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749319	28282	PASS	T	A	39429	0.907454	7	18,10,20178,19122	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749319	28603	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	42112	0.001354	0	21002,20822,32,33	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F110	N	0.000427	0.883357	2	2	C>T
ERR5749319	28881	PASS	G	A	13874	0.775551	21	8,0,6908,6791	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749319	28882	PASS	G	A	13871	0.8264	12	5,0,6970,6738	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749319	28883	PASS	G	C	13871	0.93627	3	2,0,6981,6877	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749319	28977	PASS	C	T	7072	0.925905	0	0,2,1,7050	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749319	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	37380	0.001712	356	30272,6999,8,62	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749319	29095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30307	0.024054	0	29535,2,750,0	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F274	N	0.000792	0.961279	2	2	C>T
ERR5749319	29172	PASS	A	G	30278	0.92843	0	14,0,30205,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	cAt/cGt	H300R	N	0.00062	0.92843	2	2	A>G
ERR5749319	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	60142	0.001447	0	30196,29826,55,52	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749320	241	PASS	C	T	7348	0.869352	1	2,3,3666,3661	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749320	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	13227	0.001588	0	13195,7,21,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749320	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	13227	0.001966	0	13174,7,26,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749320	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	13221	0.00121	0	12406,8,711,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749320	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	13221	9.83E-4	0	13200,8,13,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749320	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	13220	8.32E-4	0	13196,8,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749320	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	37521	5.33E-4	20	24282,13211,7,13	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749320	913	PASS	C	T	24287	0.918928	0	0,13,0,24236	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749320	1510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	21590	0.002686	0	0,21359,0,64	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G235	nsp2	0.002159	0.937304	1	1	T>C
ERR5749320	2706	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	76331	0.001166	0	38238,37971,54,53	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T634I	nsp2	0.000591	0.821437	1	1	C>T
ERR5749320	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	76371	0.001453	2147483647	38095,35858,65,2176	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749320	3037	PASS	C	T	21779	0.819505	47	1,19,10891,10733	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749320	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10973	0.001823	525	4,10944,19,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749320	3267	PASS	C	T	24404	0.973201	0	3,0,24382,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749320	3671	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	29493	8.48E-4	0	14709,14607,14,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E318K	nsp3	0.000351	0.0625	6	2	G>A
ERR5749320	5388	PASS	C	A	5857	0.960219	2147483647	0,0,5856,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749320	5986	PASS	C	T	14583	0.97888	2147483647	0,0,14581,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749320	6582	PASS	C	T	14799	0.973714	2147483647	0,0,14790,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T1288I	nsp3	0.001257	0.973714	2	2	C>T
ERR5749320	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14762	0.001219	0	0,14572,0,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749320	6954	PASS	T	C	24771	0.819063	0	0,3,0,24645	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749320	7070	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	42018	0.001761	291	17082,24829,75,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggc/Agc	G1451S	nsp3	0.000698	0.101434	3	1	G>A
ERR5749320	7926	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	26198	5.34E-4	0	0,26182,0,14	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1737	nsp3	0.000531	0.97019	5	2	CA>C
ERR5749320	11082	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	26087	8.82E-4	0	26072,0,23,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000427	0.179468	2	1	TG>T
ERR5749320	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	26087	0.002377	0	25975,0,82,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749320	11095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTT	C	26084	6.13E-4	0	26047,0,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L43	nsp6	0.000515	0.887707	7	2	CTT>C
ERR5749320	11287	PASS	GTCTGGTTTT	G	26083	0.99747	0	0,66,0,26017	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749320	11507	PASS	G	A	32107	0.907123	6	3,0,16060,15955	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Att	V179I	nsp6	0.007744	0.914418	2	2	G>A
ERR5749320	12269	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	25211	7.93E-4	0	25189,0,20,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aag/	K61	nsp8	0.000434	0.213333	2	1	GA>G
ERR5749320	12634	PASS	A	G	48004	0.891176	1	3,2,23910,24037	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcA/gcG	A181	nsp8	0.891176	0.891176	1	1	A>G
ERR5749320	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	17061	5.28E-4	0	17053,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749320	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34631	0.001415	0	17296,17244,26,27	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749320	14408	PASS	C	T	7750	0.854839	1	3,4,3871,3828	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749320	14676	PASS	C	T	15396	0.752468	0	14,0,15345,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749320	15279	PASS	C	T	23562	0.921102	0	8,0,23537,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749320	15652	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAC	G	13023	6.91E-4	0	13015,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T739	RdRp	0.000691	0.935936	2	2	GAC>G
ERR5749320	16176	PASS	T	C	23153	0.984667	0	0,1,9917,13232	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749320	16508	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	26984	0.001668	0	26910,9,61,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGt/gTt	G91V	helicase	0.000561	0.074909	2	2	G>T
ERR5749320	18747	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	30526	4.26E-4	0	30506,7,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tataat/	YN237	ExoN	0.000375	0.982946	4	2	CTA>C
ERR5749320	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29296	0.001775	0	29220,0,54,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749320	20823	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	47689	0.00239	0	26905,20647,64,51	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N55	MethTr	0.001138	0.982544	2	2	C>T
ERR5749320	20987	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	53851	6.31E-4	0	26922,26890,17,17	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L111	MethTr	0.000276	0.056129	4	2	CT>C
ERR5749320	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	26978	0.001075	0	0,26949,0,29	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TA>T
ERR5749320	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	36068	9.98E-4	11	17697,17965,16,29	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749320	21764	PASS	ATACATG	A	15953	0.998245	0	26,0,15925,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749320	21990	PASS	TTTA	T	15965	0.997808	0	0,35,10,15920	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749320	23063	PASS	A	T	321	0.679128	0	0,2,0,307	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749320	23271	PASS	C	A	27946	0.925893	0	2,0,27911,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749320	23403	PASS	A	G	27940	0.973049	0	0,7,0,27912	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749320	23604	PASS	C	A	18646	0.955755	0	9,0,18628,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749320	23709	PASS	C	T	18630	0.943371	0	0,6,1,18603	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749320	23817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	35365	9.05E-4	17	16695,18614,10,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTt/cCt	L752P	S	0.000646	0.066832	1	1	T>C
ERR5749320	24237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13109	0.001678	0	13076,0,23,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gTt	A892V	S	0.001242	0.889739	1	1	C>T
ERR5749320	24320	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	13098	7.63E-4	0	0,13063,0,10	HIGH	NONE	FRAME_SHIFT	S	aaa/	K921	S	0.000763	0.138365	4	2	CAA>C
ERR5749320	24506	PASS	T	G	20463	0.974197	0	11,0,20446,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749320	24914	PASS	G	C	49766	0.957983	0	0,1,24804,24912	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749320	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	32189	0.002485	111	22797,9298,87,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749320	25624	PASS	C	T	36194	0.983312	0	2,3,13092,23092	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Cac/Tac	H78Y	orf3a	0.00089	0.983312	1	1	C>T
ERR5749320	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	13134	0.001599	327	13077,17,8,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749320	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	50666	2.76E-4	0	4,50648,0,14	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749320	26526	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	13692	0.002775	0	0,13630,0,50	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Gca/Tca	A2S	M	0.001224	0.951192	3	1	G>T
ERR5749320	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	15372	0.001236	0	2,15351,0,19	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749320	27078	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	37323	8.04E-4	0	9,37261,0,31	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Cgt/Tgt	R186C	M	0.000415	0.05783	2	2	C>T
ERR5749320	27972	PASS	C	T	12085	0.912122	19	1,1,11984,65	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749320	28010	PASS	T	C	12002	0.933761	0	0,2,2,11987	LOW	SILENT	SYNONYMOUS_CODING	ORF8	atT/atC	I39	orf8	0.933761	0.934801	1	1	T>C
ERR5749320	28048	PASS	G	T	12015	0.913358	0	0,17,0,11992	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749320	28111	PASS	A	G	36843	0.980566	2	10,3,24804,12014	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749320	28249	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	24819	4.43E-4	0	24802,8,11,0	HIGH	NONE	FRAME_SHIFT	ORF8	ttc/	F120	orf8	0.000443	0.063605	3	2	AT>A
ERR5749320	28270	PASS	TA	T	48223	0.995977	453	192,7,24566,23463	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749320	28280	PASS	G	C	48153	0.935352	21	15,3,24605,23431	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749320	28281	PASS	A	T	48153	0.917098	6	22,14,24606,23438	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749320	28282	PASS	T	A	48154	0.909353	4	23,16,24584,23450	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749320	28881	PASS	G	A	19514	0.791124	2	3,1,9712,9597	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749320	28882	PASS	G	A	19514	0.840525	6	3,0,9775,9578	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749320	28883	PASS	G	C	19514	0.94527	0	1,0,9779,9712	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749320	28977	PASS	C	T	9893	0.930153	0	0,1,1,9870	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749320	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	48584	0.002079	671	38666,9776,4,106	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749320	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	76901	0.001131	0	38588,38171,56,54	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749320	29284	PASS	C	T	38690	0.921194	0	0,11,6,38661	LOW	SILENT	SYNONYMOUS_CODING	N	atC/atT	I337	N	0.000393	0.931014	3	2	C>T
ERR5749320	29543	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	22691	0.001058	0	10973,11651,32,34	.	.	.	.	.	.	.	0.001058	0.973475	3	1	G>T
ERR5749321	241	PASS	C	T	201	0.870647	0	0,0,100,98	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749321	323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	102	0.039216	0	0,98,0,4	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L21	leader	0.039216	0.118012	2	1	GT>G
ERR5749321	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	849	0.011779	0	839,0,10,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749321	892	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	1927	0.011936	0	0,1894,0,26	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G29	nsp2	0.000495	0.082222	2	2	T>C
ERR5749321	913	PASS	C	T	1928	0.904046	0	0,1,0,1923	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749321	932	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	1930	0.03057	0	0,1867,0,63	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gac/Tac	D43Y	nsp2	0.00048	0.184416	2	2	G>T
ERR5749321	1813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	4611	0.002386	0	0,4600,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K338	nsp2	0.001022	0.152738	4	2	TA>T
ERR5749321	3037	PASS	C	T	2476	0.796446	6	0,2,1240,1205	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749321	3267	PASS	C	T	1523	0.966513	2147483647	0,0,1523,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749321	3671	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	3810	0.009186	0	1888,1868,21,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E318K	nsp3	0.000351	0.0625	6	2	G>A
ERR5749321	5388	PASS	C	A	525	0.942857	2147483647	0,0,524,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749321	5986	PASS	C	T	2579	0.976347	2147483647	0,0,2576,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749321	6954	PASS	T	C	3144	0.825382	2147483647	0,0,0,3124	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749321	7735	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4028	0.013654	0	3966,0,59,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I1672	nsp3	0.000658	0.954659	3	2	C>T
ERR5749321	7834	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8002	0.006123	0	3949,3968,28,29	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N1705	nsp3	0.000523	0.86555	3	2	C>T
ERR5749321	11287	PASS	GTCTGGTTTT	G	8325	0.998799	0	0,10,0,8315	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749321	11747	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3335	0.015292	0	3265,3,61,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L259	nsp6	0.001145	0.737282	1	1	C>T
ERR5749321	12020	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	11882	0.005975	0	11812,0,71,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S61	nsp7	0.000994	0.968243	3	2	CT>C
ERR5749321	13059	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8017	0.00212	175	7283,713,1,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T12I	nsp10	0.000448	0.855104	3	2	C>T
ERR5749321	13176	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7281	0.007279	0	7218,0,58,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T51I	nsp10	0.002004	0.919962	2	1	C>T
ERR5749321	14120	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6109	0.017024	0	2987,2983,67,66	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCa/cTa	P227L	RdRp	0.00121	0.786944	2	2	C>T
ERR5749321	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	2449	0.006125	671	2354,51,0,44	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749321	14408	PASS	C	T	4682	0.876121	0	0,0,2340,2322	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749321	14676	PASS	C	T	1157	0.792567	2147483647	0,0,1154,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749321	15279	PASS	C	T	1975	0.901772	2147483647	0,0,1973,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749321	15924	PASS	C	T	1352	0.970414	2147483647	0,0,1352,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y828	RdRp	0.001719	0.970414	1	1	C>T
ERR5749321	16176	PASS	T	C	1847	0.978343	0	0,0,494,1351	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749321	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	4341	0.001382	0	4335,0,6,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749321	17124	PASS	T	C	5298	0.98339	0	0,0,957,4340	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcC	A296	helicase	0.000471	0.985672	2	2	T>C
ERR5749321	17135	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	960	0.010417	0	948,2,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tct/	S301	helicase	0.010417	0.96005	2	2	CT>C
ERR5749321	17615	PASS	A	G	4440	0.911487	2147483647	0,0,0,4427	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749321	18032	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3790	0.005805	70	1795,1973,22,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T599I	helicase	0.000604	0.973948	2	2	C>T
ERR5749321	19079	PASS	A	G	2489	0.957011	0	1,0,2486,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gAa/gGa	E347G	ExoN	0.001121	0.967175	2	1	A>G
ERR5749321	19164	PASS	C	T	2492	0.051364	0	0,2346,0,142	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D375	ExoN	0.000358	0.075732	4	2	C>T
ERR5749321	19854	PASS	C	T	2174	0.950322	2147483647	0,0,0,2172	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D78	endoR	0.950322	0.965654	1	1	C>T
ERR5749321	20178	PASS	C	T	300	0.853333	24	1,0,0,299	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V186	endoR	0.000533	0.867727	2	2	C>T
ERR5749321	21145	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9595	0.005524	240	5525,3995,0,64	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Ttt	L163F	MethTr	0.001379	0.921396	3	2	C>T
ERR5749321	21621	PASS	C	T	2024	0.911067	2147483647	0,0,0,2021	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCc/aTc	T20I	S	0.00148	0.944623	2	2	C>T
ERR5749321	21733	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	4096	0.014648	0	4032,2,60,0	LOW	SILENT	SYNONYMOUS_CODING	S	ccT/ccC	P57	S	0.001662	0.065814	2	1	T>C
ERR5749321	21764	PASS	ATACATG	A	4094	0.99829	0	7,0,4087,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749321	21990	PASS	TTTA	T	4095	0.999267	0	0,3,1,4091	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749321	22323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8417	0.00594	135	3903,4462,0,50	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCt/tTt	S254F	S	0.000812	0.978946	3	2	C>T
ERR5749321	23063	PASS	A	T	4172	0.88303	2147483647	0,0,0,4154	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749321	23271	PASS	C	A	2517	0.924513	2147483647	0,0,2516,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749321	23323	PASS	T	C	4977	0.948563	0	0,0,2508,2466	LOW	SILENT	SYNONYMOUS_CODING	S	atT/atC	I587	S	0.000758	0.951252	2	2	T>C
ERR5749321	23403	PASS	A	G	2517	0.965832	2147483647	0,0,0,2515	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749321	23604	PASS	C	A	3366	0.937908	2147483647	0,0,3362,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749321	23709	PASS	C	T	3362	0.930696	2147483647	0,0,0,3355	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749321	24444	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3931	0.004325	0	3910,2,17,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCg/aTg	T961M	S	0.000832	0.063732	2	2	C>T
ERR5749321	24506	PASS	T	G	3929	0.976839	2147483647	0,0,3929,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749321	24914	PASS	G	C	22138	0.959617	0	0,0,11033,11088	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749321	25276	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	1016	0.005906	0	0,1010,0,6	HIGH	NONE	FRAME_SHIFT	S	agt/	S1239	S	0.005906	0.9348	2	2	CAG>C
ERR5749321	25660	PASS	G	T	304	0.828947	171	0,10,293,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gtt/Ttt	V90F	orf3a	0.000716	0.91928	2	2	G>T
ERR5749321	27371	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	9008	0.008881	0	0,8928,0,80	HIGH	NONE	FRAME_SHIFT	ORF6	atg/	M58	orf6	0.00148	0.066731	2	2	CA>C
ERR5749321	27493	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	G	15057	0.003188	199	5980,9024,50,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Cct/Gct	P34A	orf7a	0.000794	0.971493	2	1	C>G
ERR5749321	27625	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6030	0.012438	0	5906,0,77,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Cgt/Tgt	R78C	orf7a	0.00584	0.951914	1	1	C>T
ERR5749321	27972	PASS	C	T	1355	0.892989	0	0,0,1333,16	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749321	28048	PASS	G	T	1339	0.909634	0	0,1,0,1337	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749321	28078	PASS	T	C	1342	0.974665	2147483647	0,0,0,1342	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	gTg/gCg	V62A	orf8	0.974665	0.977397	1	1	T>C
ERR5749321	28087	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	1344	0.005208	0	2,1335,0,7	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	gCt/gAt	A65D	orf8	0.001718	0.963754	2	1	C>A
ERR5749321	28111	PASS	A	G	11101	0.980362	0	1,0,9749,1343	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749321	28147	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9759	0.010964	0	9638,1,111,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	cCt/cTt	P85L	orf8	0.000438	0.981624	4	2	C>T
ERR5749321	28270	PASS	TA	T	18860	0.995811	225	79,0,9639,9142	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749321	28280	PASS	G	C	18823	0.939542	4	4,1,9653,9130	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749321	28281	PASS	A	T	18823	0.914626	10	10,3,9655,9133	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749321	28282	PASS	T	A	18823	0.909844	1	6,4,9633,9139	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749321	28456	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	10260	0.010624	0	10145,2,110,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aaG/aaC	K61N	N	0.001535	0.070307	3	2	G>C
ERR5749321	28657	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10254	0.004779	0	0,10185,0,62	LOW	SILENT	SYNONYMOUS_CODING	N	gaC/gaT	D128	N	0.00124	0.862766	1	1	C>T
ERR5749321	28881	PASS	G	A	799	0.787234	0	1,0,394,393	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749321	28882	PASS	G	A	798	0.804511	0	1,0,399,389	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749321	28883	PASS	G	C	798	0.93609	0	0,0,400,398	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749321	28977	PASS	C	T	406	0.906404	2147483647	0,0,0,406	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749321	29272	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1709	0.004681	0	0,1699,0,9	LOW	SILENT	SYNONYMOUS_CODING	N	taC/taT	Y333	N	0.001709	0.892106	1	1	C>T
ERR5749321	29370	PASS	C	T	1586	0.893443	2147483647	0,0,1584,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aCa/aTa	T366I	N	0.007888	0.893443	2	2	C>T
ERR5749321	29746	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	2095	0.004773	0	0,2080,0,10	.	.	.	.	.	.	.	0.004773	0.242549	2	1	A>G
ERR5749322	174	PASS	G	T	10184	0.740672	0	86,0,10080,0	.	.	.	.	.	.	.	0.710959	0.747093	1	1	G>T
ERR5749322	210	PASS	G	T	10303	0.784917	9	93,3,10065,129	.	.	.	.	.	.	.	0.001452	1	2	1	G>T
ERR5749322	241	PASS	C	T	20265	0.866716	5	4,9,10074,10090	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749322	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	12712	0.002989	0	12675,0,38,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749322	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	12712	6.29E-4	0	12619,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749322	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	12712	0.0059	0	12619,0,75,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749322	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12700	0.002835	0	11618,2,926,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749322	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	12700	0.002283	0	12669,2,29,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749322	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	12698	0.001024	0	12673,2,13,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749322	521	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	12708	6.3E-4	0	12688,13,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/	V86	leader	0.00063	0.731722	2	2	GT>G
ERR5749322	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	32503	8.0E-4	53	19745,12731,26,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749322	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	32503	0.001323	3	19725,12713,29,14	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749322	913	PASS	C	T	19762	0.92268	0	0,12,0,19731	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749322	2160	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAG	A	22730	5.72E-4	0	0,22717,0,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	gagaag/	EK453	nsp2	0.000572	0.089776	3	2	AAG>A
ERR5749322	2453	PASS	C	T	12004	0.735005	0	0,8,0,11857	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L550F	nsp2	0.00429	0.842201	2	2	C>T
ERR5749322	3037	PASS	C	T	19161	0.819425	42	0,14,9558,9461	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749322	3096	PASS	C	T	9631	0.932094	0	0,1,0,9623	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCa/tTa	S126L	nsp3	0.001801	0.932094	1	1	C>T
ERR5749322	3267	PASS	C	T	19802	0.970862	2147483647	0,0,19793,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749322	3832	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	13646	8.06E-4	0	13635,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L373	nsp3	0.000689	0.327273	4	2	CT>C
ERR5749322	4276	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20587	0.00102	0	0,20554,0,24	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y519	nsp3	0.00102	0.812261	1	1	C>T
ERR5749322	4693	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	18356	6.54E-4	0	18344,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/	V659	nsp3	0.000654	0.078873	1	1	TG>T
ERR5749322	4861	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAA	T	18334	7.09E-4	0	5,18307,0,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaaagt/	KS715	nsp3	0.000632	0.115789	2	1	TAA>T
ERR5749322	5388	PASS	C	A	5529	0.959486	2147483647	0,0,5528,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749322	5497	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	5526	0.001448	0	0,5518,0,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	aga/	R928	nsp3	0.000964	0.897745	3	2	CA>C
ERR5749322	5986	PASS	C	T	8450	0.975503	0	1,0,8443,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749322	6274	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	21188	7.55E-4	0	21172,0,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1186	nsp3	0.000755	0.990148	2	2	TA>T
ERR5749322	6954	PASS	T	C	15771	0.819732	0	0,2,0,15690	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749322	7067	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	29960	0.002603	255	14054,15828,78,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gaa/	E1450	nsp3	0.000274	0.059217	5	3	GA>G
ERR5749322	7239	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	28191	5.68E-4	0	14084,14098,8,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	gag/	E1508	nsp3	0.000568	0.901952	2	2	CAG>C
ERR5749322	7564	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	13576	0.001547	0	0,13555,0,21	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/	Y1617	nsp3	0.000586	0.056194	4	2	CT>C
ERR5749322	8084	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	20431	0.001322	0	20395,0,27,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1790	nsp3	0.000543	0.923413	4	2	GA>G
ERR5749322	8092	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	20427	5.39E-4	0	20417,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T1793	nsp3	0.000539	0.063953	3	2	CA>C
ERR5749322	8964	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	14539	0.002132	0	14506,2,31,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K138	nsp4	0.000553	0.981649	4	2	CA>C
ERR5749322	9391	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAT	C	29167	4.8E-4	0	14606,14549,7,7	HIGH	NONE	FRAME_SHIFT	ORF1ab	atatca/	IS280	nsp4	0.00048	0.805102	2	2	CAT>C
ERR5749322	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	33534	5.07E-4	41	18889,14627,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749322	10323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	19393	0.001134	0	0,19333,0,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749322	10595	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	15229	0.001313	0	3,15185,0,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F181L	3Cpro	0.000964	0.076408	1	1	T>C
ERR5749322	11073	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TCTTTTTTTTGTATGAAAATGCCTTTTTAC	T	21185	5.19E-4	0	21166,8,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tttttgtatgaaaatgcctttttacctttt/	FLYENAFLPF36	nsp6	0.000385	0.092251	6	2	TCTTTTTTTTGTATGAAAATGCCTTTTTAC>T
ERR5749322	11287	PASS	GTCTGGTTTT	G	21164	0.997118	76	3,56,0,21103	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749322	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	32292	0.001022	3	20359,11881,24,10	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749322	11782	PASS	A	G	20333	0.917917	0	0,1,8,20263	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaA/aaG	K270	nsp6	0.001073	0.917917	2	2	A>G
ERR5749322	12125	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	23283	0.002276	0	4,23173,0,61	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y12H	nsp8	0.000847	0.113436	1	1	T>C
ERR5749322	12269	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	23425	4.7E-4	0	23401,1,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aag/	K61	nsp8	0.000434	0.213333	2	1	GA>G
ERR5749322	12269	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAA	G	23425	5.12E-4	0	23401,1,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aag/	K61	nsp8	0.000434	0.213333	2	1	GAA>G
ERR5749322	12357	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23428	0.001152	0	0,23380,0,28	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T89I	nsp8	0.000909	0.956941	3	2	C>T
ERR5749322	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	15640	8.95E-4	0	15625,1,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749322	13378	PASS	C	T	13389	0.968482	367	1,11,13372,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acC/acT	T118	nsp10	0.002094	0.968482	1	1	C>T
ERR5749322	13994	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	14442	9.69E-4	0	14426,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L186	RdRp	0.000427	0.114441	3	2	CT>C
ERR5749322	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	19263	0.003945	2147483647	18805,188,7,252	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749322	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	37475	5.87E-4	0	18786,18696,11,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749322	14408	PASS	C	T	37475	0.846805	1	5,6,18705,18534	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749322	14676	PASS	C	T	11855	0.80911	0	5,0,11824,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749322	15026	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAT	C	17816	8.42E-4	0	17802,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tataca/	YT530	RdRp	0.000503	0.869455	2	2	CAT>C
ERR5749322	15279	PASS	C	T	18491	0.882754	0	6,0,18454,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749322	15905	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AG	A	10174	0.001278	0	10158,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggt/	G823	RdRp	0.000835	0.057692	2	1	AG>A
ERR5749322	16176	PASS	T	C	20549	0.982627	0	0,0,10362,10168	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749322	16794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	46936	7.88E-4	57	24080,22787,6,35	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	cgT/cgC	R186	helicase	0.000354	0.077626	2	2	T>C
ERR5749322	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	24102	0.001992	0	24051,0,48,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749322	17756	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	12711	8.65E-4	0	12698,2,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K508	helicase	0.000865	0.165644	4	2	GA>G
ERR5749322	18647	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTG	C	53009	2.83E-4	45	26282,26712,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctgag/	PE203	ExoN	0.000283	0.970507	4	2	CTG>C
ERR5749322	18658	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	26303	0.001026	0	26269,6,27,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tgt/	C207	ExoN	0.000507	0.115741	3	2	TG>T
ERR5749322	19343	PASS	C	T	12863	0.192257	0	10137,0,2692,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A435V	ExoN	0.000519	0.192257	7	2	C>T
ERR5749322	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16884	0.001777	0	16844,0,31,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749322	20178	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCAA	C	16887	5.33E-4	0	2,16876,0,9	MODERATE	NONE	CODON_DELETION	ORF1ab	caa/	Q188	endoR	0.000533	0.867727	2	2	CCAA>C
ERR5749322	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16070	0.001307	0	16030,0,22,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749322	21077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	22353	4.92E-4	0	6,22334,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K141	MethTr	0.000492	0.955529	4	2	CAA>C
ERR5749322	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22774	0.001712	1	11132,11340,21,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749322	21764	PASS	ATACATG	A	12174	0.996386	0	44,0,12130,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749322	21990	PASS	TTTA	T	12176	0.997947	0	0,25,2,12149	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749322	21991	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTA	T	12179	8.21E-4	0	5,12162,0,10	HIGH	NONE	FRAME_SHIFT	S	tat/	Y144	S	0.00078	0.991378	2	1	TTA>T
ERR5749322	22030	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	17792	5.62E-4	0	17778,4,10,0	HIGH	NONE	FRAME_SHIFT	S	ttc/	F157	S	0.000562	0.115047	2	2	GT>G
ERR5749322	22227	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	17783	0.001125	0	0,17763,0,20	HIGH	NONE	FRAME_SHIFT	S	tta/	L223	S	0.000419	0.824305	2	2	CT>C
ERR5749322	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29406	0.001326	12	14495,14842,26,14	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749322	23063	PASS	A	T	14518	0.878082	0	0,2,6,14438	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749322	23271	PASS	C	A	24419	0.923297	0	4,0,24390,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749322	23403	PASS	A	G	24413	0.971204	0	0,4,0,24376	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749322	23604	PASS	C	A	14590	0.943043	0	20,0,14564,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749322	23709	PASS	C	T	14573	0.950662	0	0,2,0,14549	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749322	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	25181	8.74E-4	17	10574,14585,15,7	HIGH	NONE	FRAME_SHIFT	S	ttg/	L753	S	0.000334	0.080808	2	2	CT>C
ERR5749322	24127	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAACGGCCTTACTG	T	23361	5.56E-4	33	12776,10585,13,0	HIGH	NONE	FRAME_SHIFT	S	aacggccttactgtt/	NGLTV856	S	0.000324	0.111888	4	1	TAACGGCCTTACTG>T
ERR5749322	24320	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	12770	0.002114	0	0,12740,0,27	HIGH	NONE	FRAME_SHIFT	S	aaa/	K921	S	0.000763	0.138365	4	2	CA>C
ERR5749322	24506	PASS	T	G	17206	0.977915	0	3,0,17200,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749322	24899	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	43708	4.58E-4	0	21861,21830,10,10	HIGH	NONE	FRAME_SHIFT	S	atc/	I1114	S	0.000315	0.09021	5	3	CA>C
ERR5749322	24914	PASS	G	C	43561	0.961663	0	0,0,21698,21819	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749322	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	12094	0.002481	559	12013,26,7,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749322	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	12049	7.47E-4	0	12040,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749322	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	48006	3.12E-4	0	0,47991,0,15	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749322	26270	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	58692	6.64E-4	3	10592,48031,10,34	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	aCa/aTa	T9I	E	0.000586	0.930791	3	2	C>T
ERR5749322	26526	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	10606	0.001509	0	2,10568,0,29	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Gca/Tca	A2S	M	0.001224	0.951192	3	1	G>T
ERR5749322	26710	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTTG	C	15410	6.49E-4	0	15271,135,10,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtttt/ttt	CF64F	M	0.000649	0.102857	1	1	CTTG>C
ERR5749322	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	G	15328	6.52E-4	0	7,15307,0,10	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/	ACLVGLMWLSYFIASF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT>G
ERR5749322	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGT	G	15328	7.18E-4	0	7,15295,0,11	HIGH	NONE	FRAME_SHIFT	M	cttgta/	LV87	M	0.000483	0.053997	3	1	GCTTGT>G
ERR5749322	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	15328	9.79E-4	0	7,15295,0,15	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749322	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	15327	0.00261	0	5,15276,0,40	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749322	27402	PASS	T	G	24393	0.905711	0	0,57,18,24315	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	atT/atG	I3M	orf7a	0.000551	0.905711	3	3	T>G
ERR5749322	27403	PASS	A	T	24393	0.916	0	0,13,18,24319	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Att/Ttt	I4F	orf7a	0.000512	0.916	3	2	A>T
ERR5749322	27534	PASS	T	A	15	0.933333	11	1,0,0,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	caT/caA	H47Q	orf7a	0.002615	0.933333	2	2	T>A
ERR5749322	27972	PASS	C	T	10626	0.90448	32	3,2,10495,83	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749322	28048	PASS	G	T	10548	0.927569	0	0,11,7,10525	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749322	28111	PASS	A	G	32349	0.979598	0	5,2,21791,10538	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749322	28250	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TCTG	21791	0.002432	0	21737,1,53,0	MODERATE	NONE	CODON_INSERTION	ORF8	ttc/CTGttc	F120LF	orf8	0.000494	0.993968	5	3	T>TCTG
ERR5749322	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21793	0.001744	0	21699,6,40,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749322	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	21787	0.002479	0	21733,6,54,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749322	28270	PASS	TA	T	42370	0.994996	478	208,9,21518,20640	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749322	28280	PASS	G	C	42293	0.938311	11	9,2,21563,20623	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749322	28281	PASS	A	T	42293	0.919679	32	26,6,21552,20621	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749322	28282	PASS	T	A	42294	0.914669	51	43,10,21503,20640	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749322	28651	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	25347	5.13E-4	0	0,25334,0,13	HIGH	NONE	FRAME_SHIFT	N	aaa/	K127	N	0.000502	0.918117	3	2	CA>C
ERR5749322	28881	PASS	G	A	19824	0.742887	22	10,1,9711,9761	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749322	28882	PASS	G	A	19821	0.829373	15	6,0,9882,9736	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749322	28883	PASS	G	C	19823	0.941583	12	0,4,9908,9886	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749322	28977	PASS	C	T	10094	0.934912	0	0,2,0,10072	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749322	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	67861	0.001135	0	34041,33659,48,45	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749322	29311	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	34174	5.27E-4	0	13,34143,0,18	HIGH	NONE	FRAME_SHIFT	N	aaa/	K347	N	0.000335	0.790798	3	2	CA>C
ERR5749322	29774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11223	0.003119	0	0,11177,0,35	.	.	.	.	.	.	.	0.002525	0.973955	1	1	C>T
ERR5749323	241	PASS	C	T	10477	0.870478	3	0,2,5221,5228	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749323	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	13062	0.001225	0	13050,1,16,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749323	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	13062	7.66E-4	0	13010,1,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749323	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	13062	0.00268	0	13010,1,35,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749323	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	13054	0.002528	0	11947,2,1017,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749323	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	13054	0.002145	0	13024,2,28,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749323	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	33116	9.06E-4	14	19999,13077,24,6	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749323	913	PASS	C	T	20020	0.92013	0	0,11,0,19993	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749323	1510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	18636	0.003488	0	1,18394,0,75	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G235	nsp2	0.002159	0.937304	1	1	T>C
ERR5749323	3037	PASS	C	T	19101	0.830794	30	0,10,9540,9413	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749323	3267	PASS	C	T	19621	0.973498	0	3,0,19613,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749323	5388	PASS	C	A	5742	0.956461	2147483647	0,0,5735,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749323	5986	PASS	C	T	12190	0.97539	0	0,0,12182,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749323	6944	PASS	A	G	16110	0.185475	3	1,11487,1,4446	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ata/Gta	I1409V	nsp3	0.185475	0.185475	1	1	A>G
ERR5749323	6954	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	7	0.857143	2147483647	0,0,0,7	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749323	7105	PASS	C	T	17522	0.948807	217	1,6,17505,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acC/acT	T1462	nsp3	0.948807	0.948807	1	1	C>T
ERR5749323	8603	PASS	T	C	11810	0.969094	201	6,2,0,11792	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Ctc	F17L	nsp4	0.002607	0.974959	2	1	T>C
ERR5749323	8964	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	16344	6.12E-4	0	16331,3,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K138	nsp4	0.000553	0.981649	4	2	CA>C
ERR5749323	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	19587	0.002604	0	19506,0,66,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749323	11287	PASS	GTCTGGTTTT	G	19586	0.997243	51	2,52,0,19532	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749323	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	32248	0.00155	0	16097,16053,26,27	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749323	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	9903	0.003534	2739	9677,74,0,149	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749323	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	19266	9.86E-4	0	9662,9596,10,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749323	14408	PASS	C	T	19266	0.839718	15	0,5,9621,9505	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749323	14676	PASS	C	T	13032	0.80686	0	6,0,12982,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749323	15279	PASS	C	T	21282	0.884738	0	3,0,21247,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749323	15379	PASS	A	G	42424	0.947742	0	3,3,21193,21152	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Agc/Ggc	S647G	RdRp	0.000745	0.947742	2	2	A>G
ERR5749323	16176	PASS	T	C	20240	0.98083	3	0,2,10008,10217	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749323	17615	PASS	A	G	14965	0.910458	0	0,2,3,14915	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749323	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	25376	0.001182	0	25345,0,30,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749323	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	24187	4.13E-4	0	1,24176,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749323	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28373	0.002044	0	28291,0,59,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749323	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	31043	7.41E-4	0	15488,15535,11,12	HIGH	NONE	FRAME_SHIFT	S	ctt/Tctt	L5S?	S	0.000394	0.091869	4	1	G>GT
ERR5749323	21764	PASS	ATACATG	A	12179	0.99844	0	19,0,12160,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749323	21990	PASS	TTTA	T	12183	0.194041	21	0,9819,3,2361	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749323	21995	PASS	TACC	T	12181	0.803054	21	3,2396,0,9782	MODERATE	NONE	CODON_DELETION	S	cac/	H146	S	0.803054	0.803054	1	1	TACC>T
ERR5749323	21998	PASS	C	T	33618	0.657088	42	5,7,21423,2377	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Cac/Tac	H146Y	S	0.002747	0.657088	1	1	C>T
ERR5749323	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	14772	0.002099	0	0,14728,0,31	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749323	23063	PASS	A	T	14419	0.869755	0	0,3,0,14359	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749323	23271	PASS	C	A	20640	0.912258	0	3,0,20617,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749323	23403	PASS	A	G	20636	0.969325	0	0,3,0,20623	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749323	23604	PASS	C	A	15408	0.931789	0	10,0,15384,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749323	23709	PASS	C	T	15381	0.942006	0	0,7,2,15350	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749323	24506	PASS	T	G	17570	0.974445	0	5,0,17565,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749323	24914	PASS	G	C	38392	0.959705	0	0,0,19133,19235	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749323	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	25665	0.003	115	17473,8091,87,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749323	25437	PASS	G	T	17786	0.969189	0	5,0,17749,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	ttG/ttT	L15F	orf3a	0.001128	0.971411	2	2	G>T
ERR5749323	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	19101	0.001623	343	19013,19,16,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749323	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	45624	3.51E-4	0	1,45606,0,16	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749323	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	12407	0.001773	0	0,12384,0,22	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749323	27972	PASS	C	T	10718	0.902127	39	2,2,10633,47	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749323	28048	PASS	G	T	10674	0.920929	0	0,13,0,10652	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749323	28111	PASS	A	G	28320	0.979237	15	8,0,17627,10679	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749323	28192	PASS	T	C	17634	0.980889	0	2,0,17616,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	gTg/gCg	V100A	orf8	0.001134	0.980889	2	1	T>C
ERR5749323	28270	PASS	TA	T	34200	0.994708	396	182,10,17397,16622	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749323	28271	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AA	A	34199	0.001082	67	17531,16629,34,3	.	.	.	.	.	.	.	0.000482	0.924941	3	2	AA>A
ERR5749323	28280	PASS	G	C	34134	0.939591	10	10,3,17439,16610	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749323	28281	PASS	A	T	34134	0.919054	41	26,4,17434,16617	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749323	28282	PASS	T	A	34136	0.911442	9	22,12,17417,16617	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749323	28881	PASS	G	A	17434	0.74957	36	12,0,8547,8588	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749323	28882	PASS	G	A	17433	0.829117	6	3,0,8706,8588	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749323	28883	PASS	G	C	17433	0.93868	0	0,0,8718,8704	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749323	28977	PASS	C	T	8883	0.935945	2147483647	0,0,0,8866	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749323	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	54064	9.99E-4	1	27155,26828,38,33	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749324	241	PASS	C	T	3230	0.863777	3	0,1,1608,1606	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749324	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	9580	8.35E-4	0	9569,0,8,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749324	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	9579	9.4E-4	0	9526,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749324	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	9579	0.001566	0	9526,0,15,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749324	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	9579	0.003027	0	9526,0,29,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749324	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	9570	0.002403	0	8754,0,728,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749324	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	9572	0.00188	0	9538,3,18,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttatg/gtg	VM84V	leader	0.000554	0.991848	4	1	GTTA>G
ERR5749324	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	9572	0.001463	0	9538,3,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749324	520	PASS	GGTT	G	9579	0.051154	3	9080,10,489,1	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttgag/gag	VE86E	leader	0.000583	0.051154	1	1	GGTT>G
ERR5749324	656	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	9595	0.003022	0	1,9559,0,31	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gct/Cct	A131P	leader	0.001202	0.131429	1	1	G>C
ERR5749324	657	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9595	0.001772	0	1,9565,0,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A131V	leader	0.001202	0.365979	3	1	C>T
ERR5749324	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	23605	0.001398	32	13980,9591,29,4	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749324	823	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13993	0.001215	0	13964,2,22,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V6	nsp2	0.001213	0.901722	1	1	C>T
ERR5749324	850	PASS	C	A	27925	0.076956	5	12816,12752,1151,1200	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggA	G15	nsp2	0.000947	0.076956	2	1	C>A
ERR5749324	913	PASS	C	T	13994	0.918251	0	0,3,0,13966	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749324	1191	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	13358	7.49E-4	0	0,13348,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N130	nsp2	0.000749	0.916048	3	2	CA>C
ERR5749324	3037	PASS	C	T	20425	0.81787	26	2,14,10209,10084	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749324	3096	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10276	0.002919	0	0,10234,0,31	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCa/tTa	S126L	nsp3	0.001801	0.932094	1	1	C>T
ERR5749324	3183	PASS	A	G	26213	0.985465	20	0,5,15922,10279	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gAa/gGa	E155G	nsp3	0.985465	0.985465	1	1	A>G
ERR5749324	3267	PASS	C	T	15927	0.970867	2147483647	0,0,15908,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749324	4331	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25839	0.0012	19	9843,15915,7,31	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L538	nsp3	0.000987	0.928955	1	1	C>T
ERR5749324	4423	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	9866	0.001419	0	9839,13,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K569	nsp3	0.00063	0.953796	2	2	CA>C
ERR5749324	5388	PASS	C	A	4221	0.963042	2147483647	0,0,4218,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749324	5575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4224	0.01018	0	2,4177,0,44	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y952	nsp3	0.01018	0.961493	1	1	C>T
ERR5749324	5724	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13521	0.001553	0	13485,0,23,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T1002I	nsp3	0.001553	0.866667	1	1	C>T
ERR5749324	5986	PASS	C	T	10310	0.975849	0	1,0,10301,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749324	6274	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	17808	0.001516	0	17781,0,27,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1186	nsp3	0.000755	0.990148	2	2	TA>T
ERR5749324	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9982	0.001903	0	0,9856,0,30	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749324	6936	PASS	C	T	31825	0.91447	18	0,7,15664,16001	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S1406F	nsp3	0.000553	0.91447	2	2	C>T
ERR5749324	6936	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	31814	0.001352	126	15730,16052,0,43	HIGH	NONE	FRAME_SHIFT+STOP_GAINED	ORF1ab	aaa/Taaa	K1407*?	nsp3	0.000553	0.91447	2	2	C>CT
ERR5749324	6954	PASS	T	C	16131	0.816316	0	0,2,0,16032	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749324	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	17937	0.001617	34	13503,4405,29,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749324	11073	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TCTTTTTTTTGTATGAAAATGC	T	20222	4.95E-4	0	20209,1,10,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	tttttgtatgaaaatgccttttta/tta	FLYENAFL36L	nsp6	0.000385	0.092251	6	2	TCTTTTTTTTGTATGAAAATGC>T
ERR5749324	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20222	0.001385	0	20154,1,30,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749324	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	20215	0.001682	0	20146,0,51,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749324	11104	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	20205	0.001534	0	20090,0,33,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccT/ccC	P44	nsp6	0.000866	0.675414	2	1	T>C
ERR5749324	11152	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20185	0.001437	0	20109,0,32,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V60	nsp6	0.000678	0.974465	2	2	C>T
ERR5749324	11220	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	20866	7.67E-4	44	18997,20148,0,16	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtc/	V84	nsp6	0.000767	0.057907	2	2	TG>T
ERR5749324	11287	PASS	GTCTGGTTTT	G	20203	0.997773	0	0,45,0,20158	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749324	11344	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29649	0.001315	6	9418,20187,9,32	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I124	nsp6	0.001229	0.964849	1	1	C>T
ERR5749324	11674	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17543	0.001197	0	17509,5,23,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y234	nsp6	0.00054	0.985782	3	2	C>T
ERR5749324	11956	PASS	C	T	18152	0.915271	0	2,0,18115,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D38	nsp7	0.00119	0.936616	1	1	C>T
ERR5749324	12459	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34325	0.002389	25	17233,17000,56,28	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T123I	nsp8	0.000658	0.986093	1	1	C>T
ERR5749324	13134	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	13562	9.59E-4	0	13549,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	atc/	I38	nsp10	0.000682	0.107576	2	2	CA>C
ERR5749324	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	13557	9.59E-4	0	13546,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749324	13384	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	13126	6.09E-4	0	13118,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggt/	G121	nsp10	0.000578	0.056161	3	3	CG>C
ERR5749324	13459	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTT	G	13124	9.14E-4	0	13098,0,12,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ttttta/tta	FL7L	nsp11	0.000691	0.060726	5	2	GTTT>G
ERR5749324	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26213	0.001144	0	13095,13063,17,17	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749324	14168	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	13194	7.58E-4	0	0,13183,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	atatta/	IL244	RdRp	0.000479	0.314961	1	1	CTA>C
ERR5749324	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	11991	0.004837	3086	11660,141,4,184	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749324	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	23176	0.00164	2	11632,11530,21,17	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749324	14408	PASS	C	T	23176	0.83375	4	13,8,11554,11373	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749324	14599	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTATTACTAGA	C	9838	9.15E-4	0	9827,2,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttactagataaa/	LLDK388	RdRp	0.000639	0.922766	3	2	CTATTACTAGA>C
ERR5749324	14676	PASS	C	T	9834	0.788896	0	2,0,9799,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749324	15240	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14704	0.001768	0	14650,18,26,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N600	RdRp	0.000934	0.931284	2	2	C>T
ERR5749324	15279	PASS	C	T	14686	0.878524	0	1,0,14650,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749324	15493	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	14689	0.001498	0	3,14645,0,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gcc/Ccc	A685P	RdRp	0.001408	0.076816	3	2	G>C
ERR5749324	15960	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8854	0.001581	0	8837,0,14,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A840	RdRp	0.001581	0.81574	1	1	C>T
ERR5749324	16176	PASS	T	C	15078	0.980899	7	2,0,6215,8857	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749324	16792	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CGT	C	36948	3.79E-4	27	17840,19094,1,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	gta/	V187	helicase	0.000335	0.072562	5	2	CGT>C
ERR5749324	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAA	G	17841	0.001233	0	17793,0,22,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GAA>G
ERR5749324	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	23974	0.001043	0	23949,0,25,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749324	18699	PASS	T	C	23974	0.98002	0	2,0,23967,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcC	A220	ExoN	0.001034	0.98002	1	1	T>C
ERR5749324	19096	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCA	G	16538	7.26E-4	0	16417,109,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cag/	Q354	ExoN	0.000726	0.105058	3	2	GCA>G
ERR5749324	19524	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14693	0.001293	0	0,14658,0,19	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ctC/ctT	L495	ExoN	0.000745	0.953697	2	2	C>T
ERR5749324	20148	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	14241	9.13E-4	0	0,14228,0,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N177	endoR	0.000513	0.969223	2	2	CA>C
ERR5749324	20445	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	23064	0.001041	0	14,23026,0,24	HIGH	NONE	FRAME_SHIFT	ORF1ab	aac/aaAc	N277K?	endoR	0.000518	0.059736	4	2	T>TA
ERR5749324	20719	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	17276	5.21E-4	0	0,17267,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctatta/	LL21	MethTr	0.000341	0.209091	2	2	CTA>C
ERR5749324	20844	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	35640	3.65E-4	35	18303,17324,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tataat/	YN63	MethTr	0.000293	0.905571	5	2	CTA>C
ERR5749324	20987	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	36479	3.29E-4	0	18252,18217,6,6	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L111	MethTr	0.000276	0.056129	4	2	CT>C
ERR5749324	21077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	18328	0.001582	0	8,18291,0,29	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K141	MethTr	0.000492	0.955529	4	2	CA>C
ERR5749324	21304	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	23524	5.1E-4	0	6,23506,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	cgc/	R216	MethTr	0.000411	0.605296	3	2	CG>C
ERR5749324	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23149	0.004449	0	11300,11515,57,58	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749324	21707	PASS	C	T	22948	0.072032	8	10469,10756,813,900	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Cat/Tat	H49Y	S	0.001048	0.072032	1	1	C>T
ERR5749324	21762	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTATACA	C	11286	0.002215	0	11261,0,25,0	MODERATE	NONE	CODON_DELETION	S	atacat/	IH68	S	0.001297	0.875707	2	2	CTATACA>C
ERR5749324	21764	PASS	ATACATG	A	11286	0.995215	0	49,0,11232,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749324	21812	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11285	0.001506	0	11254,0,17,0	LOW	SILENT	SYNONYMOUS_CODING	S	Cta/Tta	L84	S	0.001506	0.06449	1	1	C>T
ERR5749324	21990	PASS	TTTA	T	11292	0.997786	0	0,25,5,11262	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749324	22690	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	15552	0.001479	0	15297,4,27,0	LOW	SILENT	SYNONYMOUS_CODING	S	acT/acC	T376	S	0.000815	0.051311	2	1	T>C
ERR5749324	22759	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	15562	5.78E-4	0	0,15553,0,9	HIGH	NONE	FRAME_SHIFT	S	ttt/	F400	S	0.000578	0.12649	2	2	AT>A
ERR5749324	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	15575	0.001541	0	0,15539,0,25	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749324	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29194	0.001096	0	13599,15550,15,18	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749324	23063	PASS	A	T	13588	0.857521	0	0,3,0,13520	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749324	23170	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	30188	8.61E-4	41	16544,13617,24,2	HIGH	NONE	FRAME_SHIFT	S	aaa/	K537	S	0.000408	0.975449	3	2	CA>C
ERR5749324	23271	PASS	C	A	16558	0.925716	0	2,0,16532,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749324	23403	PASS	A	G	16554	0.965628	0	0,3,0,16520	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749324	23604	PASS	C	A	13611	0.945632	0	9,0,13598,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749324	23664	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27008	0.001074	0	13416,13535,15,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCa/gTa	A701V	S	0.000837	0.918	2	2	C>T
ERR5749324	23709	PASS	C	T	13600	0.940956	0	0,5,0,13568	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749324	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	23171	0.002072	23	9545,13578,10,38	HIGH	NONE	FRAME_SHIFT	S	ttg/	L753	S	0.000334	0.080808	2	2	CT>C
ERR5749324	23817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	23171	0.001856	31	9511,13560,30,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTt/cCt	L752P	S	0.000646	0.066832	1	1	T>C
ERR5749324	24320	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	10730	0.002796	0	0,10690,0,30	HIGH	NONE	FRAME_SHIFT	S	aaa/	K921	S	0.000763	0.138365	4	2	CA>C
ERR5749324	24320	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	10730	9.32E-4	0	0,10690,0,10	HIGH	NONE	FRAME_SHIFT	S	aaa/	K921	S	0.000763	0.138365	4	2	CAA>C
ERR5749324	24506	PASS	T	G	14878	0.975266	0	14,0,14863,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749324	24914	PASS	G	C	38470	0.960749	3	1,0,19168,19268	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749324	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	7960	0.003392	319	7903,19,12,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749324	25916	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	7929	0.001387	0	5,7913,0,11	HIGH	NONE	FRAME_SHIFT	ORF3a	aca/	T176	orf3a	0.001191	0.964713	2	2	CA>C
ERR5749324	26013	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	32741	8.86E-4	0	32693,0,29,0	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	ttC/ttT	F207	orf3a	0.000839	0.974528	1	1	C>T
ERR5749324	26270	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	41766	7.9E-4	9	9013,32683,4,34	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	aCa/aTa	T9I	E	0.000586	0.930791	3	2	C>T
ERR5749324	26333	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9020	0.002217	0	8988,0,20,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	aCa/aTa	T30I	E	0.00158	0.943221	1	1	C>T
ERR5749324	26681	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12334	0.001297	0	12250,62,16,0	LOW	SILENT	SYNONYMOUS_CODING	M	ttC/ttT	F53	M	0.001297	0.074505	1	1	C>T
ERR5749324	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	12271	6.52E-4	0	6,12262,0,8	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749324	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	12271	7.33E-4	0	1,12261,0,9	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749324	26895	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29363	8.85E-4	0	29318,1,30,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Cat/Tat	H125Y	M	0.000874	0.97046	1	1	C>T
ERR5749324	27389	PASS	C	T	18995	0.899553	0	0,8,36,18889	.	.	.	.	.	.	.	0.001157	0.899553	2	1	C>T
ERR5749324	27476	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	37938	8.96E-4	2	18916,18974,21,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	aCa/aTa	T28I	orf7a	0.000547	0.22827	4	2	C>T
ERR5749324	27577	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAATT	C	18941	8.98E-4	0	18923,0,17,0	HIGH	NONE	FRAME_SHIFT	ORF7a	caattt/	QF62	orf7a	0.000614	0.952205	4	2	CAATT>C
ERR5749324	27741	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	18933	8.98E-4	0	0,18899,0,17	HIGH	NONE	FRAME_SHIFT	ORF7a	aaaaga/	KR117	orf7a	0.000363	0.954278	3	2	CAA>C
ERR5749324	27972	PASS	C	T	9152	0.901115	0	0,0,9040,78	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749324	28048	PASS	G	T	9074	0.91911	0	0,5,0,9057	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749324	28111	PASS	A	G	25827	0.979401	8	1,3,16731,9081	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749324	28250	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TCTG	16731	8.37E-4	0	16717,1,14,0	MODERATE	NONE	CODON_INSERTION	ORF8	ttc/CTGttc	F120LF	orf8	0.000494	0.993968	5	3	T>TCTG
ERR5749324	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16729	0.001973	0	16641,2,36,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749324	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	16726	0.001256	0	16706,2,21,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749324	28270	PASS	TA	T	32363	0.995241	292	133,7,16537,15672	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749324	28270	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAA	T	32363	4.33E-4	46	133,7,7,7	.	.	.	.	.	.	.	0.000322	1	2	1	TAA>T
ERR5749324	28280	PASS	G	C	32297	0.925906	35	16,1,16564,15650	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749324	28281	PASS	A	T	32297	0.894448	34	23,4,16532,15664	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749324	28282	PASS	T	A	32298	0.869404	2	19,15,16434,15671	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749324	28603	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	39023	0.001076	0	19471,19320,25,24	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F110	N	0.000427	0.883357	2	2	C>T
ERR5749324	28651	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	19560	5.11E-4	0	1,19548,0,10	HIGH	NONE	FRAME_SHIFT	N	aaa/	K127	N	0.000502	0.918117	3	2	CA>C
ERR5749324	28881	PASS	G	A	12415	0.767217	0	0,0,6156,6105	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749324	28882	PASS	G	A	12415	0.824164	3	2,0,6206,6076	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749324	28883	PASS	G	C	12415	0.945147	3	0,1,6217,6185	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749324	28977	PASS	C	T	6313	0.930144	0	0,1,0,6293	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749324	29095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28111	0.00185	0	28040,6,53,0	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F274	N	0.000792	0.961279	2	2	C>T
ERR5749324	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	55785	0.001111	0	28010,27659,46,43	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749324	29311	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	28112	7.83E-4	0	9,28081,0,22	HIGH	NONE	FRAME_SHIFT	N	aaa/	K347	N	0.000335	0.790798	3	2	CA>C
ERR5749325	241	PASS	C	T	766	0.86423	0	0,0,380,383	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749325	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	3876	0.004902	0	3859,0,19,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749325	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	3876	0.002322	0	3849,0,9,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749325	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	3876	0.003612	0	3849,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749325	657	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3881	0.008245	0	3,3802,0,40	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A131V	leader	0.001202	0.365979	3	1	C>T
ERR5749325	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTAAAGTCATTT	C	23624	4.66E-4	6	19725,3880,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctaaagtcattt/	LKSF140	leader	0.000316	0.135802	3	2	CTAAAGTCATTT>C
ERR5749325	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	23624	0.002201	10	19693,3876,48,4	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749325	745	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19753	0.001671	0	19710,0,36,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N160	leader	0.001671	0.915927	1	1	C>T
ERR5749325	841	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	G	39429	9.89E-4	3	19697,19648,20,25	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggG	G12	nsp2	0.000771	0.932538	2	1	C>G
ERR5749325	913	PASS	C	T	19747	0.918418	0	0,3,0,19719	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749325	932	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAC	G	19752	0.001114	0	0,19730,0,22	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T44	nsp2	0.00048	0.184416	2	2	GAC>G
ERR5749325	1652	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATT	A	12302	0.001057	0	12288,4,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	att/	I283	nsp2	0.001057	0.98088	2	2	ATT>A
ERR5749325	1813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	12276	0.002444	0	0,12229,0,32	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcA	A336	nsp2	0.001022	0.152738	4	2	T>A
ERR5749325	2062	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22714	0.001277	0	22597,40,40,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A419	nsp2	0.001265	0.822961	2	1	C>T
ERR5749325	2185	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	22698	0.00141	0	2,22664,0,32	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L462S?	nsp2	0.000441	0.963529	4	3	G>GT
ERR5749325	2232	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29573	8.45E-4	4	6868,22657,9,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A476V	nsp2	0.000499	0.381237	2	2	C>T
ERR5749325	2453	PASS	C	T	6872	0.725116	0	0,5,0,6775	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L550F	nsp2	0.00429	0.842201	2	2	C>T
ERR5749325	2494	PASS	G	T	6875	0.950836	0	0,2,0,6868	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gaG/gaT	E563D	nsp2	0.002624	0.951457	2	2	G>T
ERR5749325	3037	PASS	C	T	7638	0.830977	15	0,5,3814,3769	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749325	3267	PASS	C	T	17556	0.971121	0	2,0,17547,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749325	3335	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	34899	0.001289	88	17449,17212,71,162	HIGH	NONSENSE	STOP_GAINED	ORF1ab	Gaa/Taa	E206*	nsp3	0.001289	0.891976	4	3	G>T
ERR5749325	4234	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	21208	9.9E-4	94	10604,10513,16,73	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gaC/gaA	D505E	nsp3	0.00099	0.714088	3	3	C>A
ERR5749325	4237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTA	T	21207	0.001132	0	10602,10581,12,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	ata/	I508	nsp3	0.000302	0.918634	2	2	TTA>T
ERR5749325	4578	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	12332	0.001297	0	0,12311,0,19	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cTt/cCt	L620P	nsp3	0.000519	0.082979	2	2	T>C
ERR5749325	5178	PASS	C	T	7727	0.88249	0	0,7,0,7635	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T820I	nsp3	0.00175	0.88249	2	1	C>T
ERR5749325	5388	PASS	C	A	1815	0.960882	2147483647	0,0,1814,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749325	5986	PASS	C	T	7068	0.974958	2147483647	0,0,7066,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749325	6310	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17302	0.001272	0	17260,0,22,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	agC/agT	S1197	nsp3	0.00099	0.94715	2	2	C>T
ERR5749325	6543	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6225	0.003052	0	6203,0,20,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T1275I	nsp3	0.001888	0.955595	1	1	C>T
ERR5749325	6954	PASS	T	C	13139	0.828374	0	0,1,0,13060	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749325	7945	PASS	C	T	15149	0.950558	246	7,1,0,15134	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y1742	nsp3	0.001244	0.950558	2	2	C>T
ERR5749325	8512	PASS	A	G	4940	0.8	2147483647	0,0,0,4906	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caA/caG	Q1931	nsp3	0.8	0.822278	1	1	A>G
ERR5749325	8669	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	6872	0.002183	0	6857,0,15,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F39L	nsp4	0.000973	0.22449	1	1	T>C
ERR5749325	8692	PASS	C	T	6872	0.976135	2147483647	0,0,6866,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y46	nsp4	0.967679	0.97884	1	1	C>T
ERR5749325	9198	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	13033	0.001074	0	0,13019,0,14	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F216	nsp4	0.000543	0.93476	4	2	CT>C
ERR5749325	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	8987	0.002225	16	7161,1806,20,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749325	10702	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13874	0.001225	0	425,13426,0,18	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D216	3Cpro	0.000396	0.098214	2	2	C>T
ERR5749325	11073	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	19383	0.001135	0	19345,0,24,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTc/tCc	F34S	nsp6	0.000385	0.092251	6	2	T>C
ERR5749325	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	19383	0.002631	0	18800,0,51,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749325	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	19376	0.001755	0	19315,0,55,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749325	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTATGAAAATGCCTTT	G	19375	0.001239	0	19352,0,24,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	tatgaaaatgccttttta/tta	YENAFL38L	nsp6	0.000477	0.901695	5	2	GTATGAAAATGCCTTT>G
ERR5749325	11152	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	19353	0.00124	0	19330,0,24,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K61	nsp6	0.000678	0.974465	2	2	CA>C
ERR5749325	11287	PASS	GTCTGGTTTT	G	19373	0.99778	0	0,43,0,19330	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749325	11511	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9592	0.001772	0	4791,4751,9,10	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T180I	nsp6	0.001772	0.119454	1	1	C>T
ERR5749325	11750	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	33077	0.001119	0	16828,16150,32,28	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L260F	nsp6	0.001019	0.70989	2	1	C>T
ERR5749325	12125	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	15336	0.001891	0	1,15270,0,32	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y12H	nsp8	0.000847	0.113436	1	1	T>C
ERR5749325	12269	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	8959	0.002009	0	8941,0,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aag/	K61	nsp8	0.000434	0.213333	2	1	GA>G
ERR5749325	12456	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	21277	0.001034	0	12296,8951,14,10	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cTt/cCt	L122P	nsp8	0.001034	0.090643	1	1	T>C
ERR5749325	12459	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21278	0.001269	85	12313,8935,1,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T123I	nsp8	0.000658	0.986093	1	1	C>T
ERR5749325	12741	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18085	0.001438	0	5762,12293,8,19	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T19I	nsp9	0.000486	0.962552	2	2	C>T
ERR5749325	13459	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTT	G	10893	0.002387	0	10852,13,26,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L8	nsp11	0.000691	0.060726	5	2	GTT>G
ERR5749325	14408	PASS	C	T	927	0.820928	0	0,0,461,457	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749325	14676	PASS	C	T	10089	0.789573	0	16,0,10052,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749325	14724	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10084	0.001388	0	10039,9,21,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F428	RdRp	0.000952	0.789267	3	2	C>T
ERR5749325	15279	PASS	C	T	10474	0.878938	2147483647	0,0,10465,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749325	15493	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	10477	0.001432	0	2,10457,0,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gcc/Ccc	A685P	RdRp	0.001408	0.076816	3	2	G>C
ERR5749325	15652	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAC	G	14245	9.13E-4	0	14233,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T739	RdRp	0.000691	0.935936	2	2	GAC>G
ERR5749325	16176	PASS	T	C	11672	0.977553	16	0,24,1867,9775	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749325	16468	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19744	0.002988	1	17814,1865,56,4	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ccc/Tcc	P78S	helicase	0.001077	0.977186	1	1	C>T
ERR5749325	16794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	29371	4.77E-4	28	11496,17861,0,14	HIGH	NONE	FRAME_SHIFT	ORF1ab	gta/	V187	helicase	0.000354	0.077626	2	2	TG>T
ERR5749325	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAA	G	11495	0.001392	0	11467,0,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GAA>G
ERR5749325	18501	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28837	8.67E-4	0	0,28735,0,29	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y154	ExoN	0.000336	0.857143	4	2	C>T
ERR5749325	18647	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	50278	7.56E-4	90	21332,28888,0,38	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P203L	ExoN	0.000283	0.970507	4	2	C>T
ERR5749325	18658	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	21348	5.62E-4	0	21323,13,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tgt/	C207	ExoN	0.000507	0.115741	3	2	TG>T
ERR5749325	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	21335	8.44E-4	0	21317,0,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749325	19011	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23011	0.001608	0	22960,0,39,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D324	ExoN	0.000408	0.975746	4	2	C>T
ERR5749325	19763	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25339	9.87E-4	0	12580,12634,14,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T48I	endoR	0.000987	0.809304	2	1	C>T
ERR5749325	20178	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCAA	C	7929	0.001766	0	2,7913,0,14	MODERATE	NONE	CODON_DELETION	ORF1ab	caa/	Q188	endoR	0.000533	0.867727	2	2	CCAA>C
ERR5749325	20420	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	20255	0.001481	0	65,20160,0,30	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F268	endoR	0.000383	0.069626	2	1	AT>A
ERR5749325	20445	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	20267	0.001826	0	49,20181,0,37	HIGH	NONE	FRAME_SHIFT	ORF1ab	aac/	N277	endoR	0.000518	0.059736	4	2	TA>T
ERR5749325	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22916	9.16E-4	0	22860,0,21,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749325	20825	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	42039	0.001237	139	19112,22863,0,53	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T56I	MethTr	0.001237	0.202489	2	1	C>T
ERR5749325	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAA	T	19111	0.001099	0	0,19060,0,21	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TAA>T
ERR5749325	21077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	19118	8.89E-4	0	4,19097,0,17	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K141	MethTr	0.000492	0.955529	4	2	CA>C
ERR5749325	21123	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	38661	0.001267	18	19527,19085,16,33	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F156	MethTr	0.000257	0.90982	5	2	GT>G
ERR5749325	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15987	0.001063	0	7831,7967,9,10	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749325	21658	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8046	0.001989	0	0,8023,0,17	LOW	SILENT	SYNONYMOUS_CODING	S	ttC/ttT	F32	S	0.001649	0.937508	2	2	C>T
ERR5749325	21733	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	9039	0.002876	0	8989,8,26,0	LOW	SILENT	SYNONYMOUS_CODING	S	ccT/ccC	P57	S	0.001662	0.065814	2	1	T>C
ERR5749325	21764	PASS	ATACATG	A	9031	0.997675	0	20,0,9010,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749325	21790	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	9031	0.001882	0	9004,0,17,0	LOW	SILENT	SYNONYMOUS_CODING	S	acT/acC	T76	S	0.001442	0.063712	3	2	T>C
ERR5749325	21990	PASS	TTTA	T	9035	0.997344	0	0,24,4,9007	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749325	22717	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	27242	9.18E-4	2	13565,13591,13,17	LOW	SILENT	SYNONYMOUS_CODING	S	acT/acC	T385	S	0.000395	0.918478	3	2	T>C
ERR5749325	22771	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AG	A	13674	7.31E-4	0	0,13664,0,10	HIGH	NONE	FRAME_SHIFT	S	ggt/	G404	S	0.000511	0.112051	3	3	AG>A
ERR5749325	22787	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	13674	0.001389	0	0,13655,0,19	HIGH	NONE	FRAME_SHIFT	S	atc/	I410	S	0.000599	0.053914	2	2	CA>C
ERR5749325	23063	PASS	A	T	9006	0.868421	0	0,1,0,8968	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749325	23249	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21806	0.001376	0	21708,0,33,0	HIGH	NONSENSE	STOP_GAINED	S	Caa/Taa	Q563*	S	0.001376	0.082558	1	1	C>T
ERR5749325	23271	PASS	C	A	21799	0.925593	0	2,0,21779,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749325	23323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	42190	7.58E-4	4	21698,20246,17,22	LOW	SILENT	SYNONYMOUS_CODING	S	atT/atC	I587	S	0.000758	0.951252	2	2	T>C
ERR5749325	23403	PASS	A	G	21792	0.970999	0	0,2,0,21778	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749325	23522	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGT	G	9184	0.001307	0	9171,1,12,0	HIGH	NONE	FRAME_SHIFT	S	gaacatgtcaacaactcatatgagtgtgacatacccattggtgcaggtata/	EHVNNSYECDIPIGAGI654	S	0.00053	0.959726	5	2	GAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGT>G
ERR5749325	23604	PASS	C	A	9182	0.944021	0	7,0,9167,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749325	23709	PASS	C	T	9182	0.944892	0	0,1,12,9158	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749325	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	14981	6.01E-4	7	5797,9175,1,8	HIGH	NONE	FRAME_SHIFT	S	ttg/	L753	S	0.000334	0.080808	2	2	CT>C
ERR5749325	23817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	14981	0.001335	16	5794,9157,3,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTt/cCt	L752P	S	0.000646	0.066832	1	1	T>C
ERR5749325	24010	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATTTATTGAAGATCTAC	A	5849	0.002052	0	58,5780,0,12	HIGH	NONE	FRAME_SHIFT	S	attgaagatctacttttc/	IEDLLF818	S	0.000455	0.926398	4	2	ATTTATTGAAGATCTAC>A
ERR5749325	24237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7751	0.001806	0	7731,0,15,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gTt	A892V	S	0.001242	0.889739	1	1	C>T
ERR5749325	24506	PASS	T	G	12314	0.972064	0	7,0,12305,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749325	24899	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	34959	3.43E-4	0	17470,17472,6,6	HIGH	NONE	FRAME_SHIFT	S	caaatc/	QI1113	S	0.000315	0.09021	5	3	CAA>C
ERR5749325	24914	PASS	G	C	34815	0.961798	0	1,2,17323,17464	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749325	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	23121	0.001384	40	16570,6502,44,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749325	25413	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16696	0.004552	0	16604,0,77,0	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	atC/atT	I7	orf3a	0.00145	0.968329	2	1	C>T
ERR5749325	25572	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16694	0.001557	0	0,16653,0,28	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	tcC/tcT	S60	orf3a	0.000543	0.959687	4	2	C>T
ERR5749325	25587	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	16695	5.99E-4	0	0,16685,0,10	HIGH	NONE	FRAME_SHIFT	ORF3a	aag/	K67	orf3a	0.000598	0.813206	6	2	CA>C
ERR5749325	25626	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19766	0.004503	1	3052,16610,17,83	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	caC/caT	H78	orf3a	0.000403	0.915633	3	2	C>T
ERR5749325	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	3119	0.009298	463	3064,22,4,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749325	26013	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21300	0.001174	0	21266,0,25,0	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	ttC/ttT	F207	orf3a	0.000839	0.974528	1	1	C>T
ERR5749325	26091	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAAT	C	21269	0.002022	0	21227,3,43,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF3a	aataaa/aaa	NK234K	orf3a	0.000569	0.128212	4	2	CAAT>C
ERR5749325	26159	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTAATCCAG	T	21266	5.64E-4	0	0,21254,0,12	HIGH	NONE	FRAME_SHIFT	ORF3a	ccagtaatg/	PVM258	orf3a	0.000311	0.053032	2	2	TTAATCCAG>T
ERR5749325	26256	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29470	0.001527	20	8163,21240,5,41	LOW	SILENT	SYNONYMOUS_CODING	E	ttC/ttT	F4	E	0.000748	0.969561	2	2	C>T
ERR5749325	26532	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	8170	0.001836	0	0,8152,0,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Tcc/Ccc	S4P	M	0.001836	0.05891	2	2	T>C
ERR5749325	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	9179	0.003486	0	0,9135,0,32	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749325	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTTT	G	9179	9.8E-4	0	0,9135,0,9	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgtttgcg/gcg	ACLVGLMWLSYFIASFRLFA85A	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTTT>G
ERR5749325	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	9183	0.003267	0	0,9153,0,30	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749325	26895	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25290	0.002096	0	25212,5,57,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Cat/Tat	H125Y	M	0.000874	0.97046	1	1	C>T
ERR5749325	27340	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAT	A	33242	4.51E-4	0	16634,16595,7,8	HIGH	NONE	FRAME_SHIFT	ORF6	aataaa/	NK47	orf6	0.000451	0.25	2	2	AAT>A
ERR5749325	27741	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	17569	5.69E-4	0	15,17544,0,10	HIGH	NONE	FRAME_SHIFT	ORF7a	aaaaga/	KR117	orf7a	0.000363	0.954278	3	2	CAA>C
ERR5749325	27972	PASS	C	T	6051	0.903652	0	0,0,5990,36	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749325	28048	PASS	G	T	6020	0.925083	0	0,5,0,6010	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749325	28111	PASS	A	G	23429	0.980025	0	2,0,17399,6018	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749325	28239	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTGTTTTAGATTTCATCTA	G	17402	5.75E-4	0	17392,0,10,0	HIGH	NONE	FRAME_SHIFT+STOP_LOST+SPLICE_SITE_REGION	ORF8	gttgttttagatttcatctaa/	VVLDFI*116	orf8	0.000417	0.984998	9	2	GTTGTTTTAGATTTCATCTA>G
ERR5749325	28270	PASS	TA	T	33793	0.995413	339	146,6,17193,16445	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749325	28280	PASS	G	C	33730	0.937355	35	13,0,17223,16430	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749325	28281	PASS	A	T	33730	0.916899	38	20,2,17214,16426	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749325	28282	PASS	T	A	33732	0.908722	12	27,14,17183,16443	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749325	28651	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	17936	5.02E-4	0	1,17926,0,9	HIGH	NONE	FRAME_SHIFT	N	aaa/	K127	N	0.000502	0.918117	3	2	CA>C
ERR5749325	28674	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17937	0.001338	0	0,17898,0,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gCa/gTa	A134V	N	0.001338	0.958634	1	1	C>T
ERR5749325	28881	PASS	G	A	13025	0.776046	9	4,0,6518,6354	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749325	28882	PASS	G	A	13025	0.831939	3	2,0,6581,6348	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749325	28883	PASS	G	C	13025	0.947409	0	0,0,6594,6428	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749325	28977	PASS	C	T	6693	0.934559	0	0,3,0,6674	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749325	29095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28022	0.001392	0	27962,0,41,0	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F274	N	0.000792	0.961279	2	2	C>T
ERR5749325	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	55655	8.09E-4	0	27954,27630,30,28	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749325	29284	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	28020	3.93E-4	0	0,28009,0,11	HIGH	NONE	FRAME_SHIFT	N	aaa/	K338	N	0.000393	0.931014	3	2	CAA>C
ERR5749325	29679	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	13236	9.07E-4	0	6625,6599,6,6	.	.	.	.	.	.	.	0.000443	0.838763	2	1	CT>C
ERR5749325	29733	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6642	0.002108	0	1,6619,0,15	.	.	.	.	.	.	.	0.001821	0.915943	2	1	C>T
ERR5749326	241	PASS	C	T	875	0.845714	0	0,0,436,433	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749326	507	PASS	ATGGTCATGTTATGGT	A	4223	0.081932	0	3846,0,346,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749326	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGT	A	4223	0.008051	0	3846,0,34,0	MODERATE	NONE	CODON_DELETION	ORF1ab	ggtcatgtt/	GHV82	leader	0.000686	0.081932	3	1	ATGGTCATGT>A
ERR5749326	509	PASS	GGTCATGTTA	G	4222	0.081241	0	3839,0,343,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749326	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	4222	0.00829	0	3839,0,35,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749326	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	4219	0.049775	0	4008,1,210,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749326	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	4215	0.004033	0	4196,1,17,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttatg/gtg	VM84V	leader	0.000554	0.991848	4	1	GTTA>G
ERR5749326	517	PASS	TATG	T	4214	0.476744	3	2206,0,2008,1	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749326	520	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTT	G	4214	0.030612	0	4084,1,129,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttgag/gag	VE86E	leader	0.000583	0.051154	1	1	GGTT>G
ERR5749326	635	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4231	0.021508	0	0,4119,0,109	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgt/Tgt	R124C	leader	0.00148	0.880435	1	1	C>T
ERR5749326	657	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	4232	0.004726	0	0,4198,0,29	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A131D	leader	0.001202	0.365979	3	1	C>A
ERR5749326	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	11826	0.001607	10	7577,4230,16,3	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749326	695	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	11826	0.001945	71	7588,4209,4,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gac/Tac	D144Y	leader	0.001683	0.073625	1	1	G>T
ERR5749326	913	PASS	C	T	7590	0.913175	0	0,3,0,7583	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749326	929	PASS	A	G	7591	0.968384	0	0,1,0,7582	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Att/Gtt	I42V	nsp2	0.000823	0.987013	3	2	A>G
ERR5749326	1027	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	8610	0.002555	157	8576,0,17,6	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccT/ccC	P74	nsp2	0.001454	0.276316	1	1	T>C
ERR5749326	2453	PASS	C	T	6139	0.803388	0	0,5,0,6071	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L550F	nsp2	0.00429	0.842201	2	2	C>T
ERR5749326	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	27792	0.001439	2136	13857,12960,34,859	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749326	3037	PASS	C	T	6470	0.828284	15	0,5,3233,3177	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749326	3267	PASS	C	T	8335	0.970486	2147483647	0,0,8334,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749326	3671	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GA	8940	0.002013	0	4465,4462,9,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/aaAt	N319K?	nsp3	0.000351	0.0625	6	2	G>GA
ERR5749326	3832	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	3689	0.002982	0	3678,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTg	L373F?	nsp3	0.000689	0.327273	4	2	C>CT
ERR5749326	4237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTA	T	16602	6.02E-4	0	8303,8290,5,5	HIGH	NONE	FRAME_SHIFT	ORF1ab	ata/	I508	nsp3	0.000302	0.918634	2	2	TTA>T
ERR5749326	5388	PASS	C	A	2043	0.961821	2147483647	0,0,2040,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749326	5892	PASS	C	T	6367	0.912046	0	0,5,0,6354	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCc/aTc	T1058I	nsp3	0.012179	0.912046	1	1	C>T
ERR5749326	5986	PASS	C	T	33	0.939394	2147483647	0,0,33,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749326	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	5202	0.006536	0	5,5163,0,34	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L1328S?	nsp3	0.000731	0.14377	4	2	C>CT
ERR5749326	6954	PASS	T	C	10144	0.819006	2147483647	0,0,0,10066	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749326	6990	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10168	0.001574	0	0,9979,0,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S1424F	nsp3	0.000504	0.101156	4	2	C>T
ERR5749326	7834	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	22938	5.23E-4	0	11471,11455,6,6	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L1706	nsp3	0.000523	0.86555	3	2	CT>C
ERR5749326	8137	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	9329	0.003537	0	9275,1,48,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtG/gtT	V1806	nsp3	0.002602	0.762515	2	1	G>T
ERR5749326	9060	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATTGTT	A	8771	0.002166	0	8750,2,19,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tattgttat/	YCY169	nsp4	0.000621	0.433333	5	2	ATTGTT>A
ERR5749326	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	7400	0.002162	2	6806,578,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749326	10323	PASS	A	G	10802	0.955008	0	0,1,0,10788	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749326	10369	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10818	0.002034	0	4,10785,0,24	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	cgC/cgT	R105	3Cpro	0.001225	0.120075	1	1	C>T
ERR5749326	10702	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	9002	0.001111	0	359,8633,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	agg/	R217	3Cpro	0.000396	0.098214	2	2	CAG>C
ERR5749326	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	14163	0.005013	0	14074,0,86,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749326	11287	PASS	GTCTGGTTTT	G	14162	0.993716	0	0,89,0,14073	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749326	14408	PASS	C	T	1002	0.842315	0	0,0,499,496	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749326	14676	PASS	C	T	5042	0.830028	0	1,0,5027,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749326	15029	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	6832	0.00483	0	6773,0,37,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tAt/tGt	Y530C	RdRp	0.00483	0.266667	1	1	A>G
ERR5749326	15279	PASS	C	T	8063	0.887387	0	1,0,8046,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749326	16176	PASS	T	C	5667	0.980413	0	0,0,2292,3374	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749326	16508	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	12632	0.001662	0	12604,0,28,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGt/gTt	G91V	helicase	0.000561	0.074909	2	2	G>T
ERR5749326	17749	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GC	G	6573	0.001521	0	6563,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gct/	A505	helicase	0.001521	0.987943	4	2	GC>G
ERR5749326	18131	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5274	0.003034	0	5250,1,20,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T31I	ExoN	0.0025	0.853992	1	1	C>T
ERR5749326	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	17481	0.00103	0	17463,0,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749326	18744	PASS	C	T	17479	0.948224	0	3,0,17432,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y235	ExoN	0.000912	0.953624	2	2	C>T
ERR5749326	18813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	34872	0.001549	0	17246,17414,31,31	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaT/gaC	D258	ExoN	0.000618	0.934482	1	1	T>C
ERR5749326	19034	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTGG	T	13099	6.11E-4	0	13091,0,8,0	MODERATE	NONE	CODON_DELETION	ORF1ab	ggt/	G333	ExoN	0.000384	0.060908	2	2	TTGG>T
ERR5749326	19299	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	8449	0.001065	0	8440,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gta/	V421	ExoN	0.001065	0.987656	2	2	TG>T
ERR5749326	19521	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	8449	0.001894	0	0,8426,0,20	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taT/taC	Y494	ExoN	0.001343	0.957831	1	1	T>C
ERR5749326	21004	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	24055	9.98E-4	0	12001,11990,12,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gca/Cca	A116P	MethTr	0.000749	0.857814	3	1	G>C
ERR5749326	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15496	0.001033	0	7574,7739,10,11	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749326	21764	PASS	ATACATG	A	6814	0.997358	0	18,0,6796,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749326	21786	PASS	G	T	6814	0.058409	0	6388,0,426,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gGt/gTt	G75V	S	0.001992	0.058409	1	1	G>T
ERR5749326	21987	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTGTTTA	G	6816	0.00132	0	2,6805,0,9	MODERATE	NONE	CODON_DELETION	S	gtttat/	VY143	S	0.000998	0.922156	5	2	GTGTTTA>G
ERR5749326	21990	PASS	TTTA	T	6816	0.994425	0	0,38,2,6776	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749326	22293	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	17267	0.001274	31	4998,12247,0,22	HIGH	NONE	FRAME_SHIFT	S	tta/	L244	S	0.000308	0.160511	4	1	TA>T
ERR5749326	22363	PASS	G	T	4999	0.956591	2147483647	0,0,4996,0	LOW	SILENT	SYNONYMOUS_CODING	S	gtG/gtT	V267	S	0.004714	0.976137	1	1	G>T
ERR5749326	22600	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	16485	5.46E-4	11	11477,4999,9,0	HIGH	NONE	FRAME_SHIFT	S	ttt/	F347	S	0.000471	0.963998	3	3	AT>A
ERR5749326	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	11484	0.001393	0	0,11464,0,17	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749326	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19476	0.001335	15	7978,11461,5,21	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749326	23063	PASS	A	T	7975	0.865956	2147483647	0,0,0,7937	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749326	23271	PASS	C	A	9191	0.91372	2147483647	0,0,9175,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749326	23403	PASS	A	G	9187	0.967889	0	0,2,0,9179	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749326	23522	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTA	G	7570	0.001189	0	7561,0,9,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	gaacatgtcaacaactcatatgagtgtgacatacccattggtgcaggtata/gta	EHVNNSYECDIPIGAGI654V	S	0.00053	0.959726	5	2	GAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTA>G
ERR5749326	23604	PASS	C	A	7568	0.936971	0	2,0,7563,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749326	23709	PASS	C	T	7566	0.929421	0	0,5,9,7541	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749326	23802	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	G	7573	0.001717	0	3,7550,0,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCt/aGt	T747S	S	0.001717	0.977181	3	2	C>G
ERR5749326	24010	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATTTATTGAAGATCTAC	A	4339	0.001613	0	45,4288,0,7	HIGH	NONE	FRAME_SHIFT	S	attgaagatctacttttc/	IEDLLF818	S	0.000455	0.926398	4	2	ATTTATTGAAGATCTAC>A
ERR5749326	24127	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TTTG	10636	0.001034	43	6351,4285,0,11	MODERATE	NONE	CODON_INSERTION	S	aac/TTGaac	N856LN	S	0.000324	0.111888	4	1	T>TTTG
ERR5749326	24320	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	6343	0.002207	0	0,6329,0,14	HIGH	NONE	FRAME_SHIFT	S	aaa/	K921	S	0.000763	0.138365	4	2	CA>C
ERR5749326	24506	PASS	T	G	8932	0.975481	0	2,0,8930,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749326	24899	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	25638	6.24E-4	0	12820,12804,8,8	HIGH	NONE	FRAME_SHIFT	S	atc/	I1114	S	0.000315	0.09021	5	3	CA>C
ERR5749326	24914	PASS	G	C	25548	0.959645	0	1,1,12722,12800	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749326	25422	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGGAACTGTAACTTTGAAGCAAGGTGAAATCAA	T	13093	0.001298	0	13076,0,17,0	HIGH	NONE	FRAME_SHIFT	ORF3a	actgtaactttgaagcaaggtgaaatcaaggat/	TVTLKQGEIKD12	orf3a	0.000545	0.213989	6	1	TGGAACTGTAACTTTGAAGCAAGGTGAAATCAA>T
ERR5749326	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	1817	0.005504	0	1807,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749326	26072	PASS	A	G	16236	0.953498	0	2,0,16217,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cAt/cGt	H227R	orf3a	0.951608	0.953498	1	1	A>G
ERR5749326	26151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CGG	C	16225	7.4E-4	0	0,16213,0,12	HIGH	NONE	FRAME_SHIFT	ORF3a	gga/	G254	orf3a	0.000501	0.913698	4	2	CGG>C
ERR5749326	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	6418	0.001402	0	0,6409,0,9	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749326	27461	PASS	G	T	12129	0.972957	0	0,3,0,12123	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	tGt/tTt	C23F	orf7a	0.002221	0.974441	1	1	G>T
ERR5749326	27972	PASS	C	T	3385	0.897193	20	1,1,3351,15	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749326	27996	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	6732	0.00609	14	3324,3341,42,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	Gac/Tac	D35Y	orf8	0.00609	0.077158	2	1	G>T
ERR5749326	28048	PASS	G	T	3372	0.910439	0	0,2,0,3365	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749326	28111	PASS	A	G	18494	0.97756	0	5,1,15097,3371	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749326	28270	PASS	TA	T	29230	0.994937	346	145,5,14902,14180	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749326	28280	PASS	G	C	29165	0.936054	1	5,3,14936,14167	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749326	28281	PASS	A	T	29165	0.915721	4	13,8,14933,14167	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749326	28282	PASS	T	A	29166	0.911815	0	6,6,14902,14181	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749326	28406	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTACCCAATA	T	15128	6.61E-4	0	9,15109,0,10	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	N	ttacccaataat/tat	LPNN45Y	N	0.00043	0.921074	3	2	TTACCCAATA>T
ERR5749326	28603	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	25753	4.27E-4	1	12867,12875,6,5	HIGH	NONE	FRAME_SHIFT	N	tac/	Y111	N	0.000427	0.883357	2	2	CT>C
ERR5749326	28657	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12907	0.00124	0	0,12881,0,21	LOW	SILENT	SYNONYMOUS_CODING	N	gaC/gaT	D128	N	0.00124	0.862766	1	1	C>T
ERR5749326	28881	PASS	G	A	3567	0.742641	0	0,0,1774,1735	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749326	28882	PASS	G	A	3567	0.811326	0	1,0,1788,1737	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749326	28883	PASS	G	C	3567	0.940566	0	0,0,1790,1776	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749326	28977	PASS	C	T	1812	0.94426	2147483647	0,0,0,1808	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749326	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	18192	0.003188	627	16362,1748,1,64	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749326	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	32507	0.001661	0	16301,16098,34,35	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749326	29511	PASS	G	T	8025	0.800125	282	0,114,3469,4438	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGt/aTt	S413I	N	0.800125	0.828395	1	1	G>T
ERR5749326	29635	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8039	0.003234	0	3446,4556,11,16	LOW	SILENT	SYNONYMOUS_CODING	ORF10	taC/taT	Y26	orf10	0.001133	0.928275	1	1	C>T
ERR5749326	29781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	3464	0.002887	0	0,3450,0,11	.	.	.	.	.	.	.	0.00173	0.972321	2	1	G>T
ERR5749327	71	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	603	0.031509	0	583,0,19,0	.	.	.	.	.	.	.	0.002088	0.926791	2	1	C>T
ERR5749327	241	PASS	C	T	789	0.818758	0	0,0,389,387	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749327	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	3732	0.00268	0	3449,0,273,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749327	913	PASS	C	T	16752	0.917502	0	0,12,0,16718	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749327	1323	PASS	G	A	12321	0.969402	0	1,0,12319,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGt/gAt	G173D	nsp2	0.966688	0.969402	1	1	G>A
ERR5749327	1813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	11482	0.002177	0	0,11436,0,28	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcA	A336	nsp2	0.001022	0.152738	4	2	T>A
ERR5749327	2947	PASS	C	T	3611	0.860703	0	1,0,3600,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G76	nsp3	0.001938	0.860703	2	2	C>T
ERR5749327	3037	PASS	C	T	7177	0.81803	18	0,6,3581,3546	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749327	3267	PASS	C	T	14853	0.968828	0	1,0,14842,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749327	3575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	6718	0.001042	0	6711,0,7,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/ttTa	L287F?	nsp3	0.000594	0.059126	3	1	G>GT
ERR5749327	3817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	10296	7.77E-4	12	3578,6710,0,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K367	nsp3	0.000777	0.972816	2	2	CA>C
ERR5749327	4551	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10439	0.002203	0	0,10408,0,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T611I	nsp3	0.001721	0.897919	3	2	C>T
ERR5749327	5388	PASS	C	A	1854	0.949838	2147483647	0,0,1853,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749327	5986	PASS	C	T	6788	0.976871	0	1,0,6785,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749327	6568	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	6155	9.75E-4	0	6149,0,6,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/aaAt	N1284K?	nsp3	0.000975	0.974638	3	3	C>CA
ERR5749327	6579	PASS	T	C	6153	0.967496	2147483647	0,0,6152,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cTt/cCt	L1287P	nsp3	0.003451	0.968477	2	1	T>C
ERR5749327	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	6132	0.001794	0	0,6053,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/TTctt	L1328F?	nsp3	0.000731	0.14377	4	2	C>CTT
ERR5749327	6954	PASS	T	C	11686	0.823036	0	0,1,0,11614	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749327	7926	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	15280	0.001178	0	0,15259,0,18	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1737	nsp3	0.000531	0.97019	5	2	CAA>C
ERR5749327	8368	PASS	G	T	4956	0.950161	2147483647	0,0,4954,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcG/gcT	A1883	nsp3	0.947284	0.950161	1	1	G>T
ERR5749327	8950	PASS	C	T	17440	0.977236	4	0,1,11533,5899	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I132	nsp4	0.002808	0.982604	1	1	C>T
ERR5749327	9060	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATTGTT	A	11534	9.54E-4	0	11523,2,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tattgttat/	YCY169	nsp4	0.000621	0.433333	5	2	ATTGTT>A
ERR5749327	10156	PASS	C	T	11356	0.889134	64	5,2,11344,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D34	3Cpro	0.001207	0.949463	1	1	C>T
ERR5749327	10533	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	11981	8.35E-4	0	11971,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tac/	Y161	3Cpro	0.000835	0.917216	4	2	GT>G
ERR5749327	11073	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	16168	0.001175	0	16129,0,23,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTc/tCc	F34S	nsp6	0.000385	0.092251	6	2	T>C
ERR5749327	11073	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TC	16168	0.001856	0	16138,0,30,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/Cttt	F35L?	nsp6	0.000385	0.092251	6	2	T>TC
ERR5749327	11287	PASS	GTCTGGTTTT	G	16160	0.998948	0	0,17,0,16143	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749327	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	20685	0.001402	12	15699,4937,30,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749327	12131	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	14458	0.002075	0	0,14411,0,36	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gct/Act	A14T	nsp8	0.002075	0.897455	1	1	G>A
ERR5749327	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	10503	0.001999	0	10482,0,21,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749327	14408	PASS	C	T	670	0.838806	0	0,0,336,331	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749327	14676	PASS	C	T	8859	0.737555	0	2,0,8822,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749327	14805	PASS	C	T	8854	0.895302	0	0,8,0,8819	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y455	RdRp	0.001051	0.904964	2	2	C>T
ERR5749327	15279	PASS	C	T	8680	0.8803	0	1,0,8669,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749327	16176	PASS	T	C	9119	0.978945	0	0,1,1177,7938	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749327	16506	PASS	T	C	16156	0.970785	62	11,2,16121,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttT/ttC	F90	helicase	0.966062	0.970785	1	1	T>C
ERR5749327	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	20341	0.001082	0	20319,0,22,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749327	19011	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	19860	9.06E-4	0	19842,0,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K325	ExoN	0.000408	0.975746	4	2	CAA>C
ERR5749327	19114	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	39502	0.00119	7	19617,19729,36,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Aaa/Gaa	K359E	ExoN	0.00119	0.098958	2	2	A>G
ERR5749327	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7693	0.00312	0	7661,0,26,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749327	20455	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	19341	0.001499	0	0,19259,0,34	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Ctc	F279L	endoR	0.001499	0.055699	1	1	T>C
ERR5749327	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	16805	7.74E-4	0	0,16792,0,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TA>T
ERR5749327	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	17352	0.002478	1	8636,8675,20,23	HIGH	NONE	FRAME_SHIFT	S	ctt/Tctt	L5S?	S	0.000394	0.091869	4	1	G>GT
ERR5749327	21764	PASS	ATACATG	A	7780	0.998586	0	11,0,7769,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749327	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	7780	0.002185	0	7763,0,17,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749327	21990	PASS	TTTA	T	7787	0.998716	0	0,10,0,7777	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749327	22801	PASS	G	T	12179	0.887758	0	0,2,0,12155	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggT	G413	S	0.001101	0.887758	3	2	G>T
ERR5749327	23063	PASS	A	T	7082	0.863315	0	0,3,0,7053	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749327	23271	PASS	C	A	18128	0.917917	0	1,0,18111,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749327	23403	PASS	A	G	18122	0.967112	0	0,3,0,18107	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749327	23525	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8513	0.001645	0	8498,0,14,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Cat/Tat	H655Y	S	0.001101	0.97751	2	2	C>T
ERR5749327	23604	PASS	C	A	8510	0.944301	0	8,0,8489,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749327	23709	PASS	C	T	8502	0.943896	2147483647	0,0,0,8493	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749327	24506	PASS	T	G	9494	0.976511	0	2,0,9490,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749327	24914	PASS	G	C	31169	0.958741	3	1,0,15537,15610	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749327	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	19363	0.002634	77	14662,4633,66,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749327	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	1979	0.009601	417	1942,10,0,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749327	26493	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	8157	0.001962	0	0,8141,0,16	.	.	.	.	.	.	.	0.001082	0.069277	3	1	G>GT
ERR5749327	26510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	8157	0.001839	0	0,8132,0,19	.	.	.	.	.	.	.	0.001235	0.933642	2	1	T>C
ERR5749327	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	7357	0.002039	0	0,7342,0,15	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749327	27312	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	14028	0.001497	0	14008,0,21,0	HIGH	NONE	FRAME_SHIFT	ORF6	aat/aaAt	N39K?	orf6	0.000911	0.088458	4	2	T>TA
ERR5749327	27972	PASS	C	T	3897	0.911727	22	1,1,3869,10	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749327	28048	PASS	G	T	3881	0.920124	0	0,2,0,3878	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749327	28111	PASS	A	G	20771	0.979972	0	6,1,16865,3887	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749327	28195	PASS	G	T	16879	0.896025	0	15,0,16853,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	cGt/cTt	R101L	orf8	0.000851	0.926081	3	2	G>T
ERR5749327	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	16851	7.71E-4	0	16841,1,13,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749327	28270	PASS	TA	T	32727	0.993675	423	202,13,16601,15919	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749327	28271	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AA	A	32726	0.001069	100	16754,15932,35,0	.	.	.	.	.	.	.	0.000482	0.924941	3	2	AA>A
ERR5749327	28280	PASS	G	C	32659	0.937016	14	14,4,16663,15904	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749327	28281	PASS	A	T	32659	0.908172	9	14,6,16662,15901	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749327	28282	PASS	T	A	32662	0.913416	1	13,10,16628,15916	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749327	28881	PASS	G	A	7508	0.76585	18	7,0,3709,3683	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749327	28882	PASS	G	A	7507	0.824564	0	0,0,3758,3678	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749327	28883	PASS	G	C	7507	0.948448	0	0,0,3767,3736	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749327	28977	PASS	C	T	3818	0.897328	0	0,3,0,3811	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749327	29095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22830	0.001445	0	22783,0,34,0	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F274	N	0.000792	0.961279	2	2	C>T
ERR5749327	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	45319	0.001147	0	22759,22480,33,30	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749328	222	PASS	C	T	12497	0.055773	0	5810,5849,400,403	.	.	.	.	.	.	.	0.002134	0.864859	1	1	C>T
ERR5749328	241	PASS	C	T	12479	0.844218	9	0,4,6185,6227	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749328	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	11730	8.53E-4	0	11721,1,10,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749328	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	11729	0.003666	0	11673,1,43,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749328	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	11725	0.002985	0	10747,6,879,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749328	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	11724	7.68E-4	0	11703,6,9,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749328	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	29585	6.76E-4	5	17816,11740,15,5	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749328	913	PASS	C	T	17828	0.906888	0	0,12,0,17785	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749328	1824	PASS	C	T	15753	0.940138	0	0,8,0,15732	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCc/gTc	A340V	nsp2	0.00173	0.940138	2	1	C>T
ERR5749328	2185	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	20919	6.21E-4	0	5,20901,0,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L462S?	nsp2	0.000441	0.963529	4	3	G>GT
ERR5749328	2775	PASS	A	C	62	0.951613	2147483647	0,0,0,62	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aCg	K19T	nsp3	0.000437	0.951613	3	2	A>C
ERR5749328	3037	PASS	C	T	19195	0.823548	17	5,16,9601,9453	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749328	3267	PASS	C	T	17318	0.97084	0	1,0,17304,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749328	4956	PASS	A	C	14890	0.98818	41	1,0,0,14884	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gAa/gCa	E746A	nsp3	0.98818	0.98818	1	1	A>C
ERR5749328	5388	PASS	C	A	5610	0.959893	2147483647	0,0,5608,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749328	5986	PASS	C	T	12270	0.972861	2147483647	0,0,12255,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749328	6954	PASS	T	C	19379	0.815986	0	0,12,2,19254	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749328	8664	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22397	0.011341	0	22120,0,265,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T37I	nsp4	0.003182	0.985915	1	1	C>T
ERR5749328	8964	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14887	0.009673	0	14726,9,149,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCa/tTa	S137L	nsp4	0.000553	0.981649	4	2	C>T
ERR5749328	9532	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29513	0.037983	7	14533,13782,631,553	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F326	nsp4	0.000899	0.966959	1	1	C>T
ERR5749328	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	29513	0.001355	115	15132,14341,40,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749328	10015	PASS	C	T	5600	0.858929	0	0,2,0,5585	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y487	nsp4	0.858929	0.858929	1	1	C>T
ERR5749328	11287	PASS	GTCTGGTTTT	G	14959	0.997326	0	0,40,0,14919	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749328	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	32674	8.26E-4	4	19188,13442,13,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749328	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	10151	7.88E-4	0	10144,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749328	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	13696	0.004819	2147483647	13375,76,4,237	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749328	14408	PASS	C	T	26628	0.840769	0	0,0,13322,13133	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749328	14676	PASS	C	T	10509	0.832905	0	1,0,10483,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749328	15279	PASS	C	T	19376	0.898276	0	2,0,19350,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749328	16176	PASS	T	C	18097	0.980107	0	0,0,9803,8286	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749328	17615	PASS	A	G	14250	0.904561	0	0,2,3,14197	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749328	19186	PASS	C	A	20516	0.96164	0	0,12,0,20487	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cta/Ata	L383I	ExoN	0.000709	0.96164	4	3	C>A
ERR5749328	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29904	0.00194	0	29824,0,61,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749328	21764	PASS	ATACATG	A	11972	0.994738	0	63,0,11909,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749328	21990	PASS	TTTA	T	11976	0.998414	0	0,19,2,11955	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749328	23063	PASS	A	T	11561	0.859009	0	0,1,0,11495	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749328	23271	PASS	C	A	17721	0.922465	0	2,0,17696,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749328	23403	PASS	A	G	17715	0.967203	0	0,3,0,17699	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749328	23604	PASS	C	A	14295	0.947184	0	8,0,14282,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749328	23709	PASS	C	T	14281	0.929907	0	0,5,1,14248	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749328	24506	PASS	T	G	14597	0.973693	0	9,0,14583,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749328	24914	PASS	G	C	34436	0.959868	0	0,1,17142,17262	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749328	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	21845	0.001373	536	21753,16,10,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749328	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	21963	0.001275	1048	21639,133,92,72	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749328	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	10396	0.001924	0	1,10374,0,20	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749328	27972	PASS	C	T	10719	0.903909	20	1,1,10631,48	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749328	28048	PASS	G	T	10676	0.919164	0	0,22,0,10652	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749328	28111	PASS	A	G	24360	0.97812	8	4,0,13667,10687	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749328	28270	PASS	TA	T	26425	0.99508	293	126,5,13486,12809	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749328	28280	PASS	G	C	26371	0.936142	14	8,1,13519,12797	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749328	28281	PASS	A	T	26371	0.90937	10	16,7,13514,12792	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749328	28282	PASS	T	A	26374	0.911921	0	15,13,13480,12803	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749328	28292	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	27183	9.2E-4	0	13546,13612,12,13	HIGH	NONE	FRAME_SHIFT	N	aat/	N8	N	0.000304	0.055324	4	2	CA>C
ERR5749328	28881	PASS	G	A	14250	0.753965	15	6,0,7062,6967	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749328	28882	PASS	G	A	14249	0.824549	9	4,0,7146,6969	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749328	28883	PASS	G	C	14248	0.941606	0	0,0,7152,7079	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749328	28977	PASS	C	T	7264	0.924009	0	0,0,1,7252	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749328	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	42033	7.61E-4	0	21113,20860,19,20	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749329	241	PASS	C	T	11505	0.862147	0	0,0,5717,5745	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749329	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	15214	0.003812	0	15159,0,58,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749329	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	15214	7.89E-4	0	15195,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749329	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	15195	0.002106	0	13958,2,1143,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749329	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	38153	3.41E-4	2	22901,15242,9,4	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749329	913	PASS	C	T	22893	0.916787	0	0,10,0,22851	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749329	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	83542	0.001496	2147483647	41702,39097,92,2452	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749329	3037	PASS	C	T	24746	0.839893	30	3,18,12366,12221	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749329	3177	PASS	C	T	38066	0.903273	5	4,0,25581,12447	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P153L	nsp3	0.000773	0.96008	3	2	C>T
ERR5749329	3267	PASS	C	T	25603	0.96809	0	2,0,25590,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749329	5170	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	14331	6.98E-4	0	2,14319,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T819	nsp3	0.000565	0.894036	2	2	CCA>C
ERR5749329	5388	PASS	C	A	7824	0.954882	2147483647	0,0,7819,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749329	5986	PASS	C	T	18036	0.974828	0	3,0,18023,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749329	6954	PASS	T	C	29145	0.818151	0	0,1,0,28995	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749329	7067	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAA	G	52768	6.44E-4	119	23509,29224,34,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gaa/	E1450	nsp3	0.000274	0.059217	5	3	GAA>G
ERR5749329	7070	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	52768	0.001213	185	23381,29216,64,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggc/Agc	G1451S	nsp3	0.000698	0.101434	3	1	G>A
ERR5749329	7070	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	52768	0.001725	274	23381,29216,97,5	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggc/Tgc	G1451C	nsp3	0.000698	0.101434	3	1	G>T
ERR5749329	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	33329	0.0015	93	21577,11702,50,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749329	10323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	25370	9.46E-4	0	0,25284,0,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749329	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	27182	0.00195	0	26289,5,53,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749329	11082	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	27160	4.42E-4	0	27162,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000427	0.179468	2	1	TG>T
ERR5749329	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	27160	0.001915	0	27068,0,75,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749329	11287	PASS	GTCTGGTTTT	G	27164	0.998675	0	0,36,0,27128	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749329	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	50333	7.75E-4	19	29923,20335,16,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749329	12125	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	24127	8.7E-4	0	2,24034,0,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y12H	nsp8	0.000847	0.113436	1	1	T>C
ERR5749329	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	36599	0.001093	0	18269,18240,21,22	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749329	14120	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	41818	0.001817	0	20839,20841,45,45	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCa/cTa	P227L	RdRp	0.00121	0.786944	2	2	C>T
ERR5749329	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	8994	0.003224	2101	8770,95,3,122	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749329	14408	PASS	C	T	17461	0.844912	0	1,1,8711,8645	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749329	14676	PASS	C	T	15552	0.799318	0	9,0,15508,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749329	15279	PASS	C	T	25579	0.892646	0	2,0,25546,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749329	16176	PASS	T	C	25409	0.981699	0	1,2,12568,12829	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749329	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	34772	3.74E-4	0	34759,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749329	19016	PASS	T	C	30709	0.16106	0	25662,0,5024,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTc/tCc	F326S	ExoN	0.16106	0.16106	1	1	T>C
ERR5749329	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	35230	0.001362	0	35144,4,54,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749329	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	38604	9.07E-4	0	38510,0,36,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749329	21304	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	44452	7.87E-4	0	3,44384,0,46	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgc/Agc	R216S	MethTr	0.000411	0.605296	3	2	C>A
ERR5749329	21305	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	44452	9.0E-4	0	3,44355,0,40	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cGc/cAc	R216H	MethTr	0.000727	0.703943	1	1	G>A
ERR5749329	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	42010	6.19E-4	0	20540,20982,14,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749329	21762	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTATACA	C	17699	0.001356	0	17673,2,24,0	MODERATE	NONE	CODON_DELETION	S	atacat/	IH68	S	0.001297	0.875707	2	2	CTATACA>C
ERR5749329	21764	PASS	ATACATG	A	17699	0.997458	0	44,0,17652,2	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749329	21889	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	17683	0.001074	0	6,17515,0,37	LOW	SILENT	SYNONYMOUS_CODING	S	acT/acC	T109	S	0.00091	0.065772	2	2	T>C
ERR5749329	21990	PASS	TTTA	T	17712	0.998645	0	0,24,14,17674	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749329	22792	PASS	C	T	21615	0.949572	0	0,7,0,21588	LOW	SILENT	SYNONYMOUS_CODING	S	atC/atT	I410	S	0.000722	0.949572	3	3	C>T
ERR5749329	23063	PASS	A	T	3739	0.856379	0	0,3,0,3710	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749329	23271	PASS	C	A	25772	0.921038	0	2,0,25746,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749329	23403	PASS	A	G	25764	0.969492	0	0,3,0,25750	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749329	23575	PASS	C	T	21901	0.868317	0	1,0,21838,0	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C671	S	0.001569	0.894896	2	2	C>T
ERR5749329	23604	PASS	C	A	21896	0.942136	0	20,0,21868,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749329	23709	PASS	C	T	21883	0.943518	0	0,12,0,21838	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749329	24506	PASS	T	G	22224	0.973362	0	9,0,22213,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749329	24914	PASS	G	C	53539	0.960739	2	2,1,26669,26842	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749329	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	33831	8.28E-4	47	24994,8788,38,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749329	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	21550	0.001763	718	21441,31,9,30	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749329	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	21489	9.31E-4	0	21468,0,20,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749329	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	17879	7.83E-4	0	2,17862,0,14	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749329	27807	PASS	C	T	28380	0.965257	0	0,11,0,28351	LOW	SILENT	SYNONYMOUS_CODING	ORF7b	Cta/Tta	L18	orf7b	0.000505	0.965257	2	2	C>T
ERR5749329	27855	PASS	C	A	36	0.25	84	26,0,0,10	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7b	Ctg/Atg	L34M	orf7b	0.25	0.25	1	1	C>A
ERR5749329	27972	PASS	C	T	26	0.961538	2147483647	0,0,26,0	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749329	28048	PASS	G	T	26	0.846154	2147483647	0,0,0,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749329	28111	PASS	A	G	25336	0.981015	0	3,0,25294,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749329	28239	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTGTTTT	G	25305	5.14E-4	0	25290,1,13,0	HIGH	NONE	FRAME_SHIFT	ORF8	gttgtttta/	VVL116	orf8	0.000417	0.984998	9	2	GTTGTTTT>G
ERR5749329	28270	PASS	TA	T	49142	0.995584	572	221,4,25006,23919	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749329	28280	PASS	G	C	49052	0.936761	28	16,2,25055,23898	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749329	28281	PASS	A	T	49052	0.916252	32	30,8,25036,23903	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749329	28282	PASS	T	A	49052	0.912216	25	21,5,25000,23915	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749329	28370	PASS	A	T	25305	0.946374	0	0,2,0,25277	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Agt/Tgt	S33C	N	0.935248	0.946374	1	1	A>T
ERR5749329	28795	PASS	A	G	9985	0.97356	0	3,0,9979,0	LOW	SILENT	SYNONYMOUS_CODING	N	gaA/gaG	E174	N	0.97356	0.979058	1	1	A>G
ERR5749329	28881	PASS	G	A	19619	0.752383	12	5,0,9684,9646	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749329	28882	PASS	G	A	19618	0.820318	4	7,3,9807,9606	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749329	28883	PASS	G	C	19618	0.944541	3	0,1,9828,9777	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749329	28977	PASS	C	T	9983	0.939497	0	0,3,0,9964	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749329	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	84128	9.98E-4	0	42253,41740,55,52	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749330	241	PASS	C	T	8143	0.851775	6	0,2,4049,4041	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749330	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10202	0.001764	0	9455,2,720,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749330	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	32074	4.05E-4	18	21830,10222,13,0	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749330	913	PASS	C	T	21847	0.916327	0	0,8,0,21808	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749330	3037	PASS	C	T	16906	0.801313	60	0,20,8451,8291	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749330	3267	PASS	C	T	20957	0.969843	0	3,0,20944,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749330	5388	PASS	C	A	5652	0.962491	2147483647	0,0,5647,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749330	5986	PASS	C	T	11572	0.972347	2147483647	0,0,11563,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749330	6706	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	10656	0.001408	0	0,10641,0,15	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1330	nsp3	0.000687	0.883999	2	2	CA>C
ERR5749330	6762	PASS	C	T	32345	0.963518	4	0,1,21653,10663	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T1348I	nsp3	0.001474	0.966761	2	1	C>T
ERR5749330	6954	PASS	T	C	21589	0.823892	0	0,4,0,21479	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749330	7067	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	37229	7.79E-4	38	15527,21649,35,16	HIGH	NONSENSE	STOP_GAINED	ORF1ab	Gaa/Taa	E1450*	nsp3	0.000274	0.059217	5	3	G>T
ERR5749330	7070	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	37229	0.001262	152	15503,21659,47,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggc/Agc	G1451S	nsp3	0.000698	0.101434	3	1	G>A
ERR5749330	8664	PASS	C	T	20043	0.959637	2147483647	0,0,20023,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T37I	nsp4	0.003182	0.985915	1	1	C>T
ERR5749330	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	24026	0.001124	55	14744,9255,27,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749330	10077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	7777	0.002315	472	1,7729,17,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTc/tCc	F8S	3Cpro	0.001833	0.454545	1	1	T>C
ERR5749330	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	23420	0.00158	0	23341,0,62,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749330	11287	PASS	GTCTGGTTTT	G	23423	0.99842	0	0,37,0,23386	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749330	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	36002	0.001055	13	23710,12217,32,7	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749330	12162	PASS	A	G	38869	0.976537	2	6,3,21076,17769	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cAg/cGg	Q24R	nsp8	0.000894	0.982497	1	1	A>G
ERR5749330	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	19493	0.001385	0	19437,0,28,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749330	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	13556	5.9E-4	0	13549,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749330	13356	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	32262	8.06E-4	0	18673,13549,16,11	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T111I	nsp10	0.000806	0.091518	1	1	C>T
ERR5749330	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	37322	0.001045	0	18651,18592,23,24	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749330	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	9374	0.005761	3076	9129,68,2,173	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749330	14408	PASS	C	T	18193	0.84472	4	1,3,9079,8983	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749330	14676	PASS	C	T	14189	0.784622	0	5,0,14137,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749330	15279	PASS	C	T	21767	0.879175	0	3,0,21736,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749330	16176	PASS	T	C	20055	0.98185	0	0,0,8322,11727	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749330	16939	PASS	T	C	19316	0.959205	0	0,0,19301,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Tta/Cta	L235	helicase	0.000959	0.959205	2	2	T>C
ERR5749330	17615	PASS	A	G	15074	0.930941	0	0,3,0,15037	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749330	18246	PASS	C	T	11823	0.962784	0	0,4,0,11810	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y69	ExoN	0.960724	0.984848	1	1	C>T
ERR5749330	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	25434	8.65E-4	0	25412,0,22,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749330	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23290	0.001288	0	23239,0,30,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749330	21764	PASS	ATACATG	A	12231	0.996893	0	38,0,12193,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749330	21990	PASS	TTTA	T	12234	0.997793	0	0,27,2,12205	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749330	23063	PASS	A	T	13749	0.855117	0	0,5,0,13665	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749330	23271	PASS	C	A	23819	0.916915	0	4,0,23798,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749330	23403	PASS	A	G	23809	0.968121	0	0,3,0,23786	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749330	23604	PASS	C	A	14598	0.956775	0	7,0,14582,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749330	23709	PASS	C	T	14580	0.924417	0	0,5,0,14550	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749330	24506	PASS	T	G	19412	0.975376	0	9,0,19402,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749330	24914	PASS	G	C	37703	0.960428	0	0,1,18777,18886	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749330	25571	PASS	C	T	18033	0.916431	0	0,5,3,18006	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	tCc/tTc	S60F	orf3a	0.001558	0.922217	1	1	C>T
ERR5749330	25855	PASS	G	T	13849	0.895444	0	0,35,1,13804	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gac/Tac	D155Y	orf3a	0.001326	0.969697	1	1	G>T
ERR5749330	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	12022	9.15E-4	0	0,12011,0,11	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749330	27972	PASS	C	T	9394	0.904514	63	2,3,9331,31	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749330	28048	PASS	G	T	9380	0.921535	0	0,6,0,9370	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749330	28111	PASS	A	G	32357	0.977779	1	3,2,22964,9377	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749330	28270	PASS	TA	T	44502	0.994967	506	220,9,22678,21600	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749330	28280	PASS	G	C	44414	0.937362	13	15,5,22742,21584	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749330	28281	PASS	A	T	44414	0.910771	44	25,3,22727,21582	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749330	28282	PASS	T	A	44417	0.907715	2	12,15,22689,21593	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749330	28881	PASS	G	A	16708	0.771906	2	3,1,8277,8222	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749330	28882	PASS	G	A	16708	0.829782	24	9,0,8343,8186	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749330	28883	PASS	G	C	16708	0.946134	0	2,1,8364,8329	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749330	28977	PASS	C	T	8512	0.928806	0	0,1,1,8501	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749330	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	39069	7.93E-4	124	30518,8474,7,28	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749330	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	60650	0.001303	0	30452,30078,46,45	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749331	241	PASS	C	T	18368	0.85649	0	0,1,9102,9180	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749331	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	14813	7.43E-4	0	14799,4,11,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749331	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	14813	7.43E-4	0	14789,4,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749331	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	14809	0.002904	0	13600,11,1143,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749331	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	42558	3.29E-4	13	27707,14829,13,1	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749331	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27711	0.001155	0	0,27659,0,34	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749331	913	PASS	C	T	27711	0.907762	0	0,17,0,27650	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749331	1510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	30938	0.003394	0	0,30483,0,116	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G235	nsp2	0.002159	0.937304	1	1	T>C
ERR5749331	2702	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	54412	8.09E-4	2147483647	53987,40,72,199	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F633V	nsp2	0.000632	0.333333	1	1	T>G
ERR5749331	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	107786	0.001856	2147483647	53832,49724,101,3839	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749331	3037	PASS	C	T	21920	0.804151	55	2,25,10950,10729	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749331	3177	PASS	C	T	37132	0.902672	9	13,11,26039,10999	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P153L	nsp3	0.000773	0.96008	3	2	C>T
ERR5749331	3267	PASS	C	T	26098	0.966473	0	3,0,26076,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749331	4675	PASS	A	G	16667	0.962981	0	2,0,16648,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaA/aaG	K652	nsp3	0.015625	0.967819	2	2	A>G
ERR5749331	5388	PASS	C	A	6402	0.957669	0	1,0,6396,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749331	5986	PASS	C	T	14671	0.975394	0	3,0,14655,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749331	6954	PASS	T	C	33223	0.816904	0	0,9,0,33048	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749331	7528	PASS	C	T	21396	0.900823	0	0,8,25,21326	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V1603	nsp3	0.002527	0.916131	1	1	C>T
ERR5749331	7564	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	21418	7.47E-4	0	1,21399,0,16	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/	Y1617	nsp3	0.000586	0.056194	4	2	CT>C
ERR5749331	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	40125	4.49E-4	67	17008,23098,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749331	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	23243	0.001162	0	23185,2,50,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749331	11287	PASS	GTCTGGTTTT	G	23238	0.997891	0	0,48,0,23189	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749331	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	45366	8.38E-4	14	29059,16239,20,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749331	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	43264	0.001086	0	21605,21543,26,26	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749331	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	13715	0.006781	2147483647	13341,109,5,258	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749331	14408	PASS	C	T	26543	0.831067	0	1,1,13268,13048	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749331	14676	PASS	C	T	17306	0.825841	0	8,0,17247,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749331	15279	PASS	C	T	32308	0.882877	0	3,0,32259,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749331	16176	PASS	T	C	25349	0.980078	17	5,0,11231,14104	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749331	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	31300	3.83E-4	0	0,31288,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749331	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	33843	0.001655	0	33760,0,60,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749331	21304	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	30759	0.044475	9	1,28892,1,1841	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgc/Agc	R216S	MethTr	0.000411	0.605296	3	2	C>A
ERR5749331	21305	PASS	G	A	30759	0.051042	9	1,28830,1,1851	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cGc/cAc	R216H	MethTr	0.000727	0.703943	1	1	G>A
ERR5749331	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	40514	6.91E-4	3	19848,20198,16,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749331	21764	PASS	ATACATG	A	14176	0.998448	0	22,0,14154,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749331	21994	PASS	TTAC	T	43153	0.328042	2147483647	28973,22,8,14148	MODERATE	NONE	CODON_DELETION	S	tac/	Y145	S	0.000341	0.347498	1	1	TTAC>T
ERR5749331	22450	PASS	C	T	9199	0.801935	18	2,1,9049,38	LOW	SILENT	SYNONYMOUS_CODING	S	ctC/ctT	L296	S	0.00215	0.803846	1	1	C>T
ERR5749331	23063	PASS	A	T	12750	0.848706	0	0,3,0,12672	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749331	23271	PASS	C	A	28290	0.921456	0	2,0,28261,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749331	23403	PASS	A	G	28273	0.962332	0	0,2,0,28252	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749331	23604	PASS	C	A	17483	0.934851	0	12,0,17465,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749331	23709	PASS	C	T	17464	0.935525	0	0,8,0,17430	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749331	23817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	42301	9.46E-4	1	24778,17459,23,19	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTt/cCt	L752P	S	0.000646	0.066832	1	1	T>C
ERR5749331	24506	PASS	T	G	25149	0.975665	0	8,0,25132,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749331	24914	PASS	G	C	37863	0.955894	0	0,1,18832,18984	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749331	25290	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	11250	0.001422	0	8,11213,0,29	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tGt/tTt	C1243F	S	0.001422	0.869662	1	1	G>T
ERR5749331	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	29636	0.001721	125	18330,11233,61,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749331	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	33875	0.001506	632	33737,19,29,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749331	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	33826	9.76E-4	0	33793,0,33,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749331	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	34123	0.001729	2497	33632,203,99,154	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749331	27972	PASS	C	T	11513	0.898984	0	0,0,11434,41	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749331	28048	PASS	G	T	11475	0.910937	0	0,21,1,11444	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749331	28111	PASS	A	G	32268	0.978214	3	5,1,20766,11479	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749331	28270	PASS	TA	T	40052	0.994832	509	210,6,20506,19339	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749331	28280	PASS	G	C	39962	0.935264	37	17,1,20535,19321	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749331	28281	PASS	A	T	39962	0.912292	49	32,5,20534,19310	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749331	28282	PASS	T	A	39965	0.907244	25	37,14,20478,19331	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749331	28881	PASS	G	A	18038	0.768433	0	1,0,8984,8795	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749331	28882	PASS	G	A	18038	0.831578	0	2,1,9055,8798	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749331	28883	PASS	G	C	18038	0.94057	3	0,1,9070,8948	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749331	28977	PASS	C	T	9219	0.893481	0	0,0,2,9192	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749331	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	40622	9.6E-4	0	20410,20152,24,23	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749331	29736	PASS	G	T	9259	0.78205	0	0,342,0,8908	.	.	.	.	.	.	.	0.78205	0.987769	2	1	G>T
ERR5749332	241	PASS	C	T	6895	0.858013	0	0,0,3434,3438	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749332	412	PASS	C	T	9492	0.983986	0	1,0,9488,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G49	leader	0.968277	0.983986	1	1	C>T
ERR5749332	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	9483	0.008225	0	9401,6,78,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749332	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	9483	0.002214	0	9419,6,21,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749332	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	9483	0.002953	0	9419,6,28,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749332	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	9477	0.001688	0	8835,8,480,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749332	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	9477	0.002216	0	9448,8,21,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749332	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	9477	8.44E-4	0	9448,8,8,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttatg/gtg	VM84V	leader	0.000554	0.991848	4	1	GTTA>G
ERR5749332	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	9475	0.001689	0	9447,8,16,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749332	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	27941	5.37E-4	23	18438,9486,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749332	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	27941	0.001074	9	18413,9479,24,6	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749332	913	PASS	C	T	18449	0.918966	0	0,8,2,18415	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749332	1594	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15792	0.0019	0	12,15738,0,31	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S263	nsp2	0.0019	0.963177	1	1	C>T
ERR5749332	1813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	15987	0.001251	0	0,15931,0,32	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcA	A336	nsp2	0.001022	0.152738	4	2	T>A
ERR5749332	3037	PASS	C	T	14903	0.811045	48	0,16,7437,7329	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749332	3177	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	26054	9.6E-4	38	18520,7497,35,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cAt	P153H	nsp3	0.000773	0.96008	3	2	C>A
ERR5749332	3267	PASS	C	T	18552	0.971701	0	1,0,18538,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749332	5388	PASS	C	A	4850	0.951134	2147483647	0,0,4847,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749332	5986	PASS	C	T	10843	0.971687	0	1,0,10830,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749332	6185	PASS	C	T	10844	0.92844	0	0,1,0,10830	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cac/Tac	H1156Y	nsp3	0.910265	0.954999	1	1	C>T
ERR5749332	6954	PASS	T	C	19286	0.821943	0	0,2,0,19164	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749332	7067	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	35688	4.2E-4	50	16329,19344,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gaa/	E1450	nsp3	0.000274	0.059217	5	3	GA>G
ERR5749332	7600	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13784	0.002249	0	0,13736,0,32	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C1627	nsp3	0.001321	0.973632	1	1	C>T
ERR5749332	7926	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	18196	6.05E-4	0	0,18184,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1737	nsp3	0.000531	0.97019	5	2	CAA>C
ERR5749332	9286	PASS	C	T	7034	0.971567	0	1,0,7027,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N244	nsp4	0.949239	0.971567	1	1	C>T
ERR5749332	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	18978	0.001528	0	18931,0,36,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749332	11199	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	37809	7.14E-4	0	18766,18884,14,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCc/gTc	A76V	nsp6	0.000309	0.056758	3	2	C>T
ERR5749332	11287	PASS	GTCTGGTTTT	G	18977	0.997365	0	0,50,0,18927	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749332	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	31810	9.12E-4	4	19976,11785,16,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749332	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10693	0.004489	2147483647	10415,88,3,183	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749332	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	20728	7.72E-4	0	10398,10333,8,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749332	14408	PASS	C	T	20728	0.840168	15	0,5,10350,10198	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749332	14676	PASS	C	T	11842	0.762033	0	6,0,11784,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749332	15279	PASS	C	T	18933	0.902181	0	3,0,18905,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749332	16176	PASS	T	C	16619	0.980625	0	0,0,7721,8892	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749332	17615	PASS	A	G	13054	0.910755	0	0,2,1,13009	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749332	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24557	0.002403	0	24485,0,59,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749332	21764	PASS	ATACATG	A	10450	0.99799	0	21,0,10429,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749332	21990	PASS	TTTA	T	10454	0.998469	0	0,16,3,10435	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749332	22432	PASS	C	T	7287	0.592425	0	2,0,7093,3	LOW	SILENT	SYNONYMOUS_CODING	S	gaC/gaT	D290	S	0.002959	0.755028	1	1	C>T
ERR5749332	23063	PASS	A	T	12170	0.861627	0	0,4,0,12102	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749332	23271	PASS	C	A	19981	0.924228	0	3,0,19959,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749332	23403	PASS	A	G	19977	0.970216	0	0,4,0,19955	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749332	23522	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAACATGTCAACAACTCATA	G	13321	6.01E-4	0	13310,2,8,0	HIGH	NONE	FRAME_SHIFT	S	gaacatgtcaacaactcatat/	EHVNNSY654	S	0.00053	0.959726	5	2	GAACATGTCAACAACTCATA>G
ERR5749332	23604	PASS	C	A	13317	0.942705	0	7,0,13301,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749332	23709	PASS	C	T	13293	0.939141	0	0,3,0,13277	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749332	24506	PASS	T	G	16008	0.972451	0	9,0,15994,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749332	24914	PASS	G	C	32358	0.959917	0	0,0,16133,16209	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749332	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	21933	0.001094	23	15500,6395,32,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749332	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	40263	4.47E-4	0	0,40245,0,18	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749332	26509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10222	0.002446	0	0,10185,0,26	.	.	.	.	.	.	.	0.000852	0.946613	3	1	C>T
ERR5749332	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	10593	7.55E-4	0	0,10581,0,8	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749332	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	10595	0.001605	0	0,10575,0,17	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749332	27065	PASS	G	A	27581	0.751351	0	0,2,4,27258	LOW	SILENT	SYNONYMOUS_CODING	M	ttG/ttA	L181	M	0.001008	0.897124	3	2	G>A
ERR5749332	27972	PASS	C	T	9389	0.898711	37	2,2,9291,50	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749332	28048	PASS	G	T	9344	0.924336	0	0,11,0,9331	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749332	28111	PASS	A	G	27016	0.979086	0	4,2,17650,9346	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749332	28198	PASS	G	T	17658	0.932099	0	15,0,17595,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tGt/tTt	C102F	orf8	0.000718	0.94386	4	2	G>T
ERR5749332	28270	PASS	TA	T	34293	0.993701	546	215,5,17358,16719	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749332	28271	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AA	A	34288	0.001342	133	17521,16725,46,0	.	.	.	.	.	.	.	0.000482	0.924941	3	2	AA>A
ERR5749332	28280	PASS	G	C	34223	0.938404	16	11,2,17433,16704	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749332	28281	PASS	A	T	34223	0.915905	22	21,6,17430,16703	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749332	28282	PASS	T	A	34225	0.913893	7	14,7,17402,16718	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749332	28321	PASS	G	T	17646	0.944463	0	0,10,3,17599	LOW	SILENT	SYNONYMOUS_CODING	N	acG/acT	T16	N	0.00045	0.947809	3	2	G>T
ERR5749332	28881	PASS	G	A	14987	0.733302	9	4,0,7366,7347	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749332	28882	PASS	G	A	14987	0.823781	3	2,0,7491,7350	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749332	28883	PASS	G	C	14988	0.944155	1	3,4,7501,7464	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749332	28977	PASS	C	T	7630	0.932503	2147483647	0,0,0,7611	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749332	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	51355	8.96E-4	0	25804,25482,25,24	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749332	29492	PASS	T	C	8840	0.925	0	4,0,8810,8	LOW	SILENT	SYNONYMOUS_CODING	N	Ttg/Ctg	L407	N	0.029032	0.925	1	1	T>C
ERR5749332	29642	PASS	C	T	8861	0.919761	0	0,1,4,8849	HIGH	NONSENSE	STOP_GAINED	ORF10	Caa/Taa	Q29*	orf10	0.001806	0.941176	2	2	C>T
ERR5749333	241	PASS	C	T	12807	0.866167	2	1,3,6345,6411	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749333	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	12255	0.002203	0	12228,3,27,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749333	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	12252	0.001061	0	12183,4,13,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749333	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	12252	0.003999	0	12183,4,49,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749333	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12241	0.002532	0	11258,4,856,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749333	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	12241	0.001225	0	12222,4,15,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749333	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	36545	3.28E-4	19	24258,12273,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749333	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	36545	9.3E-4	11	24234,12267,28,6	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749333	745	PASS	C	T	24269	0.913387	0	1,0,24246,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N160	leader	0.001671	0.915927	1	1	C>T
ERR5749333	913	PASS	C	T	24257	0.919487	0	0,5,0,24224	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749333	1643	PASS	A	T	19148	0.973783	261	6,8,19129,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Aac/Tac	N280Y	nsp2	0.001863	0.97665	1	1	A>T
ERR5749333	3037	PASS	C	T	20416	0.813235	57	0,19,10207,10035	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749333	3267	PASS	C	T	22972	0.970573	0	1,0,22962,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749333	3320	PASS	G	T	22944	0.745293	0	295,0,22623,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Ttt	V201F	nsp3	0.001049	0.745293	2	2	G>T
ERR5749333	5388	PASS	C	A	7053	0.962711	2147483647	0,0,7048,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749333	5986	PASS	C	T	12633	0.977203	2147483647	0,0,12627,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749333	6573	PASS	C	T	12659	0.956632	0	1,0,12644,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S1285F	nsp3	0.001862	0.957014	1	1	C>T
ERR5749333	6954	PASS	T	C	24718	0.817097	0	0,2,2,24598	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749333	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	33959	0.001266	133	16604,17312,43,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749333	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	22841	0.002277	0	22758,0,72,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749333	11287	PASS	GTCTGGTTTT	G	22843	0.998074	0	0,44,0,22799	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749333	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	40341	0.001339	3	25597,14666,38,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749333	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	43090	0.001369	0	21505,21463,31,31	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749333	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	15605	0.004293	2147483647	15279,103,5,213	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749333	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	30392	6.91E-4	0	15253,15140,11,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749333	14408	PASS	C	T	30392	0.84927	21	0,7,15194,15000	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749333	14676	PASS	C	T	15118	0.795806	0	13,0,15044,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749333	15279	PASS	C	T	25796	0.888936	0	9,0,25751,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749333	16176	PASS	T	C	22388	0.981508	0	0,0,10422,11961	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749333	18658	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	25623	5.07E-4	0	25598,11,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tgt/	C207	ExoN	0.000507	0.115741	3	2	TG>T
ERR5749333	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	25612	9.76E-4	0	25587,0,25,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749333	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29984	0.002134	0	29896,0,68,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749333	21764	PASS	ATACATG	A	12935	0.995903	0	53,0,12882,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749333	21990	PASS	TTTA	T	12942	0.9966	0	0,44,6,12892	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749333	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	17384	0.001266	0	0,17344,0,25	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749333	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	31989	8.75E-4	0	14582,17364,12,16	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749333	23063	PASS	A	T	14585	0.885362	0	0,4,0,14517	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749333	23271	PASS	C	A	25742	0.923821	0	5,0,25717,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749333	23403	PASS	A	G	25733	0.968484	0	0,5,1,25708	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749333	23604	PASS	C	A	16760	0.943735	0	11,0,16734,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749333	23709	PASS	C	T	16741	0.944687	0	0,5,2,16709	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749333	24506	PASS	T	G	21185	0.975974	0	9,0,21170,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749333	24914	PASS	G	C	39156	0.958525	0	0,0,19513,19625	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749333	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	23840	0.002265	710	23712,31,24,32	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749333	26526	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	13189	0.001516	0	1,13157,0,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Gca/Aca	A2T	M	0.001224	0.951192	3	1	G>A
ERR5749333	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	G	12879	6.21E-4	0	0,12859,0,8	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/	ACLVGLMWLSYFIASF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT>G
ERR5749333	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	12879	6.21E-4	0	0,12859,0,8	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749333	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	12880	0.002795	0	0,12840,0,36	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749333	27972	PASS	C	T	11820	0.903723	18	1,1,11704,83	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749333	28048	PASS	G	T	11747	0.921938	0	0,19,1,11718	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749333	28095	PASS	A	T	11759	0.962497	108	3,1,0,11737	HIGH	NONSENSE	STOP_GAINED	ORF8	Aaa/Taa	K68*	orf8	0.002672	0.967672	2	2	A>T
ERR5749333	28111	PASS	A	G	30524	0.978574	0	5,3,18756,11750	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749333	28237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GATC	18755	0.001173	0	18731,1,22,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_INSERTION	ORF8	cgt/cgATCt	R115RS	orf8	0.000442	0.966707	4	2	G>GATC
ERR5749333	28245	PASS	T	G	18696	0.950471	0	23,0,18619,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	Tta/Gta	L118V	orf8	0.019165	0.950471	2	2	T>G
ERR5749333	28249	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	ATC	18695	0.001016	0	18659,1,19,0	HIGH	NONE	FRAME_SHIFT	ORF8	ttc/CTttc	F120L?	orf8	0.000443	0.063605	3	2	A>ATC
ERR5749333	28250	PASS	T	TCTG	18631	0.99109	0	191,0,18465,0	MODERATE	NONE	CODON_INSERTION	ORF8	ttc/CTGttc	F120LF	orf8	0.000494	0.993968	5	3	T>TCTG
ERR5749333	28250	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TATG	18631	0.001503	8	191,0,27,1	MODERATE	NONE	CODON_INSERTION	ORF8	ttc/ATGttc	F120MF	orf8	0.000494	0.993968	5	3	T>TATG
ERR5749333	28253	PASS	CA	C	18631	0.993666	0	118,0,18512,1	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749333	28254	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	ATC	18631	0.001396	0	18604,1,26,0	HIGH	NONE	FRAME_SHIFT+STOP_LOST+SPLICE_SITE_REGION	ORF8	taa/tCTaa	*122S?	orf8	0.000541	0.914398	3	2	A>ATC
ERR5749333	28270	PASS	TA	T	35926	0.994322	418	197,11,18427,17295	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749333	28280	PASS	G	C	35810	0.945267	12	11,3,18452,17282	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749333	28281	PASS	A	T	35810	0.919129	10	15,6,18439,17268	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749333	28282	PASS	T	A	35811	0.879423	4	15,19,18402,17267	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749333	28881	PASS	G	A	21381	0.763435	14	8,1,10573,10514	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749333	28882	PASS	G	A	21379	0.828757	12	5,0,10673,10499	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749333	28883	PASS	G	C	21379	0.94228	0	0,0,10695,10665	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749333	28977	PASS	C	T	10916	0.923415	0	0,9,1,10886	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749333	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	55071	0.001144	0	27641,27331,38,38	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749333	29253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27722	9.02E-4	0	0,27652,0,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCg/tTg	S327L	N	0.000361	0.053998	4	2	C>T
ERR5749334	241	PASS	C	T	11528	0.86008	1	2,3,5748,5736	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749334	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	9674	0.001861	0	8995,0,667,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749334	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20400	9.8E-4	0	0,20356,0,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749334	913	PASS	C	T	20400	0.907157	0	0,12,0,20366	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749334	3037	PASS	C	T	19618	0.815017	52	1,21,9799,9660	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749334	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	9900	0.001919	516	3,9866,19,4	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749334	3267	PASS	C	T	19512	0.971248	2147483647	0,0,19499,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749334	5388	PASS	C	A	5613	0.961518	2147483647	0,0,5608,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749334	5986	PASS	C	T	13255	0.976084	2147483647	0,0,13241,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749334	6762	PASS	C	T	34301	0.963762	0	2,1,22295,11983	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T1348I	nsp3	0.001474	0.966761	2	1	C>T
ERR5749334	6954	PASS	T	C	22238	0.82458	0	0,2,0,22131	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749334	8664	PASS	C	T	21278	0.95305	0	1,0,21258,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T37I	nsp4	0.003182	0.985915	1	1	C>T
ERR5749334	11074	PASS	C	CT	21021	0.065886	0	19354,1,1385,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CT
ERR5749334	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	21021	0.009609	0	19354,1,202,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749334	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21021	0.003092	0	20915,1,77,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749334	11082	PASS	TG	T	20931	0.093402	0	19065,0,1955,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000427	0.179468	2	1	TG>T
ERR5749334	11083	PASS	G	T	20931	0.86231	0	4,0,18899,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749334	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GTT	20931	0.003918	0	20235,0,82,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/tTTat	Y38F?	nsp6	0.000477	0.901695	5	2	G>GTT
ERR5749334	11287	PASS	GTCTGGTTTT	G	21014	0.99862	0	0,28,0,20985	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749334	12125	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	18092	0.001105	0	4,17998,0,28	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y12H	nsp8	0.000847	0.113436	1	1	T>C
ERR5749334	12162	PASS	A	G	40135	0.976504	0	5,4,22019,18090	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cAg/cGg	Q24R	nsp8	0.000894	0.982497	1	1	A>G
ERR5749334	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28995	0.001276	3	14478,14443,20,25	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749334	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	8914	0.004712	2397	8700,69,4,135	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749334	14408	PASS	C	T	17339	0.873753	7	2,6,8651,8578	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749334	14676	PASS	C	T	12973	0.756803	0	5,0,12924,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749334	15279	PASS	C	T	20320	0.898081	2147483647	0,0,20291,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749334	16176	PASS	T	C	19795	0.979793	3	1,0,8875,10911	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749334	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	20831	8.64E-4	0	20813,0,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749334	16939	PASS	T	C	20804	0.951019	0	0,0,20778,2	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Tta/Cta	L235	helicase	0.000959	0.959205	2	2	T>C
ERR5749334	17615	PASS	A	G	16263	0.902355	0	0,0,2,16209	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749334	18246	PASS	C	T	11886	0.961383	0	0,3,0,11875	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y69	ExoN	0.960724	0.984848	1	1	C>T
ERR5749334	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	25315	8.69E-4	0	25293,0,22,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749334	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	25230	7.13E-4	0	0,25212,0,18	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749334	19961	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27751	0.008648	0	27487,0,249,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aTg	T114M	endoR	0.008648	0.927928	1	1	C>T
ERR5749334	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27746	0.00137	0	27693,0,39,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749334	21764	PASS	ATACATG	A	13178	0.997875	0	28,0,13150,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749334	21990	PASS	TTTA	T	13181	0.997496	0	0,33,3,13145	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749334	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30582	8.83E-4	8	14828,15711,9,18	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749334	23063	PASS	A	T	14833	0.845412	0	0,3,0,14749	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749334	23271	PASS	C	A	23228	0.910109	139	5,4,23193,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749334	23403	PASS	A	G	23216	0.97295	0	0,3,1,23199	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749334	23604	PASS	C	A	16223	0.946187	0	11,0,16204,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749334	23709	PASS	C	T	16207	0.940334	0	0,4,0,16182	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749334	24506	PASS	T	G	17612	0.973711	0	11,0,17599,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749334	24914	PASS	G	C	38296	0.959186	0	0,1,19075,19185	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749334	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	26137	0.001148	47	18507,7577,41,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749334	25496	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	37206	6.72E-4	117	18440,18290,153,301	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aTa/aGa	I35R	orf3a	0.000369	0.96555	3	2	T>G
ERR5749334	25571	PASS	C	T	18645	0.91778	0	0,13,0,18612	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	tCc/tTc	S60F	orf3a	0.001558	0.922217	1	1	C>T
ERR5749334	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	16506	0.001757	363	16437,19,14,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749334	25855	PASS	G	T	16459	0.908621	0	0,37,0,16409	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gac/Tac	D155Y	orf3a	0.001326	0.969697	1	1	G>T
ERR5749334	27972	PASS	C	T	10639	0.90281	42	1,2,10558,45	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749334	28048	PASS	G	T	10596	0.919592	0	0,16,0,10575	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749334	28111	PASS	A	G	33241	0.978611	1	5,1,22628,10594	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749334	28270	PASS	TA	T	43890	0.994782	476	223,13,22335,21326	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749334	28280	PASS	G	C	43792	0.937157	29	11,0,22389,21305	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749334	28281	PASS	A	T	43792	0.909687	30	29,8,22360,21308	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749334	28282	PASS	T	A	43797	0.90335	3	19,14,22282,21325	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749334	28881	PASS	G	A	14042	0.77959	0	0,0,6965,6900	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749334	28882	PASS	G	A	14042	0.83236	6	3,0,7026,6868	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749334	28883	PASS	G	C	14043	0.944955	6	0,2,7038,6993	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749334	28977	PASS	C	T	7125	0.929403	0	0,0,1,7117	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749334	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	39667	0.001311	267	32505,7063,8,47	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749334	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	64647	0.001299	1	32448,32070,56,52	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749335	145	PASS	T	C	8174	0.955346	0	1,0,8160,0	.	.	.	.	.	.	.	0.955346	0.955346	1	1	T>C
ERR5749335	241	PASS	C	T	13669	0.816446	0	0,1,5489,8089	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749335	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	12545	0.002232	0	12518,0,28,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749335	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	12545	8.77E-4	0	12498,0,11,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749335	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	12545	0.002391	0	12498,0,30,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749335	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12543	0.001834	0	11677,4,763,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749335	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	12542	9.57E-4	0	12527,4,12,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749335	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	12542	8.77E-4	0	12523,4,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749335	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	12542	7.18E-4	0	12526,4,9,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749335	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	35508	8.17E-4	9	22908,12562,23,6	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749335	913	PASS	C	T	22924	0.921218	0	0,14,0,22878	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749335	1390	PASS	T	C	23499	0.968424	0	1,0,23477,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaT/aaC	N195	nsp2	0.0033	0.968424	1	1	T>C
ERR5749335	1510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	23481	0.002513	0	0,23198,0,69	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G235	nsp2	0.002159	0.937304	1	1	T>C
ERR5749335	3037	PASS	C	T	20247	0.820912	63	0,21,10119,9988	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749335	3267	PASS	C	T	20334	0.96705	0	2,0,20321,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749335	3811	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	39205	0.002015	0	27387,11723,55,25	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ctC/ctT	L364	nsp3	0.002015	0.946635	1	1	C>T
ERR5749335	3959	PASS	A	G	27341	0.913902	0	9,0,27288,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Atc/Gtc	I414V	nsp3	0.913902	0.913902	1	1	A>G
ERR5749335	4573	PASS	C	T	15071	0.844138	0	0,10,0,15024	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N618	nsp3	0.001686	0.844138	2	2	C>T
ERR5749335	5388	PASS	C	A	6568	0.957217	2147483647	0,0,6566,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749335	5986	PASS	C	T	13478	0.97277	0	1,0,13472,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749335	6954	PASS	T	C	25060	0.828452	0	0,14,0,24915	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749335	7239	PASS	C	T	48201	0.901952	0	3,3,23992,24126	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCa/gTa	A1507V	nsp3	0.000568	0.901952	2	2	C>T
ERR5749335	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	32724	3.67E-4	41	14866,17846,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749335	10252	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17453	0.015585	0	17141,1,291,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F66	3Cpro	0.000645	0.943062	2	2	C>T
ERR5749335	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	17966	0.001781	0	17911,0,48,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749335	11287	PASS	GTCTGGTTTT	G	17963	0.99794	0	0,37,0,17926	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749335	12269	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	25252	4.75E-4	0	25239,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aag/	K61	nsp8	0.000434	0.213333	2	1	GA>G
ERR5749335	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	31297	9.59E-4	0	15631,15595,16,16	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749335	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	13504	0.005036	2147483647	13159,106,7,218	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749335	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	26221	8.77E-4	0	13144,13074,12,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749335	14408	PASS	C	T	26221	0.849929	3	5,8,13074,12943	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749335	14676	PASS	C	T	13611	0.791492	0	6,0,13559,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749335	15279	PASS	C	T	24516	0.892642	0	3,0,24468,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749335	16176	PASS	T	C	20783	0.981187	0	0,0,9662,11120	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749335	17615	PASS	A	G	14620	0.915595	2147483647	0,0,0,14574	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749335	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	23405	8.55E-4	0	23385,0,20,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749335	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30917	0.001714	0	30839,0,58,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749335	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28942	0.001244	3	14195,14430,19,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749335	21764	PASS	ATACATG	A	13189	0.996361	0	48,0,13140,1	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749335	21990	PASS	TTTA	T	13201	0.998561	0	0,19,11,13171	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749335	23063	PASS	A	T	10330	0.874927	0	0,1,0,10286	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749335	23271	PASS	C	A	22795	0.924852	0	1,0,22772,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749335	23403	PASS	A	G	22789	0.969327	0	0,4,0,22769	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749335	23604	PASS	C	A	14976	0.93957	0	14,0,14953,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749335	23625	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14974	0.002538	0	14920,1,40,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gTt	A688V	S	0.002362	0.901054	2	2	C>T
ERR5749335	23709	PASS	C	T	14966	0.948684	0	0,7,3,14936	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749335	24506	PASS	T	G	18620	0.975027	0	6,0,18612,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749335	24914	PASS	G	C	25102	0.963031	0	0,0,12496,12581	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749335	25290	PASS	G	T	8360	0.859689	319	12,12,0,8330	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tGt/tTt	C1243F	S	0.001422	0.869662	1	1	G>T
ERR5749335	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	21768	0.005053	257	13290,8342,123,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749335	26774	PASS	G	A	9277	0.943732	0	0,5,1,9239	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	atG/atA	M84I	M	0.000483	0.943732	7	2	G>A
ERR5749335	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	9282	0.001293	0	1,9268,0,12	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749335	27625	PASS	C	T	22252	0.951914	0	2,0,22127,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Cgt/Tgt	R78C	orf7a	0.00584	0.951914	1	1	C>T
ERR5749335	27972	PASS	C	T	9498	0.899663	0	0,0,9428,42	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749335	28001	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	18890	0.001112	0	9418,9426,14,14	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ccG/ccA	P36	orf8	0.00085	0.830607	2	1	G>A
ERR5749335	28048	PASS	G	T	9468	0.923849	0	0,13,0,9450	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749335	28111	PASS	A	G	25632	0.978542	2	2,2,16145,9472	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749335	28270	PASS	TA	T	31385	0.994775	419	166,4,15906,15315	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749335	28280	PASS	G	C	31325	0.938037	12	11,3,15957,15303	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749335	28281	PASS	A	T	31325	0.916648	21	19,5,15945,15305	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749335	28282	PASS	T	A	31329	0.911456	11	14,5,15909,15321	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749335	28881	PASS	G	A	13120	0.813491	11	7,1,6520,6443	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749335	28882	PASS	G	A	13119	0.826968	4	4,1,6555,6439	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749335	28883	PASS	G	C	13119	0.945042	3	0,1,6573,6527	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749335	28960	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	6675	0.005094	0	3,6625,0,45	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	caG/caT	Q229H	N	0.00273	0.921139	2	2	G>T
ERR5749335	28977	PASS	C	T	6676	0.930647	0	0,1,3,6666	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749335	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	35725	8.4E-4	0	17932,17742,17,17	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749336	241	PASS	C	T	16	0.75	0	0,0,8,8	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749336	843	PASS	CTGA	C	1355	0.050923	0	644,642,35,34	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gatggc/ggc	DG14G	nsp2	0.000301	0.050923	4	2	CTGA>C
ERR5749336	913	PASS	C	T	679	0.92489	2147483647	0,0,0,679	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749336	1813	PASS	T	TA	467	0.059957	0	0,439,0,28	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggt/Aggt	G339R?	nsp2	0.001022	0.152738	4	2	T>TA
ERR5749336	2403	PASS	CA	C	259	0.061776	0	0,243,0,16	HIGH	NONE	FRAME_SHIFT	ORF1ab	aag/	K534	nsp2	0.000951	0.061776	2	1	CA>C
ERR5749336	3037	PASS	C	T	166	0.777108	0	0,0,84,80	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749336	3267	PASS	C	T	416	0.978365	2147483647	0,0,415,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749336	4607	PASS	A	T	544	0.051471	0	0,507,0,36	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Atg/Ttg	M630L	nsp3	0.051471	0.051471	1	1	A>T
ERR5749336	5388	PASS	C	A	51	0.960784	2147483647	0,0,51,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749336	5986	PASS	C	T	232	0.987069	2147483647	0,0,232,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749336	6762	PASS	C	T	708	0.957627	0	0,0,423,283	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T1348I	nsp3	0.001474	0.966761	2	1	C>T
ERR5749336	6954	PASS	T	C	421	0.826603	2147483647	0,0,0,420	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749336	8664	PASS	C	T	142	0.985915	2147483647	0,0,142,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T37I	nsp4	0.003182	0.985915	1	1	C>T
ERR5749336	8906	PASS	T	C	142	0.091549	0	0,128,0,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F118L	nsp4	0.005779	0.091549	2	1	T>C
ERR5749336	10386	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	1510	0.007947	33	754,744,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	tca/	S113	3Cpro	0.000642	0.160456	4	2	CT>C
ERR5749336	11095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	848	0.004717	0	844,0,4,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L43	nsp6	0.000515	0.887707	7	2	CT>C
ERR5749336	11287	PASS	GTCTGGTTTT	G	848	0.997642	0	0,2,0,846	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749336	12162	PASS	A	G	1956	0.968814	0	0,0,174,1780	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cAg/cGg	Q24R	nsp8	0.000894	0.982497	1	1	A>G
ERR5749336	14408	PASS	C	T	22	0.818182	0	0,0,11,11	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749336	14676	PASS	C	T	336	0.791667	2147483647	0,0,335,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749336	15279	PASS	C	T	399	0.874687	2147483647	0,0,397,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749336	15951	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	395	0.027848	0	384,0,11,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I837	RdRp	0.027848	0.334146	1	1	C>T
ERR5749336	16176	PASS	T	C	450	0.991111	0	0,0,55,394	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749336	16524	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	1338	0.007474	0	1326,0,12,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acA/acG	T96	helicase	0.00047	0.926983	2	2	A>G
ERR5749336	16939	PASS	T	C	485	0.954639	2147483647	0,0,482,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Tta/Cta	L235	helicase	0.000959	0.959205	2	2	T>C
ERR5749336	17122	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCT	G	831	0.013237	42	334,486,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctctac/	LY297	helicase	0.000476	0.056834	3	2	GCT>G
ERR5749336	17615	PASS	A	G	423	0.929078	2147483647	0,0,0,423	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749336	18246	PASS	C	T	264	0.984848	2147483647	0,0,0,264	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y69	ExoN	0.960724	0.984848	1	1	C>T
ERR5749336	18504	PASS	A	G	1179	0.094148	0	0,1049,0,117	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaA/aaG	K155	ExoN	0.000518	0.094148	4	3	A>G
ERR5749336	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	241	0.045643	0	230,0,11,0	HIGH	NONE	FRAME_SHIFT+STOP_GAINED	ORF1ab	gat/Tgat	D124*?	endoR	0.000884	0.981982	5	2	C>CT
ERR5749336	21764	PASS	ATACATG	A	626	0.998403	0	1,0,625,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749336	21990	PASS	TTTA	T	626	1.0	2147483647	0,0,0,626	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749336	23042	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	474	0.031646	0	0,456,0,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Cca	S494P	S	0.030769	0.900602	1	1	T>C
ERR5749336	23063	PASS	A	T	475	0.865263	2147483647	0,0,0,473	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749336	23271	PASS	C	A	1076	0.925651	2147483647	0,0,1075,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749336	23403	PASS	A	G	1076	0.967472	2147483647	0,0,0,1075	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749336	23604	PASS	C	A	525	0.921905	2147483647	0,0,524,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749336	23709	PASS	C	T	523	0.927342	2147483647	0,0,0,523	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749336	24506	PASS	T	G	606	0.971947	2147483647	0,0,606,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749336	24914	PASS	G	C	2422	0.962428	0	0,0,1209,1213	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749336	25571	PASS	C	T	2504	0.911342	0	0,1,0,2499	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	tCc/tTc	S60F	orf3a	0.001558	0.922217	1	1	C>T
ERR5749336	25572	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	2504	0.018371	0	0,2458,0,46	HIGH	NONE	FRAME_SHIFT	ORF3a	atc/	I62	orf3a	0.000543	0.959687	4	2	CA>C
ERR5749336	25855	PASS	G	T	33	0.969697	2147483647	0,0,0,33	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gac/Tac	D155Y	orf3a	0.001326	0.969697	1	1	G>T
ERR5749336	26717	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	629	0.012719	0	310,308,4,4	LOW	SILENT	SYNONYMOUS_CODING	M	ttT/ttC	F65	M	0.001602	0.063291	2	2	T>C
ERR5749336	27493	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2185	0.018307	10	1100,1043,15,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Cct/Tct	P34S	orf7a	0.000794	0.971493	2	1	C>T
ERR5749336	27972	PASS	C	T	80	0.95	2147483647	0,0,80,0	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749336	28048	PASS	G	T	80	0.9375	2147483647	0,0,0,80	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749336	28111	PASS	A	G	2907	0.977984	0	1,0,2824,80	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749336	28270	PASS	TA	T	5482	0.995075	63	26,1,2788,2667	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749336	28280	PASS	G	C	5470	0.938757	0	1,0,2796,2662	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749336	28281	PASS	A	T	5470	0.925594	2	3,1,2793,2665	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749336	28282	PASS	T	A	5470	0.909141	0	1,1,2786,2664	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749336	28881	PASS	G	A	125	0.784	0	0,0,63,59	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749336	28882	PASS	G	A	125	0.816	0	0,0,62,61	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749336	28883	PASS	G	C	125	0.936	0	0,0,63,62	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749336	28977	PASS	C	T	64	0.9375	2147483647	0,0,0,64	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749337	241	PASS	C	T	15748	0.867285	0	0,0,7837,7847	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749337	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	12351	0.002186	0	12327,0,27,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749337	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	12351	0.0017	0	12311,0,21,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749337	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12339	0.001783	0	11342,2,914,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749337	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	12339	0.001621	0	12317,2,20,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749337	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	31789	0.001258	1	19388,12358,26,14	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749337	913	PASS	C	T	19394	0.912241	0	0,8,0,19356	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749337	1510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	19636	0.004023	0	0,19370,0,89	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G235	nsp2	0.002159	0.937304	1	1	T>C
ERR5749337	1813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	16528	0.001271	0	0,16486,0,24	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcA	A336	nsp2	0.001022	0.152738	4	2	T>A
ERR5749337	3037	PASS	C	T	22540	0.802972	82	0,27,11265,11049	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749337	3177	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	29372	9.19E-4	55	17989,11345,33,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cAt	P153H	nsp3	0.000773	0.96008	3	2	C>A
ERR5749337	3267	PASS	C	T	18026	0.970321	0	1,0,18016,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749337	4578	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTAACGATC	T	13084	8.41E-4	0	1,13072,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	aacgatctaaat/	NDLN621	nsp3	0.000519	0.082979	2	2	TTAACGATC>T
ERR5749337	5170	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	10849	7.37E-4	0	0,10841,0,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T819	nsp3	0.000565	0.894036	2	2	CCA>C
ERR5749337	5388	PASS	C	A	7641	0.95799	2147483647	0,0,7636,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749337	5986	PASS	C	T	14082	0.974435	0	3,0,14072,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749337	6954	PASS	T	C	21896	0.813025	0	0,4,0,21775	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749337	7764	PASS	C	T	22557	0.963337	0	1,0,22540,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCc/tTc	S1682F	nsp3	0.001052	0.964731	1	1	C>T
ERR5749337	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	30658	3.59E-4	28	16867,13780,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749337	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	16204	0.001913	0	16149,0,45,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749337	11287	PASS	GTCTGGTTTT	G	16198	0.998024	0	0,31,0,16166	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749337	11464	PASS	G	T	14718	0.902704	0	11,0,14684,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atT	M164I	nsp6	0.001064	0.906658	2	2	G>T
ERR5749337	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29406	0.001394	0	14690,14638,23,23	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749337	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	14523	0.0042	2147483647	14187,79,8,242	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749337	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	28241	8.85E-4	0	14172,14066,13,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749337	14408	PASS	C	T	28242	0.859819	16	2,10,14120,13937	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749337	14676	PASS	C	T	11726	0.772216	0	2,0,11691,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749337	15279	PASS	C	T	20245	0.891479	0	2,0,20215,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749337	16176	PASS	T	C	19577	0.979466	0	0,0,10833,8733	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749337	17799	PASS	A	G	12564	0.974292	0	3,0,12555,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtA/gtG	V521	helicase	0.001548	0.98027	1	1	A>G
ERR5749337	18457	PASS	C	T	26332	0.951352	0	2,0,26309,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cca/Tca	P140S	ExoN	0.001253	0.951352	2	1	C>T
ERR5749337	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	32261	0.001922	0	32181,0,64,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749337	21658	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14836	0.027164	0	0,14397,0,430	LOW	SILENT	SYNONYMOUS_CODING	S	ttC/ttT	F32	S	0.001649	0.937508	2	2	C>T
ERR5749337	21764	PASS	ATACATG	A	14049	0.997793	0	31,0,14018,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749337	21990	PASS	TTTA	T	14050	0.99879	0	0,17,0,14033	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749337	23063	PASS	A	T	12605	0.861008	0	0,4,0,12529	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749337	23271	PASS	C	A	18943	0.928206	2147483647	0,0,18923,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749337	23403	PASS	A	G	18932	0.964346	0	0,2,0,18916	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749337	23541	PASS	A	T	16479	0.913041	0	3,0,16463,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tAt/tTt	Y660F	S	0.000911	0.950734	4	2	A>T
ERR5749337	23604	PASS	C	A	16476	0.951566	0	11,0,16460,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749337	23709	PASS	C	T	16441	0.930844	0	0,6,1,16399	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749337	23817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	32986	9.09E-4	0	16484,16457,17,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTt/cCt	L752P	S	0.000646	0.066832	1	1	T>C
ERR5749337	24506	PASS	T	G	16706	0.972704	0	9,0,16696,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749337	24914	PASS	G	C	35081	0.956957	0	0,0,17490,17570	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749337	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	24250	0.001526	50	17718,6480,47,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749337	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	22630	0.001149	258	22539,17,16,11	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749337	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	22602	7.08E-4	0	22586,0,16,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749337	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	22746	0.001275	1338	22400,119,107,89	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749337	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	12205	0.002212	0	0,12176,0,27	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749337	27972	PASS	C	T	12082	0.899686	78	4,4,11988,44	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749337	28001	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	24039	9.57E-4	0	11988,12004,14,14	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ccG/ccA	P36	orf8	0.00085	0.830607	2	1	G>A
ERR5749337	28048	PASS	G	T	12041	0.9172	0	0,15,0,12021	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749337	28093	PASS	C	T	12054	0.222499	2	5,9264,0,2775	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tCt/tTt	S67F	orf8	0.001515	0.967675	1	1	C>T
ERR5749337	28111	PASS	A	G	12054	0.975444	0	0,1,5,12044	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749337	28270	PASS	TA	T	16217	0.999445	0	0,8,6,16202	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749337	28280	PASS	G	C	16220	0.911714	0	0,0,6,16191	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749337	28281	PASS	A	T	16220	0.922565	0	0,4,6,16194	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749337	28282	PASS	T	A	16221	0.94914	0	0,7,6,16205	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749337	28881	PASS	G	A	14456	0.742806	16	9,1,7139,7078	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749337	28882	PASS	G	A	14453	0.824189	0	3,3,7232,7083	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749337	28883	PASS	G	C	14455	0.941128	6	3,0,7246,7196	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749337	28977	PASS	C	T	7373	0.923912	0	0,2,0,7357	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749337	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	47565	0.001009	0	23902,23595,31,29	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749337	29774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9869	0.003952	0	1,9814,0,43	.	.	.	.	.	.	.	0.002525	0.973955	1	1	C>T
ERR5749338	174	PASS	G	T	12967	0.710959	0	139,0,12805,0	.	.	.	.	.	.	.	0.710959	0.747093	1	1	G>T
ERR5749338	241	PASS	C	T	25824	0.864699	0	2,3,12852,12880	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749338	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	10246	0.00205	0	10223,4,21,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749338	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	10247	0.001952	20	10213,4,19,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749338	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10240	0.002148	3	9345,6,827,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749338	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	10240	8.79E-4	0	10223,8,9,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749338	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	10240	7.81E-4	0	10220,8,8,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749338	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	32792	4.88E-4	15	22514,10257,15,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749338	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	32792	0.002135	8	22474,10240,54,16	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749338	1059	PASS	C	T	8596	0.912052	0	2,0,8587,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCc/aTc	T85I	nsp2	0.001728	0.920973	1	1	C>T
ERR5749338	1594	PASS	C	T	24604	0.963177	0	0,7,0,24586	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S263	nsp2	0.0019	0.963177	1	1	C>T
ERR5749338	2692	PASS	A	T	60	0.933333	0	0,0,59,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acA/acT	T629	nsp2	0.888889	0.933333	1	1	A>T
ERR5749338	3037	PASS	C	T	15193	0.821365	48	0,16,7593,7493	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749338	5230	PASS	G	T	15143	0.891303	0	0,11,0,15095	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaG/aaT	K837N	nsp3	0.002515	0.902519	1	1	G>T
ERR5749338	8139	PASS	C	T	26644	0.403093	13	14382,11,12193,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCc/tTc	S1807F	nsp3	0.001297	0.889336	1	1	C>T
ERR5749338	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	30509	3.93E-4	48	12041,18456,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749338	10323	PASS	A	G	13508	0.963281	0	0,2,0,13499	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749338	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20481	0.001562	0	20414,2,36,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749338	11082	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	20474	5.86E-4	0	20467,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000427	0.179468	2	1	TG>T
ERR5749338	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	20474	0.0021	0	20395,0,63,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749338	11287	PASS	GTCTGGTTTT	G	20469	0.998486	28	1,30,0,20438	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749338	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	34208	8.48E-4	2	23118,11036,23,8	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749338	12459	PASS	C	T	38357	0.985583	12	5,2,13492,24850	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T123I	nsp8	0.000658	0.986093	1	1	C>T
ERR5749338	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	41652	0.00132	0	20794,20747,30,30	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749338	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	9841	0.004776	2562	9654,48,2,133	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749338	14408	PASS	C	T	19216	0.847107	4	1,3,9598,9503	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749338	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	26282	6.09E-4	0	2,26264,0,16	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749338	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23452	0.001834	0	23389,0,43,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749338	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	33934	0.001267	2	16543,16980,22,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749338	21614	PASS	C	T	17119	0.928442	0	0,6,0,17099	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L18F	S	0.001194	0.949239	2	2	C>T
ERR5749338	21801	PASS	A	C	9196	0.946172	0	6,0,9182,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gCt	D80A	S	0.005484	0.946172	2	2	A>C
ERR5749338	22206	PASS	A	G	22704	0.950097	0	0,4,0,22679	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D215G	S	0.002035	0.950097	2	1	A>G
ERR5749338	22280	PASS	ACTTTACTTG	A	22720	0.997799	0	0,50,0,22670	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	cttgctttacat/cat	LALH242H	S	0.00046	0.997799	1	1	ACTTTACTTG>A
ERR5749338	22813	PASS	G	T	16305	0.937872	0	0,7,0,16295	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aaG/aaT	K417N	S	0.937872	0.94113	1	1	G>T
ERR5749338	23012	PASS	G	A	17602	0.909158	20	8,0,9112,8464	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gaa/Aaa	E484K	S	0.001756	0.909912	2	1	G>A
ERR5749338	23063	PASS	A	T	9225	0.88206	0	0,2,0,9181	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749338	23403	PASS	A	G	24898	0.969676	2147483647	0,0,0,24887	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749338	23664	PASS	C	T	24112	0.914731	9	0,4,11759,12299	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCa/gTa	A701V	S	0.000837	0.918	2	2	C>T
ERR5749338	25469	PASS	C	T	13239	0.940479	0	1,0,13212,11	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	tCa/tTa	S26L	orf3a	0.001214	0.959377	2	2	C>T
ERR5749338	25563	PASS	G	T	13242	0.871319	0	0,44,1,13189	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	caG/caT	Q57H	orf3a	0.001456	0.886549	2	1	G>T
ERR5749338	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	25871	0.001198	312	25783,14,21,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749338	25687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	25844	9.67E-4	0	25814,0,27,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gct/Act	A99T	orf3a	0.000967	0.944569	1	1	G>A
ERR5749338	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	25844	6.96E-4	0	25826,0,18,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749338	25720	PASS	G	T	25842	0.951784	0	20,0,25811,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gct/Tct	A110S	orf3a	0.947933	0.951784	1	1	G>T
ERR5749338	25904	PASS	C	T	25852	0.805199	317	9,3,0,25714	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	tCa/tTa	S171L	orf3a	0.000757	0.83473	1	1	C>T
ERR5749338	26456	PASS	C	T	15222	0.927736	0	0,5,0,15180	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	cCt/cTt	P71L	E	0.001544	0.927736	1	1	C>T
ERR5749338	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	9239	0.002381	0	0,9215,0,22	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749338	27312	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	13935	0.001507	0	13915,0,21,0	HIGH	NONE	FRAME_SHIFT	ORF6	aat/aaAt	N39K?	orf6	0.000911	0.088458	4	2	T>TA
ERR5749338	28200	PASS	T	G	23128	0.978468	0	10,0,23112,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	Tcg/Gcg	S103A	orf8	0.000751	0.981434	2	2	T>G
ERR5749338	28253	PASS	C	T	23072	0.950286	0	17,0,23038,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749338	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	23072	6.5E-4	0	23057,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749338	28254	PASS	A	C	23072	0.914398	0	62,0,22991,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	Atc/Ctc	I121L	orf8	0.000541	0.914398	3	2	A>C
ERR5749338	28310	PASS	C	T	23094	0.918594	0	0,9,0,23038	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Ccc/Tcc	P13S	N	0.00095	0.92832	2	1	C>T
ERR5749338	28887	PASS	C	T	18670	0.814997	9	2,7,9296,9121	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aCt/aTt	T205I	N	0.002174	0.814997	2	2	C>T
ERR5749338	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	29771	9.07E-4	95	20378,9342,3,25	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749338	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	40520	8.39E-4	0	20327,20119,26,24	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749339	241	PASS	C	T	501	0.88024	0	0,0,250,249	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749339	913	PASS	C	T	1296	0.895833	2147483647	0,0,0,1292	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749339	2110	PASS	C	T	608	0.805921	2147483647	0,0,0,604	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N435	nsp2	0.024426	0.811371	1	1	C>T
ERR5749339	2144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	608	0.037829	0	0,578,0,29	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtc/Ttc	V447F	nsp2	0.004278	0.752119	2	1	G>T
ERR5749339	3037	PASS	C	T	1071	0.796452	3	0,1,534,526	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749339	3267	PASS	C	T	1210	0.971901	2147483647	0,0,1210,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749339	5388	PASS	C	A	358	0.941341	2147483647	0,0,358,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749339	5512	PASS	C	T	356	0.932584	2147483647	0,0,0,356	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N931	nsp3	0.002299	0.987013	1	1	C>T
ERR5749339	5986	PASS	C	T	1289	0.976726	2147483647	0,0,1288,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749339	6954	PASS	T	C	2776	0.806556	2147483647	0,0,0,2762	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749339	7600	PASS	C	T	1517	0.973632	2147483647	0,0,0,1517	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C1627	nsp3	0.001321	0.973632	1	1	C>T
ERR5749339	8084	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	1666	0.004202	0	1660,0,7,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1790	nsp3	0.000543	0.923413	4	2	GA>G
ERR5749339	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	2254	0.011535	4	2107,121,26,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749339	11095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	8373	0.020423	0	8201,0,171,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L43	nsp6	0.000515	0.887707	7	2	CT>C
ERR5749339	11287	PASS	GTCTGGTTTT	G	8375	0.998925	0	0,9,0,8366	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749339	12809	PASS	C	T	478	0.880753	2147483647	0,0,478,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Ttt	L42F	nsp9	0.001562	1	1	1	C>T
ERR5749339	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5764	0.004684	0	2864,2859,16,16	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749339	14120	PASS	C	T	5834	0.729688	3	0,1,2904,2854	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCa/cTa	P227L	RdRp	0.00121	0.786944	2	2	C>T
ERR5749339	14408	PASS	C	T	184	0.788043	0	0,0,93,90	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749339	14676	PASS	C	T	1313	0.83473	2147483647	0,0,1312,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749339	15279	PASS	C	T	1228	0.887622	2147483647	0,0,1227,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749339	16176	PASS	T	C	1739	0.981024	0	0,0,484,1254	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749339	18079	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	713	0.023843	0	694,0,19,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gta/Ata	V14I	ExoN	0.003215	0.944695	2	1	G>A
ERR5749339	20091	PASS	C	CA	853	0.051583	0	0,809,0,44	HIGH	NONE	FRAME_SHIFT	ORF1ab	caa/Acaa	Q159T?	endoR	0.000368	0.051583	1	1	C>CA
ERR5749339	21145	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	5888	0.011209	231	3312,2501,2,72	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Att	L163I	MethTr	0.001379	0.921396	3	2	C>A
ERR5749339	21764	PASS	ATACATG	A	2727	0.996333	0	9,0,2717,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749339	21990	PASS	TTTA	T	2730	0.996703	0	0,9,2,2719	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749339	22225	PASS	G	T	4219	0.923679	0	0,4,0,4212	LOW	SILENT	SYNONYMOUS_CODING	S	tcG/tcT	S221	S	0.001195	0.94526	3	1	G>T
ERR5749339	22289	PASS	G	T	4222	0.915917	0	0,2,0,4215	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gct/Tct	A243S	S	0.000446	0.915917	3	2	G>T
ERR5749339	23063	PASS	A	T	1288	0.874224	2147483647	0,0,0,1283	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749339	23271	PASS	C	A	1552	0.925902	2147483647	0,0,1550,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749339	23403	PASS	A	G	1552	0.965851	2147483647	0,0,0,1551	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749339	23604	PASS	C	A	1569	0.950924	0	1,0,1567,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749339	23709	PASS	C	T	1568	0.935587	2147483647	0,0,0,1567	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749339	24506	PASS	T	G	2580	0.974806	2147483647	0,0,2580,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749339	24914	PASS	G	C	9776	0.956424	0	0,0,4864,4906	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749339	25523	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	5687	0.001407	0	0,5125,0,561	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	gGa/gTa	G44V	orf3a	0.000994	0.895931	1	1	G>T
ERR5749339	25531	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	5973	0.002846	0	0,5283,0,690	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Att/Ttt	I47F	orf3a	0.000473	0.975891	5	2	A>T
ERR5749339	25553	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	6355	0.026279	0	0,6188,0,167	HIGH	NONE	FRAME_SHIFT	ORF3a	gtt/Tgtt	V55C?	orf3a	0.001165	0.868131	3	2	C>CT
ERR5749339	25555	PASS	G	T	6355	0.886703	2147483647	0,0,0,6346	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gtt/Ttt	V55F	orf3a	0.000552	0.900573	5	2	G>T
ERR5749339	25555	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	6355	0.035563	0	0,6128,0,226	HIGH	NONE	FRAME_SHIFT	ORF3a	cag/Tcag	Q57S?	orf3a	0.000552	0.900573	5	2	G>GT
ERR5749339	25636	PASS	A	T	6585	0.068641	6	184,5922,9,469	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Aac/Tac	N82Y	orf3a	0.068641	0.068641	1	1	A>T
ERR5749339	26775	PASS	GCTTGT	G	1426	0.053997	0	0,1314,0,77	HIGH	NONE	FRAME_SHIFT	M	cttgta/	LV87	M	0.000483	0.053997	3	1	GCTTGT>G
ERR5749339	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	1426	0.024544	0	0,1314,0,35	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749339	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	1426	0.020337	0	0,1397,0,29	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749339	27972	PASS	C	T	396	0.901515	0	0,0,388,6	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749339	28048	PASS	G	T	389	0.935733	2147483647	0,0,0,388	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749339	28095	PASS	A	T	395	0.959494	89	4,0,0,391	HIGH	NONSENSE	STOP_GAINED	ORF8	Aaa/Taa	K68*	orf8	0.002672	0.967672	2	2	A>T
ERR5749339	28111	PASS	A	G	8469	0.980281	0	2,0,8072,391	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749339	28270	PASS	TA	T	15671	0.996235	134	60,3,7995,7617	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749339	28280	PASS	G	C	15643	0.936905	0	3,3,8000,7604	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749339	28281	PASS	A	T	15643	0.918302	14	8,1,7997,7611	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749339	28282	PASS	T	A	15643	0.909161	6	5,1,7971,7619	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749339	28292	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	16076	9.95E-4	0	8013,8047,8,8	HIGH	NONE	FRAME_SHIFT	N	aat/	N8	N	0.000304	0.055324	4	2	CA>C
ERR5749339	28881	PASS	G	A	482	0.759336	0	0,0,239,237	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749339	28882	PASS	G	A	482	0.819502	0	0,0,242,239	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749339	28883	PASS	G	C	482	0.910788	0	0,0,242,239	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749339	28977	PASS	C	T	243	0.942387	2147483647	0,0,0,243	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749340	241	PASS	C	T	114	0.903509	0	0,0,57,57	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749340	292	PASS	C	T	57	0.947368	2147483647	0,0,0,57	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N9	leader	0.939339	0.96124	1	1	C>T
ERR5749340	913	PASS	C	T	5163	0.905481	0	0,8,0,5144	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749340	1492	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	2092	0.00478	0	0,2074,0,11	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgT/tgC	C229	nsp2	0.000868	0.321508	3	3	T>C
ERR5749340	2250	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	1821	0.013729	0	1793,0,27,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGa/gCa	G482A	nsp2	0.013729	0.06689	1	1	G>C
ERR5749340	3037	PASS	C	T	1273	0.812254	6	0,2,635,629	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749340	3267	PASS	C	T	4901	0.966333	2147483647	0,0,4897,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749340	3802	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	2821	0.003899	71	627,2183,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N363	nsp3	0.000554	0.064198	4	2	TA>T
ERR5749340	4960	PASS	G	T	2806	0.062723	0	0,2628,0,178	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtG/gtT	V747	nsp3	0.000673	0.062723	2	2	G>T
ERR5749340	5388	PASS	C	A	315	0.952381	2147483647	0,0,315,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749340	5986	PASS	C	T	1812	0.974614	2147483647	0,0,1810,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749340	6516	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	4788	0.007728	154	1848,2900,38,0	HIGH	NONSENSE	STOP_GAINED	ORF1ab	tTa/tAa	L1266*	nsp3	0.000479	0.186047	4	2	T>A
ERR5749340	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	1880	0.007447	0	0,1866,0,14	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L1328S?	nsp3	0.000731	0.14377	4	2	C>CT
ERR5749340	6954	PASS	T	C	3635	0.806052	0	0,2,0,3619	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749340	6982	PASS	C	T	3645	0.911934	0	0,1,0,3639	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C1421	nsp3	0.001915	0.911934	1	1	C>T
ERR5749340	7764	PASS	C	T	6778	0.95869	0	1,0,6772,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCc/tTc	S1682F	nsp3	0.001052	0.964731	1	1	C>T
ERR5749340	8254	PASS	A	G	3660	0.959563	2147483647	0,0,0,3652	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atA/atG	I1845M	nsp3	0.000412	0.959563	2	2	A>G
ERR5749340	9473	PASS	G	A	90	0.888889	2147483647	0,0,0,90	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gct/Act	A307T	nsp4	0.888889	1	1	1	G>A
ERR5749340	11287	PASS	GTCTGGTTTT	G	9357	0.987496	0	0,117,0,9240	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749340	11991	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	8559	0.011684	0	8451,0,102,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gAa/gGa	E50G	nsp7	0.003937	0.05063	1	1	A>G
ERR5749340	13459	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	3729	0.001877	0	3722,0,7,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L8	nsp11	0.000691	0.060726	5	2	GT>G
ERR5749340	14408	PASS	C	T	128	0.875	0	0,0,63,63	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749340	14676	PASS	C	T	2744	0.818878	0	1,0,2733,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749340	15279	PASS	C	T	2644	0.87292	2147483647	0,0,2639,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749340	16176	PASS	T	C	3274	0.978925	0	0,0,263,3009	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749340	20544	PASS	C	T	5838	0.975334	2147483647	0,0,5836,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S308	endoR	0.000834	0.975334	2	1	C>T
ERR5749340	21657	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TCA	T	1965	0.016794	0	0,1932,0,33	HIGH	NONE	FRAME_SHIFT	S	acacgt/	TR33	S	0.000702	0.06812	2	2	TCA>T
ERR5749340	21764	PASS	ATACATG	A	3173	0.997164	0	9,0,3164,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749340	21987	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	3173	0.006303	0	0,3152,0,20	HIGH	NONE	FRAME_SHIFT	S	ggt/	G142	S	0.000998	0.922156	5	2	GT>G
ERR5749340	21990	PASS	TTTA	T	3173	0.991176	0	0,28,0,3145	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749340	21991	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTAT	T	3174	0.006301	0	1,3153,0,20	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.00078	0.991378	2	1	TTAT>T
ERR5749340	23063	PASS	A	T	2306	0.847355	0	0,1,0,2285	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749340	23271	PASS	C	A	6773	0.915842	2147483647	0,0,6762,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749340	23403	PASS	A	G	6764	0.971023	0	0,1,0,6762	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749340	23604	PASS	C	A	2517	0.924116	0	5,0,2508,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749340	23709	PASS	C	T	2515	0.93837	0	0,2,0,2508	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749340	24320	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	2443	0.008596	0	0,2422,0,21	HIGH	NONE	FRAME_SHIFT	S	ttg/Attg	L922I?	S	0.000763	0.138365	4	2	C>CA
ERR5749340	24506	PASS	T	G	4237	0.976398	0	1,0,4236,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749340	24914	PASS	G	C	18046	0.958162	3	1,0,8985,9053	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749340	25626	PASS	C	T	9500	0.900737	0	0,4,283,9202	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	caC/caT	H78	orf3a	0.000403	0.915633	3	2	C>T
ERR5749340	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	304	0.042763	174	284,7,0,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749340	27577	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAATTTGCTTTTGCTTGTCCTGACGGCGTAAAACACGTCTATCAGTT	C	4702	0.004892	0	4679,0,23,0	HIGH	NONE	FRAME_SHIFT	ORF7a	caatttgcttttgcttgtcctgacggcgtaaaacacgtctatcagtta/	QFAFACPDGVKHVYQL62	orf7a	0.000614	0.952205	4	2	CAATTTGCTTTTGCTTGTCCTGACGGCGTAAAACACGTCTATCAGTT>C
ERR5749340	27972	PASS	C	T	738	0.892954	0	0,0,731,5	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749340	28048	PASS	G	T	732	0.903005	0	0,3,0,729	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749340	28111	PASS	A	G	12244	0.975662	9	1,1,11502,735	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749340	28147	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	11510	0.007906	0	11417,2,91,0	HIGH	NONE	FRAME_SHIFT	ORF8	aca/Taca	T87Y?	orf8	0.000438	0.981624	4	2	C>CT
ERR5749340	28270	PASS	TA	T	22183	0.995086	230	110,7,11349,10725	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749340	28280	PASS	G	C	22141	0.94124	26	10,0,11372,10719	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749340	28281	PASS	A	T	22141	0.909308	19	16,4,11362,10719	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749340	28282	PASS	T	A	22142	0.910216	27	13,1,11342,10733	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749340	28292	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	22886	6.99E-4	0	11398,11472,8,8	HIGH	NONE	FRAME_SHIFT	N	aat/	N8	N	0.000304	0.055324	4	2	CA>C
ERR5749340	28378	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	11507	0.005909	0	0,11433,0,73	LOW	SILENT	SYNONYMOUS_CODING	N	gcG/gcT	A35	N	0.001609	0.060482	3	1	G>T
ERR5749340	28881	PASS	G	A	783	0.745849	3	1,0,381,389	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749340	28882	PASS	G	A	783	0.804598	0	0,0,391,380	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749340	28883	PASS	G	C	783	0.950192	0	0,0,391,390	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749340	28977	PASS	C	T	398	0.922111	2147483647	0,0,0,398	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749340	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	15140	0.001849	0	7596,7504,16,15	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749341	77	PASS	T	C	161	0.074534	0	149,0,12,0	.	.	.	.	.	.	.	0.074534	0.074534	1	1	T>C
ERR5749341	97	PASS	A	T	161	0.068323	0	150,0,11,0	.	.	.	.	.	.	.	0.068323	0.068323	1	1	A>T
ERR5749341	241	PASS	C	T	321	0.866044	0	0,0,160,158	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749341	323	PASS	GT	G	161	0.118012	0	0,142,0,19	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L21	leader	0.039216	0.118012	2	1	GT>G
ERR5749341	695	PASS	G	T	2309	0.073625	1385	1810,312,0,187	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gac/Tac	D144Y	leader	0.001683	0.073625	1	1	G>T
ERR5749341	913	PASS	C	T	1809	0.882808	0	0,1,0,1805	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749341	1656	PASS	T	C	1101	0.970936	2147483647	0,0,1100,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gTt/gCt	V284A	nsp2	0.970936	0.970936	1	1	T>C
ERR5749341	2639	PASS	G	A	1876	0.076226	0	1733,0,143,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E612K	nsp2	0.076226	0.076226	1	1	G>A
ERR5749341	2768	PASS	G	T	1873	0.758142	0	0,285,0,1586	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggt/Tgt	G17C	nsp3	0.758142	0.758142	1	1	G>T
ERR5749341	2823	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	1875	0.035733	0	0,1802,0,71	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cTt/cCt	L35P	nsp3	0.035733	0.069143	1	1	T>C
ERR5749341	2862	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAGA	C	2089	0.03303	30	213,1807,0,69	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gaagta/gta	EV49V	nsp3	0.000547	0.850688	4	2	CAGA>C
ERR5749341	3037	PASS	C	T	417	0.803357	0	0,0,210,204	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749341	3267	PASS	C	T	1587	0.973535	2147483647	0,0,1587,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749341	3466	PASS	TG	T	1588	0.051008	0	0,1507,0,81	HIGH	NONE	FRAME_SHIFT	ORF1ab	gga/	G250	nsp3	0.000976	0.051008	3	3	TG>T
ERR5749341	4668	PASS	C	T	710	0.969014	2147483647	0,0,710,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S650F	nsp3	0.002266	0.970109	2	1	C>T
ERR5749341	4693	PASS	TG	T	710	0.078873	0	654,0,56,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/	V659	nsp3	0.000654	0.078873	1	1	TG>T
ERR5749341	5388	PASS	C	A	140	0.978571	2147483647	0,0,140,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749341	5986	PASS	C	T	371	0.975741	2147483647	0,0,371,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749341	6678	PASS	T	C	1343	0.071482	0	620,607,54,51	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1320T	nsp3	0.000822	0.071482	2	1	T>C
ERR5749341	6954	PASS	T	C	1096	0.796533	2147483647	0,0,0,1092	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749341	7658	PASS	A	T	1416	0.055791	121	406,929,0,81	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Att/Ttt	I1647F	nsp3	0.001526	0.055791	1	1	A>T
ERR5749341	7740	PASS	A	T	406	0.078818	0	374,0,32,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gAt/gTt	D1674V	nsp3	0.000834	0.078818	3	2	A>T
ERR5749341	8964	PASS	C	T	1168	0.050514	0	1108,0,60,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCa/tTa	S137L	nsp4	0.000553	0.981649	4	2	C>T
ERR5749341	10045	PASS	TG	T	323	0.052632	0	0,306,0,17	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/	V498	nsp4	0.003321	0.052632	2	2	TG>T
ERR5749341	11199	PASS	CCA	C	8175	0.056758	0	3852,3860,234,230	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T77	nsp6	0.000309	0.056758	3	2	CCA>C
ERR5749341	11287	PASS	GTCTGGTTTT	G	4107	0.99927	0	0,3,0,4104	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749341	11504	PASS	G	T	553	0.052441	0	260,256,18,19	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gta/Tta	V178L	nsp6	0.052441	0.052441	1	1	G>T
ERR5749341	12024	PASS	C	T	6555	0.052021	0	6202,0,349,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCc/tTc	S61F	nsp7	0.002605	0.052021	1	1	C>T
ERR5749341	13134	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	3386	0.042233	0	3243,0,143,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	atc/	I38	nsp10	0.000682	0.107576	2	2	CA>C
ERR5749341	13459	PASS	GT	G	1268	0.060726	0	1191,0,77,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L8	nsp11	0.000691	0.060726	5	2	GT>G
ERR5749341	13468	PASS	CG	C	1268	0.076498	0	1171,0,97,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggg/	G10	nsp11	0.000713	0.076498	2	2	CG>C
ERR5749341	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	2141	0.00794	724	2090,6,3,39	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749341	14408	PASS	C	T	4166	0.845175	3	0,1,2087,2042	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749341	14676	PASS	C	T	702	0.82906	2147483647	0,0,701,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749341	15096	PASS	T	C	480	0.941667	2147483647	0,0,0,480	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaT/aaC	N552	RdRp	0.941667	0.970182	1	1	T>C
ERR5749341	15277	PASS	C	T	716	0.326816	0	462,0,254,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cac/Tac	H613Y	RdRp	0.006345	0.326816	1	1	C>T
ERR5749341	15279	PASS	C	T	716	0.903631	2147483647	0,0,716,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749341	15493	PASS	G	C	716	0.076816	0	0,658,0,58	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gcc/Ccc	A685P	RdRp	0.001408	0.076816	3	2	G>C
ERR5749341	15905	PASS	AG	A	1196	0.057692	0	1127,0,69,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggt/	G823	RdRp	0.000835	0.057692	2	1	AG>A
ERR5749341	16176	PASS	T	C	1386	0.970418	0	0,1,190,1195	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749341	16792	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CGTG	C	4551	0.026807	347	2160,2269,0,122	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	cgtgta/cta	RV186L	helicase	0.000335	0.072562	5	2	CGTG>C
ERR5749341	18086	PASS	C	T	264	0.075758	0	238,0,26,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T16I	ExoN	0.001699	0.075758	1	1	C>T
ERR5749341	18304	PASS	T	C	1271	0.071597	95	913,264,93,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Ctc	F89L	ExoN	0.003096	0.071597	1	1	T>C
ERR5749341	18357	PASS	T	C	1007	0.057597	0	947,0,59,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccT/ccC	P106	ExoN	0.001226	0.057597	1	1	T>C
ERR5749341	18897	PASS	TG	T	6509	0.060685	0	0,6114,0,395	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/	V287	ExoN	0.00046	0.060685	3	3	TG>T
ERR5749341	19096	PASS	G	T	257	0.105058	0	228,1,28,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gca/Tca	A353S	ExoN	0.000726	0.105058	3	2	G>T
ERR5749341	19269	PASS	C	T	1076	0.945167	2147483647	0,0,1076,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N410	ExoN	0.000773	0.954777	2	2	C>T
ERR5749341	19293	PASS	T	G	1076	0.060409	0	1011,0,65,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	agT/agG	S418R	ExoN	0.002704	0.060409	2	2	T>G
ERR5749341	20179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	273	0.043956	0	0,261,0,12	HIGH	NONSENSE	STOP_GAINED	ORF1ab	Caa/Taa	Q187*	endoR	0.001915	0.20339	1	1	C>T
ERR5749341	20203	PASS	A	G	273	0.054945	0	0,257,0,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Act/Gct	T195A	endoR	0.054945	0.054945	1	1	A>G
ERR5749341	20445	PASS	TA	T	3482	0.059736	0	0,3274,0,208	HIGH	NONE	FRAME_SHIFT	ORF1ab	aac/	N277	endoR	0.000518	0.059736	4	2	TA>T
ERR5749341	20455	PASS	T	C	3483	0.055699	0	0,3263,0,211	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Ctc	F279L	endoR	0.001499	0.055699	1	1	T>C
ERR5749341	20951	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3034	0.038893	0	2908,0,122,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCa/tTa	S98L	MethTr	0.000431	0.138667	3	3	C>T
ERR5749341	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	1953	0.049667	4	931,921,44,53	HIGH	NONE	FRAME_SHIFT	S	ctt/Tctt	L5S?	S	0.000394	0.091869	4	1	G>GT
ERR5749341	21736	PASS	C	T	643	0.122862	0	560,0,81,0	LOW	SILENT	SYNONYMOUS_CODING	S	ttC/ttT	F58	S	0.001596	0.804427	3	2	C>T
ERR5749341	21764	PASS	ATACATG	A	643	1.0	2147483647	0,0,643,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749341	21990	PASS	TTTA	T	643	1.0	2147483647	0,0,0,643	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749341	22289	PASS	G	T	1834	0.065431	0	0,1705,0,129	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gct/Tct	A243S	S	0.000446	0.915917	3	2	G>T
ERR5749341	23043	PASS	C	T	1025	0.056585	0	0,946,0,75	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCa/tTa	S494L	S	0.000881	0.056585	2	2	C>T
ERR5749341	23063	PASS	A	T	1029	0.859087	2147483647	0,0,0,1021	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749341	23271	PASS	C	A	4959	0.920145	2147483647	0,0,4954,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749341	23403	PASS	A	G	4958	0.960871	0	0,2,0,4947	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749341	23604	PASS	C	A	608	0.947368	0	1,0,606,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749341	23709	PASS	C	T	608	0.929276	2147483647	0,0,0,608	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749341	24506	PASS	T	G	1107	0.971093	2147483647	0,0,1107,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749341	24914	PASS	G	C	14904	0.959273	0	0,0,7425,7466	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749341	24998	PASS	G	T	7505	0.804131	0	0,29,0,7473	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Tac	D1146Y	S	0.001186	0.846993	3	1	G>T
ERR5749341	25496	PASS	T	G	12713	0.071659	2	5773,5735,587,606	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aTa/aGa	I35R	orf3a	0.000369	0.96555	3	2	T>G
ERR5749341	26060	PASS	C	T	1785	0.807283	2147483647	0,0,1772,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aCt/aTt	T223I	orf3a	0.000459	0.822477	2	2	C>T
ERR5749341	26564	PASS	A	G	2139	0.071529	396	904,1074,0,158	LOW	SILENT	SYNONYMOUS_CODING	M	aaA/aaG	K14	M	0.003994	0.071529	1	1	A>G
ERR5749341	27567	PASS	CTTTAGCACTCAA	C	2340	0.998291	0	4,0,2336,0	MODERATE	NONE	CODON_DELETION	ORF7a	agcactcaattt/	STQF60	orf7a	0.000449	0.998291	4	1	CTTTAGCACTCAA>C
ERR5749341	28095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	5	0.8	0	0,1,0,4	HIGH	NONSENSE	STOP_GAINED	ORF8	Aaa/Taa	K68*	orf8	0.002672	0.967672	2	2	A>T
ERR5749341	28111	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	5	0.6	2147483647	0,0,0,5	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749341	28147	PASS	C	T	6639	0.981624	2147483647	0,0,6638,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	cCt/cTt	P85L	orf8	0.000438	0.981624	4	2	C>T
ERR5749341	28237	PASS	G	T	6638	0.966707	0	1,0,6636,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	cGt/cTt	R115L	orf8	0.000442	0.966707	4	2	G>T
ERR5749341	28253	PASS	C	T	6637	0.246798	0	4891,0,1738,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749341	28270	PASS	TA	T	5630	0.99929	0	0,4,1,5625	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749341	28273	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	ATGTTTCT	12222	0.0018	56	6586,5629,22,0	HIGH	NONE	FRAME_SHIFT+START_LOST	N	atg/TGTTTCTatg	M1CFY?	N	0.000399	0.842333	4	1	A>ATGTTTCT
ERR5749341	28280	PASS	G	C	5630	0.912789	0	0,0,1,5620	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749341	28281	PASS	A	T	5630	0.921314	0	0,0,1,5626	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749341	28282	PASS	T	A	5631	0.938199	0	0,3,1,5627	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749341	28341	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6637	0.02923	0	0,6420,0,210	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCa/tTa	S23L	N	0.02923	0.05919	1	1	C>T
ERR5749341	28881	PASS	G	A	416	0.769231	0	0,0,202,209	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749341	28882	PASS	G	A	416	0.802885	0	0,0,207,200	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749341	28883	PASS	G	C	416	0.930288	0	0,0,207,209	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749341	28977	PASS	C	T	211	0.905213	2147483647	0,0,0,211	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749341	29171	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1598	0.016896	0	1569,0,29,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Cat/Tat	H300Y	N	0.00121	0.854685	2	2	C>T
ERR5749341	29492	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	620	0.029032	0	592,0,20,0	LOW	SILENT	SYNONYMOUS_CODING	N	Ttg/Ctg	L407	N	0.029032	0.925	1	1	T>C
ERR5749342	241	PASS	C	T	181	0.812155	0	0,0,90,89	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749342	913	PASS	C	T	802	0.859102	0	0,1,0,801	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749342	932	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAC	G	802	0.006234	0	0,797,0,5	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T44	nsp2	0.00048	0.184416	2	2	GAC>G
ERR5749342	1874	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	4120	0.00267	0	0,4105,0,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gca/Cca	A357P	nsp2	0.001611	0.344371	2	1	G>C
ERR5749342	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	3998	0.004002	469	2008,1814,2,161	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749342	3037	PASS	C	T	1674	0.778375	0	0,0,838,818	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749342	3267	PASS	C	T	810	0.979012	2147483647	0,0,810,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749342	4578	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTAACGATC	T	1086	0.003683	0	0,1082,0,4	HIGH	NONE	FRAME_SHIFT	ORF1ab	aacgatctaaat/	NDLN621	nsp3	0.000519	0.082979	2	2	TTAACGATC>T
ERR5749342	5388	PASS	C	A	745	0.954362	2147483647	0,0,744,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749342	5986	PASS	C	T	2318	0.970233	2147483647	0,0,2318,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749342	6606	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1811	0.008835	0	1793,0,18,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S1296F	nsp3	0.002262	0.945412	1	1	C>T
ERR5749342	6659	PASS	A	G	1811	0.056322	0	1690,0,116,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Agt/Ggt	S1314G	nsp3	0.001866	0.056322	1	1	A>G
ERR5749342	6706	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	1799	0.004447	0	0,1791,0,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1330	nsp3	0.000687	0.883999	2	2	CA>C
ERR5749342	6954	PASS	T	C	3648	0.771656	2147483647	0,0,0,3598	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749342	6990	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	3665	0.006548	0	0,3641,0,24	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L1425	nsp3	0.000504	0.101156	4	2	CT>C
ERR5749342	7834	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTT	C	8612	0.003484	0	4295,4287,15,15	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L1706	nsp3	0.000523	0.86555	3	2	CTT>C
ERR5749342	7926	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4331	0.005541	0	0,4304,0,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCa/gTa	A1736V	nsp3	0.000531	0.97019	5	2	C>T
ERR5749342	8381	PASS	A	G	1891	0.954521	0	21,0,1867,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Agt/Ggt	S1888G	nsp3	0.954521	0.954521	1	1	A>G
ERR5749342	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	3124	0.004481	0	3019,91,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749342	9697	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	6015	0.001995	42	3012,2982,0,14	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taT/taC	Y381	nsp4	0.001995	0.05887	1	1	T>C
ERR5749342	10116	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6143	0.006511	14	5367,727,44,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T21I	3Cpro	0.001266	0.952096	1	1	C>T
ERR5749342	10323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	5410	0.007024	0	0,5346,0,40	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749342	11104	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	5813	0.005161	0	5758,0,36,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccT/ccC	P44	nsp6	0.000866	0.675414	2	1	T>C
ERR5749342	11287	PASS	GTCTGGTTTT	G	5811	0.998623	0	0,8,0,5803	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749342	11507	PASS	G	A	2800	0.872143	0	1,0,1404,1377	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Att	V179I	nsp6	0.007744	0.914418	2	2	G>A
ERR5749342	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	3187	0.003138	13	1757,1418,9,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749342	12025	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8751	0.003314	0	8709,0,33,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S61	nsp7	0.001295	0.948026	1	1	C>T
ERR5749342	12067	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	17446	0.002121	0	8709,8667,21,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atA	M75I	nsp7	0.001146	0.086511	2	1	G>A
ERR5749342	12374	PASS	C	T	2286	0.932196	0	0,46,0,2238	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Ttt	L95F	nsp8	0.001063	0.932196	1	1	C>T
ERR5749342	12459	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4929	0.002637	50	2642,2270,0,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T123I	nsp8	0.000658	0.986093	1	1	C>T
ERR5749342	12513	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2643	0.00454	0	2629,0,12,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aTg	T141M	nsp8	0.000794	0.984064	2	2	C>T
ERR5749342	13115	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5537	0.002528	0	5514,0,16,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L31	nsp10	0.001806	0.922167	1	1	C>T
ERR5749342	13994	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	2765	0.003255	0	2756,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L186	RdRp	0.000427	0.114441	3	2	CT>C
ERR5749342	14408	PASS	C	T	133	0.834586	0	0,0,67,66	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749342	14676	PASS	C	T	651	0.829493	2147483647	0,0,651,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749342	14925	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1658	0.004825	0	1650,0,8,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V495	RdRp	0.002531	0.98996	1	1	C>T
ERR5749342	15279	PASS	C	T	1203	0.897756	2147483647	0,0,1201,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749342	15371	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2400	0.00375	0	1194,1188,7,7	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aTg	T644M	RdRp	0.00056	0.786959	4	2	C>T
ERR5749342	16176	PASS	T	C	1267	0.95659	0	0,0,567,700	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749342	16293	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	567	0.010582	0	561,0,6,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C19	helicase	0.001538	0.968351	1	1	C>T
ERR5749342	16575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3786	0.004226	0	3766,0,19,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D113	helicase	0.001088	0.827968	1	1	C>T
ERR5749342	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAA	G	4740	0.002954	0	4720,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GAA>G
ERR5749342	17999	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	3808	0.004464	41	2054,1735,17,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aAa	T588K	helicase	0.001094	0.974498	2	1	C>A
ERR5749342	18501	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1056	0.007576	0	0,1039,0,9	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y154	ExoN	0.000336	0.857143	4	2	C>T
ERR5749342	19227	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2287	0.011369	0	0,2256,0,27	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S396	ExoN	0.002586	0.982286	2	2	C>T
ERR5749342	19263	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5579	0.00233	21	3276,2286,14,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N408	ExoN	0.000943	0.943181	2	2	C>T
ERR5749342	19343	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTTTTGTTAA	C	3291	0.002431	0	3283,0,8,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	tttgttaattta/tta	FVNL436L	ExoN	0.000519	0.192257	7	2	CTTTTGTTAA>C
ERR5749342	19524	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3290	0.006383	0	0,3262,0,23	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ctC/ctT	L495	ExoN	0.000745	0.953697	2	2	C>T
ERR5749342	20233	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8601	0.006511	0	8542,0,56,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ccc/Tcc	P205S	endoR	0.000964	0.980008	2	1	C>T
ERR5749342	20823	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2636	0.004173	19	1766,858,12,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N55	MethTr	0.001138	0.982544	2	2	C>T
ERR5749342	21134	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	8659	0.003003	24	6855,1776,27,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cAa/cGa	Q159R	MethTr	0.001194	0.689661	1	1	A>G
ERR5749342	21234	PASS	C	T	6881	0.598605	0	5,0,6754,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A192	MethTr	0.000472	0.857572	5	2	C>T
ERR5749342	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3429	0.019248	0	1653,1665,36,36	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749342	21660	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1720	0.008721	0	1,1701,0,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T33I	S	0.008721	0.937304	1	1	C>T
ERR5749342	21764	PASS	ATACATG	A	3288	0.99635	0	12,0,3276,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749342	21786	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	3288	0.010645	0	3246,0,39,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gGt/gTt	G75V	S	0.001992	0.058409	1	1	G>T
ERR5749342	21990	PASS	TTTA	T	3289	0.993007	0	0,23,1,3265	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749342	22295	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6783	0.001769	46	2771,3994,12,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Cat/Tat	H245Y	S	0.000662	0.930915	2	2	C>T
ERR5749342	22927	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	2803	0.004638	0	2788,0,13,0	LOW	SILENT	SYNONYMOUS_CODING	S	ttG/ttA	L455	S	0.000791	0.909717	4	3	G>A
ERR5749342	23063	PASS	A	T	2798	0.827377	0	0,1,0,2772	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749342	23271	PASS	C	A	914	0.923414	2147483647	0,0,911,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749342	23403	PASS	A	G	913	0.945235	2147483647	0,0,0,912	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749342	23604	PASS	C	A	2759	0.952519	2147483647	0,0,2758,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749342	23634	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2759	0.004712	0	2745,0,14,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tTc	S691F	S	0.00071	0.931159	2	2	C>T
ERR5749342	23709	PASS	C	T	2753	0.917544	0	0,2,0,2749	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749342	23712	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATT	A	2753	0.004359	0	0,2741,0,12	HIGH	NONE	FRAME_SHIFT	S	ttt/	F718	S	0.000679	0.958955	3	2	ATT>A
ERR5749342	24320	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	2518	0.002383	0	0,2511,0,6	HIGH	NONE	FRAME_SHIFT	S	aaa/	K921	S	0.000763	0.138365	4	2	CAA>C
ERR5749342	24370	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2526	0.004751	0	0,2508,0,16	LOW	SILENT	SYNONYMOUS_CODING	S	gaC/gaT	D936	S	0.004751	0.899498	1	1	C>T
ERR5749342	24444	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2539	0.009059	0	2513,2,23,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCg/aTg	T961M	S	0.000832	0.063732	2	2	C>T
ERR5749342	24506	PASS	T	G	2537	0.974773	2147483647	0,0,2536,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749342	24914	PASS	G	C	9238	0.951829	3	1,0,4607,4625	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749342	25555	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	8324	0.001922	0	0,8291,0,31	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gtt/Ttt	V55F	orf3a	0.000552	0.900573	5	2	G>T
ERR5749342	26510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	1512	0.00463	0	0,1500,0,7	.	.	.	.	.	.	.	0.001235	0.933642	2	1	T>C
ERR5749342	26730	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	5043	0.004561	0	2514,2507,12,11	HIGH	NONE	FRAME_SHIFT	M	tac/	Y71	M	0.000371	0.919543	3	2	GT>G
ERR5749342	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	2538	0.016154	0	0,2497,0,41	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749342	26958	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7520	0.003324	0	7493,0,25,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Cgt/Tgt	R146C	M	0.00096	0.122326	1	1	C>T
ERR5749342	27240	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAT	G	5932	0.002697	0	5916,0,16,0	HIGH	NONE	FRAME_SHIFT	ORF6	atatta/	IL14	orf6	0.000521	0.117458	2	2	GAT>G
ERR5749342	27297	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5932	0.002866	0	5903,0,17,0	LOW	SILENT	SYNONYMOUS_CODING	ORF6	atC/atT	I32	orf6	0.000978	0.91266	1	1	C>T
ERR5749342	27625	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6184	0.006792	0	6137,0,44,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Cgt/Tgt	R78C	orf7a	0.00584	0.951914	1	1	C>T
ERR5749342	27741	PASS	C	T	6180	0.060518	0	0,5746,0,403	LOW	SILENT	SYNONYMOUS_CODING	ORF7a	ctC/ctT	L116	orf7a	0.000363	0.954278	3	2	C>T
ERR5749342	27741	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	6180	0.003722	0	0,6157,0,23	HIGH	NONE	FRAME_SHIFT	ORF7a	aga/	R118	orf7a	0.000363	0.954278	3	2	CA>C
ERR5749342	27972	PASS	C	T	1183	0.893491	0	0,0,1173,7	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749342	28048	PASS	G	T	1176	0.879252	0	0,6,0,1168	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749342	28111	PASS	A	G	8270	0.976904	0	2,0,7090,1177	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749342	28249	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	7090	0.004513	0	7058,1,32,0	HIGH	NONE	FRAME_SHIFT	ORF8	ttc/	F120	orf8	0.000443	0.063605	3	2	AT>A
ERR5749342	28270	PASS	TA	T	13529	0.994161	69	65,15,7002,6448	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749342	28271	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAATGTCTGAT	A	13528	0.0017	0	7051,6452,12,11	HIGH	NONE	START_LOST+CODON_DELETION	N	atgtctgat/	MSD1	N	0.000482	0.924941	3	2	AAAATGTCTGAT>A
ERR5749342	28280	PASS	G	C	13507	0.925298	0	3,3,7009,6441	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749342	28281	PASS	A	T	13507	0.900422	5	9,4,7007,6439	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749342	28282	PASS	T	A	13509	0.893552	0	7,6,6997,6444	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749342	28382	PASS	T	C	7093	0.944593	0	0,2,0,7084	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Tca/Cca	S37P	N	0.944593	0.944593	1	1	T>C
ERR5749342	28651	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	8808	0.002044	0	0,8790,0,18	HIGH	NONE	FRAME_SHIFT	N	aaa/	K127	N	0.000502	0.918117	3	2	CA>C
ERR5749342	28657	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8812	0.001702	0	0,8785,0,20	LOW	SILENT	SYNONYMOUS_CODING	N	gaC/gaT	D128	N	0.00124	0.862766	1	1	C>T
ERR5749342	28881	PASS	G	A	453	0.726269	0	0,0,228,216	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749342	28882	PASS	G	A	453	0.812362	0	0,0,228,219	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749342	28883	PASS	G	C	453	0.92936	0	0,0,231,220	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749342	28887	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	458	0.019651	1	223,220,7,5	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aCt/aTt	T205I	N	0.002174	0.814997	2	2	C>T
ERR5749342	28977	PASS	C	T	234	0.884615	2147483647	0,0,0,233	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749342	29077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAATGT	C	5088	0.002358	0	5076,0,12,0	HIGH	NONE	FRAME_SHIFT	N	aatgtaaca/	NVT269	N	0.000408	0.88565	3	2	CAATGT>C
ERR5749342	29736	PASS	GGCCACGCGGAGTAC	G	2044	0.987769	0	0,24,0,2019	.	.	.	.	.	.	.	0.78205	0.987769	2	1	GGCCACGCGGAGTAC>G
ERR5749342	29738	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCACGCGGAGTACGA	C	2044	0.005382	0	0,2033,0,11	.	.	.	.	.	.	.	0.001703	0.890671	2	1	CCACGCGGAGTACGA>C
ERR5749343	179	PASS	T	G	10400	0.857981	0	29,0,10368,1	.	.	.	.	.	.	.	0.850195	0.857981	1	1	T>G
ERR5749343	241	PASS	C	T	20721	0.868829	0	4,5,10297,10324	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749343	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	8848	0.002599	0	8823,0,23,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749343	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	8849	0.001582	0	8800,1,14,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749343	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	8849	0.003051	0	8800,1,27,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749343	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	8839	0.00181	0	8167,1,577,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749343	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	8839	0.002715	0	8814,1,24,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749343	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	8839	0.001471	0	8821,1,13,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749343	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	28471	4.21E-4	16	19598,8858,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749343	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	28470	4.92E-4	0	19540,8850,10,4	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749343	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	28470	0.002248	56	19540,8850,60,4	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749343	913	PASS	C	T	19602	0.915468	0	0,5,0,19560	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749343	2445	PASS	C	T	14170	0.815808	0	0,11,3,14056	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T547I	nsp2	0.001663	0.815808	1	1	C>T
ERR5749343	3037	PASS	C	T	17625	0.825532	27	0,9,8808,8686	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749343	3267	PASS	C	T	18832	0.971644	2147483647	0,0,18821,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749343	3832	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	23369	8.13E-4	0	23347,2,19,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L373	nsp3	0.000689	0.327273	4	2	CT>C
ERR5749343	4136	PASS	G	T	39169	0.973985	2	0,2,15795,23355	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Ttt	V473F	nsp3	0.00075	0.974623	4	2	G>T
ERR5749343	5388	PASS	C	A	5350	0.955701	2147483647	0,0,5343,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749343	5986	PASS	C	T	11730	0.973743	2147483647	0,0,11718,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749343	6954	PASS	T	C	21143	0.802204	0	0,5,1,20984	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749343	7564	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	14489	9.66E-4	0	0,14475,0,14	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/	Y1617	nsp3	0.000586	0.056194	4	2	CT>C
ERR5749343	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	30114	8.97E-4	86	14363,15723,27,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749343	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	17712	0.002484	0	17646,0,60,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749343	11287	PASS	GTCTGGTTTT	G	17713	0.996782	0	0,56,0,17656	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749343	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	33260	0.001022	2	21138,12068,24,11	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749343	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	15965	0.001441	0	15915,0,25,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749343	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27348	0.001901	0	13647,13611,28,29	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749343	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	13498	0.001926	1831	13241,137,8,105	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749343	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	26340	0.001746	0	13208,13107,23,23	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749343	14408	PASS	C	T	26340	0.849051	11	4,11,13139,12978	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749343	14676	PASS	C	T	12104	0.77809	0	8,0,12055,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749343	15279	PASS	C	T	20295	0.89697	0	3,0,20265,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749343	16176	PASS	T	C	18212	0.982484	0	0,0,8612,9592	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749343	17747	PASS	C	T	11280	0.967376	0	4,0,11272,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P504L	helicase	0.000839	0.968462	2	2	C>T
ERR5749343	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28890	0.002146	0	28808,0,64,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749343	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28828	9.37E-4	0	28755,0,27,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749343	21034	PASS	C	T	19368	0.910471	0	0,8,1,19308	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L126F	MethTr	0.001871	0.915185	1	1	C>T
ERR5749343	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	31888	7.53E-4	0	15672,15908,13,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749343	21764	PASS	ATACATG	A	11667	0.996314	0	43,0,11624,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749343	21990	PASS	TTTA	T	11675	0.996574	0	0,40,6,11629	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749343	22927	PASS	G	T	11649	0.898446	0	32,0,11606,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	ttG/ttT	L455F	S	0.000791	0.909717	4	3	G>T
ERR5749343	23063	PASS	A	T	11627	0.860669	0	0,4,0,11573	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749343	23271	PASS	C	A	20246	0.923343	0	0,0,20219,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749343	23403	PASS	A	G	20238	0.97732	0	0,5,0,20224	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749343	23604	PASS	C	A	14005	0.938379	0	8,0,13985,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749343	23709	PASS	C	T	13997	0.938844	0	0,6,5,13974	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749343	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	30616	5.88E-4	12	16590,14008,14,4	HIGH	NONE	FRAME_SHIFT	S	ttg/	L753	S	0.000334	0.080808	2	2	CT>C
ERR5749343	24506	PASS	T	G	16606	0.978622	0	3,0,16601,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749343	24914	PASS	G	C	32177	0.960779	3	1,0,16032,16120	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749343	25429	PASS	G	T	15664	0.905197	0	20,0,15625,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gta/Tta	V13L	orf3a	0.00064	0.906678	5	2	G>T
ERR5749343	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	22000	0.0015	207	21906,23,24,10	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749343	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	22132	0.00113	913	21722,142,162,73	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749343	25954	PASS	G	T	67552	0.983657	1	4,3,45566,21960	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Ggt/Tgt	G188C	orf3a	0.983612	0.984476	1	1	G>T
ERR5749343	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	45504	3.08E-4	0	0,45490,0,14	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749343	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	11150	8.97E-4	0	2,11136,0,10	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749343	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	11151	0.00269	0	2,11115,0,30	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749343	27972	PASS	C	T	10306	0.907141	38	1,2,10206,70	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749343	28048	PASS	G	T	10239	0.923039	0	0,12,0,10224	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749343	28111	PASS	A	G	29973	0.978214	0	5,2,19710,10246	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749343	28270	PASS	TA	T	38256	0.995347	414	177,7,19462,18616	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749343	28280	PASS	G	C	38186	0.940607	23	16,3,19495,18596	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749343	28281	PASS	A	T	38186	0.919787	24	24,7,19503,18599	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749343	28282	PASS	T	A	38188	0.910495	4	22,15,19433,18607	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749343	28881	PASS	G	A	17143	0.763635	11	7,1,8463,8452	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749343	28882	PASS	G	A	17143	0.83276	2	3,1,8569,8438	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749343	28883	PASS	G	C	17143	0.943942	3	0,1,8586,8539	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749343	28977	PASS	C	T	8735	0.925816	0	0,3,0,8717	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749343	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	52658	8.74E-4	0	26431,26137,30,29	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749343	29721	PASS	C	T	8157	0.880471	0	0,2,3,8133	.	.	.	.	.	.	.	0.001062	0.880471	2	1	C>T
ERR5749344	241	PASS	C	T	15336	0.872066	0	0,1,7643,7644	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749344	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	10695	0.001309	0	10682,3,14,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749344	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	10695	0.002244	0	10656,3,24,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749344	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10689	0.002058	0	10051,3,569,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749344	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	10689	0.001778	0	10667,3,19,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749344	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	38042	4.73E-4	3	27315,10707,15,3	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749344	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	38040	0.00113	4	27289,10701,34,9	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749344	913	PASS	C	T	27311	0.898905	0	0,14,0,27250	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749344	2702	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	37408	8.82E-4	2290	37113,36,74,106	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F633V	nsp2	0.000632	0.333333	1	1	T>G
ERR5749344	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	74198	0.001563	2147483647	37052,34547,58,2369	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749344	3037	PASS	C	T	28082	0.810127	67	1,26,14035,13782	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749344	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	14190	0.001691	713	6,14149,25,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749344	3267	PASS	C	T	26188	0.971934	0	2,0,26167,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749344	4331	PASS	C	T	40268	0.919713	8	2,0,14871,25344	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L538	nsp3	0.000987	0.928955	1	1	C>T
ERR5749344	5388	PASS	C	A	8074	0.962844	2147483647	0,0,8073,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749344	5986	PASS	C	T	17122	0.974945	0	2,0,17112,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749344	6954	PASS	T	C	24284	0.814899	0	0,5,4,24129	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749344	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	38819	9.02E-4	87	21618,17166,35,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749344	10077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	8088	0.001978	291	10,8046,12,4	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTc/tCc	F8S	3Cpro	0.001833	0.454545	1	1	T>C
ERR5749344	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	24409	0.001229	0	24349,0,51,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749344	11287	PASS	GTCTGGTTTT	G	24405	0.997419	0	0,63,0,24342	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749344	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	46523	9.24E-4	1	28566,17876,29,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749344	12125	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	25523	0.001019	0	17,25379,0,39	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y12H	nsp8	0.000847	0.113436	1	1	T>C
ERR5749344	12388	PASS	T	C	29243	0.955477	0	0,4,0,29221	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaT/gaC	D99	nsp8	0.001786	0.961473	1	1	T>C
ERR5749344	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	26225	0.002097	0	26112,0,57,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749344	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34633	0.001011	1	17300,17255,20,22	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749344	13536	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17329	0.002655	0	6,17235,0,66	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y32	RdRp	0.002208	0.799427	1	1	C>T
ERR5749344	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	22209	0.006169	2147483647	21566,171,8,453	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749344	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	42949	6.99E-4	0	21545,21397,15,15	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749344	14408	PASS	C	T	42949	0.844234	2	1,2,21457,21146	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749344	14676	PASS	C	T	15308	0.773778	0	8,0,15243,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749344	15279	PASS	C	T	25243	0.894902	0	7,0,25202,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749344	16176	PASS	T	C	22580	0.978875	0	0,0,10593,11982	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749344	18504	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	37014	7.56E-4	0	0,36452,0,505	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K155N	ExoN	0.000518	0.094148	4	3	A>C
ERR5749344	19011	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27518	0.001454	0	27468,0,42,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D324	ExoN	0.000408	0.975746	4	2	C>T
ERR5749344	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	36880	0.001518	0	36792,0,63,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749344	21255	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	81522	5.64E-4	4	42324,39119,33,23	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcG/gcA	A199	MethTr	0.000341	0.917425	4	2	G>A
ERR5749344	21752	PASS	T	A	18108	0.958416	0	1,0,18091,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tgg/Agg	W64R	S	0.958416	0.958416	1	1	T>A
ERR5749344	21762	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTATACA	C	18108	0.001767	0	18076,0,32,0	MODERATE	NONE	CODON_DELETION	S	atacat/	IH68	S	0.001297	0.875707	2	2	CTATACA>C
ERR5749344	21764	PASS	ATACATG	A	18108	0.996797	0	58,0,18050,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749344	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	18108	5.52E-4	0	18098,0,10,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749344	21990	PASS	TTTA	T	18110	0.99735	0	0,48,1,18061	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749344	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	38185	0.001048	0	19400,18723,20,21	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749344	23063	PASS	A	T	19398	0.858748	0	0,5,0,19301	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749344	23271	PASS	C	A	27585	0.924814	0	1,0,27557,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749344	23403	PASS	A	G	27569	0.966811	0	0,1,2,27548	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749344	23604	PASS	C	A	21256	0.940629	0	12,0,21239,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749344	23709	PASS	C	T	21241	0.93635	0	0,13,0,21194	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749344	23914	PASS	A	G	18808	0.965493	0	4,0,18789,0	LOW	SILENT	SYNONYMOUS_CODING	S	caA/caG	Q784	S	0.003876	0.965493	1	1	A>G
ERR5749344	24506	PASS	T	G	20077	0.974747	0	10,0,20060,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749344	24742	PASS	A	C	43027	0.985986	7	11,4,22940,20065	LOW	SILENT	SYNONYMOUS_CODING	S	gtA/gtC	V1060	S	0.985986	0.985986	1	1	A>C
ERR5749344	24914	PASS	G	C	45643	0.958132	3	0,2,22751,22859	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749344	25603	PASS	C	T	26878	0.924436	315	9,2,1,26851	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	Cta/Tta	L71	orf3a	0.001967	0.924436	1	1	C>T
ERR5749344	25673	PASS	T	C	70	0.4	26	11,31,0,28	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749344	25794	PASS	T	G	230	0.095652	18	10,136,0,83	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749344	26510	PASS	T	G	12538	0.933642	0	0,16,0,12517	.	.	.	.	.	.	.	0.001235	0.933642	2	1	T>G
ERR5749344	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	18861	0.001379	0	0,18830,0,26	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749344	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	18861	7.42E-4	0	0,18847,0,14	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749344	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	18862	0.002439	0	0,18809,0,46	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749344	27506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	54566	7.15E-4	5	26312,28204,19,28	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	gGa/gTa	G38V	orf7a	0.000715	0.985435	4	2	G>T
ERR5749344	27625	PASS	C	T	26306	0.951342	0	1,0,26262,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Cgt/Tgt	R78C	orf7a	0.00584	0.951914	1	1	C>T
ERR5749344	27754	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	26333	0.001253	0	6,26227,0,95	HIGH	NONSENSE	STOP_GAINED	ORF7a	Gaa/Taa	E121*	orf7a	0.001253	0.928716	1	1	G>T
ERR5749344	27972	PASS	C	T	17497	0.901469	60	1,3,17334,104	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749344	28048	PASS	G	T	17399	0.914363	0	0,22,0,17363	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749344	28111	PASS	A	G	39513	0.976236	0	3,3,22087,17410	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749344	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22084	0.001585	0	21999,5,36,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749344	28270	PASS	TA	T	42542	0.99551	366	183,13,21846,20505	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749344	28280	PASS	G	C	42479	0.936745	6	8,3,21902,20500	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749344	28281	PASS	A	T	42479	0.913416	38	30,6,21881,20500	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749344	28282	PASS	T	A	42482	0.911939	1	19,15,21834,20509	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749344	28881	PASS	G	A	25016	0.764511	30	11,0,12412,12241	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749344	28882	PASS	G	A	25015	0.825944	6	3,0,12552,12206	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749344	28883	PASS	G	C	25015	0.942435	1	2,3,12567,12425	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749344	28977	PASS	C	T	12729	0.921753	0	0,5,0,12692	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749344	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	82821	0.001292	0	41569,41087,70,66	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749345	241	PASS	C	T	10764	0.8534	3	0,2,5335,5367	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749345	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	10933	7.32E-4	0	10929,4,8,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749345	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	10938	0.002103	0	10897,9,23,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749345	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	10923	7.32E-4	0	10905,10,8,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749345	515	PASS	GTTA	G	10918	0.991848	0	90,0,10819,10	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttatg/gtg	VM84V	leader	0.000554	0.991848	4	1	GTTA>G
ERR5749345	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	36997	4.59E-4	14	26025,10953,16,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749345	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	36995	3.24E-4	9	25955,10937,11,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749345	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	36995	0.002514	17	25955,10937,76,17	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749345	913	PASS	C	T	26036	0.91819	0	0,19,1,25974	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749345	1510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	24879	0.003618	0	0,24587,0,97	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G235	nsp2	0.002159	0.937304	1	1	T>C
ERR5749345	3037	PASS	C	T	21877	0.824062	36	0,12,10922,10802	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749345	3177	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	37098	7.82E-4	49	26043,11008,41,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cAt	P153H	nsp3	0.000773	0.96008	3	2	C>A
ERR5749345	3267	PASS	C	T	26083	0.972894	0	1,0,26057,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749345	5388	PASS	C	A	5765	0.960104	2147483647	0,0,5762,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749345	5640	PASS	A	T	22477	0.921164	0	1260,0,21215,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cAa/cTa	Q974L	nsp3	0.002387	0.921164	1	1	A>T
ERR5749345	5986	PASS	C	T	14627	0.976755	0	1,0,14613,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749345	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13909	0.001366	0	5,13755,0,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749345	6954	PASS	T	C	25775	0.818739	0	0,4,1,25625	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749345	7097	PASS	A	G	22025	0.985062	144	3,4,22016,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Att/Gtt	I1460V	nsp3	0.980962	0.985062	1	1	A>G
ERR5749345	9130	PASS	G	T	17588	0.960712	2147483647	0,0,0,17582	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtG/gtT	V192	nsp4	0.001321	0.963415	2	1	G>T
ERR5749345	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	32302	4.33E-4	39	16274,16014,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749345	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	23721	0.001644	0	23656,0,54,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749345	11287	PASS	GTCTGGTTTT	G	23714	0.997807	0	0,52,0,23662	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749345	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	39594	0.001616	1	19770,19706,34,37	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749345	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	15117	0.003638	2147483647	14833,96,7,177	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749345	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	29534	5.42E-4	0	14813,14736,9,7	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749345	14408	PASS	C	T	29534	0.849394	6	3,7,14729,14598	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749345	14599	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15225	0.002365	0	15173,6,39,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L387	RdRp	0.000639	0.922766	3	2	C>T
ERR5749345	14676	PASS	C	T	15212	0.811136	0	8,0,15178,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749345	15279	PASS	C	T	26017	0.892724	0	5,0,25972,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749345	16176	PASS	T	C	21524	0.981695	14	4,0,9390,12117	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749345	16946	PASS	C	T	21564	0.949314	0	3,0,21522,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCa/gTa	A237V	helicase	0.001418	0.951893	1	1	C>T
ERR5749345	17615	PASS	A	G	17724	0.906567	0	0,1,0,17660	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749345	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	24044	0.00104	0	24019,0,25,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749345	19079	PASS	A	G	30099	0.967175	0	6,0,30078,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gAa/gGa	E347G	ExoN	0.001121	0.967175	2	1	A>G
ERR5749345	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	30149	7.3E-4	0	0,30127,0,22	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749345	19854	PASS	C	T	24057	0.962921	975	32,7,0,23994	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D78	endoR	0.950322	0.965654	1	1	C>T
ERR5749345	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27398	0.001095	0	27346,1,33,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749345	20786	PASS	A	T	18	0.555556	40	0,6,11,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAt/aTt	N43I	MethTr	0.001392	1	1	1	A>T
ERR5749345	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34925	8.59E-4	0	17107,17400,16,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749345	21764	PASS	ATACATG	A	14248	0.998105	0	27,0,14221,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749345	21990	PASS	TTTA	T	14252	0.996983	0	0,43,5,14204	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749345	22280	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ACTTTACTTG	A	25952	0.001195	0	3,25918,0,31	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	cttgctttacat/cat	LALH242H	S	0.00046	0.997799	1	1	ACTTTACTTG>A
ERR5749345	22630	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	19357	0.001137	0	19313,1,24,0	LOW	SILENT	SYNONYMOUS_CODING	S	aaG/aaA	K356	S	0.001137	0.921237	2	2	G>A
ERR5749345	23063	PASS	A	T	14046	0.86352	38	1,1,0,13978	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749345	23271	PASS	C	A	27094	0.927143	0	2,0,27065,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749345	23403	PASS	A	G	27083	0.972123	0	0,9,0,27060	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749345	23604	PASS	C	A	17411	0.94716	0	11,0,17390,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749345	23709	PASS	C	T	17398	0.942752	0	0,14,2,17357	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749345	23817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	39149	8.43E-4	6	21694,17399,22,11	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTt/cCt	L752P	S	0.000646	0.066832	1	1	T>C
ERR5749345	24237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13041	0.001304	0	13012,0,19,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gTt	A892V	S	0.001242	0.889739	1	1	C>T
ERR5749345	24506	PASS	T	G	20766	0.975344	0	10,0,20753,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749345	24914	PASS	G	C	37568	0.960764	0	0,0,18729,18827	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749345	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	27529	0.00138	71	19307,8166,48,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749345	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	29645	0.001079	0	29613,0,32,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749345	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	29848	0.001072	1297	29465,193,77,84	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749345	25904	PASS	C	T	29656	0.821992	632	19,5,0,29499	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	tCa/tTa	S171L	orf3a	0.000757	0.83473	1	1	C>T
ERR5749345	26314	PASS	G	A	12200	0.874836	196	4,8,12152,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	Gtg/Atg	V24M	E	0.874836	0.874836	1	1	G>A
ERR5749345	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	11941	0.003015	0	0,11905,0,36	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749345	27513	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	26953	0.01139	0	26607,3,324,0	HIGH	NONSENSE	STOP_GAINED	ORF7a	taC/taA	Y40*	orf7a	0.001863	0.982462	2	2	C>A
ERR5749345	27643	PASS	C	T	26487	0.858006	0	6,0,26370,9	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Cct/Tct	P84S	orf7a	0.00166	0.858006	2	1	C>T
ERR5749345	27972	PASS	C	T	13198	0.901576	40	1,2,13079,72	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749345	28048	PASS	G	T	13132	0.917834	0	0,27,1,13098	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749345	28111	PASS	A	G	34730	0.980766	1	5,4,21578,13132	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749345	28250	PASS	T	C	21549	0.918604	0	6,0,21496,7	LOW	SILENT	SYNONYMOUS_CODING	ORF8	gaT/gaC	D119	orf8	0.000494	0.993968	5	3	T>C
ERR5749345	28270	PASS	TA	T	41828	0.994908	416	204,14,21295,20320	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749345	28271	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AA	A	41825	0.0011	132	21445,20336,46,0	.	.	.	.	.	.	.	0.000482	0.924941	3	2	AA>A
ERR5749345	28280	PASS	G	C	41762	0.937479	14	10,2,21364,20312	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749345	28281	PASS	A	T	41762	0.904554	30	27,7,21348,20307	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749345	28282	PASS	T	A	41763	0.9081	6	22,14,21306,20320	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749345	28881	PASS	G	A	19489	0.776643	18	7,0,9647,9576	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749345	28882	PASS	G	A	19489	0.835548	2	3,1,9747,9575	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749345	28883	PASS	G	C	19490	0.946537	2	1,2,9759,9706	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749345	28957	PASS	C	T	9903	0.94436	0	0,1,0,9895	LOW	SILENT	SYNONYMOUS_CODING	N	aaC/aaT	N228	N	0.01097	0.950683	1	1	C>T
ERR5749345	28977	PASS	C	T	9907	0.929444	0	0,6,0,9889	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749345	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	34048	7.93E-4	91	24106,9871,4,24	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749345	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	47918	7.3E-4	0	24064,23785,25,25	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749346	241	PASS	C	T	16212	0.865347	0	2,3,8074,8078	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749346	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	12589	7.94E-4	0	12582,0,10,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749346	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	12592	0.001191	0	12563,3,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749346	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12586	0.00151	0	11862,3,675,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749346	657	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12613	0.004519	0	3,12539,0,62	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A131V	leader	0.001202	0.365979	3	1	C>T
ERR5749346	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	35784	7.27E-4	3	23142,12606,19,7	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749346	913	PASS	C	T	23160	0.918005	0	0,9,0,23117	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749346	1230	PASS	A	G	14666	0.969658	2147483647	0,0,0,14656	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K142R	nsp2	0.00129	0.969658	2	2	A>G
ERR5749346	1544	PASS	G	T	23323	0.936929	0	0,5,0,23314	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gct/Tct	A247S	nsp2	0.00161	0.936929	2	1	G>T
ERR5749346	3037	PASS	C	T	19423	0.835916	33	0,11,9694,9609	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749346	3267	PASS	C	T	23582	0.973539	0	3,0,23568,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749346	4276	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17371	0.001324	51	1,17332,2,25	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y519	nsp3	0.00102	0.812261	1	1	C>T
ERR5749346	4331	PASS	C	T	31867	0.928955	0	0,1,14484,17354	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L538	nsp3	0.000987	0.928955	1	1	C>T
ERR5749346	5388	PASS	C	A	5304	0.955694	2147483647	0,0,5301,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749346	5944	PASS	C	T	12794	0.977177	315	4,10,12770,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D1075	nsp3	0.002228	0.977177	1	1	C>T
ERR5749346	5986	PASS	C	T	12783	0.975436	2147483647	0,0,12777,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749346	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12361	0.001375	0	0,12215,0,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749346	6954	PASS	T	C	25808	0.832843	0	0,5,3,25674	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749346	7067	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	46498	4.3E-4	70	20590,25888,20,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gaa/	E1450	nsp3	0.000274	0.059217	5	3	GA>G
ERR5749346	8327	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12500	0.0032	0	12438,11,45,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Ttt	L1870F	nsp3	0.001407	0.90398	1	1	C>T
ERR5749346	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	30143	0.001261	106	15730,14375,38,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749346	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	23148	0.001858	0	23074,0,68,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749346	11287	PASS	GTCTGGTTTT	G	23144	0.998099	0	0,44,0,23100	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749346	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	39808	0.001281	13	25895,13838,27,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749346	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	19763	0.001063	0	19718,0,22,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749346	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	33029	0.001605	0	16490,16437,28,29	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749346	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	15004	0.004066	2147483647	14683,97,6,216	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749346	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	29244	6.84E-4	0	14659,14583,10,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749346	14408	PASS	C	T	29244	0.844071	2	1,2,14598,14437	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749346	14676	PASS	C	T	14705	0.822305	0	9,0,14664,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749346	15096	PASS	T	C	19481	0.969303	0	0,1,6,19467	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaT/aaC	N552	RdRp	0.941667	0.970182	1	1	T>C
ERR5749346	15279	PASS	C	T	23670	0.902197	0	3,0,23636,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749346	16176	PASS	T	C	21544	0.981155	5	0,3,9696,11837	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749346	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	24940	9.62E-4	0	24912,0,24,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749346	18887	PASS	A	G	24939	0.130719	0	0,21541,0,3363	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cAc/cGc	H283R	ExoN	0.130719	0.130719	1	1	A>G
ERR5749346	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28338	0.002153	0	28253,0,65,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749346	20091	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	28282	4.6E-4	0	0,28269,0,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	caa/Acaa	Q159T?	endoR	0.000368	0.051583	1	1	C>CA
ERR5749346	21255	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	55438	6.85E-4	113	28675,26687,40,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcG/gcC	A199	MethTr	0.000341	0.917425	4	2	G>C
ERR5749346	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	39183	7.4E-4	2	19165,19551,14,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749346	21764	PASS	ATACATG	A	12643	0.996045	0	50,0,12593,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749346	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	12643	6.33E-4	0	12635,0,8,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749346	21990	PASS	TTTA	T	12653	0.998182	0	0,23,6,12624	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749346	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	32627	9.81E-4	2	14527,18055,13,20	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749346	23063	PASS	A	T	14531	0.881357	0	0,1,0,14469	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749346	23271	PASS	C	A	24950	0.913026	0	3,0,24916,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749346	23403	PASS	A	G	24945	0.971257	0	0,2,0,24929	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749346	23604	PASS	C	A	15970	0.93851	0	13,0,15944,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749346	23709	PASS	C	T	15954	0.946722	0	0,3,1,15929	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749346	24506	PASS	T	G	19778	0.976742	0	8,0,19767,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749346	24914	PASS	G	C	38933	0.96119	0	0,0,19404,19512	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749346	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	20350	0.001376	441	20277,9,13,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749346	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	20323	7.87E-4	0	20307,0,16,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749346	26681	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12926	0.024679	6	12527,65,323,3	LOW	SILENT	SYNONYMOUS_CODING	M	ttC/ttT	F53	M	0.001297	0.074505	1	1	C>T
ERR5749346	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	12855	0.001867	0	0,12824,0,24	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749346	27402	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	19417	0.001236	0	1,19358,0,27	LOW	SILENT	SYNONYMOUS_CODING	ORF7a	atT/atC	I3	orf7a	0.000551	0.905711	3	3	T>C
ERR5749346	27972	PASS	C	T	11103	0.908583	0	0,0,11017,45	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749346	28048	PASS	G	T	11070	0.921771	0	0,14,0,11050	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749346	28095	PASS	A	T	11081	0.961285	181	5,0,0,11072	HIGH	NONSENSE	STOP_GAINED	ORF8	Aaa/Taa	K68*	orf8	0.002672	0.967672	2	2	A>T
ERR5749346	28111	PASS	A	G	34812	0.979346	0	2,1,23727,11073	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749346	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23715	9.7E-4	0	23645,1,23,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749346	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	23706	4.22E-4	0	23704,1,10,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749346	28270	PASS	TA	T	46074	0.995225	505	218,9,23422,22432	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749346	28280	PASS	G	C	45981	0.93643	21	8,0,23474,22412	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749346	28281	PASS	A	T	45981	0.917662	41	28,5,23462,22410	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749346	28282	PASS	T	A	45983	0.913577	17	28,12,23415,22428	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749346	28881	PASS	G	A	19585	0.784427	0	2,1,9648,9557	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749346	28882	PASS	G	A	19584	0.862541	6	5,1,9680,9551	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749346	28883	PASS	G	C	19584	0.943781	0	4,4,9691,9647	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749346	28884	PASS	G	C	19584	0.935815	12	0,4,9692,9648	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gGa/gCa	G204A	N	0.004552	0.935815	1	1	G>C
ERR5749346	28977	PASS	C	T	10292	0.938593	0	0,2,0,10275	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749346	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	59494	0.001345	0	29854,29512,49,48	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749347	239	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTC	T	17515	5.71E-4	0	8725,8780,5,5	.	.	.	.	.	.	.	0.000495	0.25	4	1	TTC>T
ERR5749347	241	PASS	C	T	17515	0.859092	0	0,0,8713,8729	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749347	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	10093	0.001486	0	10074,8,15,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749347	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	10099	8.91E-4	0	10021,14,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749347	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	10099	0.004456	0	10021,14,45,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749347	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10101	0.00198	5	9128,21,854,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749347	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	10101	9.9E-4	0	10070,21,10,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749347	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	10099	0.001386	0	10056,22,14,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749347	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	38217	3.66E-4	15	28105,10091,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749347	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	38219	0.001779	15	28049,10081,58,10	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749347	913	PASS	C	T	28104	0.911614	0	0,14,0,28042	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749347	2453	PASS	C	T	18432	0.739258	0	0,27,1,18143	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L550F	nsp2	0.00429	0.842201	2	2	C>T
ERR5749347	2702	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	55638	7.19E-4	2147483647	55251,42,79,158	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F633V	nsp2	0.000632	0.333333	1	1	T>G
ERR5749347	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	110361	0.001187	2147483647	55104,51688,107,3185	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749347	3037	PASS	C	T	24676	0.821608	87	1,33,12321,12138	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749347	3267	PASS	C	T	30593	0.97081	2147483647	0,0,30576,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749347	4508	PASS	G	A	44898	0.685019	45	18,1,21536,22341	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtg/Atg	V597M	nsp3	0.000445	0.685019	2	2	G>A
ERR5749347	4508	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTGGTTGATTATGGTGCTAGATTTTACTTTTACACCAGTAAAACAACTGTAGCGTCACTTATCAACACACTT	G	44898	4.45E-4	57	22327,22551,0,20	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtggttgattatggtgctagattttacttttacaccagtaaaacaactgtagcgtcacttatcaacacactt/	VVDYGARFYFYTSKTTVASLINTL597	nsp3	0.000445	0.685019	2	2	GTGGTTGATTATGGTGCTAGATTTTACTTTTACACCAGTAAAACAACTGTAGCGTCACTTATCAACACACTT>G
ERR5749347	5388	PASS	C	A	6975	0.964014	2147483647	0,0,6971,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749347	5986	PASS	C	T	17348	0.973369	0	1,0,17330,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749347	6311	PASS	A	C	35103	0.973136	0	25,0,35038,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Aca/Cca	T1198P	nsp3	0.002365	0.973136	2	2	A>C
ERR5749347	6954	PASS	T	C	34237	0.816251	0	0,8,10,34026	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749347	8796	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	69957	2.57E-4	0	35018,34921,9,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/	Y82	nsp4	0.000257	0.25	2	2	GT>G
ERR5749347	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	36476	8.22E-4	85	18888,17558,30,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749347	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	32603	0.001227	0	32513,2,44,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749347	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	32591	0.001197	0	32512,0,68,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749347	11287	PASS	GTCTGGTTTT	G	32586	0.997023	0	0,97,0,32489	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749347	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	50256	7.36E-4	3	33952,16229,23,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749347	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	22290	9.87E-4	0	22235,0,24,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749347	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	45837	0.001309	0	22874,22817,33,34	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749347	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12304	0.004064	2966	12010,112,7,171	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749347	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	23882	0.001214	0	11986,11885,15,14	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749347	14408	PASS	C	T	23882	0.840508	10	5,12,11915,11744	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749347	14676	PASS	C	T	19737	0.822212	0	13,0,19674,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749347	15279	PASS	C	T	31416	0.880475	0	4,0,31373,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749347	16176	PASS	T	C	25652	0.978325	0	0,0,9930,15708	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749347	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	27387	8.03E-4	0	27365,0,22,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749347	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	35235	0.002526	0	35104,0,94,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749347	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	43727	8.46E-4	0	43634,0,37,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749347	21764	PASS	ATACATG	A	16590	0.996745	0	54,0,16535,1	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749347	21990	PASS	TTTA	T	16602	0.997049	0	0,49,13,16540	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749347	22289	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTTA	G	32820	5.79E-4	0	5,32796,0,19	HIGH	NONE	FRAME_SHIFT	S	gctttacat/	ALH243	S	0.000446	0.915917	3	2	GCTTTA>G
ERR5749347	22290	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	32821	4.27E-4	0	5,32802,0,14	HIGH	NONE	FRAME_SHIFT	S	tta/	L244	S	0.000389	0.578006	2	2	CT>C
ERR5749347	23063	PASS	A	T	17948	0.858313	0	0,6,0,17858	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749347	23271	PASS	C	A	33377	0.925098	0	1,0,33342,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749347	23403	PASS	A	G	33364	0.968439	0	0,9,0,33322	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749347	23604	PASS	C	A	19709	0.939926	0	13,0,19683,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749347	23709	PASS	C	T	19680	0.928404	0	0,7,3,19627	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749347	24127	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TTTG	39656	4.54E-4	38	15605,24057,0,18	MODERATE	NONE	CODON_INSERTION	S	aac/TTGaac	N856LN	S	0.000324	0.111888	4	1	T>TTTG
ERR5749347	24127	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TTTTTG	39656	4.03E-4	33	15605,24057,0,16	HIGH	NONE	FRAME_SHIFT+STOP_GAINED	S	aac/TTTTGaac	N856F*?	S	0.000324	0.111888	4	1	T>TTTTTG
ERR5749347	24506	PASS	T	G	27437	0.974742	0	8,0,27425,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749347	24914	PASS	G	C	44904	0.959001	0	0,0,22381,22485	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749347	25481	PASS	G	T	46436	0.899776	137	4,61,23289,23062	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cGc/cTc	R30L	orf3a	0.000794	0.899776	2	1	G>T
ERR5749347	25496	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	46552	7.3E-4	691	23186,22771,83,480	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aTa/aGa	I35R	orf3a	0.000369	0.96555	3	2	T>G
ERR5749347	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	27199	0.001066	372	27086,31,14,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749347	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	27341	0.001097	1289	26931,172,118,90	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749347	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	58943	2.71E-4	0	6,58917,0,16	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749347	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	15924	0.00113	0	0,15903,0,18	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749347	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	15925	0.003391	0	0,15862,0,54	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749347	27371	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25347	0.00213	0	53,25188,0,65	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF6	cCa/cTa	P57L	orf6	0.00148	0.066731	2	2	C>T
ERR5749347	27972	PASS	C	T	15244	0.895237	150	7,9,15081,109	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749347	28048	PASS	G	T	15143	0.908605	0	0,26,0,15105	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749347	28077	PASS	G	C	15156	0.974466	0	0,1,1,15149	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	Gtg/Ctg	V62L	orf8	0.00228	0.974466	2	1	G>C
ERR5749347	28093	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15174	0.00257	0	11,15108,0,40	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tCt/tTt	S67F	orf8	0.001515	0.967675	1	1	C>T
ERR5749347	28111	PASS	A	G	45333	0.974257	1	14,9,30146,15147	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749347	28239	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTGTTTTAGATTTCATCTAAACGAACAAACTAA	G	30165	6.3E-4	0	30142,2,19,0	HIGH	NONE	FRAME_SHIFT+STOP_LOST+SPLICE_SITE_REGION	ORF8	gttgttttagatttcatctaa/	VVLDFI*116	orf8	0.000417	0.984998	9	2	GTTGTTTTAGATTTCATCTAAACGAACAAACTAA>G
ERR5749347	28270	PASS	TA	T	58385	0.994656	745	311,10,29761,28312	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749347	28271	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AA	A	58378	5.31E-4	73	30024,28324,30,1	.	.	.	.	.	.	.	0.000482	0.924941	3	2	AA>A
ERR5749347	28280	PASS	G	C	58284	0.933635	54	29,3,29849,28280	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749347	28281	PASS	A	T	58285	0.896646	71	49,8,29825,28289	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749347	28282	PASS	T	A	58288	0.896119	12	38,21,29759,28304	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749347	28406	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTACCCAATA	T	30191	4.31E-4	0	20,30156,0,13	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	N	ttacccaataat/tat	LPNN45Y	N	0.00043	0.921074	3	2	TTACCCAATA>T
ERR5749347	28881	PASS	G	A	26611	0.752659	18	14,3,13140,13082	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749347	28882	PASS	G	A	26609	0.832989	6	8,3,13327,13023	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749347	28883	PASS	G	C	26608	0.942724	0	1,0,13345,13224	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749347	28977	PASS	C	T	13555	0.931169	2147483647	0,0,0,13521	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749347	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	53719	0.001247	314	40110,13476,8,68	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749347	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	79731	0.001367	1	40024,39541,71,66	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749348	241	PASS	C	T	371	0.881402	0	0,0,185,184	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749348	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	4181	0.003348	0	4165,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749348	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	4180	0.004067	0	3894,0,268,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749348	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	4181	0.001674	0	4173,1,7,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749348	673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	22069	0.00435	697	17884,4089,0,96	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggc/	G137	leader	0.000454	0.602236	3	2	CG>C
ERR5749348	676	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22069	0.001586	265	17877,4143,3,42	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G137	leader	0.000799	0.919273	2	1	C>T
ERR5749348	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	22069	0.001133	20	17859,4185,25,0	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749348	913	PASS	C	T	17870	0.902126	0	0,12,0,17829	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749348	1510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	13814	0.004416	0	0,13598,0,68	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G235	nsp2	0.002159	0.937304	1	1	T>C
ERR5749348	1813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	15857	0.001829	0	0,15805,0,33	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcA	A336	nsp2	0.001022	0.152738	4	2	T>A
ERR5749348	3037	PASS	C	T	10861	0.842924	24	0,8,5429,5371	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749348	3267	PASS	C	T	16072	0.968952	0	3,0,16057,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749348	3575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	10536	0.001898	0	10516,0,20,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/ttTa	L287F?	nsp3	0.000594	0.059126	3	1	G>GT
ERR5749348	3671	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GA	20963	7.63E-4	0	10499,10451,8,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/aaAt	N319K?	nsp3	0.000351	0.0625	6	2	G>GA
ERR5749348	3802	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	14355	6.97E-4	57	3808,10537,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N363	nsp3	0.000554	0.064198	4	2	TA>T
ERR5749348	3817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	14355	8.36E-4	13	3818,10525,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K367	nsp3	0.000777	0.972816	2	2	CA>C
ERR5749348	4423	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	11380	0.001142	0	11360,7,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K569	nsp3	0.00063	0.953796	2	2	CA>C
ERR5749348	4529	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTTTAC	T	11344	0.00141	0	2,11326,0,16	HIGH	NONE	FRAME_SHIFT	ORF1ab	tacttt/	YF605	nsp3	0.000527	0.402778	3	1	TTTTAC>T
ERR5749348	4764	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	11880	6.73E-4	0	11872,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F683	nsp3	0.000673	0.93404	4	2	AT>A
ERR5749348	4960	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	11882	6.73E-4	0	1,11873,0,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	agg/	R748	nsp3	0.000673	0.062723	2	2	GA>G
ERR5749348	5192	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7390	0.003789	0	0,7355,0,29	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Ctg/Ttg	L825	nsp3	0.003789	0.912192	1	1	C>T
ERR5749348	5388	PASS	C	A	2081	0.953388	2147483647	0,0,2078,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749348	5986	PASS	C	T	9254	0.975146	2147483647	0,0,9247,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749348	6516	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	22323	0.001433	158	7094,15197,32,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	att/aAtt	I1268N?	nsp3	0.000479	0.186047	4	2	T>TA
ERR5749348	6813	PASS	C	T	18685	0.950709	0	1,1,11554,7118	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T1365I	nsp3	0.001082	0.95799	2	1	C>T
ERR5749348	6954	PASS	T	C	11528	0.826249	0	0,2,0,11462	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749348	7070	PASS	G	T	14709	0.101434	2147483647	1641,11535,1508,11	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggc/Tgc	G1451C	nsp3	0.000698	0.101434	3	1	G>T
ERR5749348	7764	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19595	0.001123	0	19519,0,23,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCc/tTc	S1682F	nsp3	0.001052	0.964731	1	1	C>T
ERR5749348	7945	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19602	0.003316	0	7,19521,0,70	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y1742	nsp3	0.001244	0.950558	2	2	C>T
ERR5749348	9060	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	16443	0.001764	0	16373,0,32,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tAt/tGt	Y169C	nsp4	0.000621	0.433333	5	2	A>G
ERR5749348	9198	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	16461	5.47E-4	0	0,16452,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F216	nsp4	0.000543	0.93476	4	2	CT>C
ERR5749348	9661	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	17131	5.84E-4	0	8789,8332,5,5	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T370	nsp4	0.000584	0.920378	2	2	CA>C
ERR5749348	9968	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	3820	0.003141	0	3802,1,14,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gca/Aca	A472T	nsp4	0.003141	0.078014	2	1	G>A
ERR5749348	10470	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12508	0.001439	0	12488,0,18,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCa/tTa	S139L	3Cpro	0.001439	0.104693	1	1	C>T
ERR5749348	10642	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	12508	0.001359	0	0,12445,0,19	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acG/acC	T196	3Cpro	0.001264	0.951979	3	1	G>C
ERR5749348	10642	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	12508	0.001599	0	0,12445,0,31	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acG/acT	T196	3Cpro	0.001264	0.951979	3	1	G>T
ERR5749348	11075	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TC	17496	0.001086	0	17476,0,19,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/tCtt	F35S?	nsp6	0.000555	0.885796	4	2	T>TC
ERR5749348	11287	PASS	GTCTGGTTTT	G	17489	0.997313	0	0,47,0,17442	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749348	11507	PASS	G	A	9366	0.897502	0	1,0,4714,4630	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Att	V179I	nsp6	0.007744	0.914418	2	2	G>A
ERR5749348	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	22409	0.001249	1	17640,4725,21,7	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749348	12125	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	18557	0.001293	0	2,18466,0,28	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y12H	nsp8	0.000847	0.113436	1	1	T>C
ERR5749348	12870	PASS	C	T	4591	0.773252	2147483647	0,0,4569,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T62I	nsp9	0.773252	0.848527	1	1	C>T
ERR5749348	13498	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	18205	0.002911	4	9078,8997,35,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Aca/Gca	T20A	RdRp	0.001341	0.952048	1	1	A>G
ERR5749348	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18216	0.002251	0	9091,9055,22,22	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749348	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	8485	0.002829	1897	8290,81,3,108	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749348	14408	PASS	C	T	16499	0.845142	9	0,3,8249,8123	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749348	14676	PASS	C	T	9012	0.822348	0	4,0,8991,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749348	15279	PASS	C	T	9938	0.8709	0	18,0,9900,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749348	15379	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AG	A	19821	9.59E-4	0	9899,9903,10,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	agc/	S647	RdRp	0.000745	0.947742	2	2	AG>A
ERR5749348	15924	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8725	0.001719	0	8702,0,15,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y828	RdRp	0.001719	0.970414	1	1	C>T
ERR5749348	15983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	8718	9.18E-4	0	8711,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T850	RdRp	0.000701	0.338235	2	1	TA>T
ERR5749348	16176	PASS	T	C	10731	0.976423	0	0,0,2003,8722	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749348	16647	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	16789	0.001549	0	0,16681,0,27	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acG/acA	T137	helicase	0.000746	0.885245	2	1	G>A
ERR5749348	16792	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CGT	C	29809	4.03E-4	27	12954,16843,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	gta/	V187	helicase	0.000335	0.072562	5	2	CGT>C
ERR5749348	18131	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6401	0.0025	0	6384,0,17,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T31I	ExoN	0.0025	0.853992	1	1	C>T
ERR5749348	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	26781	8.96E-4	0	26740,0,24,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749348	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTT	C	26781	6.35E-4	0	26740,0,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttttcc/	FS217	ExoN	0.000374	0.981963	3	2	CTT>C
ERR5749348	18813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	53416	6.18E-4	2	26458,26709,18,23	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaT/gaC	D258	ExoN	0.000618	0.934482	1	1	T>C
ERR5749348	18897	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	26790	6.72E-4	0	9,26763,0,18	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/	V287	ExoN	0.00046	0.060685	3	3	TG>T
ERR5749348	19343	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	13768	6.54E-4	0	13759,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/Tgtt	V437C?	ExoN	0.000519	0.192257	7	2	C>CT
ERR5749348	19343	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13768	0.001598	0	13729,0,25,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A435V	ExoN	0.000519	0.192257	7	2	C>T
ERR5749348	19401	PASS	T	A	13743	0.918286	0	7,0,13698,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcT/tcA	S454	ExoN	0.913864	0.918286	1	1	T>A
ERR5749348	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30149	0.001095	0	30075,0,36,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749348	20718	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	30083	8.98E-4	0	0,29910,0,30	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atA	M20I	MethTr	0.000898	0.920213	3	1	G>A
ERR5749348	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	16694	0.001498	0	0,16669,0,25	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TA>T
ERR5749348	21101	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	16700	0.001677	0	1,16650,0,45	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGt/gTt	G148V	MethTr	0.001498	0.083467	2	2	G>T
ERR5749348	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15975	0.004632	0	7780,7930,43,44	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749348	21637	PASS	C	T	8033	0.954687	0	0,1,0,8027	LOW	SILENT	SYNONYMOUS_CODING	S	ccC/ccT	P25	S	0.954687	0.96491	1	1	C>T
ERR5749348	21764	PASS	ATACATG	A	11113	0.99766	0	26,0,11087,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749348	21976	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	11120	0.001799	0	7,11089,0,21	LOW	SILENT	SYNONYMOUS_CODING	S	gaT/gaC	D138	S	0.000856	0.977603	2	2	T>C
ERR5749348	21990	PASS	TTTA	T	11120	0.998651	0	0,15,7,11098	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749348	22028	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	15492	6.45E-4	0	15474,8,10,0	HIGH	NONE	FRAME_SHIFT	S	gag/	E156	S	0.000645	1	2	1	GA>G
ERR5749348	22451	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	8815	0.001815	425	8661,19,9,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Cca	S297P	S	0.001815	0.056075	2	1	T>C
ERR5749348	22771	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AG	A	13429	5.96E-4	0	0,13421,0,8	HIGH	NONE	FRAME_SHIFT	S	ggt/	G404	S	0.000511	0.112051	3	3	AG>A
ERR5749348	23063	PASS	A	T	12255	0.859486	0	0,2,0,12195	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749348	23271	PASS	C	A	19721	0.940064	0	1,0,19707,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749348	23403	PASS	A	G	19708	0.966207	0	0,1,0,19687	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749348	23406	PASS	T	C	19708	0.949411	0	0,3,0,19695	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gTt/gCt	V615A	S	0.949411	0.956636	1	1	T>C
ERR5749348	23481	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	31881	0.001098	6	12133,19680,18,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCt/tTt	S640F	S	0.001098	0.964516	1	1	C>T
ERR5749348	23604	PASS	C	A	12155	0.945372	0	6,0,12142,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749348	23709	PASS	C	T	12145	0.93907	0	0,5,0,12124	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749348	24320	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	9157	0.003276	0	0,9127,0,30	HIGH	NONE	FRAME_SHIFT	S	aaa/	K921	S	0.000763	0.138365	4	2	CA>C
ERR5749348	24506	PASS	T	G	11895	0.97377	0	1,0,11893,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749348	24914	PASS	G	C	43459	0.957937	0	0,0,21642,21769	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749348	25207	PASS	C	T	5207	0.766084	0	0,7,0,5163	LOW	SILENT	SYNONYMOUS_CODING	S	taC/taT	Y1215	S	0.004687	0.815232	1	1	C>T
ERR5749348	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	25644	0.001443	29	20353,5236,43,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749348	25496	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	40792	9.32E-4	11	20324,20058,20,33	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aTa/aCa	I35T	orf3a	0.000369	0.96555	3	2	T>C
ERR5749348	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	2235	0.007606	293	2183,33,0,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749348	26158	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	25421	7.87E-4	0	3,25388,0,20	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF3a	gttaat/gat	VN256D	orf3a	0.000297	0.905181	6	2	GTTA>G
ERR5749348	26158	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTAATCCAGTAATGGAACCAA	G	25421	3.93E-4	0	3,25388,0,10	MODERATE	NONE	CODON_DELETION	ORF3a	aatccagtaatggaaccaatt/	NPVMEPI257	orf3a	0.000297	0.905181	6	2	GTTAATCCAGTAATGGAACCAA>G
ERR5749348	26526	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	7449	0.002953	0	0,7416,0,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Gca/Aca	A2T	M	0.001224	0.951192	3	1	G>A
ERR5749348	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	G	11665	7.72E-4	0	0,11650,0,9	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/	ACLVGLMWLSYFIASF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT>G
ERR5749348	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	11666	7.71E-4	0	0,11657,0,9	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749348	27294	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAT	C	19547	7.67E-4	0	19532,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF6	atc/	I32	orf6	0.000651	0.875122	2	2	CAT>C
ERR5749348	27403	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATTC	A	19541	5.12E-4	0	0,19531,0,10	MODERATE	NONE	CODON_DELETION	ORF7a	ctt/	L5	orf7a	0.000512	0.916	3	2	ATTC>A
ERR5749348	27494	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	35661	0.001262	1	16073,19514,21,29	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	cCt/cTt	P34L	orf7a	0.000672	0.961447	2	2	C>T
ERR5749348	27509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	35661	8.97E-4	36	16079,19541,27,8	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	aCa/aTa	T39I	orf7a	0.000843	0.067888	1	1	C>T
ERR5749348	27972	PASS	C	T	7622	0.897533	21	1,1,7555,26	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749348	28048	PASS	G	T	7589	0.917249	0	0,11,0,7576	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749348	28111	PASS	A	G	24195	0.976524	1	3,2,16586,7589	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749348	28270	PASS	TA	T	32023	0.995066	310	154,11,16374,15491	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749348	28280	PASS	G	C	31969	0.936188	14	8,1,16412,15480	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749348	28281	PASS	A	T	31969	0.911883	18	21,7,16401,15478	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749348	28282	PASS	T	A	31969	0.918139	10	13,5,16382,15488	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749348	28881	PASS	G	A	12250	0.767347	6	3,0,6079,6007	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749348	28882	PASS	G	A	12250	0.828327	6	3,0,6139,6005	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749348	28883	PASS	G	C	12250	0.942367	0	1,0,6155,6086	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749348	28977	PASS	C	T	6227	0.931428	0	0,3,0,6205	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749348	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	37932	0.003084	917	31679,6092,3,123	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749348	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	62943	0.001271	1	31605,31212,47,51	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749349	239	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTC	T	5171	0.001547	0	2580,2583,4,4	.	.	.	.	.	.	.	0.000495	0.25	4	1	TTC>T
ERR5749349	241	PASS	C	T	5171	0.871592	0	0,0,2574,2573	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749349	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	9151	0.004262	0	9111,0,39,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749349	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	9151	0.001202	0	9095,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749349	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	9151	0.004262	0	9095,0,39,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749349	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	9168	0.001745	5	8349,24,685,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749349	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	9168	0.002618	0	9120,24,24,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749349	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	9167	0.001527	0	9118,24,14,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttatg/gtg	VM84V	leader	0.000554	0.991848	4	1	GTTA>G
ERR5749349	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	9167	0.001309	0	9118,24,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749349	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	9166	9.82E-4	0	9125,24,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TA>T
ERR5749349	657	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9167	0.004254	0	3,9116,0,47	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A131V	leader	0.001202	0.365979	3	1	C>T
ERR5749349	673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29360	0.001465	115	20170,9096,9,38	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y136	leader	0.000454	0.602236	3	2	C>T
ERR5749349	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	29360	7.49E-4	16	20116,9149,20,2	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749349	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	29360	0.002146	11	20116,9149,50,13	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749349	892	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	20183	4.95E-4	0	0,20173,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K30	nsp2	0.000495	0.082222	2	2	TA>T
ERR5749349	913	PASS	C	T	20187	0.919304	0	0,9,0,20151	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749349	1813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	24473	0.001022	0	0,24421,0,30	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcA	A336	nsp2	0.001022	0.152738	4	2	T>A
ERR5749349	2151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATTGGC	A	19753	5.57E-4	0	0,19742,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	tggcttgaa/	WLE450	nsp2	0.000402	0.971954	3	2	ATTGGC>A
ERR5749349	3037	PASS	C	T	18904	0.846699	16	1,8,9436,9349	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749349	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	9549	0.002618	692	2,9517,25,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749349	3267	PASS	C	T	22697	0.97145	0	2,0,22683,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749349	4529	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTTTACTTTTACACCAGTAAAACAAC	T	17084	5.27E-4	0	17,17058,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttttacttttacaccagtaaaacaact/	FYFYTSKTT604	nsp3	0.000527	0.402778	3	1	TTTTACTTTTACACCAGTAAAACAAC>T
ERR5749349	4578	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTAACGATC	T	17094	6.44E-4	0	0,17083,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	aacgatctaaat/	NDLN621	nsp3	0.000519	0.082979	2	2	TTAACGATC>T
ERR5749349	5077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	13318	0.001427	0	13260,0,21,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtT/gtC	V786	nsp3	0.001393	0.168205	1	1	T>C
ERR5749349	5388	PASS	C	A	5611	0.960435	2147483647	0,0,5607,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749349	5986	PASS	C	T	15647	0.975395	2147483647	0,0,15630,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749349	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15131	0.001851	0	8,14948,0,36	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749349	6954	PASS	T	C	26072	0.818541	0	0,2,0,25940	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749349	8950	PASS	C	T	37652	0.978806	5	3,0,21296,16337	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I132	nsp4	0.002808	0.982604	1	1	C>T
ERR5749349	8964	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	21320	6.57E-4	0	21293,7,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K138	nsp4	0.000553	0.981649	4	2	CA>C
ERR5749349	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	20248	0.001827	30	16531,3680,37,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749349	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	29554	0.001353	0	29458,0,65,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749349	11287	PASS	GTCTGGTTTT	G	29555	0.99665	196	8,99,0,29456	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749349	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	40436	8.41E-4	4	27805,12551,22,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749349	11750	PASS	C	T	54088	0.682462	27	16,35,27681,23793	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L260F	nsp6	0.001019	0.70989	2	1	C>T
ERR5749349	11750	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	G	54088	0.002718	103	16,35,90,2425	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Gtc	L260V	nsp6	0.001019	0.70989	2	1	C>G
ERR5749349	12439	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	24028	6.66E-4	0	9,24003,0,16	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L117	nsp8	0.000666	0.637117	2	2	CT>C
ERR5749349	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	23322	0.001286	0	23258,0,30,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749349	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	19013	9.47E-4	0	18994,0,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749349	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	40590	0.001552	0	20251,20210,35,36	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749349	13994	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20329	0.001181	0	20296,0,24,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A185V	RdRp	0.000427	0.114441	3	2	C>T
ERR5749349	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	10622	0.002259	0	5321,5283,13,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749349	14408	PASS	C	T	10622	0.85144	2	1,2,5301,5221	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749349	14676	PASS	C	T	14462	0.723966	0	8,0,14388,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749349	15026	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAT	C	19085	5.76E-4	0	19076,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tataca/	YT530	RdRp	0.000503	0.869455	2	2	CAT>C
ERR5749349	15279	PASS	C	T	21143	0.897886	0	1,0,21112,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749349	15720	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23956	0.001002	0	1,23922,0,24	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D760	RdRp	0.001002	0.917823	1	1	C>T
ERR5749349	15905	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AG	A	12861	0.001322	0	12844,0,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggt/	G823	RdRp	0.000835	0.057692	2	1	AG>A
ERR5749349	16176	PASS	T	C	20018	0.981567	0	1,2,7152,12854	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749349	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAA	G	25545	5.87E-4	0	25491,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GAA>G
ERR5749349	17181	PASS	T	C	16409	0.988055	0	11,0,16387,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaT/gaC	D315	helicase	0.986595	0.991193	1	1	T>C
ERR5749349	18576	PASS	C	T	34941	0.865001	0	0,11,0,34812	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D179	ExoN	0.005404	0.876866	2	2	C>T
ERR5749349	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	31947	5.95E-4	0	31928,0,19,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749349	19164	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	30689	3.58E-4	0	0,30678,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K376	ExoN	0.000358	0.075732	4	2	CAA>C
ERR5749349	19299	PASS	T	C	22820	0.987467	0	6,0,22804,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taT/taC	Y420	ExoN	0.001065	0.987656	2	2	T>C
ERR5749349	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22027	0.001952	0	21966,0,46,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749349	20091	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	21997	5.46E-4	0	1,21984,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	caa/Acaa	Q159T?	endoR	0.000368	0.051583	1	1	C>CA
ERR5749349	20987	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	56698	4.59E-4	0	28373,28300,13,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L111	MethTr	0.000276	0.056129	4	2	CT>C
ERR5749349	21234	PASS	C	T	38760	0.65743	0	28,0,38242,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A192	MethTr	0.000472	0.857572	5	2	C>T
ERR5749349	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	37564	9.05E-4	1	18397,18749,20,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749349	21724	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTCTTACCTT	G	17056	5.86E-4	0	17033,13,10,0	HIGH	NONE	FRAME_SHIFT	S	ttcttacctttc/	FLPF55	S	0.000586	0.911899	2	2	GTTCTTACCTT>G
ERR5749349	21764	PASS	ATACATG	A	17038	0.996831	0	54,0,16984,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749349	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	17036	6.46E-4	0	17025,0,11,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749349	21990	PASS	TTTA	T	17052	0.996775	0	0,55,11,16986	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749349	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	41936	0.001002	0	18765,23100,19,25	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749349	23063	PASS	A	T	18778	0.867185	0	0,1,0,18696	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749349	23271	PASS	C	A	25611	0.919683	0	2,0,25579,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749349	23403	PASS	A	G	25607	0.977858	0	0,12,0,25580	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749349	23604	PASS	C	A	18838	0.937998	0	28,0,18798,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749349	23709	PASS	C	T	18820	0.941711	0	0,3,3,18790	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749349	24506	PASS	T	G	22110	0.973948	0	14,0,22094,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749349	24914	PASS	G	C	49025	0.959633	0	0,0,24417,24563	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749349	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	34257	0.001343	60	26152,8046,54,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749349	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	10547	0.002276	435	10469,34,4,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749349	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	10493	7.62E-4	0	10485,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749349	25844	PASS	C	T	10475	0.928687	0	0,3,6,10458	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aCt/aTt	T151I	orf3a	0.001226	0.938776	1	1	C>T
ERR5749349	26159	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTAATCCAG	T	46856	5.55E-4	0	1,46829,0,26	HIGH	NONE	FRAME_SHIFT	ORF3a	ccagtaatg/	PVM258	orf3a	0.000311	0.053032	2	2	TTAATCCAG>T
ERR5749349	26257	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	60640	2.47E-4	15	13695,46930,0,15	HIGH	NONE	FRAME_SHIFT	E	tcg/	S6	E	0.000247	0.948926	4	2	GT>G
ERR5749349	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	G	16629	6.01E-4	0	0,16558,0,10	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/	ACLVGLMWLSYFIASF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT>G
ERR5749349	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	16629	0.002947	0	0,16558,0,49	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749349	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	16629	6.01E-4	0	0,16618,0,10	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749349	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	16630	0.003788	0	0,16560,0,63	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749349	27128	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	40322	7.19E-4	0	0,40270,0,30	LOW	SILENT	SYNONYMOUS_CODING	M	ggC/ggT	G202	M	0.000719	0.147659	1	1	C>T
ERR5749349	27577	PASS	C	T	27842	0.8114	0	5,0,27579,0	HIGH	NONSENSE	STOP_GAINED	ORF7a	Caa/Taa	Q62*	orf7a	0.000614	0.952205	4	2	C>T
ERR5749349	27972	PASS	C	T	11858	0.904453	0	0,0,11725,90	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749349	28048	PASS	G	T	11788	0.925348	0	0,10,0,11769	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749349	28111	PASS	A	G	41190	0.979582	11	9,0,29370,11798	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749349	28237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTGT	G	29383	4.42E-4	0	29370,0,13,0	MODERATE	NONE	CODON_DELETION	ORF8	gtt/	V117	orf8	0.000442	0.966707	4	2	GTGT>G
ERR5749349	28247	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AGATT	A	29379	3.74E-4	0	29365,3,11,0	HIGH	NONE	FRAME_SHIFT	ORF8	gatttc/	DF119	orf8	0.000374	0.998357	3	1	AGATT>A
ERR5749349	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	29353	4.77E-4	0	29345,3,14,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749349	28270	PASS	TA	T	57184	0.994946	567	266,16,28998,27897	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749349	28270	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAA	T	57184	3.5E-4	64	266,16,10,10	.	.	.	.	.	.	.	0.000322	1	2	1	TAA>T
ERR5749349	28280	PASS	G	C	57074	0.939359	11	12,4,29061,27882	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749349	28281	PASS	A	T	57074	0.918422	20	47,23,29031,27873	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749349	28282	PASS	T	A	57077	0.914169	0	31,29,28985,27884	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749349	28292	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	58458	3.08E-4	0	29128,29288,9,9	HIGH	NONE	FRAME_SHIFT	N	aat/	N8	N	0.000304	0.055324	4	2	CAA>C
ERR5749349	28406	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTACCCAATA	T	29408	0.001258	0	18,29346,0,37	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	N	ttacccaataat/tat	LPNN45Y	N	0.00043	0.921074	3	2	TTACCCAATA>T
ERR5749349	28881	PASS	G	A	16463	0.722651	38	16,1,8037,8111	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749349	28882	PASS	G	A	16461	0.824494	4	4,1,8213,8082	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749349	28883	PASS	G	C	16461	0.942288	0	1,0,8227,8212	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749349	28977	PASS	C	T	8368	0.935707	2147483647	0,0,0,8351	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749349	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	79457	9.06E-4	0	39912,39437,43,40	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749349	29679	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	22577	4.43E-4	0	11300,11271,5,5	.	.	.	.	.	.	.	0.000443	0.838763	2	1	CT>C
ERR5749350	71	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1080	0.026852	0	1051,0,29,0	.	.	.	.	.	.	.	0.002088	0.926791	2	1	C>T
ERR5749350	241	PASS	C	T	1182	0.879865	0	0,0,586,595	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749350	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	4364	0.002062	0	4354,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749350	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	4358	0.002754	0	4032,0,314,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749350	657	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4373	0.005946	0	1,4337,0,33	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A131V	leader	0.001202	0.365979	3	1	C>T
ERR5749350	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	26236	7.62E-4	6	21845,4371,19,1	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749350	751	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21864	0.001464	0	21813,0,33,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N162	leader	0.000662	0.943591	2	2	C>T
ERR5749350	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	21854	9.15E-4	0	0,21834,0,20	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L35	nsp2	0.000551	0.081967	3	2	CT>C
ERR5749350	913	PASS	C	T	21854	0.91489	0	0,8,0,21820	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749350	929	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	21859	8.23E-4	0	0,21841,0,18	HIGH	NONE	FRAME_SHIFT	ORF1ab	att/	I42	nsp2	0.000823	0.987013	3	2	AT>A
ERR5749350	3037	PASS	C	T	8798	0.815981	30	0,10,4392,4329	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749350	3177	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	22415	9.81E-4	1	17958,4427,23,4	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cAt	P153H	nsp3	0.000773	0.96008	3	2	C>A
ERR5749350	3267	PASS	C	T	17980	0.97069	0	2,0,17970,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749350	3671	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	19486	0.002053	0	9701,9648,22,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E318K	nsp3	0.000351	0.0625	6	2	G>A
ERR5749350	3832	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5109	0.002936	0	5086,4,15,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	agC/agT	S371	nsp3	0.000689	0.327273	4	2	C>T
ERR5749350	5388	PASS	C	A	2253	0.954727	2147483647	0,0,2251,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749350	5605	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	18938	6.86E-4	26	16678,2247,7,6	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K963	nsp3	0.000409	0.095477	2	2	GA>G
ERR5749350	5986	PASS	C	T	8096	0.974308	2147483647	0,0,8089,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749350	6266	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GC	G	17743	6.76E-4	0	17729,2,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gcc/	A1183	nsp3	0.000676	0.950772	2	2	GC>G
ERR5749350	6336	PASS	C	T	17723	0.951419	0	1,0,17692,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCg/tTg	S1206L	nsp3	0.001317	0.951419	1	1	C>T
ERR5749350	6383	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	35416	0.001045	71	17596,17679,99,37	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gcc/Tcc	A1222S	nsp3	0.000859	0.05632	3	1	G>T
ERR5749350	6651	PASS	C	T	7471	0.857717	0	5,0,7436,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A1311V	nsp3	0.008493	0.857717	1	1	C>T
ERR5749350	6894	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	14588	9.6E-4	0	14575,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tgt/	C1392	nsp3	0.00096	0.897867	3	2	GT>G
ERR5749350	6954	PASS	T	C	14575	0.822985	0	0,1,0,14501	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749350	6982	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14624	0.001915	0	0,14571,0,29	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C1421	nsp3	0.001915	0.911934	1	1	C>T
ERR5749350	7674	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CGA	C	18063	9.97E-4	0	18039,6,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gac/	D1654	nsp3	0.000682	0.109264	3	2	CGA>C
ERR5749350	8123	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15834	0.002589	0	15771,0,47,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Ttt	L1802F	nsp3	0.001144	0.778589	1	1	C>T
ERR5749350	9053	PASS	G	A	15505	0.060755	0	14437,0,1065,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gta/Ata	V167I	nsp4	0.060755	0.060755	1	1	G>A
ERR5749350	9072	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30855	0.001037	1	15460,15305,16,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCc/aTc	T173I	nsp4	0.001037	0.930675	2	1	C>T
ERR5749350	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	11047	0.001086	10	8502,2533,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749350	10138	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19145	0.001097	16	14211,4906,21,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N28	3Cpro	0.000458	0.983567	3	3	C>T
ERR5749350	10386	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29630	8.77E-4	59	15363,14233,25,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T111I	3Cpro	0.000642	0.160456	4	2	C>T
ERR5749350	10615	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15401	0.001623	0	14,15333,0,33	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D187	3Cpro	0.001623	0.865067	1	1	C>T
ERR5749350	11287	PASS	GTCTGGTTTT	G	20020	0.997453	0	0,51,0,19969	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749350	12513	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CGT	C	14155	9.89E-4	0	14141,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tgtgat/	CD142	nsp8	0.000794	0.984064	2	2	CGT>C
ERR5749350	13459	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	13497	7.41E-4	0	13487,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/ttTa	L8F?	nsp11	0.000691	0.060726	5	2	G>GT
ERR5749350	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26957	8.53E-4	0	13468,13433,13,13	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749350	14408	PASS	C	T	1304	0.860429	0	0,0,652,647	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749350	14676	PASS	C	T	11347	0.725214	0	3,0,11288,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749350	14805	PASS	C	T	11343	0.9032	0	0,7,0,11308	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y455	RdRp	0.001051	0.904964	2	2	C>T
ERR5749350	15096	PASS	T	C	11425	0.966827	0	0,6,13,11402	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaT/aaC	N552	RdRp	0.941667	0.970182	1	1	T>C
ERR5749350	15240	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13190	0.00144	0	13155,13,19,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N600	RdRp	0.000934	0.931284	2	2	C>T
ERR5749350	15279	PASS	C	T	13177	0.891326	2147483647	0,0,13155,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749350	16176	PASS	T	C	12889	0.979595	0	0,1,2190,10696	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749350	16260	PASS	C	T	2191	0.961661	2147483647	0,0,2190,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C8	helicase	0.045161	0.961661	2	2	C>T
ERR5749350	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	13261	0.002111	0	13233,0,28,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749350	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	25508	6.66E-4	0	25491,0,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749350	18756	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	25506	9.8E-4	0	25456,0,40,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccG/ccT	P239	ExoN	0.000392	0.942688	3	2	G>T
ERR5749350	18800	PASS	A	G	50935	0.072445	0	23463,23398,1992,1990	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cAa/cGa	Q254R	ExoN	0.000701	0.072445	1	1	A>G
ERR5749350	19269	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	36997	9.73E-4	23	12213,24740,21,16	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N410	ExoN	0.000773	0.954777	2	2	C>T
ERR5749350	19299	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	12236	0.001553	0	12213,0,19,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taT/taC	Y420	ExoN	0.001065	0.987656	2	2	T>C
ERR5749350	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10152	0.002955	0	10117,0,32,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749350	20578	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	32352	0.001205	0	32267,0,77,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtg/Ttg	V320L	endoR	0.00085	0.958277	3	1	G>T
ERR5749350	20925	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	20685	0.001064	0	20639,0,40,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L89F	MethTr	0.001064	0.136967	2	1	G>T
ERR5749350	21101	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	20688	0.001498	0	3,20627,0,56	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGt/gTt	G148V	MethTr	0.001498	0.083467	2	2	G>T
ERR5749350	21123	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	41879	3.1E-4	39	21192,20674,0,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F156	MethTr	0.000257	0.90982	5	2	GT>G
ERR5749350	21234	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	21181	7.55E-4	0	21167,0,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/Tgtt	V194C?	MethTr	0.000472	0.857572	5	2	C>CT
ERR5749350	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	17418	0.002009	0	8676,8709,17,18	HIGH	NONE	FRAME_SHIFT	S	ctt/Tctt	L5S?	S	0.000394	0.091869	4	1	G>GT
ERR5749350	21595	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8747	0.002401	0	0,8719,0,22	LOW	SILENT	SYNONYMOUS_CODING	S	gtC/gtT	V11	S	0.001296	0.918559	3	2	C>T
ERR5749350	21764	PASS	ATACATG	A	9684	0.998451	0	16,0,9669,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749350	21817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	AT	9691	0.001135	0	9673,7,11,0	HIGH	NONE	FRAME_SHIFT+STOP_GAINED	S	aat/Taat	N87*?	S	0.000689	0.961354	3	2	A>AT
ERR5749350	21990	PASS	TTTA	T	9689	0.997936	0	0,20,4,9665	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749350	22295	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAT	C	24174	6.62E-4	23	7484,16674,0,16	HIGH	NONE	FRAME_SHIFT	S	cataga/	HR245	S	0.000662	0.930915	2	2	CAT>C
ERR5749350	22600	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	21299	7.04E-4	9	13804,7480,13,2	HIGH	NONE	FRAME_SHIFT	S	ttt/	F347	S	0.000471	0.963998	3	3	AT>A
ERR5749350	22776	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATG	A	13810	6.52E-4	0	0,13801,0,9	HIGH	NONE	FRAME_SHIFT	S	gatgaa/	DE405	S	0.000652	0.1959	2	2	ATG>A
ERR5749350	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24995	9.6E-4	23	11168,13794,4,21	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749350	23063	PASS	A	T	11158	0.871303	2147483647	0,0,0,11104	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749350	23271	PASS	C	A	24117	0.922917	0	3,0,24086,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749350	23403	PASS	A	G	24115	0.97176	0	0,8,0,24087	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749350	23604	PASS	C	A	10808	0.942358	0	9,0,10792,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749350	23709	PASS	C	T	10803	0.942516	0	0,6,0,10790	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749350	24506	PASS	T	G	14064	0.972056	0	7,0,14053,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749350	24914	PASS	G	C	40541	0.960336	0	0,0,20188,20322	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749350	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	24861	0.001528	51	17640,7168,44,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749350	25482	PASS	C	T	35384	0.83761	24	1,11,17689,17519	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgC/cgT	R30	orf3a	0.00032	0.83761	2	2	C>T
ERR5749350	25626	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21212	0.001414	23	3452,17717,0,35	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	caC/caT	H78	orf3a	0.000403	0.915633	3	2	C>T
ERR5749350	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	3486	0.004016	239	3448,18,2,12	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749350	26526	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	9615	0.00208	0	2,9571,0,30	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Gca/Tca	A2S	M	0.001224	0.951192	3	1	G>T
ERR5749350	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	9327	7.51E-4	0	0,9320,0,7	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749350	27406	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	16954	5.9E-4	0	0,16944,0,10	HIGH	NONE	FRAME_SHIFT	ORF7a	ttc/	F6	orf7a	0.00059	0.998683	2	1	CT>C
ERR5749350	27816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	22878	9.18E-4	4	5775,17082,3,18	HIGH	NONE	FRAME_SHIFT	ORF7b	tta/	L22	orf7b	0.000423	0.053007	1	1	GT>G
ERR5749350	27972	PASS	C	T	5799	0.900845	0	0,0,5753,24	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749350	28001	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	11535	0.001387	0	5753,5759,8,8	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ccG/ccA	P36	orf8	0.00085	0.830607	2	1	G>A
ERR5749350	28048	PASS	G	T	5777	0.919335	0	0,8,0,5768	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749350	28095	PASS	A	T	5780	0.959862	64	2,2,0,5764	HIGH	NONSENSE	STOP_GAINED	ORF8	Aaa/Taa	K68*	orf8	0.002672	0.967672	2	2	A>T
ERR5749350	28111	PASS	A	G	23682	0.978254	0	5,1,17892,5776	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749350	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17887	0.001677	0	17813,0,30,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749350	28270	PASS	TA	T	34771	0.994478	413	180,8,17647,16932	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749350	28270	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAA	T	34771	4.6E-4	57	180,8,8,8	.	.	.	.	.	.	.	0.000322	1	2	1	TAA>T
ERR5749350	28280	PASS	G	C	34718	0.938418	23	14,2,17700,16930	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749350	28281	PASS	A	T	34718	0.91984	37	22,3,17699,16926	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749350	28282	PASS	T	A	34721	0.910803	4	38,29,17638,16919	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749350	28881	PASS	G	A	11103	0.758083	15	5,0,5458,5478	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749350	28882	PASS	G	A	11103	0.842205	15	6,0,5543,5449	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749350	28883	PASS	G	C	11102	0.947037	0	0,0,5551,5538	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749350	28977	PASS	C	T	5660	0.933392	2147483647	0,0,0,5651	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749350	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	58145	0.00141	0	29182,28850,51,50	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749351	241	PASS	C	T	2281	0.860149	0	0,0,1136,1135	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749351	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	4180	0.001914	0	4174,0,8,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749351	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	4180	0.001435	0	4171,0,6,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749351	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	4176	0.003352	0	4162,0,14,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749351	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	4175	0.001437	0	4166,0,6,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749351	656	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	4185	0.003345	0	0,4170,0,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gct/Cct	A131P	leader	0.001202	0.131429	1	1	G>C
ERR5749351	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	17370	7.48E-4	13	13169,4185,13,0	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749351	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13178	0.001366	0	0,13142,0,19	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749351	913	PASS	C	T	13178	0.917969	0	0,9,0,13152	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749351	1685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	16048	0.001433	0	16015,0,23,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gcc/Acc	A294T	nsp2	0.001379	0.231183	3	2	G>A
ERR5749351	2453	PASS	C	T	8624	0.709879	0	0,8,0,8482	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L550F	nsp2	0.00429	0.842201	2	2	C>T
ERR5749351	3037	PASS	C	T	11350	0.817709	10	3,9,5667,5592	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749351	3267	PASS	C	T	14765	0.970945	0	3,0,14751,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749351	4021	PASS	C	T	6277	0.439223	0	0,3050,0,3205	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N434	nsp3	0.018041	0.439223	1	1	C>T
ERR5749351	4529	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTTTACTTTTACACCAGTAAAACAAC	T	11060	0.001266	0	0,11046,0,14	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttttacttttacaccagtaaaacaact/	FYFYTSKTT604	nsp3	0.000527	0.402778	3	1	TTTTACTTTTACACCAGTAAAACAAC>T
ERR5749351	5388	PASS	C	A	3009	0.954138	2147483647	0,0,3006,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749351	5986	PASS	C	T	9620	0.972453	0	1,0,9611,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749351	6337	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	17764	7.32E-4	0	17751,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F1207	nsp3	0.000579	0.91624	3	2	GT>G
ERR5749351	6954	PASS	T	C	16724	0.802679	0	0,3,0,16638	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749351	7528	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11079	0.002527	0	36,11005,0,30	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V1603	nsp3	0.002527	0.916131	1	1	C>T
ERR5749351	7564	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	11060	0.001266	0	0,11046,0,14	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/	Y1617	nsp3	0.000586	0.056194	4	2	CT>C
ERR5749351	8084	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	15102	0.001126	0	15088,0,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1790	nsp3	0.000543	0.923413	4	2	GA>G
ERR5749351	8207	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ACT	A	15095	0.001457	0	0,15073,0,22	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T1830	nsp3	0.001457	0.940954	2	2	ACT>A
ERR5749351	8697	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	7838	0.001531	0	7826,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	att/	I49	nsp4	0.000737	0.072165	1	1	CTA>C
ERR5749351	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	12047	0.001411	10	10201,1829,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749351	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20983	0.002478	0	20877,1,56,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749351	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	20976	0.001049	0	20917,0,42,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749351	11287	PASS	GTCTGGTTTT	G	20975	0.996949	0	0,64,0,20911	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749351	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22405	0.001919	0	11180,11139,24,24	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749351	14097	PASS	C	T	13182	0.972462	0	0,0,13152,6	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F219	RdRp	0.000613	0.981481	2	2	C>T
ERR5749351	14408	PASS	C	T	1921	0.841229	0	0,0,958,950	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749351	14676	PASS	C	T	8392	0.785868	0	4,0,8362,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749351	15279	PASS	C	T	11579	0.877969	0	1,0,11550,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749351	16176	PASS	T	C	11666	0.978399	2	1,1,3466,8193	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749351	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	16557	0.001752	0	16528,0,29,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749351	18357	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	22924	0.001309	0	22877,0,31,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccT/ccC	P106	ExoN	0.001226	0.057597	1	1	T>C
ERR5749351	19343	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	14518	6.89E-4	0	14508,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F436	ExoN	0.000519	0.192257	7	2	CT>C
ERR5749351	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8719	0.002409	0	8692,0,22,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749351	20420	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	27225	5.88E-4	0	53,27156,0,16	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F268	endoR	0.000383	0.069626	2	1	AT>A
ERR5749351	20481	PASS	A	G	27232	0.966106	0	0,4,23,27151	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcA/tcG	S287	endoR	0.001272	0.966106	1	1	A>G
ERR5749351	20987	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	40178	6.72E-4	3	20034,19989,60,69	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aAt	T110N	MethTr	0.000276	0.056129	4	2	C>A
ERR5749351	21077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	20157	0.001439	0	8,20120,0,29	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K141	MethTr	0.000492	0.955529	4	2	CA>C
ERR5749351	21234	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	25823	5.42E-4	0	25811,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/Tgtt	V194C?	MethTr	0.000472	0.857572	5	2	C>CT
ERR5749351	21764	PASS	ATACATG	A	11056	0.996382	0	39,0,11016,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749351	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	11056	8.14E-4	0	11047,0,9,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749351	21990	PASS	TTTA	T	11061	0.998644	0	0,15,5,11041	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749351	22450	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9303	0.00215	0	9161,102,23,0	LOW	SILENT	SYNONYMOUS_CODING	S	ctC/ctT	L296	S	0.00215	0.803846	1	1	C>T
ERR5749351	23063	PASS	A	T	11471	0.867928	0	0,2,0,11419	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749351	23271	PASS	C	A	16512	0.917212	0	2,0,16494,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749351	23403	PASS	A	G	16500	0.970545	0	0,3,0,16482	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749351	23604	PASS	C	A	11282	0.949034	0	8,0,11265,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749351	23634	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCAT	C	11275	7.1E-4	0	11264,3,8,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atcatt/att	II692I	S	0.00071	0.931159	2	2	CCAT>C
ERR5749351	23709	PASS	C	T	11269	0.939036	0	0,10,0,11238	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749351	24010	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATTTATTGAAGATCTAC	A	7105	9.85E-4	0	50,7049,0,7	HIGH	NONE	FRAME_SHIFT	S	attgaagatctacttttc/	IEDLLF818	S	0.000455	0.926398	4	2	ATTTATTGAAGATCTAC>A
ERR5749351	24506	PASS	T	G	13637	0.976168	0	2,0,13630,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749351	24914	PASS	G	C	28505	0.961059	3	1,0,14193,14291	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749351	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	24287	0.001276	21	19152,5093,39,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749351	25587	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	19223	9.88E-4	0	0,19204,0,19	HIGH	NONE	FRAME_SHIFT	ORF3a	aag/	K67	orf3a	0.000598	0.813206	6	2	CA>C
ERR5749351	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	4140	0.004348	316	4084,33,2,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749351	26044	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	27747	4.69E-4	0	27734,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF3a	caa/	Q218	orf3a	0.000469	0.102679	3	3	CA>C
ERR5749351	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	27697	3.97E-4	0	0,27686,0,11	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749351	26158	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	27697	0.001083	0	0,27667,0,30	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF3a	gttaat/gat	VN256D	orf3a	0.000297	0.905181	6	2	GTTA>G
ERR5749351	26895	PASS	C	T	25743	0.963679	68	8,2,25713,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Cat/Tat	H125Y	M	0.000874	0.97046	1	1	C>T
ERR5749351	27128	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25739	0.001127	0	0,25694,0,30	LOW	SILENT	SYNONYMOUS_CODING	M	ggC/ggT	G202	M	0.000719	0.147659	1	1	C>T
ERR5749351	27461	PASS	G	T	17763	0.974441	42	1,0,0,17757	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	tGt/tTt	C23F	orf7a	0.002221	0.974441	1	1	G>T
ERR5749351	27476	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24033	9.15E-4	20	6270,17736,1,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	aCa/aTa	T28I	orf7a	0.000547	0.22827	4	2	C>T
ERR5749351	27972	PASS	C	T	5075	0.88867	72	4,4,5028,24	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749351	28001	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	10083	0.001785	0	5026,5032,10,10	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ccG/ccA	P36	orf8	0.00085	0.830607	2	1	G>A
ERR5749351	28048	PASS	G	T	5050	0.927327	0	0,6,0,5044	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749351	28111	PASS	A	G	27747	0.978556	8	12,0,22668,5052	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749351	28270	PASS	TA	T	44004	0.995069	601	220,2,22383,21404	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749351	28280	PASS	G	C	43912	0.935052	21	15,3,22439,21375	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749351	28281	PASS	A	T	43912	0.916834	30	27,7,22427,21387	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749351	28282	PASS	T	A	43914	0.907956	6	20,12,22369,21394	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749351	28881	PASS	G	A	7696	0.742204	6	3,0,3782,3772	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749351	28882	PASS	G	A	7696	0.816918	0	1,0,3847,3765	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749351	28883	PASS	G	C	7696	0.940359	2	1,2,3849,3833	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749351	28977	PASS	C	T	3927	0.933282	2147483647	0,0,0,3921	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749351	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	48681	0.001253	1	24439,24145,39,35	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749351	29384	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	8321	0.016344	0	8172,0,146,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gac/Aac	D371N	N	0.009923	0.099057	2	2	G>A
ERR5749351	29386	PASS	C	A	8319	0.887486	0	12,0,8277,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaC/gaA	D371E	N	0.000887	0.899197	4	2	C>A
ERR5749351	29386	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	8319	0.00577	0	8267,0,48,0	HIGH	NONE	FRAME_SHIFT	N	aag/aaAg	K373K?	N	0.000887	0.899197	4	2	C>CA
ERR5749352	241	PASS	C	T	15109	0.860944	0	0,1,7432,7626	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749352	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	13919	0.001796	0	13895,4,25,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749352	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	13922	7.18E-4	0	13866,7,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749352	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	13922	0.00237	0	13866,7,33,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749352	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	13912	0.002372	0	12754,8,1054,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749352	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	13912	9.34E-4	0	13890,9,13,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749352	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	13911	7.91E-4	0	13881,9,11,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttatg/gtg	VM84V	leader	0.000554	0.991848	4	1	GTTA>G
ERR5749352	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	38733	0.001265	12	24746,13931,38,11	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749352	913	PASS	C	T	24780	0.911945	0	0,15,0,24729	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749352	2702	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	44236	7.69E-4	2687	43931,44,67,121	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F633V	nsp2	0.000632	0.333333	1	1	T>G
ERR5749352	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	87721	0.001505	2147483647	43754,40987,105,2638	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749352	3037	PASS	C	T	25556	0.820473	35	3,20,12763,12590	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749352	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12894	0.002482	831	5,12846,31,4	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749352	3267	PASS	C	T	22450	0.968641	0	2,0,22428,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749352	5388	PASS	C	A	7154	0.958625	0	0,0,7147,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749352	5986	PASS	C	T	15134	0.972843	2147483647	0,0,15121,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749352	6320	PASS	G	T	24455	0.080147	0	22037,0,2409,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Ttt	V1201F	nsp3	0.001197	0.080147	2	2	G>T
ERR5749352	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14708	0.001632	0	1,14533,0,32	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749352	6954	PASS	T	C	25318	0.821273	0	0,7,0,25187	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749352	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	39829	5.77E-4	75	18613,21192,23,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749352	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	21169	0.001181	0	21111,0,48,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749352	11287	PASS	GTCTGGTTTT	G	21166	0.998157	0	0,39,0,21127	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749352	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	40199	7.71E-4	17	24372,15763,26,6	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749352	13431	PASS	C	T	22934	0.10382	0	20455,0,2457,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCc/cTc	P136L	nsp10	0.10382	0.10382	1	1	C>T
ERR5749352	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	45791	0.001005	0	22874,22821,25,25	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749352	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	16651	0.003844	2147483647	16281,133,8,223	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749352	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	32417	9.87E-4	0	16258,16150,17,15	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749352	14408	PASS	C	T	32417	0.842274	2	5,7,16167,15959	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749352	14676	PASS	C	T	15399	0.771803	0	5,0,15353,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749352	15279	PASS	C	T	27952	0.879293	0	8,0,27889,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749352	15371	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	55789	8.25E-4	0	27853,27799,31,31	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aTg	T644M	RdRp	0.00056	0.786959	4	2	C>T
ERR5749352	16176	PASS	T	C	24687	0.979665	9	3,0,11592,13080	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749352	17615	PASS	A	G	17490	0.899485	0	0,0,2,17444	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749352	18647	PASS	C	T	58929	0.970507	6	3,9,26339,32561	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P203L	ExoN	0.000283	0.970507	4	2	C>T
ERR5749352	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	26356	0.001214	0	26324,0,32,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749352	19763	PASS	C	T	43981	0.809304	0	0,0,21821,21967	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T48I	endoR	0.000987	0.809304	2	1	C>T
ERR5749352	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34144	0.002343	0	34034,0,80,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749352	21764	PASS	ATACATG	A	15595	0.997114	0	44,0,15550,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749352	21990	PASS	TTTA	T	15598	0.996987	0	0,47,5,15546	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749352	22484	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	10330	0.003485	0	112,10130,0,42	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gta/Ata	V308I	S	0.003485	0.765485	2	1	G>A
ERR5749352	23063	PASS	A	T	12351	0.862602	0	0,3,1,12297	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749352	23271	PASS	C	A	25829	0.899957	0	3,0,25787,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749352	23277	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25830	0.001007	0	25758,1,39,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCt/aTt	T572I	S	0.001007	0.74768	1	1	C>T
ERR5749352	23403	PASS	A	G	25822	0.967624	0	0,5,0,25796	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749352	23604	PASS	C	A	17700	0.934576	0	17,0,17668,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749352	23709	PASS	C	T	17681	0.935298	0	0,8,1,17629	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749352	24506	PASS	T	G	22120	0.97396	0	14,0,22102,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749352	24914	PASS	G	C	35781	0.95956	0	0,0,17831,17923	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749352	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	29926	0.001036	528	29827,15,13,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749352	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	29890	4.68E-4	0	29875,1,14,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749352	25855	PASS	G	T	29857	0.899421	0	0,63,2,29772	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gac/Tac	D155Y	orf3a	0.001326	0.969697	1	1	G>T
ERR5749352	26208	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	61035	9.34E-4	0	2,60928,0,66	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	agC/agT	S272	orf3a	0.000315	0.922222	2	2	C>T
ERR5749352	26256	PASS	C	T	74213	0.969561	9	4,7,13160,61029	LOW	SILENT	SYNONYMOUS_CODING	E	ttC/ttT	F4	E	0.000748	0.969561	2	2	C>T
ERR5749352	26526	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	13170	0.001291	0	2,13131,0,28	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Gca/Tca	A2S	M	0.001224	0.951192	3	1	G>T
ERR5749352	26748	PASS	A	G	11510	0.926238	0	0,0,17,11481	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Atc/Gtc	I76V	M	0.001056	0.926238	2	1	A>G
ERR5749352	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	11531	0.001041	0	1,11518,0,12	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749352	27972	PASS	C	T	11113	0.903446	19	1,1,11023,57	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749352	28048	PASS	G	T	11069	0.924654	0	0,15,2,11043	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749352	28111	PASS	A	G	29392	0.978055	10	6,0,18300,11073	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749352	28270	PASS	TA	T	35505	0.995465	395	162,5,18066,17278	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749352	28280	PASS	G	C	35449	0.93509	30	19,3,18096,17262	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749352	28281	PASS	A	T	35449	0.914807	35	35,10,18088,17262	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749352	28282	PASS	T	A	35454	0.909347	22	28,10,18019,17277	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749352	28881	PASS	G	A	14204	0.736623	42	15,0,6983,6978	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749352	28882	PASS	G	A	14203	0.82391	15	6,0,7094,6964	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749352	28883	PASS	G	C	14203	0.942407	3	0,1,7115,7071	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749352	28977	PASS	C	T	7269	0.920209	0	0,3,3,7246	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749352	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	41600	0.00101	0	20869,20652,28,26	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749353	241	PASS	C	T	12498	0.858697	0	0,1,6219,6229	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749353	442	PASS	C	T	14216	0.297974	0	9409,0,4787,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G59	leader	0.001641	0.297974	2	2	C>T
ERR5749353	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	14187	8.46E-4	0	14183,0,12,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749353	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	14189	0.002326	0	14144,2,33,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749353	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	14178	0.002328	0	12974,4,1128,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749353	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	14178	6.35E-4	0	14165,4,9,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749353	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	14173	0.001058	0	14154,4,15,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749353	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	33019	3.94E-4	3	18792,14210,9,4	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749353	913	PASS	C	T	18796	0.91296	0	0,20,0,18726	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749353	3037	PASS	C	T	21881	0.810795	60	0,20,10931,10751	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749353	3267	PASS	C	T	18970	0.969689	0	4,0,18956,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749353	5170	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	13209	6.81E-4	0	1,13199,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T819	nsp3	0.000565	0.894036	2	2	CCA>C
ERR5749353	5388	PASS	C	A	6457	0.957411	2147483647	0,0,6454,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749353	5986	PASS	C	T	14080	0.973437	0	2,0,14067,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749353	6954	PASS	T	C	21776	0.82917	0	0,3,2,21657	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749353	7067	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	44326	3.38E-4	42	22469,21842,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gaa/	E1450	nsp3	0.000274	0.059217	5	3	GA>G
ERR5749353	8123	PASS	C	T	22008	0.770674	0	5,0,21778,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Ttt	L1802F	nsp3	0.001144	0.778589	1	1	C>T
ERR5749353	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	30257	0.001818	123	17870,12331,55,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749353	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	18926	0.001479	0	18866,1,50,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749353	11287	PASS	GTCTGGTTTT	G	18923	0.997728	0	0,41,0,18880	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749353	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	33270	0.001383	1	16615,16556,25,27	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749353	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	17245	0.004929	2147483647	16841,124,4,271	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749353	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	33522	3.88E-4	0	16821,16716,7,6	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749353	14408	PASS	C	T	33522	0.848428	2	3,5,16737,16565	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749353	14676	PASS	C	T	12873	0.791424	0	7,0,12820,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749353	15279	PASS	C	T	20661	0.882387	0	2,0,20623,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749353	16176	PASS	T	C	23005	0.980004	0	0,0,11844,11148	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749353	17615	PASS	A	G	17190	0.902094	0	0,1,0,17146	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749353	17626	PASS	C	T	17199	0.940345	0	0,16,0,17159	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cat/Tat	H464Y	helicase	0.001039	0.946125	2	2	C>T
ERR5749353	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	26562	7.91E-4	0	26541,0,21,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749353	19296	PASS	G	A	20687	0.975734	215	2,6,20678,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttG/ttA	L419	ExoN	0.000586	0.977017	2	2	G>A
ERR5749353	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29344	0.002113	0	29254,0,66,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749353	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	32354	8.35E-4	0	32283,0,27,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749353	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	31011	0.00129	3	15161,15467,22,29	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749353	21764	PASS	ATACATG	A	14002	0.995572	0	62,0,13937,3	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749353	21817	PASS	A	G	13999	0.961354	0	1,0,13977,5	LOW	SILENT	SYNONYMOUS_CODING	S	ccA/ccG	P85	S	0.000689	0.961354	3	2	A>G
ERR5749353	21990	PASS	TTTA	T	14005	0.997929	0	0,29,5,13971	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749353	23063	PASS	A	T	15675	0.860478	0	0,2,0,15597	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749353	23271	PASS	C	A	20556	0.910099	0	2,0,20528,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749353	23403	PASS	A	G	20554	0.968084	0	0,4,1,20542	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749353	23604	PASS	C	A	17408	0.936523	30	15,1,17384,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749353	23709	PASS	C	T	17395	0.941477	0	0,4,1,17367	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749353	24506	PASS	T	G	18794	0.974513	0	9,0,18778,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749353	24914	PASS	G	C	41420	0.95775	0	0,0,20636,20751	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749353	25496	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	39230	6.63E-4	8	19250,19296,342,306	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aTa/aGa	I35R	orf3a	0.000369	0.96555	3	2	T>G
ERR5749353	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	16474	0.001518	458	16394,24,6,19	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749353	25690	PASS	G	T	16431	0.971091	0	4,0,16420,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Ggc/Tgc	G100C	orf3a	0.971091	0.979849	1	1	G>T
ERR5749353	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	16431	8.52E-4	0	16417,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749353	26157	PASS	TGTTA	T	48251	0.122153	0	1,42356,0,5894	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749353	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	14747	8.14E-4	0	0,14729,0,12	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749353	27493	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26585	0.001806	3	22532,4000,39,9	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Cct/Tct	P34S	orf7a	0.000794	0.971493	2	1	C>T
ERR5749353	27513	PASS	C	T	22583	0.977859	29	3,1,22550,6	LOW	SILENT	SYNONYMOUS_CODING	ORF7a	taC/taT	Y40	orf7a	0.001863	0.982462	2	2	C>T
ERR5749353	27972	PASS	C	T	12582	0.906056	22	0,1,12454,72	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749353	28048	PASS	G	T	12523	0.909047	0	0,17,2,12499	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749353	28111	PASS	A	G	31156	0.977372	1	6,3,18609,12526	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749353	28270	PASS	TA	T	35928	0.994517	430	193,9,18368,17363	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749353	28280	PASS	G	C	35840	0.93976	21	11,1,18395,17354	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749353	28281	PASS	A	T	35840	0.915402	39	25,4,18399,17346	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749353	28282	PASS	T	A	35840	0.908287	21	24,8,18356,17365	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749353	28881	PASS	G	A	18825	0.761965	12	4,0,9254,9327	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749353	28882	PASS	G	A	18825	0.825923	21	8,0,9364,9286	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749353	28883	PASS	G	C	18826	0.943217	9	0,4,9384,9420	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749353	28977	PASS	C	T	9514	0.933992	2147483647	0,0,0,9496	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749353	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	61032	0.001032	0	30639,30292,41,39	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749354	241	PASS	C	T	715	0.857343	0	0,0,357,356	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749354	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	2415	0.007453	0	2391,0,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749354	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	2412	0.00539	0	2399,0,13,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749354	676	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8158	0.006006	259	5733,2372,1,52	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G137	leader	0.000799	0.919273	2	1	C>T
ERR5749354	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	8158	0.003064	36	5709,2424,25,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749354	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	8158	0.002819	34	5706,2423,23,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749354	913	PASS	C	T	5731	0.905078	0	0,5,0,5718	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749354	1813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	9106	0.003185	0	0,9068,0,30	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcA	A336	nsp2	0.001022	0.152738	4	2	T>A
ERR5749354	2062	PASS	C	T	5593	0.742893	0	0,0,5547,14	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A419	nsp2	0.001265	0.822961	2	1	C>T
ERR5749354	2305	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	5819	0.002062	0	5803,0,13,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaG/aaA	K500	nsp2	0.000443	0.070409	4	3	G>A
ERR5749354	2498	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GA	5818	0.001031	0	0,5812,0,6	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/aAca	T566N?	nsp2	0.001031	0.07717	2	2	G>GA
ERR5749354	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	19098	9.43E-4	1561	9561,8911,12,572	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749354	2775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	9605	0.001874	0	0,9554,0,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K19R	nsp3	0.000437	0.951613	3	2	A>G
ERR5749354	2862	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAGAAGT	C	11680	0.001455	12	2061,9602,0,17	MODERATE	NONE	CODON_DELETION	ORF1ab	gaagta/	EV49	nsp3	0.000547	0.850688	4	2	CAGAAGT>C
ERR5749354	2925	PASS	C	T	2061	0.89083	2147483647	0,0,2057,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S69F	nsp3	0.89083	0.89083	1	1	C>T
ERR5749354	3037	PASS	C	T	4101	0.819312	3	0,1,2053,2022	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749354	3177	PASS	C	T	7418	0.906713	0	0,0,5347,2059	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P153L	nsp3	0.000773	0.96008	3	2	C>T
ERR5749354	3267	PASS	C	T	5359	0.970144	0	1,0,5356,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749354	3671	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GA	9258	8.64E-4	0	4631,4622,4,4	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/aaAt	N319K?	nsp3	0.000351	0.0625	6	2	G>GA
ERR5749354	3802	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAA	T	8028	0.002118	63	3364,4647,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N363	nsp3	0.000554	0.064198	4	2	TAA>T
ERR5749354	4136	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	9336	7.5E-4	12	5961,3368,7,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/	V473	nsp3	0.00075	0.974623	4	2	GT>G
ERR5749354	4276	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5959	0.002014	0	0,5942,0,14	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y519	nsp3	0.00102	0.812261	1	1	C>T
ERR5749354	4764	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	6561	0.001372	0	6552,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F683	nsp3	0.000673	0.93404	4	2	AT>A
ERR5749354	5230	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	5124	0.002537	0	0,5094,0,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaG/aaT	K837N	nsp3	0.002515	0.902519	1	1	G>T
ERR5749354	5388	PASS	C	A	1733	0.95326	2147483647	0,0,1732,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749354	5986	PASS	C	T	5061	0.976684	2147483647	0,0,5060,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749354	6954	PASS	T	C	9552	0.826738	0	0,4,0,9510	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749354	7811	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAT	C	11439	0.001224	0	11427,1,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H1698	nsp3	0.000971	0.883442	2	2	CAT>C
ERR5749354	8123	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7394	0.005139	0	7328,0,49,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Ttt	L1802F	nsp3	0.001144	0.778589	1	1	C>T
ERR5749354	8964	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7954	0.002514	0	7928,2,20,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCa/tTa	S137L	nsp4	0.000553	0.981649	4	2	C>T
ERR5749354	8964	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	7954	0.00528	0	7910,2,42,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K138	nsp4	0.000553	0.981649	4	2	CA>C
ERR5749354	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	7086	0.008326	18	6436,591,59,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749354	10502	PASS	TTTA	T	7967	0.998494	0	16,0,7955,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	tttaac/tac	FN150Y	3Cpro	0.000992	0.998494	3	2	TTTA>T
ERR5749354	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	13786	0.002829	0	13714,0,57,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749354	11152	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13775	0.002105	0	13714,0,29,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V60	nsp6	0.000678	0.974465	2	2	C>T
ERR5749354	11199	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27461	9.1E-4	0	13638,13704,15,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCc/gTc	A76V	nsp6	0.000309	0.056758	3	2	C>T
ERR5749354	11287	PASS	GTCTGGTTTT	G	13780	0.993977	0	0,83,0,13697	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749354	11747	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5943	0.002356	0	5921,2,15,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L259	nsp6	0.001145	0.737282	1	1	C>T
ERR5749354	11767	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11867	0.002107	0	5906,5901,15,15	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	agC/agT	S265	nsp6	0.000949	0.854102	1	1	C>T
ERR5749354	12269	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	6546	0.001528	0	6536,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aag/	K61	nsp8	0.000434	0.213333	2	1	GA>G
ERR5749354	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	7777	0.002057	0	7756,0,16,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749354	13176	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8980	0.002004	0	8955,0,21,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T51I	nsp10	0.002004	0.919962	2	1	C>T
ERR5749354	13384	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	7675	0.001694	0	7649,0,23,0	HIGH	NONSENSE	STOP_GAINED	ORF1ab	tgC/tgA	C120*	nsp10	0.000578	0.056161	3	3	C>A
ERR5749354	13468	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	7672	0.001564	0	7659,1,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggg/	G10	nsp11	0.000713	0.076498	2	2	CG>C
ERR5749354	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15323	0.00137	0	7655,7636,11,12	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749354	13990	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6707	0.002087	0	6692,0,14,0	HIGH	NONSENSE	STOP_GAINED	ORF1ab	Caa/Taa	Q184*	RdRp	0.002087	0.5	2	2	C>T
ERR5749354	13994	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	6707	0.00164	0	6696,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTg	L186F?	RdRp	0.000427	0.114441	3	2	C>CT
ERR5749354	14408	PASS	C	T	776	0.864691	0	0,0,387,380	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749354	14676	PASS	C	T	4282	0.725596	2147483647	0,0,4272,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749354	14925	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5532	0.002531	0	5513,4,14,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V495	RdRp	0.002531	0.98996	1	1	C>T
ERR5749354	15279	PASS	C	T	6525	0.88567	2147483647	0,0,6516,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749354	16176	PASS	T	C	5553	0.982892	0	0,0,1795,3757	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749354	16508	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	10308	0.001552	0	10282,1,23,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGt/gTt	G91V	helicase	0.000561	0.074909	2	2	G>T
ERR5749354	16792	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CGT	C	18884	0.001271	9	8561,10299,15,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	gta/	V187	helicase	0.000335	0.072562	5	2	CGT>C
ERR5749354	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	8576	0.001516	0	8563,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749354	17749	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	5676	0.003347	0	5643,1,20,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gct/Tct	A505S	helicase	0.001521	0.987943	4	2	G>T
ERR5749354	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	18848	0.001273	0	18824,0,24,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749354	19113	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22526	0.001021	0	11248,11212,15,16	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D358	ExoN	0.000461	0.125	4	3	C>T
ERR5749354	19114	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	22503	0.002177	3	11178,11222,32,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Aaa/Gaa	K359E	ExoN	0.00119	0.098958	2	2	A>G
ERR5749354	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	11295	0.001859	0	0,11274,0,21	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749354	19186	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11305	0.001415	0	0,11280,0,16	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L383	ExoN	0.000709	0.96164	4	3	C>T
ERR5749354	19763	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16280	0.002518	0	8071,8107,25,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T48I	endoR	0.000987	0.809304	2	1	C>T
ERR5749354	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5336	0.003561	0	5310,0,20,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749354	20148	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5333	0.0075	0	0,5277,0,41	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F176	endoR	0.000513	0.969223	2	2	C>T
ERR5749354	20245	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	17286	0.001157	0	17249,2,21,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Atg/Ctg	M209L	endoR	0.001027	0.060575	3	2	A>C
ERR5749354	21036	PASS	C	A	8982	0.09764	0	0,8026,0,955	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ctC/ctA	L126	MethTr	0.09764	0.09764	1	1	C>A
ERR5749354	21234	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	14790	7.44E-4	0	14781,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/Tgtt	V194C?	MethTr	0.000472	0.857572	5	2	C>CT
ERR5749354	21304	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14772	0.001219	0	0,14750,0,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgc/Tgc	R216C	MethTr	0.000411	0.605296	3	2	C>T
ERR5749354	21462	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	5817	0.002922	0	5797,0,17,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaT/aaC	N268	MethTr	0.00078	0.959051	2	2	T>C
ERR5749354	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	11566	0.001729	0	5762,5786,9,11	HIGH	NONE	FRAME_SHIFT	S	ctt/Tctt	L5S?	S	0.000394	0.091869	4	1	G>GT
ERR5749354	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11549	0.003117	0	5626,5750,20,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749354	21736	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	6750	0.001778	0	6736,2,12,0	HIGH	NONE	FRAME_SHIFT	S	tcc/	S60	S	0.001596	0.804427	3	2	CT>C
ERR5749354	21764	PASS	ATACATG	A	6748	0.998222	0	12,0,6736,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749354	21846	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13461	0.001263	0	6728,6698,10,10	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCt/aTt	T95I	S	0.001104	0.788523	1	1	C>T
ERR5749354	21990	PASS	TTTA	T	6749	0.996148	0	0,26,1,6722	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749354	22290	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	11118	0.002339	0	0,11092,0,26	HIGH	NONE	FRAME_SHIFT	S	tta/	L244	S	0.000389	0.578006	2	2	CT>C
ERR5749354	22293	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	16243	0.001539	39	5125,11093,0,25	HIGH	NONE	FRAME_SHIFT	S	tta/	L244	S	0.000308	0.160511	4	1	TA>T
ERR5749354	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	11071	0.001716	0	0,11047,0,20	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749354	23040	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	6866	0.001893	0	11,6820,0,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cAa/cGa	Q493R	S	0.001893	0.933049	1	1	A>G
ERR5749354	23063	PASS	A	T	6868	0.867938	2147483647	0,0,0,6842	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749354	23271	PASS	C	A	5917	0.911949	0	1,0,5904,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749354	23403	PASS	A	G	5911	0.970733	2147483647	0,0,0,5911	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749354	23525	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6782	0.003686	0	6756,0,26,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Cat/Tat	H655Y	S	0.001101	0.97751	2	2	C>T
ERR5749354	23604	PASS	C	A	6779	0.947632	0	4,0,6771,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749354	23625	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6775	0.002362	0	6752,0,18,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gTt	A688V	S	0.002362	0.901054	2	2	C>T
ERR5749354	23709	PASS	C	T	6774	0.943756	0	0,1,0,6762	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749354	24127	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TTTTTG	3305	0.003631	0	1,3304,0,12	HIGH	NONE	FRAME_SHIFT+STOP_GAINED	S	aac/TTTTGaac	N856F*?	S	0.000324	0.111888	4	1	T>TTTTTG
ERR5749354	24127	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	3305	0.002118	0	1,3309,0,7	HIGH	NONE	FRAME_SHIFT	S	aac/	N856	S	0.000324	0.111888	4	1	TA>T
ERR5749354	24320	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	5968	0.004692	0	11,5929,0,28	HIGH	NONE	FRAME_SHIFT	S	aaa/	K921	S	0.000763	0.138365	4	2	CA>C
ERR5749354	24444	PASS	C	T	8724	0.063732	0	8139,3,573,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCg/aTg	T961M	S	0.000832	0.063732	2	2	C>T
ERR5749354	24506	PASS	T	G	8721	0.971219	0	5,0,8714,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749354	24914	PASS	G	C	21988	0.96207	0	0,0,10968,11010	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749354	24949	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AATAGGAATT	A	11062	0.001446	0	0,11046,0,16	MODERATE	NONE	CODON_DELETION	S	ataggaatt/	IGI1130	S	0.001446	0.963384	2	2	AATAGGAATT>A
ERR5749354	25413	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	13009	0.002152	0	12957,0,44,0	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	atC/atA	I7	orf3a	0.00145	0.968329	2	1	C>A
ERR5749354	25422	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGGAACTGTA	T	13008	7.69E-4	0	12998,0,10,0	MODERATE	NONE	CODON_DELETION	ORF3a	ggaactgta/	GTV11	orf3a	0.000545	0.213989	6	1	TGGAACTGTA>T
ERR5749354	25429	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTAACTT	G	13006	6.92E-4	0	12988,0,9,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF3a	gtaactttg/gtg	VTL13V	orf3a	0.00064	0.906678	5	2	GTAACTT>G
ERR5749354	25429	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTAACTTTGAAGCAAGGTGAAATCA	G	13006	6.92E-4	0	12988,0,9,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF3a	gtaactttgaagcaaggtgaaatcaag/gag	VTLKQGEIK13E	orf3a	0.00064	0.906678	5	2	GTAACTTTGAAGCAAGGTGAAATCA>G
ERR5749354	25555	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	13004	0.001538	0	0,12975,0,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gtt/Ttt	V55F	orf3a	0.000552	0.900573	5	2	G>T
ERR5749354	25596	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	13011	0.001691	0	0,12983,0,24	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	agA/agG	R68	orf3a	0.001691	0.988281	1	1	A>G
ERR5749354	25904	PASS	C	T	1684	0.827197	53	2,2,0,1672	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	tCa/tTa	S171L	orf3a	0.000757	0.83473	1	1	C>T
ERR5749354	26013	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14360	0.001532	0	14329,0,24,0	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	ttC/ttT	F207	orf3a	0.000839	0.974528	1	1	C>T
ERR5749354	26509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5781	0.002422	0	0,5759,0,16	.	.	.	.	.	.	.	0.000852	0.946613	3	1	C>T
ERR5749354	26571	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTTGAACAATGGAACCTAGTAATAGGTTTCCTA	C	5831	0.001372	0	5823,0,8,0	HIGH	NONE	FRAME_SHIFT	M	gaacaatggaacctagtaataggtttcctattc/	EQWNLVIGFLF18	M	0.000508	0.905823	3	2	CTTGAACAATGGAACCTAGTAATAGGTTTCCTA>C
ERR5749354	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	5816	0.002751	0	0,5800,0,16	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749354	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	5816	0.002063	0	0,5804,0,12	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749354	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	5817	0.002579	0	0,5802,0,15	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749354	27312	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	11895	0.001513	0	11877,0,18,0	HIGH	NONE	FRAME_SHIFT	ORF6	aat/aaAt	N39K?	orf6	0.000911	0.088458	4	2	T>TA
ERR5749354	27557	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13032	0.001381	0	13004,0,19,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	gCa/gTa	A55V	orf7a	0.000949	0.267468	2	2	C>T
ERR5749354	27972	PASS	C	T	2767	0.897	20	0,1,2728,26	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749354	28048	PASS	G	T	2744	0.917274	0	0,2,0,2737	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749354	28111	PASS	A	G	15855	0.980826	3	2,1,13103,2745	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749354	28147	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	13111	6.86E-4	0	13102,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF8	ttt/	F86	orf8	0.000438	0.981624	4	2	CT>C
ERR5749354	28192	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	13111	0.001297	0	13084,0,17,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	gTg/gCg	V100A	orf8	0.001134	0.980889	2	1	T>C
ERR5749354	28237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTGT	G	13117	0.001067	0	13093,10,14,0	MODERATE	NONE	CODON_DELETION	ORF8	gtt/	V117	orf8	0.000442	0.966707	4	2	GTGT>G
ERR5749354	28249	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	13112	0.001907	0	13077,10,25,0	HIGH	NONE	FRAME_SHIFT	ORF8	ttc/	F120	orf8	0.000443	0.063605	3	2	AT>A
ERR5749354	28270	PASS	TA	T	25353	0.99503	330	135,4,12920,12307	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749354	28280	PASS	G	C	25289	0.93511	6	3,0,12943,12286	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749354	28281	PASS	A	T	25289	0.916446	4	8,4,12946,12289	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749354	28282	PASS	T	A	25291	0.910798	3	7,10,12911,12290	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749354	28406	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTACCCAATA	T	13132	0.001828	0	9,13099,0,24	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	N	ttacccaataat/tat	LPNN45Y	N	0.00043	0.921074	3	2	TTACCCAATA>T
ERR5749354	28412	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	13133	0.00198	0	9,13069,0,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Aat/Gat	N47D	N	0.00198	0.965453	2	1	A>G
ERR5749354	28881	PASS	G	A	2275	0.743297	0	1,0,1123,1120	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749354	28882	PASS	G	A	2275	0.829451	0	1,0,1141,1113	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749354	28883	PASS	G	C	2275	0.942418	0	0,0,1145,1130	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749354	28977	PASS	C	T	1166	0.944254	2147483647	0,0,0,1163	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749354	29077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAATGT	C	13695	8.03E-4	0	13684,0,11,0	HIGH	NONE	FRAME_SHIFT	N	aatgtaaca/	NVT269	N	0.000408	0.88565	3	2	CAATGT>C
ERR5749354	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	27155	0.002025	0	13612,13458,36,35	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749354	29311	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	13697	0.001095	0	1,13681,0,15	HIGH	NONE	FRAME_SHIFT	N	aaa/	K347	N	0.000335	0.790798	3	2	CA>C
ERR5749354	29738	PASS	C	T	3055	0.890671	0	0,1,0,3046	.	.	.	.	.	.	.	0.001703	0.890671	2	1	C>T
ERR5749355	241	PASS	C	T	9955	0.862983	0	0,0,4964,4958	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749355	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	9714	0.001441	0	9700,1,14,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749355	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	9709	0.00206	0	8989,2,689,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749355	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	9709	8.24E-4	0	9699,2,8,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749355	673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26130	0.001263	67	16400,9684,7,29	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y136	leader	0.000454	0.602236	3	2	C>T
ERR5749355	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	26130	6.12E-4	7	16395,9718,13,3	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749355	913	PASS	C	T	16402	0.912267	0	0,13,0,16372	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749355	1225	PASS	C	T	11668	0.928522	2147483647	0,0,0,11641	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ctC/ctT	L140	nsp2	0.928522	0.929115	1	1	C>T
ERR5749355	3037	PASS	C	T	14902	0.815662	39	0,13,7438,7358	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749355	3267	PASS	C	T	15819	0.968898	0	1,0,15812,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749355	4280	PASS	G	A	13289	0.885845	0	0,1,2,13237	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gta/Ata	V521I	nsp3	0.002822	0.896067	2	1	G>A
ERR5749355	5388	PASS	C	A	4494	0.956831	2147483647	0,0,4493,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749355	5986	PASS	C	T	9488	0.974494	2147483647	0,0,9481,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749355	6954	PASS	T	C	17366	0.815789	0	0,2,0,17275	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749355	7067	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	31174	0.001411	160	13694,17415,45,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Caa	E1450Q	nsp3	0.000274	0.059217	5	3	G>C
ERR5749355	7070	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	31174	0.001091	124	13710,17422,35,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggc/Agc	G1451S	nsp3	0.000698	0.101434	3	1	G>A
ERR5749355	7423	PASS	C	T	13104	0.970543	0	3,0,13078,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1568	nsp3	0.000941	0.970543	2	2	C>T
ERR5749355	7564	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	13091	8.4E-4	0	0,13080,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/	Y1617	nsp3	0.000586	0.056194	4	2	CT>C
ERR5749355	8084	PASS	G	A	19598	0.916165	0	10,0,19562,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E1789K	nsp3	0.000543	0.923413	4	2	G>A
ERR5749355	8084	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GA	19598	0.019594	0	19214,0,384,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctc/Actc	L1791T?	nsp3	0.000543	0.923413	4	2	G>GA
ERR5749355	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	21614	0.001527	77	12316,9265,33,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749355	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	17314	0.001675	0	17259,0,43,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749355	11287	PASS	GTCTGGTTTT	G	17312	0.999134	0	0,15,0,17297	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749355	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	9905	0.003332	2527	9705,55,3,134	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749355	14408	PASS	C	T	19340	0.844623	6	0,2,9661,9542	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749355	14676	PASS	C	T	10812	0.829726	0	6,0,10780,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749355	15279	PASS	C	T	17256	0.886706	0	2,0,17221,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749355	16176	PASS	T	C	16701	0.981199	2	0,2,7805,8887	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749355	17615	PASS	A	G	11763	0.919408	2147483647	0,0,0,11737	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749355	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	19488	6.16E-4	0	19476,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749355	19328	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	14142	7.78E-4	0	14130,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F431	ExoN	0.000459	0.937906	4	2	CT>C
ERR5749355	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19676	0.002948	0	19604,0,58,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749355	20091	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	19654	7.12E-4	0	3,19637,0,14	HIGH	NONE	FRAME_SHIFT	ORF1ab	caa/Acaa	Q159T?	endoR	0.000368	0.051583	1	1	C>CA
ERR5749355	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26782	0.001494	1	13065,13360,26,30	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749355	21764	PASS	ATACATG	A	9769	0.994063	0	58,0,9711,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749355	21990	PASS	TTTA	T	9775	0.999079	0	0,9,4,9762	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749355	23063	PASS	A	T	11323	0.868851	0	0,1,0,11279	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749355	23271	PASS	C	A	18023	0.915552	0	1,0,17999,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749355	23403	PASS	A	G	18020	0.97303	0	0,3,0,17999	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749355	23604	PASS	C	A	12256	0.950228	0	11,0,12238,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749355	23709	PASS	C	T	12240	0.936111	0	0,5,0,12221	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749355	24506	PASS	T	G	14938	0.974428	0	6,0,14931,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749355	24914	PASS	G	C	30582	0.96135	0	0,0,15236,15330	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749355	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	9919	0.001411	0	0,9901,0,14	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749355	27972	PASS	C	T	7590	0.902767	41	2,2,7541,25	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749355	28048	PASS	G	T	7587	0.922499	0	0,8,0,7575	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749355	28111	PASS	A	G	25049	0.9796	10	1,3,17439,7595	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749355	28270	PASS	TA	T	33790	0.995383	353	155,7,17228,16406	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749355	28280	PASS	G	C	33718	0.939765	9	8,2,17260,16403	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749355	28281	PASS	A	T	33718	0.917522	23	14,2,17252,16396	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749355	28282	PASS	T	A	33719	0.911326	1	13,10,17213,16404	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749355	28881	PASS	G	A	13887	0.786131	5	6,2,6888,6819	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749355	28882	PASS	G	A	13886	0.836022	12	5,0,6953,6802	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749355	28883	PASS	G	C	13886	0.945989	3	0,1,6966,6906	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749355	28977	PASS	C	T	7052	0.927964	0	0,1,0,7029	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749355	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	45512	0.001362	0	22853,22573,34,34	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749356	241	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8	0.875	0	0,0,4,4	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749356	906	PASS	C	T	122	0.081967	0	0,110,0,12	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749356	913	PASS	C	T	122	0.942623	2147483647	0,0,0,122	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749356	1824	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	41	0.073171	0	0,38,0,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCc/gAc	A340D	nsp2	0.00173	0.940138	2	1	C>A
ERR5749356	3037	PASS	C	T	120	0.858333	0	0,0,59,59	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749356	3177	PASS	C	T	168	0.910714	0	0,0,107,61	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P153L	nsp3	0.000773	0.96008	3	2	C>T
ERR5749356	3267	PASS	C	T	107	0.981308	2147483647	0,0,107,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749356	3870	PASS	A	G	65	0.938462	2147483647	0,0,65,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K384R	nsp3	0.938462	0.94487	1	1	A>G
ERR5749356	4918	PASS	C	T	106	0.971698	2147483647	0,0,0,106	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I733	nsp3	0.94545	0.971698	1	1	C>T
ERR5749356	5388	PASS	C	A	27	0.888889	2147483647	0,0,27,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749356	5986	PASS	C	T	24	1.0	2147483647	0,0,24,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749356	6954	PASS	T	C	152	0.828947	2147483647	0,0,0,152	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749356	10291	PASS	A	G	837	0.117085	0	360,359,59,59	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggA/ggG	G79	3Cpro	0.117085	0.117085	1	1	A>G
ERR5749356	10632	PASS	C	T	146	0.89726	2147483647	0,0,0,144	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCa/gTa	A193V	3Cpro	0.875555	0.89726	1	1	C>T
ERR5749356	11074	PASS	C	CT	598	0.130435	0	552,0,78,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CT
ERR5749356	11287	PASS	GTCTGGTTTT	G	598	1.0	2147483647	0,0,0,598	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749356	12020	PASS	C	T	2163	0.9681	2147483647	0,0,2161,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Ttt	L60F	nsp7	0.000994	0.968243	3	2	C>T
ERR5749356	12452	PASS	C	A	342	0.078947	258	292,23,0,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cct/Act	P121T	nsp8	0.078947	0.078947	1	1	C>A
ERR5749356	12456	PASS	T	C	342	0.090643	18	261,50,31,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cTt/cCt	L122P	nsp8	0.001034	0.090643	1	1	T>C
ERR5749356	14408	PASS	C	T	114	0.903509	0	0,0,57,56	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749356	14676	PASS	C	T	63	0.809524	2147483647	0,0,63,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749356	15279	PASS	C	T	96	0.875	2147483647	0,0,96,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749356	16176	PASS	T	C	126	1.0	0	0,0,43,83	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749356	17068	PASS	T	C	296	0.081081	0	0,272,0,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tct/Cct	S278P	helicase	0.081081	0.081081	1	1	T>C
ERR5749356	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	55	0.036364	0	0,53,0,2	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TA>T
ERR5749356	21764	PASS	ATACATG	A	140	0.992857	0	1,0,139,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749356	21990	PASS	TTTA	T	142	0.978873	0	0,7,0,139	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749356	23063	PASS	A	T	252	0.853175	2147483647	0,0,0,250	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749356	23271	PASS	C	A	47	0.93617	2147483647	0,0,47,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749356	23403	PASS	A	G	47	0.957447	2147483647	0,0,0,47	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749356	23604	PASS	C	A	123	0.926829	2147483647	0,0,123,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749356	23709	PASS	C	T	123	0.97561	2147483647	0,0,0,123	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749356	24506	PASS	T	G	43	0.953488	2147483647	0,0,43,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749356	24914	PASS	G	C	2724	0.959985	0	0,0,1355,1368	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749356	25048	PASS	A	G	1404	0.111823	11	27,1216,0,160	LOW	SILENT	SYNONYMOUS_CODING	S	ccA/ccG	P1162	S	0.111823	0.111823	1	1	A>G
ERR5749356	26208	PASS	C	T	270	0.922222	0	0,1,0,269	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	agC/agT	S272	orf3a	0.000315	0.922222	2	2	C>T
ERR5749356	27972	PASS	C	T	55	0.872727	2147483647	0,0,55,0	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749356	28048	PASS	G	T	55	0.963636	2147483647	0,0,0,55	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749356	28111	PASS	A	G	1257	0.981702	0	0,0,1202,55	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749356	28270	PASS	TA	T	2505	0.992016	62	22,0,1270,1215	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749356	28280	PASS	G	C	2500	0.946	3	2,0,1279,1213	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749356	28281	PASS	A	T	2500	0.9128	3	2,0,1279,1214	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749356	28282	PASS	T	A	2500	0.9132	3	2,0,1277,1214	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749356	28881	PASS	G	A	25	0.72	0	0,0,13,12	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749356	28882	PASS	G	A	25	0.84	0	0,0,13,12	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749356	28883	PASS	G	C	25	0.96	0	0,0,13,12	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749356	28977	PASS	C	T	12	1.0	2147483647	0,0,0,12	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749356	29778	PASS	G	A	50	0.38	0	0,30,0,20	.	.	.	.	.	.	.	0.001972	0.38	2	1	G>A
ERR5749357	239	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTC	T	14784	6.76E-4	0	7363,7411,5,5	.	.	.	.	.	.	.	0.000495	0.25	4	1	TTC>T
ERR5749357	241	PASS	C	T	14780	0.861773	3	0,2,7344,7372	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749357	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	11549	0.002165	0	11519,7,25,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749357	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	11549	7.79E-4	0	11458,6,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749357	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	11549	0.001818	0	11458,6,21,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749357	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	11549	0.004156	33	11458,6,46,2	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749357	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	11542	0.001819	0	10794,8,595,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749357	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	11542	0.001993	17	11510,9,22,1	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749357	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	30211	5.3E-4	20	18631,11558,15,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749357	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	30211	0.001324	3	18620,11537,22,18	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749357	913	PASS	C	T	18646	0.918535	0	0,11,0,18619	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749357	3037	PASS	C	T	19223	0.818655	35	1,15,9598,9493	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749357	3267	PASS	C	T	18618	0.971748	0	1,0,18602,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749357	5388	PASS	C	A	5717	0.955746	0	1,0,5714,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749357	5986	PASS	C	T	12528	0.97342	0	1,0,12512,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749357	6954	PASS	T	C	21354	0.819893	0	0,5,5,21193	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749357	7674	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20554	0.001119	0	20515,7,23,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCg/gTg	A1652V	nsp3	0.000682	0.109264	3	2	C>T
ERR5749357	8139	PASS	C	T	22374	0.889336	0	1,0,22286,5	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCc/tTc	S1807F	nsp3	0.001297	0.889336	1	1	C>T
ERR5749357	9430	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14170	0.001411	0	5,14100,0,20	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I292	nsp4	0.001411	0.960894	1	1	C>T
ERR5749357	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	29279	0.002254	190	15027,14186,66,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749357	10029	PASS	C	T	6450	0.12186	0	0,5609,0,838	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCc/aTc	T492I	nsp4	0.12186	0.12186	1	1	C>T
ERR5749357	10193	PASS	G	A	16984	0.869819	0	3,0,16961,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E47K	3Cpro	0.000774	0.869819	2	2	G>A
ERR5749357	10195	PASS	A	T	16984	0.96114	0	10,0,16968,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gaA/gaT	E47D	3Cpro	0.951998	0.969772	1	1	A>T
ERR5749357	11074	PASS	C	CT	17789	0.05717	0	16561,13,1017,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CT
ERR5749357	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	17789	0.008264	0	16561,13,147,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749357	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17789	0.003654	0	17662,13,72,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749357	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	17789	0.007027	0	17648,13,125,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000965	0.945355	5	2	CT>C
ERR5749357	11082	PASS	TG	T	17718	0.067897	0	16571,3,1203,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000427	0.179468	2	1	TG>T
ERR5749357	11083	PASS	G	T	17718	0.589457	2	5545,0,10913,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749357	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	17718	0.022519	0	17234,3,399,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/tTat	Y38L?	nsp6	0.000477	0.901695	5	2	G>GT
ERR5749357	11287	PASS	GTCTGGTTTT	G	17766	0.996904	0	0,53,0,17711	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749357	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	34733	0.001036	11	20806,13861,17,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749357	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	10937	0.001371	0	10922,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749357	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28420	0.001795	0	14185,14146,26,26	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749357	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	13701	0.004963	2147483647	13336,144,4,211	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749357	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	26555	0.002184	0	13292,13222,30,28	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749357	14408	PASS	C	T	26555	0.8537	18	0,6,13226,13093	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749357	14676	PASS	C	T	12043	0.76177	0	2,0,12014,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749357	15279	PASS	C	T	20380	0.965015	0	2,0,20367,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749357	16176	PASS	T	C	19292	0.981443	6	3,0,9904,9378	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749357	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28865	0.002287	0	28776,0,71,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749357	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28234	9.56E-4	0	28170,0,27,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749357	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30469	0.001313	1	14945,15196,21,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749357	21764	PASS	ATACATG	A	11726	0.995651	0	51,0,11675,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749357	21990	PASS	TTTA	T	11734	0.996421	0	0,42,7,11685	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749357	22981	PASS	T	C	12694	0.861194	0	3,0,12615,0	LOW	SILENT	SYNONYMOUS_CODING	S	taT/taC	Y473	S	0.001557	0.861194	3	2	T>C
ERR5749357	23063	PASS	A	T	12701	0.875364	0	0,4,6,12630	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749357	23271	PASS	C	A	20161	0.926591	0	1,0,20140,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749357	23403	PASS	A	G	20160	0.970437	0	0,4,0,20138	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749357	23604	PASS	C	A	15153	0.947007	0	12,0,15132,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749357	23709	PASS	C	T	15128	0.944474	0	0,2,5,15105	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749357	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	31638	6.01E-4	1	16471,15147,11,8	HIGH	NONE	FRAME_SHIFT	S	ttg/	L753	S	0.000334	0.080808	2	2	CT>C
ERR5749357	23817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	31638	8.53E-4	4	16449,15134,17,10	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTt/cCt	L752P	S	0.000646	0.066832	1	1	T>C
ERR5749357	24010	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATTTATTGAAGATCTAC	A	16612	6.62E-4	0	164,16439,0,11	HIGH	NONE	FRAME_SHIFT	S	attgaagatctacttttc/	IEDLLF818	S	0.000455	0.926398	4	2	ATTTATTGAAGATCTAC>A
ERR5749357	24237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11812	0.001355	0	11782,0,17,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gTt	A892V	S	0.001242	0.889739	1	1	C>T
ERR5749357	24506	PASS	T	G	16708	0.976418	0	6,0,16700,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749357	24914	PASS	G	C	34532	0.948598	0	0,1,17194,17314	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749357	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	22828	0.001183	31	16104,6680,34,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749357	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	21515	0.001255	173	21419,17,21,8	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749357	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	21616	6.01E-4	0	21603,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749357	25782	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21600	0.001204	0	21505,0,27,0	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	tgC/tgT	C130	orf3a	0.000916	0.955348	1	1	C>T
ERR5749357	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	47145	4.03E-4	0	2,47123,0,19	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749357	26158	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTAATCCAGTA	G	47145	2.97E-4	0	2,47124,0,14	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaatccagta/	VNPV256	orf3a	0.000297	0.905181	6	2	GTTAATCCAGTA>G
ERR5749357	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	G	12049	9.13E-4	0	5,12017,0,11	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/	ACLVGLMWLSYFIASF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT>G
ERR5749357	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	12049	9.13E-4	0	5,12017,0,11	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749357	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	12049	6.64E-4	0	5,12036,0,8	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749357	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	12049	0.002573	0	5,12008,0,31	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749357	27527	PASS	C	T	20373	0.973593	244	4,8,20346,4	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	cCa/cTa	P45L	orf7a	0.001708	0.973593	1	1	C>T
ERR5749357	27577	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAATT	C	20367	0.002995	0	20294,8,61,0	HIGH	NONE	FRAME_SHIFT	ORF7a	caattt/	QF62	orf7a	0.000614	0.952205	4	2	CAATT>C
ERR5749357	27972	PASS	C	T	10617	0.906	0	0,0,10508,74	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749357	28048	PASS	G	T	10550	0.921422	0	0,16,0,10521	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749357	28111	PASS	A	G	28648	0.97944	1	6,2,18077,10553	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749357	28270	PASS	TA	T	35084	0.995097	421	167,4,17852,17060	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749357	28280	PASS	G	C	35020	0.936322	18	12,2,17903,17033	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749357	28281	PASS	A	T	35020	0.912935	12	19,8,17888,17048	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749357	28282	PASS	T	A	35024	0.905922	0	21,20,17839,17053	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749357	28881	PASS	G	A	16432	0.792843	9	6,1,8144,8082	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749357	28882	PASS	G	A	16432	0.82601	9	4,0,8213,8071	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749357	28883	PASS	G	C	16435	0.94104	0	1,0,8230,8185	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749357	28977	PASS	C	T	8367	0.927095	0	0,8,2,8335	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749357	29095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24921	9.23E-4	0	24880,7,23,0	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F274	N	0.000792	0.961279	2	2	C>T
ERR5749357	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	49471	0.001193	0	24838,24545,38,36	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749358	241	PASS	C	T	879	0.866894	0	0,0,441,437	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749358	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13036	0.002531	1	9191,3800,25,12	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L140	leader	0.000316	0.135802	3	2	C>T
ERR5749358	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	13036	6.9E-4	11	9208,3819,9,0	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749358	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	9213	0.001194	0	0,9202,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTg	L35F?	nsp2	0.000551	0.081967	3	2	C>CT
ERR5749358	913	PASS	C	T	9213	0.902963	0	0,4,0,9186	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749358	3037	PASS	C	T	8728	0.808089	27	0,9,4358,4306	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749358	3267	PASS	C	T	11046	0.969129	2147483647	0,0,11044,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749358	4285	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGA	G	10649	9.39E-4	0	0,10639,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	gag/	E523	nsp3	0.000939	0.899038	2	2	GGA>G
ERR5749358	5388	PASS	C	A	2668	0.949775	2147483647	0,0,2667,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749358	5497	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	2668	0.002624	0	0,2661,0,7	HIGH	NONE	FRAME_SHIFT	ORF1ab	aga/	R928	nsp3	0.000964	0.897745	3	2	CA>C
ERR5749358	5986	PASS	C	T	7684	0.977746	0	1,0,7678,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749358	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	6685	0.011219	0	0,6609,0,75	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L1328S?	nsp3	0.000731	0.14377	4	2	C>CT
ERR5749358	6954	PASS	T	C	13450	0.812714	0	0,4,1,13367	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749358	7067	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	16926	0.009985	960	3265,13483,164,14	HIGH	NONSENSE	STOP_GAINED	ORF1ab	Gaa/Taa	E1450*	nsp3	0.000274	0.059217	5	3	G>T
ERR5749358	7735	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CGTTGATAGT	C	15199	6.58E-4	0	15184,0,10,0	MODERATE	NONE	CODON_DELETION	ORF1ab	gatagtgtt/	DSV1674	nsp3	0.000658	0.954659	3	2	CGTTGATAGT>C
ERR5749358	8950	PASS	C	T	17298	0.978263	5	0,1,11941,5351	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I132	nsp4	0.002808	0.982604	1	1	C>T
ERR5749358	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	9726	0.001028	4	8454,1262,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749358	10642	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	12654	0.001264	0	0,12610,0,18	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acG/acC	T196	3Cpro	0.001264	0.951979	3	1	G>C
ERR5749358	11075	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTTTTTTTGTATGAAAATGCCTTTTTACC	T	16524	6.05E-4	0	16514,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tttttgtatgaaaatgcctttttacctttt/	FLYENAFLPF36	nsp6	0.000555	0.885796	4	2	TTTTTTTTGTATGAAAATGCCTTTTTACC>T
ERR5749358	11287	PASS	GTCTGGTTTT	G	16517	0.998729	0	0,21,0,16496	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749358	12125	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	14362	0.001601	0	4,14285,0,28	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y12H	nsp8	0.000847	0.113436	1	1	T>C
ERR5749358	14408	PASS	C	T	2818	0.847409	3	0,1,1410,1389	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749358	14676	PASS	C	T	6999	0.842978	0	3,0,6981,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749358	15279	PASS	C	T	10196	0.875343	0	1,0,10184,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749358	15981	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	6043	0.001324	0	6035,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gta/	V848	RdRp	0.001324	0.965686	2	2	CG>C
ERR5749358	16176	PASS	T	C	9043	0.980427	0	0,0,2994,6042	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749358	17181	PASS	T	C	7267	0.991193	0	9,0,7257,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaT/gaC	D315	helicase	0.986595	0.991193	1	1	T>C
ERR5749358	17795	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTG	C	8107	0.00111	0	8098,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gta/	V521	helicase	0.00111	0.966723	2	2	CTG>C
ERR5749358	18576	PASS	C	T	12909	0.864745	0	0,3,0,12877	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D179	ExoN	0.005404	0.876866	2	2	C>T
ERR5749358	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	20710	0.001207	0	20685,0,25,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749358	19164	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	17264	5.21E-4	0	0,17255,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttc/Attc	F377I?	ExoN	0.000358	0.075732	4	2	C>CA
ERR5749358	19483	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	10989	0.002275	0	0,10939,0,39	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gct/Tct	A482S	ExoN	0.001112	0.089844	3	1	G>T
ERR5749358	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9432	0.001908	0	9411,0,18,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749358	21234	PASS	C	T	18648	0.857572	0	8,0,18587,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A192	MethTr	0.000472	0.857572	5	2	C>T
ERR5749358	21764	PASS	ATACATG	A	8904	0.996855	18	26,1,8872,4	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749358	21990	PASS	TTTA	T	8901	0.996854	0	0,28,1,8872	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749358	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22857	9.63E-4	5	9879,12948,12,10	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749358	23063	PASS	A	T	9886	0.866377	0	0,1,0,9837	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749358	23271	PASS	C	A	12664	0.922773	2147483647	0,0,12653,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749358	23294	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	12663	0.001816	0	12628,0,29,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gat/Tat	D578Y	S	0.001754	0.102649	2	1	G>T
ERR5749358	23403	PASS	A	G	12659	0.964768	0	0,1,0,12643	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749358	23604	PASS	C	A	9946	0.934044	0	5,0,9935,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749358	23709	PASS	C	T	9933	0.935669	0	0,4,0,9913	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749358	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	17244	0.001102	11	7291,9934,4,15	HIGH	NONE	FRAME_SHIFT	S	ttg/	L753	S	0.000334	0.080808	2	2	CT>C
ERR5749358	24506	PASS	T	G	12326	0.971037	0	7,0,12317,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749358	24899	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	31598	4.43E-4	0	15807,15778,7,7	HIGH	NONE	FRAME_SHIFT	S	caaatc/	QI1113	S	0.000315	0.09021	5	3	CAA>C
ERR5749358	24914	PASS	G	C	31488	0.958714	0	0,0,15685,15785	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749358	25391	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTA	T	14890	0.001679	0	14865,0,25,0	HIGH	NONE	FRAME_SHIFT+START_LOST	ORF3a	atg/	M1	orf3a	0.000585	0.191026	1	1	TTA>T
ERR5749358	25844	PASS	C	T	4472	0.919946	0	0,1,0,4466	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aCt/aTt	T151I	orf3a	0.001226	0.938776	1	1	C>T
ERR5749358	25855	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	4474	0.002459	0	0,4459,0,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gac/Tac	D155Y	orf3a	0.001326	0.969697	1	1	G>T
ERR5749358	26208	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	22392	5.36E-4	0	1,22379,0,12	HIGH	NONE	FRAME_SHIFT	ORF3a	gtg/	V273	orf3a	0.000315	0.922222	2	2	CG>C
ERR5749358	26493	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	8318	0.001082	0	0,8309,0,9	.	.	.	.	.	.	.	0.001082	0.069277	3	1	GT>G
ERR5749358	27506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	33897	0.001092	13	18174,15623,26,11	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	gGa/gCa	G38A	orf7a	0.000715	0.985435	4	2	G>C
ERR5749358	27506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	33897	0.001475	0	18174,15623,34,28	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	gGa/gTa	G38V	orf7a	0.000715	0.985435	4	2	G>T
ERR5749358	27577	PASS	C	T	33320	0.854592	1	3,4,18181,15033	HIGH	NONSENSE	STOP_GAINED	ORF7a	Caa/Taa	Q62*	orf7a	0.000614	0.952205	4	2	C>T
ERR5749358	27604	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	36425	0.001455	0	18203,18100,27,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Gta/Ata	V71I	orf7a	0.001008	0.967671	3	2	G>A
ERR5749358	27672	PASS	TCAAGAACTTTACTCTCCAATTTTTCTTATTGTTGCGGCAATAGTGTTTATAACACTTTGCTTCACACTCAAAAGAAAG	T	17824	0.999439	0	0,331,0,17814	MODERATE	NONE	CODON_DELETION	ORF7a	caagaactttactctccaatttttcttattgttgcggcaatagtgtttataacactttgcttcacactcaaaagaaag/	QELYSPIFLIVAAIVFITLCFTLKRK94	orf7a	0.00102	0.999439	2	1	TCAAGAACTTTACTCTCCAATTTTTCTTATTGTTGCGGCAATAGTGTTTATAACACTTTGCTTCACACTCAAAAGAAAG>T
ERR5749358	27972	PASS	C	T	5980	0.89699	19	1,1,5926,32	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749358	28048	PASS	G	T	5947	0.920632	0	0,7,0,5940	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749358	28111	PASS	A	G	21674	0.975639	0	3,1,15711,5946	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749358	28270	PASS	TA	T	30399	0.995164	346	145,5,15520,14732	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749358	28280	PASS	G	C	30334	0.935782	4	4,1,15554,14721	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749358	28281	PASS	A	T	30334	0.91554	21	15,3,15545,14713	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749358	28282	PASS	T	A	30337	0.90411	5	14,8,15506,14730	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749358	28881	PASS	G	A	6299	0.7525	3	2,0,3116,3097	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749358	28882	PASS	G	A	6299	0.828862	0	1,1,3152,3090	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749358	28883	PASS	G	C	6299	0.943642	0	0,0,3157,3141	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749358	28903	PASS	G	T	3197	0.889271	0	0,18,0,3177	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	atG/atT	M210I	N	0.009291	0.889271	2	2	G>T
ERR5749358	28977	PASS	C	T	3210	0.92866	0	0,1,0,3198	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749358	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	48672	0.001356	0	24432,24133,42,41	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749358	29253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	24500	4.08E-4	0	0,24490,0,10	HIGH	NONE	FRAME_SHIFT	N	gga/	G328	N	0.000361	0.053998	4	2	CG>C
ERR5749358	29311	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	24517	7.75E-4	0	12,24486,0,19	HIGH	NONE	FRAME_SHIFT	N	aaa/	K347	N	0.000335	0.790798	3	2	CA>C
ERR5749359	241	PASS	C	T	22588	0.858686	3	0,2,11227,11274	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749359	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	14361	0.003482	0	14297,9,50,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749359	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	14367	6.26E-4	0	14231,17,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749359	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	14367	0.001183	0	14231,17,17,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749359	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	14367	0.005847	0	14231,17,84,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749359	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	14375	0.002087	7	13061,34,1064,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749359	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	14375	0.002435	0	14306,34,35,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749359	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTT	G	14375	7.65E-4	0	14310,34,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/	V84	leader	0.000554	0.991848	4	1	GTT>G
ERR5749359	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	14375	6.96E-4	0	14310,34,10,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttatg/gtg	VM84V	leader	0.000554	0.991848	4	1	GTTA>G
ERR5749359	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	14375	6.96E-4	0	14310,34,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749359	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	14375	8.35E-4	0	14268,37,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TA>T
ERR5749359	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	14375	0.003757	8	14268,37,53,1	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749359	526	PASS	G	T	24655	0.101764	2147483647	10600,10298,3729,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gaG/gaT	E87D	leader	0.101764	0.101764	1	1	G>T
ERR5749359	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	44676	0.001142	48	30263,14361,48,3	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749359	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	44677	3.58E-4	5	30199,14336,13,3	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749359	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	44677	0.002529	19	30199,14336,89,24	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749359	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30290	8.58E-4	0	0,30231,0,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749359	913	PASS	C	T	30291	0.908884	0	0,19,0,30203	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749359	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	107066	0.001392	2147483647	53503,49946,74,3293	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749359	3037	PASS	C	T	24046	0.811029	67	1,26,12006,11827	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749359	3095	PASS	T	C	12099	0.950988	0	0,4,0,12087	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tca/Cca	S126P	nsp3	0.937591	0.970297	1	1	T>C
ERR5749359	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12152	0.002057	667	15,12102,27,4	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749359	3177	PASS	C	T	40908	0.881955	6	7,6,28763,12083	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P153L	nsp3	0.000773	0.96008	3	2	C>T
ERR5749359	3267	PASS	C	T	28797	0.969268	0	1,0,28777,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749359	3832	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34236	8.18E-4	0	34189,5,28,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	agC/agT	S371	nsp3	0.000689	0.327273	4	2	C>T
ERR5749359	4578	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTAACGATC	T	20362	5.89E-4	0	0,20350,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	aacgatctaaat/	NDLN621	nsp3	0.000519	0.082979	2	2	TTAACGATC>T
ERR5749359	5178	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17147	0.00175	0	4,17081,0,37	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T820I	nsp3	0.00175	0.88249	2	1	C>T
ERR5749359	5388	PASS	C	A	8977	0.961568	2147483647	0,0,8975,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749359	5986	PASS	C	T	16354	0.975725	0	2,0,16336,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749359	6954	PASS	T	C	32583	0.797195	0	0,7,5,32377	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749359	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	40826	3.67E-4	47	19728,21083,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749359	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	27116	0.001291	0	27044,0,52,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749359	11287	PASS	GTCTGGTTTT	G	27108	0.996495	0	0,93,0,27013	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749359	12374	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	32921	0.001063	0	1,32857,0,35	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Ttt	L95F	nsp8	0.001063	0.932196	1	1	C>T
ERR5749359	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	23452	9.81E-4	0	23403,0,24,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749359	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	43346	9.69E-4	0	21655,21590,24,24	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749359	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12527	0.004231	2828	12223,134,4,164	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749359	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	24334	0.002753	0	12177,12103,35,32	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749359	14408	PASS	C	T	24334	0.834717	4	3,6,12117,11983	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749359	14676	PASS	C	T	18846	0.77348	0	7,0,18776,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749359	15279	PASS	C	T	31774	0.891672	0	1,0,31738,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749359	15960	PASS	C	T	14637	0.799003	0	1,0,14575,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A840	RdRp	0.001581	0.81574	1	1	C>T
ERR5749359	16176	PASS	T	C	27373	0.982063	6	1,5,12724,14635	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749359	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	35329	3.4E-4	0	2,35315,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749359	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	38308	0.001984	0	38203,2,78,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749359	21764	PASS	ATACATG	A	15723	0.997647	0	37,0,15686,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749359	21990	PASS	TTTA	T	15726	0.997011	0	0,47,3,15676	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749359	22290	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	30140	5.64E-4	0	0,30123,0,17	HIGH	NONE	FRAME_SHIFT	S	tta/	L244	S	0.000389	0.578006	2	2	CT>C
ERR5749359	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	36634	7.92E-4	1	16188,20371,12,18	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749359	23063	PASS	A	T	16196	0.863855	0	0,3,3,16124	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749359	23271	PASS	C	A	31102	0.926146	0	1,0,31059,4	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749359	23403	PASS	A	G	31091	0.96655	0	0,3,1,31048	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749359	23604	PASS	C	A	19659	0.949692	0	13,0,19638,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749359	23709	PASS	C	T	19641	0.932234	0	0,6,8,19588	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749359	23817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	45055	7.1E-4	2	25360,19635,21,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTt/cCt	L752P	S	0.000646	0.066832	1	1	T>C
ERR5749359	24010	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATTTATTGAAGATCTAC	A	25542	4.7E-4	0	204,25322,0,12	HIGH	NONE	FRAME_SHIFT	S	attgaagatctacttttc/	IEDLLF818	S	0.000455	0.926398	4	2	ATTTATTGAAGATCTAC>A
ERR5749359	24127	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TTTTTG	40815	4.41E-4	35	15458,25357,0,18	HIGH	NONE	FRAME_SHIFT+STOP_GAINED	S	aac/TTTTGaac	N856F*?	S	0.000324	0.111888	4	1	T>TTTTTG
ERR5749359	24127	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	40815	4.17E-4	3	15437,25386,8,9	HIGH	NONE	FRAME_SHIFT	S	aac/	N856	S	0.000324	0.111888	4	1	TA>T
ERR5749359	24432	PASS	A	T	41948	0.941141	8	11,2,26475,15440	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cAa/cTa	Q957L	S	0.935743	0.949489	1	1	A>T
ERR5749359	24506	PASS	T	G	26488	0.974252	0	13,0,26473,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749359	24914	PASS	G	C	43277	0.955034	0	0,0,21555,21700	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749359	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	31529	0.001047	37	21281,10196,39,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749359	25495	PASS	A	G	42526	0.893971	0	5,5,21134,21327	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Ata/Gta	I35V	orf3a	0.000735	0.911134	2	1	A>G
ERR5749359	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	31696	0.001451	578	31569,23,23,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749359	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	31649	6.0E-4	0	31630,0,19,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749359	25726	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	31647	9.48E-4	0	31593,0,45,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gtc/Ttc	V112F	orf3a	0.000948	0.982899	1	1	G>T
ERR5749359	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	31875	0.001569	1574	31335,196,197,117	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749359	26013	PASS	C	T	61278	0.967427	0	11,0,61230,0	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	ttC/ttT	F207	orf3a	0.000839	0.974528	1	1	C>T
ERR5749359	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	61163	5.72E-4	0	6,61117,0,35	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749359	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	14682	0.001294	0	1,14646,0,19	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749359	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTTT	G	14682	6.81E-4	0	1,14646,0,10	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgtttgcg/gcg	ACLVGLMWLSYFIASFRLFA85A	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTTT>G
ERR5749359	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	14682	0.001158	0	1,14661,0,17	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749359	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	14682	0.004904	0	0,14599,0,72	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749359	27972	PASS	C	T	14223	0.902833	0	1,0,14098,83	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749359	28048	PASS	G	T	14150	0.924664	0	0,15,1,14127	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749359	28111	PASS	A	G	42967	0.980217	17	1,5,28789,14154	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749359	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	28782	4.86E-4	0	28763,12,14,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749359	28270	PASS	TA	T	55914	0.995457	593	251,9,28450,27210	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749359	28280	PASS	G	C	55810	0.938326	15	16,5,28490,27187	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749359	28281	PASS	A	T	55810	0.919584	35	33,9,28491,27179	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749359	28282	PASS	T	A	55812	0.914678	11	37,21,28419,27190	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749359	28407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TACCCAATA	T	28823	3.82E-4	0	13,28795,0,11	HIGH	NONE	FRAME_SHIFT	N	cccaataat/	PNN46	N	0.000382	0.179673	1	1	TACCCAATA>T
ERR5749359	28881	PASS	G	A	25093	0.770534	18	7,0,12413,12341	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749359	28882	PASS	G	A	25092	0.833094	21	11,1,12546,12283	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749359	28883	PASS	G	C	25091	0.942609	0	1,1,12569,12481	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749359	28977	PASS	C	T	12800	0.928828	0	0,3,0,12771	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749359	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	45582	0.001207	214	32768,12721,6,51	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749359	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	65124	8.91E-4	1	32696,32328,39,35	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749360	174	PASS	G	T	344	0.747093	0	1,0,342,0	.	.	.	.	.	.	.	0.710959	0.747093	1	1	G>T
ERR5749360	241	PASS	C	T	688	0.896802	0	0,0,344,343	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749360	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	724	0.009669	0	714,0,7,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749360	657	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	729	0.021948	0	3,708,0,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A131V	leader	0.001202	0.365979	3	1	C>T
ERR5749360	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	11091	0.003336	2	10329,725,36,1	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749360	843	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20683	0.001402	0	10326,10309,16,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P13L	nsp2	0.000301	0.050923	4	2	C>T
ERR5749360	1059	PASS	C	T	6580	0.920973	0	2,0,6571,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCc/aTc	T85I	nsp2	0.001728	0.920973	1	1	C>T
ERR5749360	1594	PASS	C	T	6917	0.961544	0	0,3,0,6885	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S263	nsp2	0.0019	0.963177	1	1	C>T
ERR5749360	2084	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18511	0.002323	0	9217,9229,23,23	HIGH	NONSENSE	STOP_GAINED	ORF1ab	Cag/Tag	Q427*	nsp2	0.001943	0.253112	1	1	C>T
ERR5749360	2692	PASS	A	T	18	0.888889	2147483647	0,0,18,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acA/acT	T629	nsp2	0.888889	0.933333	1	1	A>T
ERR5749360	3037	PASS	C	T	5132	0.805144	9	0,3,2565,2517	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749360	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	2607	0.006904	454	2,2585,19,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749360	3466	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12374	0.001697	0	0,12338,0,30	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H249Q	nsp3	0.000976	0.051008	3	3	T>G
ERR5749360	3483	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	16489	0.001819	36	4113,12341,0,31	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGa/gCa	G255A	nsp3	0.001819	0.962114	2	1	G>C
ERR5749360	3671	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	8196	0.00244	1	4092,4085,9,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N319	nsp3	0.000351	0.0625	6	2	GA>G
ERR5749360	4280	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	7088	0.002822	0	0,7064,0,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gta/Cta	V521L	nsp3	0.002822	0.896067	2	1	G>C
ERR5749360	4338	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	17181	0.001921	75	10052,7096,33,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	att/	I541	nsp3	0.000366	0.051643	2	2	CTA>C
ERR5749360	4573	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	10082	0.001686	0	0,10060,0,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaC/aaA	N618K	nsp3	0.001686	0.844138	2	2	C>A
ERR5749360	5178	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	6461	0.001857	0	34,6401,0,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aAt	T820N	nsp3	0.00175	0.88249	2	1	C>A
ERR5749360	5184	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6462	0.004643	0	34,6386,0,32	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P822L	nsp3	0.004643	0.894684	2	2	C>T
ERR5749360	5230	PASS	G	T	6432	0.902519	0	0,5,0,6414	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaG/aaT	K837N	nsp3	0.002515	0.902519	1	1	G>T
ERR5749360	6516	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	15781	0.001774	37	4327,11426,0,28	HIGH	NONE	FRAME_SHIFT	ORF1ab	att/aAtt	I1268N?	nsp3	0.000479	0.186047	4	2	T>TA
ERR5749360	6706	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	4316	0.002085	0	0,4307,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1330	nsp3	0.000687	0.883999	2	2	CA>C
ERR5749360	6954	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	11754	0.001872	0	0,11732,0,22	HIGH	NONE	FRAME_SHIFT	ORF1ab	att/	I1413	nsp3	0.001872	0.892308	2	2	TA>T
ERR5749360	7528	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8189	0.00867	8	62,8041,2,78	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V1603	nsp3	0.002527	0.916131	1	1	C>T
ERR5749360	7674	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13696	0.002482	0	13653,3,37,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCg/gTg	A1652V	nsp3	0.000682	0.109264	3	2	C>T
ERR5749360	7771	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	13689	0.001972	0	13646,0,32,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H1684Q	nsp3	0.001343	1	2	2	T>G
ERR5749360	7843	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27221	8.45E-4	0	13537,13612,13,13	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N1708	nsp3	0.000845	0.916161	2	2	C>T
ERR5749360	7926	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	13691	0.003506	0	0,13643,0,48	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1737	nsp3	0.000531	0.97019	5	2	CA>C
ERR5749360	8084	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GA	5776	0.001385	0	5769,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctc/Actc	L1791T?	nsp3	0.000543	0.923413	4	2	G>GA
ERR5749360	8137	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	5765	0.002602	0	5741,0,16,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtG/gtC	V1806	nsp3	0.002602	0.762515	2	1	G>C
ERR5749360	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	5497	0.001819	2	4971,516,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749360	10116	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14210	0.001619	23	11112,3070,24,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T21I	3Cpro	0.001266	0.952096	1	1	C>T
ERR5749360	10296	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22194	0.002839	0	11033,10964,33,34	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S81F	3Cpro	0.002839	0.925159	1	1	C>T
ERR5749360	10323	PASS	A	G	11129	0.965046	2147483647	0,0,0,11116	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749360	10533	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTACATGCACCATATGGAA	G	13704	0.001022	0	13691,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	atgcaccatatggaattacca/	MHHMELP162	3Cpro	0.000835	0.917216	4	2	GTTACATGCACCATATGGAA>G
ERR5749360	11073	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	18681	0.001713	0	18638,0,35,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTc/tGc	F34C	nsp6	0.000385	0.092251	6	2	T>G
ERR5749360	11095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18675	0.001339	0	18623,0,27,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A41	nsp6	0.000515	0.887707	7	2	C>T
ERR5749360	11095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTTTTTACCT	C	18675	0.001124	0	18645,0,21,0	MODERATE	NONE	CODON_DELETION	ORF1ab	ttacctttt/	LPF43	nsp6	0.000515	0.887707	7	2	CTTTTTACCT>C
ERR5749360	11199	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	37190	9.95E-4	0	18458,18559,20,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCc/gTc	A76V	nsp6	0.000309	0.056758	3	2	C>T
ERR5749360	11287	PASS	GTCTGGTTTT	G	18672	0.995501	0	0,84,0,18588	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749360	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	18044	0.001386	18	14944,3057,26,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749360	12459	PASS	C	T	13231	0.986093	3	0,1,7442,5787	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T123I	nsp8	0.000658	0.986093	1	1	C>T
ERR5749360	12513	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7443	0.003628	0	7412,0,27,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aTg	T141M	nsp8	0.000794	0.984064	2	2	C>T
ERR5749360	12781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2981	0.00369	0	2964,4,11,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y32	nsp9	0.001869	0.974683	2	2	C>T
ERR5749360	13134	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	10603	0.001132	0	10591,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	atc/	I38	nsp10	0.000682	0.107576	2	2	CA>C
ERR5749360	13459	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	11677	0.001285	0	11663,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L8	nsp11	0.000691	0.060726	5	2	GT>G
ERR5749360	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23332	0.001243	0	11648,11622,17,17	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749360	14408	PASS	C	T	613	0.849918	0	0,0,306,301	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749360	14805	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7140	0.002521	0	0,7120,0,19	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y455	RdRp	0.001051	0.904964	2	2	C>T
ERR5749360	15237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8319	0.001803	0	8298,5,15,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H599	RdRp	0.001014	0.955128	2	2	C>T
ERR5749360	15797	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	11032	0.001722	0	0,10985,0,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cTt/cCt	L786P	RdRp	0.001418	0.07734	2	1	T>C
ERR5749360	18658	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTGTCTATGTG	T	18096	0.002431	0	18050,2,44,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	tgttgtctatgtgat/tat	CCLCD207Y	ExoN	0.000507	0.115741	3	2	TGTTGTCTATGTG>T
ERR5749360	18747	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	18089	0.001106	0	18044,0,28,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtA	V236	ExoN	0.000375	0.982946	4	2	C>A
ERR5749360	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18680	0.001874	0	0,18626,0,43	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCc/gTc	A371V	ExoN	0.00034	0.247423	2	2	C>T
ERR5749360	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	18680	0.002463	0	0,18634,0,46	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749360	19188	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	18691	6.96E-4	0	0,18678,0,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	tgg/	W385	ExoN	0.000427	0.06319	2	1	AT>A
ERR5749360	19269	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25987	0.001655	48	7283,18649,1,43	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N410	ExoN	0.000773	0.954777	2	2	C>T
ERR5749360	19343	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	7290	0.001646	0	7278,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F436	ExoN	0.000519	0.192257	7	2	CT>C
ERR5749360	19483	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	7283	0.002746	0	0,7249,0,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gct/Act	A482T	ExoN	0.001112	0.089844	3	1	G>A
ERR5749360	20091	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	4698	0.00149	0	0,4691,0,7	HIGH	NONE	FRAME_SHIFT	ORF1ab	caa/Acaa	Q159T?	endoR	0.000368	0.051583	1	1	C>CA
ERR5749360	20148	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	4703	0.00489	0	0,4680,0,23	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N177	endoR	0.000513	0.969223	2	2	CA>C
ERR5749360	20178	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCAA	C	4708	0.002336	0	4,4693,0,11	MODERATE	NONE	CODON_DELETION	ORF1ab	caa/	Q188	endoR	0.000533	0.867727	2	2	CCAA>C
ERR5749360	20320	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21043	0.001996	0	20940,0,46,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cat/Tat	H234Y	endoR	0.000651	0.916979	2	2	C>T
ERR5749360	20507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	32237	6.82E-4	101	11158,21057,22,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L297	endoR	0.000629	0.062609	1	1	AT>A
ERR5749360	20844	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTATAA	C	28691	5.23E-4	61	17510,11166,0,15	HIGH	NONE	FRAME_SHIFT	ORF1ab	aatatg/	NM64	MethTr	0.000293	0.905571	5	2	CTATAA>C
ERR5749360	21597	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	8258	0.00218	0	0,8221,0,37	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCt/tAt	S12Y	S	0.00218	0.901607	2	1	C>A
ERR5749360	21614	PASS	C	T	8259	0.912459	0	0,3,0,8244	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L18F	S	0.001194	0.949239	2	2	C>T
ERR5749360	21655	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	8266	0.003508	0	0,8234,0,30	LOW	SILENT	SYNONYMOUS_CODING	S	tcT/tcC	S31	S	0.001481	0.110354	1	1	T>C
ERR5749360	21801	PASS	A	C	6373	0.945238	0	8,0,6365,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gCt	D80A	S	0.005484	0.946172	2	2	A>C
ERR5749360	22206	PASS	A	G	12704	0.937972	0	0,1,0,12694	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D215G	S	0.002035	0.950097	2	1	A>G
ERR5749360	22280	PASS	ACTTTACTTG	A	12714	0.997562	0	0,31,0,12683	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	cttgctttacat/cat	LALH242H	S	0.00046	0.997799	1	1	ACTTTACTTG>A
ERR5749360	22690	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	13855	0.001588	0	13652,0,27,0	LOW	SILENT	SYNONYMOUS_CODING	S	acT/acC	T376	S	0.000815	0.051311	2	1	T>C
ERR5749360	22813	PASS	G	T	13895	0.94113	0	0,15,0,13879	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aaG/aaT	K417N	S	0.937872	0.94113	1	1	G>T
ERR5749360	22917	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	1801	0.005552	0	1788,0,10,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTg/cCg	L452P	S	0.005552	0.975153	2	1	T>C
ERR5749360	23012	PASS	G	A	3457	0.90512	0	1,0,1779,1667	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gaa/Aaa	E484K	S	0.001756	0.909912	2	1	G>A
ERR5749360	23063	PASS	A	T	1800	0.867778	2147483647	0,0,0,1792	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749360	23403	PASS	A	G	16346	0.975223	2147483647	0,0,0,16334	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749360	23664	PASS	C	T	11561	0.918	0	0,1,5667,5882	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCa/gTa	A701V	S	0.000837	0.918	2	2	C>T
ERR5749360	23802	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5919	0.002534	0	4,5899,0,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCt/aTt	T747I	S	0.001717	0.977181	3	2	C>T
ERR5749360	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	8901	8.99E-4	12	2986,5907,0,8	HIGH	NONE	FRAME_SHIFT	S	ttg/	L753	S	0.000334	0.080808	2	2	CT>C
ERR5749360	23817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	8901	0.003146	18	2969,5892,16,12	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTt/cCt	L752P	S	0.000646	0.066832	1	1	T>C
ERR5749360	23855	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2986	0.005358	0	2967,0,17,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Cgt/Tgt	R765C	S	0.000815	0.181818	2	2	C>T
ERR5749360	24382	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6016	0.00266	0	0,5998,0,17	LOW	SILENT	SYNONYMOUS_CODING	S	tcC/tcT	S940	S	0.002118	0.920404	2	1	C>T
ERR5749360	24899	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	29411	0.002244	0	14684,14662,33,33	HIGH	NONE	FRAME_SHIFT	S	atc/	I1114	S	0.000315	0.09021	5	3	CA>C
ERR5749360	25019	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	19312	0.001191	25	4564,14716,0,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gat/Cat	D1153H	S	0.00048	0.981297	3	2	G>C
ERR5749360	25469	PASS	C	T	13810	0.959377	0	2,0,13792,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	tCa/tTa	S26L	orf3a	0.001214	0.959377	2	2	C>T
ERR5749360	25563	PASS	G	T	13821	0.886549	0	0,36,0,13779	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	caG/caT	Q57H	orf3a	0.001456	0.886549	2	1	G>T
ERR5749360	25624	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15134	0.003238	2	1301,13781,3,49	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Cac/Tac	H78Y	orf3a	0.00089	0.983312	1	1	C>T
ERR5749360	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	1330	0.008271	203	1304,13,0,11	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749360	25720	PASS	G	T	1306	0.947933	2147483647	0,0,1305,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gct/Tct	A110S	orf3a	0.947933	0.951784	1	1	G>T
ERR5749360	25904	PASS	C	T	1313	0.81112	171	7,1,0,1296	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	tCa/tTa	S171L	orf3a	0.000757	0.83473	1	1	C>T
ERR5749360	26060	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11482	0.001568	0	11455,0,21,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aCt/aTt	T223I	orf3a	0.000459	0.822477	2	2	C>T
ERR5749360	26333	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7756	0.003223	0	7721,0,27,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	aCa/aTa	T30I	E	0.00158	0.943221	1	1	C>T
ERR5749360	26456	PASS	C	T	7736	0.927223	2147483647	0,0,0,7717	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	cCt/cTt	P71L	E	0.001544	0.927736	1	1	C>T
ERR5749360	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	5458	0.006046	0	0,5398,0,33	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749360	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	G	5458	0.004947	0	0,5398,0,27	HIGH	NONE	FRAME_SHIFT	M	cttgtaggcttgatgtggctcagctacttcattgcttctttc/	LVGLMWLSYFIASF87	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT>G
ERR5749360	27078	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21053	0.002945	0	0,20980,0,66	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Cgt/Tgt	R186C	M	0.000415	0.05783	2	2	C>T
ERR5749360	27312	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	10485	0.004101	0	10443,0,43,0	HIGH	NONE	FRAME_SHIFT	ORF6	aat/aaAt	N39K?	orf6	0.000911	0.088458	4	2	T>TA
ERR5749360	27382	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GATT	G	10522	0.001236	0	51,10458,0,13	HIGH	NONE	STOP_LOST+CODON_CHANGE_PLUS_CODON_DELETION+SPLICE_SITE_REGION	ORF6	gattaa/gaa	D*61E	orf6	0.001236	0.927964	2	2	GATT>G
ERR5749360	27598	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	12568	0.003899	0	12515,0,51,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Gac/Aac	D69N	orf7a	0.000699	0.958994	6	2	G>A
ERR5749360	27765	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12568	0.001432	0	0,12537,0,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7b	Ctt/Ttt	L4F	orf7b	0.00109	0.970449	1	1	C>T
ERR5749360	28200	PASS	T	G	21114	0.981434	0	6,0,21107,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	Tcg/Gcg	S103A	orf8	0.000751	0.981434	2	2	T>G
ERR5749360	28253	PASS	C	T	21077	0.946055	0	4,0,21056,2	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749360	28254	PASS	A	C	21077	0.912701	0	56,0,21014,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	Atc/Ctc	I121L	orf8	0.000541	0.914398	3	2	A>C
ERR5749360	28290	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	42125	0.0033	45	20881,20971,164,97	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	cCc/cAc	P6H	N	0.001339	0.943901	2	1	C>A
ERR5749360	28310	PASS	C	T	21089	0.919484	0	0,7,0,21042	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Ccc/Tcc	P13S	N	0.00095	0.92832	2	1	C>T
ERR5749360	28337	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	21103	0.001279	0	0,21047,0,29	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Aat	D22N	N	0.001279	0.935503	2	1	G>A
ERR5749360	28407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TACCCAATA	T	21120	0.002367	0	5,21065,0,50	HIGH	NONE	FRAME_SHIFT	N	cccaataat/	PNN46	N	0.000382	0.179673	1	1	TACCCAATA>T
ERR5749360	28516	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	12569	0.001273	0	12541,0,16,0	LOW	SILENT	SYNONYMOUS_CODING	N	gaT/gaC	D81	N	0.001273	0.990661	2	2	T>C
ERR5749360	28657	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12558	0.001354	0	0,12530,0,21	LOW	SILENT	SYNONYMOUS_CODING	N	gaC/gaT	D128	N	0.00124	0.862766	1	1	C>T
ERR5749360	28887	PASS	C	T	3483	0.812805	0	1,1,1730,1708	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aCt/aTt	T205I	N	0.002174	0.814997	2	2	C>T
ERR5749360	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	31229	0.001121	0	15680,15493,23,23	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749360	29311	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAAAGATCAAGTCATTTTGCTGAAT	C	15716	0.001336	0	2,15693,0,21	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	N	aaagatcaagtcattttgctgaataag/aag	KDQVILLNK347K	N	0.000335	0.790798	3	2	CAAAGATCAAGTCATTTTGCTGAAT>C
ERR5749360	29445	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTG	C	3798	0.003686	0	3784,0,14,0	HIGH	NONE	FRAME_SHIFT	N	gtg/	V392	N	0.000907	0.853797	2	2	CTG>C
ERR5749360	29733	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2254	0.005768	0	0,2240,0,14	.	.	.	.	.	.	.	0.001821	0.915943	2	1	C>T
ERR5749361	241	PASS	C	T	15164	0.871142	0	1,2,7504,7616	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749361	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	14415	0.001041	0	14401,3,15,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749361	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	14415	0.00111	0	14345,2,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749361	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	14415	7.63E-4	0	14345,2,11,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749361	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	14415	0.002428	44	14345,2,33,2	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749361	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	14406	0.001388	0	13475,5,819,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749361	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	14406	0.001111	0	14383,7,16,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749361	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	37882	9.24E-4	3	23417,14420,24,11	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749361	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23433	9.39E-4	0	0,23379,0,28	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749361	913	PASS	C	T	23433	0.915504	0	0,15,0,23388	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749361	1510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	23979	0.002544	0	0,23746,0,71	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G235	nsp2	0.002159	0.937304	1	1	T>C
ERR5749361	2508	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19714	0.008471	0	0,19519,0,174	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCc/cTc	P568L	nsp2	0.008471	0.96125	2	1	C>T
ERR5749361	3037	PASS	C	T	23597	0.826037	48	0,16,11788,11638	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749361	3267	PASS	C	T	21878	0.971798	0	3,0,21861,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749361	5388	PASS	C	A	7507	0.96097	2147483647	0,0,7504,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749361	5986	PASS	C	T	15327	0.975925	0	1,0,15323,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749361	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14399	0.001667	0	5,14255,0,35	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749361	6954	PASS	T	C	25898	0.812611	0	0,0,1,25752	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749361	7564	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	17034	7.63E-4	0	0,17021,0,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/	Y1617	nsp3	0.000586	0.056194	4	2	CT>C
ERR5749361	8092	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27094	0.001144	0	27044,0,31,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ctC/ctT	L1791	nsp3	0.000539	0.063953	3	2	C>T
ERR5749361	8664	PASS	C	T	29095	0.957828	0	4,0,29070,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T37I	nsp4	0.003182	0.985915	1	1	C>T
ERR5749361	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	35912	7.52E-4	85	17244,18641,27,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749361	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	18144	0.002315	0	18060,4,65,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749361	11287	PASS	GTCTGGTTTT	G	18144	0.998016	0	0,36,0,18108	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749361	12162	PASS	A	G	41339	0.973608	0	3,2,25225,16088	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cAg/cGg	Q24R	nsp8	0.000894	0.982497	1	1	A>G
ERR5749361	13902	PASS	T	A	21366	0.965319	0	0,14,0,21344	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gaT/gaA	D154E	RdRp	0.965319	0.965319	1	1	T>A
ERR5749361	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	14657	0.00232	2691	14417,87,6,141	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749361	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	28692	7.32E-4	1	14398,14291,12,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749361	14408	PASS	C	T	28692	0.848041	11	2,8,14332,14149	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749361	14599	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13873	0.001802	0	13841,3,27,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L387	RdRp	0.000639	0.922766	3	2	C>T
ERR5749361	14676	PASS	C	T	13867	0.728059	0	5,0,13801,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749361	15279	PASS	C	T	23965	0.900063	0	3,0,23941,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749361	16176	PASS	T	C	22469	0.982109	0	1,0,11680,10776	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749361	16939	PASS	T	C	20944	0.957315	0	2,0,20927,2	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Tta/Cta	L235	helicase	0.000959	0.959205	2	2	T>C
ERR5749361	17615	PASS	A	G	17017	0.904977	0	0,0,2,16968	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749361	18246	PASS	C	T	13931	0.961022	0	0,5,0,13918	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y69	ExoN	0.960724	0.984848	1	1	C>T
ERR5749361	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	26213	7.63E-4	0	26193,0,20,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749361	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	35313	0.001614	0	35227,0,62,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749361	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	31433	8.91E-4	0	31357,0,28,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749361	21678	PASS	C	A	16877	0.963501	64	2,9,0,16858	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P39H	S	0.963501	0.963501	1	1	C>A
ERR5749361	21764	PASS	ATACATG	A	3151	0.997461	0	8,0,3143,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749361	21990	PASS	TTTA	T	3160	0.997468	0	0,8,6,3146	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749361	23063	PASS	A	T	12593	0.881839	0	0,4,1,12537	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749361	23191	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22907	0.007771	0	22708,5,187,0	LOW	SILENT	SYNONYMOUS_CODING	S	ttC/ttT	F543	S	0.000538	0.973337	2	2	C>T
ERR5749361	23271	PASS	C	A	22893	0.928799	0	1,0,22866,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749361	23403	PASS	A	G	22881	0.969931	0	0,1,0,22863	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749361	23604	PASS	C	A	17717	0.949992	0	7,0,17704,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749361	23709	PASS	C	T	17698	0.932422	0	0,4,1,17667	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749361	24506	PASS	T	G	18716	0.974514	0	6,0,18704,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749361	24914	PASS	G	C	36587	0.960778	2	1,3,18203,18349	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749361	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	22620	0.001459	81	14627,7940,44,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749361	25555	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	14796	6.76E-4	0	2,14784,0,10	HIGH	NONE	FRAME_SHIFT	ORF3a	cag/Tcag	Q57S?	orf3a	0.000552	0.900573	5	2	G>GT
ERR5749361	25571	PASS	C	T	14799	0.914792	0	0,8,2,14770	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	tCc/tTc	S60F	orf3a	0.001558	0.922217	1	1	C>T
ERR5749361	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	28523	6.31E-4	0	28504,1,18,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749361	25909	PASS	G	A	28534	0.963447	517	15,3,0,28499	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gat/Aat	D173N	orf3a	0.963447	0.964132	1	1	G>A
ERR5749361	25916	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28537	0.001191	0	15,28479,0,36	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aCa/aTa	T175I	orf3a	0.001191	0.964713	2	2	C>T
ERR5749361	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	11826	0.001015	0	0,11812,0,12	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749361	27972	PASS	C	T	12005	0.914952	20	1,1,11907,49	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749361	28048	PASS	G	T	11968	0.927557	0	0,9,0,11951	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749361	28111	PASS	A	G	30228	0.9781	1	4,1,18244,11972	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749361	28270	PASS	TA	T	35103	0.9953	343	157,8,18046,16892	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749361	28280	PASS	G	C	35031	0.932289	20	8,0,18079,16876	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749361	28281	PASS	A	T	35031	0.910993	56	20,0,18071,16879	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749361	28282	PASS	T	A	35033	0.908429	4	16,10,18042,16887	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749361	28881	PASS	G	A	14745	0.756935	15	6,0,7283,7251	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749361	28882	PASS	G	A	14745	0.826517	6	5,1,7368,7242	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749361	28883	PASS	G	C	14746	0.946969	6	0,2,7379,7351	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749361	28977	PASS	C	T	7499	0.933324	2147483647	0,0,0,7490	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749361	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	28975	8.63E-4	86	21463,7472,5,22	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749361	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	42584	7.75E-4	0	21383,21142,20,18	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749362	241	PASS	C	T	8134	0.857143	0	0,0,4049,4052	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749362	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	10896	0.001652	0	10872,2,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749362	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10883	0.001654	0	10034,2,814,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749362	913	PASS	C	T	20022	0.905454	0	0,11,0,19972	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749362	3037	PASS	C	T	16707	0.813432	35	1,15,8347,8233	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749362	3177	PASS	C	T	28267	0.911275	2	2,2,19852,8382	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P153L	nsp3	0.000773	0.96008	3	2	C>T
ERR5749362	3267	PASS	C	T	19864	0.966422	0	2,0,19853,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749362	3870	PASS	A	G	18538	0.94487	0	2,0,18517,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K384R	nsp3	0.938462	0.94487	1	1	A>G
ERR5749362	4918	PASS	C	T	16187	0.94545	0	0,4,0,16163	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I733	nsp3	0.94545	0.971698	1	1	C>T
ERR5749362	5170	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	13077	0.001147	0	1,13061,0,15	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T819	nsp3	0.000565	0.894036	2	2	CCA>C
ERR5749362	5388	PASS	C	A	5591	0.957074	2147483647	0,0,5589,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749362	5986	PASS	C	T	12542	0.974565	0	1,0,12538,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749362	6954	PASS	T	C	22547	0.823347	0	0,3,2,22431	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749362	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	20884	0.001341	37	15080,5776,28,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749362	10632	PASS	C	T	20041	0.875555	0	0,9,0,19970	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCa/gTa	A193V	3Cpro	0.875555	0.89726	1	1	C>T
ERR5749362	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23881	0.001172	0	23815,2,34,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749362	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	23872	0.001592	0	23810,0,56,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749362	11287	PASS	GTCTGGTTTT	G	23867	0.997737	0	0,54,0,23813	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749362	12020	PASS	C	T	18043	0.968243	0	3,0,18022,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Ttt	L60F	nsp7	0.000994	0.968243	3	2	C>T
ERR5749362	12269	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	22874	4.81E-4	0	22863,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aag/	K61	nsp8	0.000434	0.213333	2	1	GA>G
ERR5749362	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34846	0.001004	0	17405,17362,20,20	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749362	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	5442	0.003491	1282	5309,52,4,75	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749362	14408	PASS	C	T	10562	0.843685	4	1,3,5277,5214	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749362	14676	PASS	C	T	14007	0.800386	0	5,0,13957,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749362	15279	PASS	C	T	22614	0.885911	0	2,0,22571,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749362	16176	PASS	T	C	19683	0.979627	0	2,2,8847,10821	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749362	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	26956	4.45E-4	0	26944,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749362	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25216	0.002181	0	25134,0,60,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749362	21764	PASS	ATACATG	A	12735	0.997566	0	31,0,12704,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749362	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	12735	7.85E-4	0	12725,0,10,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749362	21990	PASS	TTTA	T	12743	0.998117	0	0,24,7,12712	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749362	23063	PASS	A	T	14934	0.861591	0	0,3,0,14872	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749362	23271	PASS	C	A	22037	0.920316	0	2,0,22010,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749362	23403	PASS	A	G	22025	0.969489	2147483647	0,0,0,22013	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749362	23604	PASS	C	A	15737	0.937027	0	8,0,15719,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749362	23709	PASS	C	T	15726	0.94029	0	0,2,0,15704	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749362	23855	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16104	0.001987	0	16057,0,32,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Cgt/Tgt	R765C	S	0.000815	0.181818	2	2	C>T
ERR5749362	24506	PASS	T	G	21407	0.972813	0	10,0,21392,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749362	24914	PASS	G	C	39878	0.959928	3	0,2,19865,19990	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749362	25437	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAAGCAAGGTGAAATCAAGGATGCTACT	G	18684	0.008778	0	18521,0,164,0	MODERATE	NONE	CODON_DELETION	ORF3a	aagcaaggtgaaatcaaggatgctact/	KQGEIKDAT16	orf3a	0.001128	0.971411	2	2	GAAGCAAGGTGAAATCAAGGATGCTACT>G
ERR5749362	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	15680	0.001722	556	15608,15,6,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749362	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	15643	8.31E-4	0	15630,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749362	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	15739	0.001398	794	15531,86,60,52	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749362	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	12718	6.29E-4	0	0,12708,0,8	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749362	27972	PASS	C	T	10379	0.904133	23	0,1,10295,44	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749362	28048	PASS	G	T	10342	0.924096	0	0,13,0,10325	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749362	28111	PASS	A	G	32644	0.979659	0	4,2,22271,10351	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749362	28270	PASS	TA	T	43182	0.995253	479	205,8,21983,20994	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749362	28280	PASS	G	C	43095	0.936443	21	11,1,22030,20967	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749362	28281	PASS	A	T	43095	0.915791	16	23,9,22022,20972	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749362	28282	PASS	T	A	43096	0.908089	4	22,15,21955,20983	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749362	28881	PASS	G	A	14552	0.770478	9	4,0,7190,7161	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749362	28882	PASS	G	A	14552	0.834318	0	1,0,7276,7154	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749362	28883	PASS	G	C	14553	0.945716	0	2,1,7289,7256	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749362	28977	PASS	C	T	7380	0.936856	0	0,2,0,7369	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749362	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	61884	9.86E-4	0	31091,30701,37,35	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749363	241	PASS	C	T	622	0.853698	0	0,0,309,311	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749363	676	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7181	0.011976	607	5517,1563,1,97	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G137	leader	0.000799	0.919273	2	1	C>T
ERR5749363	913	PASS	C	T	5516	0.914249	0	0,5,0,5503	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749363	1415	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTT	C	4275	0.002573	0	4264,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/	L204	nsp2	0.002573	0.161017	2	2	CTT>C
ERR5749363	1684	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	10029	0.004686	0	9982,0,47,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gcc/	A294	nsp2	0.000638	0.973136	2	2	CG>C
ERR5749363	1813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	10015	0.002197	0	0,9982,0,26	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcA	A336	nsp2	0.001022	0.152738	4	2	T>A
ERR5749363	2698	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	11680	0.001712	0	11602,1,37,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaT/aaG	N631K	nsp2	0.001712	0.955854	2	2	T>G
ERR5749363	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	23250	0.002108	2029	11608,10815,16,747	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749363	3037	PASS	C	T	5901	0.821217	22	1,10,2949,2900	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749363	3267	PASS	C	T	6116	0.972531	2147483647	0,0,6113,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749363	3518	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	5220	0.001724	0	5209,2,9,0	HIGH	NONE	FRAME_SHIFT+STOP_GAINED	ORF1ab	gaa/Tgaa	E268*?	nsp3	0.001724	0.970993	2	2	G>GT
ERR5749363	3671	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	10387	0.003947	0	5157,5126,24,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E318K	nsp3	0.000351	0.0625	6	2	G>A
ERR5749363	3802	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	7704	0.001947	23	2485,5204,0,15	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N363	nsp3	0.000554	0.064198	4	2	TA>T
ERR5749363	4582	PASS	C	T	4766	0.938733	0	0,2,0,4759	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N621	nsp3	0.005644	0.938733	2	2	C>T
ERR5749363	5170	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	5193	0.001733	0	0,5184,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T819	nsp3	0.000565	0.894036	2	2	CCA>C
ERR5749363	5388	PASS	C	A	1625	0.966154	2147483647	0,0,1624,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749363	5849	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	5711	0.002101	0	0,5686,0,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cct/Act	P1044T	nsp3	0.00146	0.830206	2	1	C>A
ERR5749363	5986	PASS	C	T	5771	0.974355	0	1,0,5767,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749363	6954	PASS	T	C	9881	0.82188	0	0,2,0,9827	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749363	7067	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	10631	0.00254	5	715,9886,0,30	HIGH	NONSENSE	STOP_GAINED	ORF1ab	Gaa/Taa	E1450*	nsp3	0.000274	0.059217	5	3	G>T
ERR5749363	9016	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	12340	0.001702	0	12304,0,22,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcC	A154	nsp4	0.001138	0.950039	2	1	T>C
ERR5749363	9130	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	12334	0.00373	0	0,12278,0,55	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtG/gtT	V192	nsp4	0.001321	0.963415	2	1	G>T
ERR5749363	9402	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	732	0.005464	0	364,364,2,2	HIGH	NONE	FRAME_SHIFT	ORF1ab	ata/	I284	nsp4	0.000453	0.058824	2	2	CTA>C
ERR5749363	10189	PASS	C	T	11765	0.074883	0	10859,0,897,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acC/acT	T45	3Cpro	0.000675	0.074883	2	2	C>T
ERR5749363	10692	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	10233	0.002345	5	797,9411,0,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aAa	I213K	3Cpro	0.000956	0.982968	4	2	T>A
ERR5749363	10692	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAA	T	10233	0.003029	7	797,9405,0,31	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N214	3Cpro	0.000956	0.982968	4	2	TAA>T
ERR5749363	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	15119	0.003902	0	15048,0,69,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749363	11235	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15098	0.009008	0	0,14937,0,146	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A88V	nsp6	0.000512	0.942208	2	2	C>T
ERR5749363	11287	PASS	GTCTGGTTTT	G	15105	0.998808	0	0,18,0,15087	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749363	12125	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	16467	0.002125	0	3,16368,0,37	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y12H	nsp8	0.000847	0.113436	1	1	T>C
ERR5749363	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	11627	0.001376	0	11600,0,19,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgT/tgC	C46	nsp10	0.000528	0.198485	2	2	T>C
ERR5749363	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12148	0.001646	0	6068,6048,10,10	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749363	14098	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	7632	0.001834	0	7575,38,18,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggt/Tgt	G220C	RdRp	0.000806	0.065317	4	2	G>T
ERR5749363	14408	PASS	C	T	5876	0.841899	0	0,0,2939,2886	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749363	14676	PASS	C	T	3379	0.762356	0	2,0,3370,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749363	15279	PASS	C	T	6171	0.885432	2147483647	0,0,6159,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749363	16092	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4080	0.002941	0	0,4060,0,14	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y884	RdRp	0.002941	0.906832	1	1	C>T
ERR5749363	16176	PASS	T	C	5213	0.979283	0	0,0,1127,4086	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749363	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAA	G	9702	8.25E-4	0	9692,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GAA>G
ERR5749363	17999	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9829	0.002035	68	4103,5701,21,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T588I	helicase	0.001094	0.974498	2	1	C>T
ERR5749363	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	24889	9.64E-4	0	24865,0,24,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749363	19164	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	12467	0.001444	0	0,12449,0,18	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K376	ExoN	0.000358	0.075732	4	2	CA>C
ERR5749363	19263	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20801	0.001971	175	8275,12475,44,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N408	ExoN	0.000943	0.943181	2	2	C>T
ERR5749363	19524	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	8321	0.002884	0	0,8297,0,24	HIGH	NONE	FRAME_SHIFT	ORF1ab	gat/	D496	ExoN	0.000745	0.953697	2	2	CG>C
ERR5749363	20507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	34453	0.001277	102	14436,19973,0,44	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L297	endoR	0.000629	0.062609	1	1	AT>A
ERR5749363	20853	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	24998	0.00108	31	10529,14396,9,40	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atT	M65I	MethTr	0.000856	0.198276	2	1	G>T
ERR5749363	20925	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	10561	0.002083	0	10532,0,22,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttC	L89F	MethTr	0.001064	0.136967	2	1	G>C
ERR5749363	21004	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	21038	0.001616	47	10465,10473,26,68	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gca/Tca	A116S	MethTr	0.000749	0.857814	3	1	G>T
ERR5749363	21255	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	27087	0.001883	0	13947,13071,32,28	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcG/gcA	A199	MethTr	0.000341	0.917425	4	2	G>A
ERR5749363	21305	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	13985	0.00143	0	0,13952,0,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cGc/cAc	R216H	MethTr	0.000727	0.703943	1	1	G>A
ERR5749363	21733	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	8324	0.003364	0	8283,3,29,0	LOW	SILENT	SYNONYMOUS_CODING	S	ccT/ccC	P57	S	0.001662	0.065814	2	1	T>C
ERR5749363	21764	PASS	ATACATG	A	8321	0.997476	0	21,0,8300,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749363	21790	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAA	T	8321	0.001442	0	8309,0,12,0	HIGH	NONE	FRAME_SHIFT	S	aag/	K77	S	0.001442	0.063712	3	2	TAA>T
ERR5749363	21990	PASS	TTTA	T	8323	0.997837	0	0,18,2,8303	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749363	22225	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	12194	0.001558	0	0,12164,0,29	LOW	SILENT	SYNONYMOUS_CODING	S	tcG/tcT	S221	S	0.001195	0.94526	3	1	G>T
ERR5749363	22712	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26687	0.001986	0	13309,13271,29,29	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Cct/Tct	P384S	S	0.001254	0.842266	2	2	C>T
ERR5749363	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	13401	0.001343	0	0,13378,0,18	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749363	22803	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	13402	0.002015	0	0,13370,0,31	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cAa/cTa	Q414L	S	0.002015	0.9788	2	1	A>T
ERR5749363	23063	PASS	A	T	8610	0.862485	0	0,1,0,8574	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749363	23271	PASS	C	A	7184	0.900473	0	1,0,7173,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749363	23403	PASS	A	G	7180	0.970474	2147483647	0,0,0,7174	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749363	23604	PASS	C	A	8354	0.969595	2147483647	0,0,8354,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749363	23709	PASS	C	T	8344	0.938998	0	0,2,0,8337	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749363	23780	PASS	A	G	8356	0.96697	2147483647	0,0,0,8342	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Atg/Gtg	M740V	S	0.002014	0.967596	3	2	A>G
ERR5749363	24320	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	7488	0.002537	0	0,7469,0,19	HIGH	NONE	FRAME_SHIFT	S	aaa/	K921	S	0.000763	0.138365	4	2	CA>C
ERR5749363	24506	PASS	T	G	8849	0.971183	0	3,0,8840,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749363	24914	PASS	G	C	37222	0.954839	3	0,2,18561,18637	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749363	25350	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18044	0.001053	0	18023,2,19,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCa/cTa	P1263L	S	0.000626	0.97904	4	2	C>T
ERR5749363	25422	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGGAACTGTAACTTTG	T	18037	0.003382	0	17976,0,61,0	MODERATE	NONE	CODON_DELETION	ORF3a	ggaactgtaactttg/	GTVTL11	orf3a	0.000545	0.213989	6	1	TGGAACTGTAACTTTG>T
ERR5749363	25553	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	18023	0.001165	0	0,17984,0,30	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	gCt/gAt	A54D	orf3a	0.001165	0.868131	3	2	C>A
ERR5749363	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	1193	0.012573	193	1156,20,2,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749363	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	6339	0.001735	0	0,6328,0,11	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749363	27065	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	19311	0.001139	0	0,19275,0,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	ttG/ttC	L181F	M	0.001008	0.897124	3	2	G>C
ERR5749363	27312	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	14948	0.002676	0	14908,0,40,0	HIGH	NONE	FRAME_SHIFT	ORF6	aat/aaAt	N39K?	orf6	0.000911	0.088458	4	2	T>TA
ERR5749363	27384	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TCTC	14933	0.00154	0	0,14908,0,23	MODERATE	NONE	CODON_INSERTION+SPLICE_SITE_REGION	ORF6	taa/CTCtaa	*62L*	orf6	0.00154	0.931035	3	3	T>TCTC
ERR5749363	27476	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28354	0.00194	172	13389,14895,0,62	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	aCa/aTa	T28I	orf7a	0.000547	0.22827	4	2	C>T
ERR5749363	27476	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	28354	9.17E-4	72	13394,14934,0,26	HIGH	NONE	FRAME_SHIFT	ORF7a	acagta/	TV28	orf7a	0.000547	0.22827	4	2	CAG>C
ERR5749363	27552	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	13392	0.001867	0	13368,0,25,0	HIGH	NONE	FRAME_SHIFT	ORF7a	ttt/	F54	orf7a	0.000563	0.985801	6	1	AT>A
ERR5749363	27881	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3392	0.002948	0	3380,0,10,0	LOW	SILENT	SYNONYMOUS_CODING	ORF7b	caC/caT	H42	orf7b	0.001798	0.979167	2	2	C>T
ERR5749363	27972	PASS	C	T	3408	0.898181	39	1,2,3371,20	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749363	28048	PASS	G	T	3389	0.92033	0	0,3,0,3379	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749363	28085	PASS	G	T	3397	0.968796	155	5,0,0,3390	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	gaG/gaT	E64D	orf8	0.968796	0.968796	1	1	G>T
ERR5749363	28111	PASS	A	G	18475	0.977321	3	2,1,15073,3388	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749363	28270	PASS	TA	T	29131	0.991487	619	248,6,14782,14101	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749363	28280	PASS	G	C	29057	0.937192	44	25,3,14895,14088	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749363	28281	PASS	A	T	29057	0.917404	12	13,4,14907,14090	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749363	28282	PASS	T	A	29058	0.909216	26	25,7,14847,14097	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749363	28434	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	30676	8.15E-4	60	15563,15075,28,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aCc/aAc	T54N	N	0.000815	0.871795	4	2	C>A
ERR5749363	28881	PASS	G	A	1699	0.743378	3	2,0,839,834	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749363	28882	PASS	G	A	1699	0.842849	0	0,0,856,825	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749363	28883	PASS	G	C	1699	0.941142	0	1,0,855,842	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749363	28977	PASS	C	T	867	0.933103	2147483647	0,0,0,862	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749363	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	40195	0.001791	0	20142,19902,45,43	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749363	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	40195	0.001095	139	20142,19902,52,1	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccT	P302	N	0.000713	0.913732	2	1	G>T
ERR5749364	241	PASS	C	T	1384	0.849711	0	0,0,687,693	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749364	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	5307	0.007537	0	5262,0,40,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749364	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	5305	0.002451	0	5292,0,13,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749364	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	5306	0.001131	0	5297,2,6,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749364	520	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTT	G	5307	0.001131	0	5298,3,6,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttgag/gag	VE86E	leader	0.000583	0.051154	1	1	GGTT>G
ERR5749364	676	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19096	0.001623	174	13775,5278,2,36	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G137	leader	0.000799	0.919273	2	1	C>T
ERR5749364	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	19096	8.9E-4	22	13764,5315,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749364	913	PASS	C	T	13777	0.909922	0	0,2,0,13757	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749364	1813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	15110	0.00139	0	0,15078,0,25	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcA	A336	nsp2	0.001022	0.152738	4	2	T>A
ERR5749364	1960	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15053	0.002524	0	15007,1,38,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A385	nsp2	0.001414	0.105737	2	1	C>T
ERR5749364	3037	PASS	C	T	9777	0.819065	33	0,11,4889,4822	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749364	3177	PASS	C	T	19163	0.911914	23	0,4,14221,4915	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P153L	nsp3	0.000773	0.96008	3	2	C>T
ERR5749364	3267	PASS	C	T	14230	0.970625	0	1,0,14221,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749364	3877	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	6272	0.002232	0	5529,0,742,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcG	A386	nsp3	0.000588	0.960227	2	1	T>G
ERR5749364	4754	PASS	C	T	12516	0.947507	0	7,0,12501,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cct/Tct	P679S	nsp3	0.001054	0.947507	1	1	C>T
ERR5749364	5170	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	8725	0.001261	0	0,8714,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T819	nsp3	0.000565	0.894036	2	2	CCA>C
ERR5749364	5388	PASS	C	A	3426	0.961763	2147483647	0,0,3421,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749364	5986	PASS	C	T	9276	0.972186	2147483647	0,0,9264,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749364	6348	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	15253	0.003868	610	15113,27,33,31	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cTg/cCg	L1210P	nsp3	0.001003	0.125	2	1	T>C
ERR5749364	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9280	0.001616	0	17,9154,0,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749364	6954	PASS	T	C	15503	0.810424	2147483647	0,0,0,15415	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749364	7239	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	9113	0.002195	0	4545,4550,10,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	gag/	E1508	nsp3	0.000568	0.901952	2	2	CAG>C
ERR5749364	7423	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTT	C	10629	9.41E-4	0	10619,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F1569	nsp3	0.000941	0.970543	2	2	CTT>C
ERR5749364	8796	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	17178	0.001281	7	8577,8554,16,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aGt/aTt	S81I	nsp4	0.000257	0.25	2	2	G>T
ERR5749364	10369	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15647	0.003323	0	0,15583,0,52	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	cgC/cgT	R105	3Cpro	0.001225	0.120075	1	1	C>T
ERR5749364	10595	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	14848	0.001347	0	10,14806,0,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F181L	3Cpro	0.000964	0.076408	1	1	T>C
ERR5749364	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	19857	0.003827	0	19417,0,76,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749364	11082	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	19851	7.05E-4	0	19842,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000427	0.179468	2	1	TG>T
ERR5749364	11152	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19826	0.001211	0	19764,0,24,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V60	nsp6	0.000678	0.974465	2	2	C>T
ERR5749364	11199	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	39536	0.001214	0	19614,19718,27,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCc/gTc	A76V	nsp6	0.000309	0.056758	3	2	C>T
ERR5749364	11235	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19842	0.001008	0	0,19795,0,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A88V	nsp6	0.000512	0.942208	2	2	C>T
ERR5749364	11287	PASS	GTCTGGTTTT	G	19845	0.996221	0	0,75,0,19770	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749364	12020	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	17479	0.001144	0	17459,0,20,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S61	nsp7	0.000994	0.968243	3	2	CT>C
ERR5749364	12459	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25738	0.001321	47	13582,12116,30,4	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T123I	nsp8	0.000658	0.986093	1	1	C>T
ERR5749364	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	13616	0.00191	0	13566,0,27,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749364	12741	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	20555	4.86E-4	16	6939,13606,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/acTa	T19T?	nsp9	0.000486	0.962552	2	2	C>CT
ERR5749364	12741	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20555	0.001022	35	6938,13590,0,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T19I	nsp9	0.000486	0.962552	2	2	C>T
ERR5749364	12884	PASS	A	G	6861	0.08541	0	6246,0,602,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Aca/Gca	T67A	nsp9	0.001655	0.08541	1	1	A>G
ERR5749364	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	5872	0.001362	0	2943,2927,4,4	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749364	14408	PASS	C	T	5872	0.845368	3	0,1,2927,2905	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749364	14676	PASS	C	T	9258	0.781162	0	1,0,9228,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749364	14724	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	9255	0.001729	0	9224,15,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F429	RdRp	0.000952	0.789267	3	2	CT>C
ERR5749364	15240	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12527	0.001357	0	12498,6,20,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N600	RdRp	0.000934	0.931284	2	2	C>T
ERR5749364	15279	PASS	C	T	12521	0.97013	0	1,0,12509,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749364	15960	PASS	C	T	8573	0.807419	0	5,0,8531,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A840	RdRp	0.001581	0.81574	1	1	C>T
ERR5749364	16176	PASS	T	C	12516	0.979067	10	2,0,3936,8574	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749364	16794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	34124	0.001143	1	15481,18597,19,20	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	cgT/cgC	R186	helicase	0.000354	0.077626	2	2	T>C
ERR5749364	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	23980	6.67E-4	0	23964,0,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749364	18756	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	23974	0.001293	0	23945,0,31,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F240	ExoN	0.000392	0.942688	3	2	GT>G
ERR5749364	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	20193	6.44E-4	0	0,20180,0,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749364	19164	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	20200	4.95E-4	0	0,20190,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K376	ExoN	0.000358	0.075732	4	2	CA>C
ERR5749364	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11647	0.00146	0	11624,0,18,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749364	20445	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	23234	9.47E-4	0	0,23212,0,22	HIGH	NONE	FRAME_SHIFT	ORF1ab	aac/aaAc	N277K?	endoR	0.000518	0.059736	4	2	T>TA
ERR5749364	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAA	T	17974	7.23E-4	0	0,17957,0,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TAA>T
ERR5749364	21234	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTT	C	22935	6.98E-4	0	22920,0,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F193	MethTr	0.000472	0.857572	5	2	CTT>C
ERR5749364	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	20150	6.95E-4	0	10053,10086,7,7	HIGH	NONE	FRAME_SHIFT	S	ttt/	F4	S	0.000394	0.091869	4	1	GT>G
ERR5749364	21655	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	10128	0.001481	0	0,10101,0,16	LOW	SILENT	SYNONYMOUS_CODING	S	tcT/tcC	S31	S	0.001481	0.110354	1	1	T>C
ERR5749364	21764	PASS	ATACATG	A	11010	0.997094	0	32,0,10978,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749364	21889	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTTA	T	10995	9.1E-4	0	0,10985,0,10	MODERATE	NONE	CODON_DELETION	S	tta/	L110	S	0.00091	0.065772	2	2	TTTA>T
ERR5749364	21987	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	11018	9.98E-4	0	6,10999,0,11	HIGH	NONE	FRAME_SHIFT	S	ggt/	G142	S	0.000998	0.922156	5	2	GT>G
ERR5749364	21990	PASS	TTTA	T	11018	0.996007	0	0,44,6,10968	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749364	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	14401	0.00125	0	0,14377,0,18	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749364	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26128	9.19E-4	0	11702,14371,10,14	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749364	23063	PASS	A	T	11713	0.868778	0	0,2,0,11655	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749364	23170	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	29446	4.08E-4	47	17710,11716,0,12	HIGH	NONE	FRAME_SHIFT	S	aaa/	K537	S	0.000408	0.975449	3	2	CA>C
ERR5749364	23271	PASS	C	A	17714	0.922829	0	2,0,17687,10	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749364	23403	PASS	A	G	17690	0.965743	0	0,6,0,17669	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749364	23522	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAACATGTCAACAACTCATA	G	12043	0.001079	0	12028,2,13,0	HIGH	NONE	FRAME_SHIFT	S	gaacatgtcaacaactcatat/	EHVNNSY654	S	0.00053	0.959726	5	2	GAACATGTCAACAACTCATA>G
ERR5749364	23604	PASS	C	A	12036	0.953722	0	6,0,12028,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749364	23664	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23882	0.001298	0	11857,11949,16,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCa/gTa	A701V	S	0.000837	0.918	2	2	C>T
ERR5749364	23709	PASS	C	T	12025	0.939543	0	0,2,0,12009	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749364	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	19675	9.66E-4	3	7625,12031,9,10	HIGH	NONE	FRAME_SHIFT	S	ttg/	L753	S	0.000334	0.080808	2	2	CT>C
ERR5749364	24127	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	18300	7.1E-4	2	10662,7630,9,4	HIGH	NONE	FRAME_SHIFT	S	aac/	N856	S	0.000324	0.111888	4	1	TA>T
ERR5749364	24432	PASS	A	T	25058	0.936747	18	9,0,14370,10661	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cAa/cTa	Q957L	S	0.935743	0.949489	1	1	A>T
ERR5749364	24506	PASS	T	G	14383	0.972746	0	7,0,14375,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749364	24914	PASS	G	C	32378	0.958212	0	1,1,16133,16217	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749364	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	23323	0.001243	46	17440,5830,40,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749364	25495	PASS	A	G	34804	0.899782	2	6,4,17286,17452	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Ata/Gta	I35V	orf3a	0.000735	0.911134	2	1	A>G
ERR5749364	25587	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	17546	0.001824	0	0,17514,0,32	HIGH	NONE	FRAME_SHIFT	ORF3a	aag/	K67	orf3a	0.000598	0.813206	6	2	CA>C
ERR5749364	25624	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22463	0.00138	21	4914,17516,1,30	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Cac/Tac	H78Y	orf3a	0.00089	0.983312	1	1	C>T
ERR5749364	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	4946	0.003841	262	4904,15,6,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749364	26013	PASS	C	T	27677	0.974528	0	4,0,27662,0	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	ttC/ttT	F207	orf3a	0.000839	0.974528	1	1	C>T
ERR5749364	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	10997	0.001091	0	0,10985,0,12	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749364	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	10998	0.005092	0	0,10937,0,56	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749364	26907	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27160	0.001325	0	27111,7,37,0	LOW	SILENT	SYNONYMOUS_CODING	M	Ctg/Ttg	L129	M	0.000817	0.976032	1	1	C>T
ERR5749364	27406	PASS	CTTTTCTTGGCACTGATAACACTCGCTACTTGTGAGCTTTATCACTACCAAGAGT	C	18217	0.998683	52	2,41,0,18193	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF7a	cttttcttggcactgataacactcgctacttgtgagctttatcactaccaagagtgt/cgt	LFLALITLATCELYHYQEC5R	orf7a	0.00059	0.998683	2	1	CTTTTCTTGGCACTGATAACACTCGCTACTTGTGAGCTTTATCACTACCAAGAGT>C
ERR5749364	27972	PASS	C	T	8015	0.90418	0	0,0,7952,32	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749364	28048	PASS	G	T	7988	0.921257	0	0,13,0,7972	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749364	28111	PASS	A	G	26071	0.978405	3	4,3,18061,7988	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749364	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18072	0.001107	0	17997,4,20,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749364	28270	PASS	TA	T	18013	0.123355	105	15803,14,2201,21	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749364	28273	PASS	AATGTC	A	17797	0.842333	131	2961,26,14982,9	HIGH	NONE	FRAME_SHIFT+START_LOST	N	atgtct/	MS1	N	0.000399	0.842333	4	1	AATGTC>A
ERR5749364	28273	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	AT	17797	0.001349	0	17637,35,24,0	HIGH	NONE	FRAME_SHIFT+START_LOST	N	atg/Tatg	M1Y?	N	0.000399	0.842333	4	1	A>AT
ERR5749364	28273	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	ATGTTTCT	17797	0.015789	0	17637,35,281,0	HIGH	NONE	FRAME_SHIFT+START_LOST	N	atg/TGTTTCTatg	M1CFY?	N	0.000399	0.842333	4	1	A>ATGTTTCT
ERR5749364	28281	PASS	A	T	17791	0.811871	73	213,7,16905,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749364	28282	PASS	T	TTCTA	17798	0.841611	170	2570,29,14971,8	HIGH	NONE	FRAME_SHIFT	N	aat/TCTAaat	N4SK?	N	0.001009	0.957283	3	2	T>TTCTA
ERR5749364	28881	PASS	G	A	10678	0.75398	11	7,1,5270,5248	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749364	28882	PASS	G	A	10678	0.82787	11	7,1,5339,5241	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749364	28883	PASS	G	C	10678	0.944653	0	0,0,5349,5322	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749364	28977	PASS	C	T	5436	0.932119	2147483647	0,0,0,5423	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749364	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	53368	0.001293	0	26840,26433,41,40	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749365	241	PASS	C	T	19572	0.84861	0	1,2,9710,9744	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749365	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	16990	0.001295	0	16975,2,22,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749365	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	16991	7.06E-4	0	16934,3,12,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749365	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	16991	0.00206	0	16934,3,35,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749365	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	16978	0.002474	0	15647,4,1236,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749365	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	16974	5.89E-4	0	16961,4,10,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttatg/gtg	VM84V	leader	0.000554	0.991848	4	1	GTTA>G
ERR5749365	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	16974	8.84E-4	0	16948,4,15,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749365	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	40829	0.001151	5	23773,17006,31,16	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749365	913	PASS	C	T	23783	0.914224	0	0,15,0,23738	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749365	2702	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	44341	8.57E-4	2147483647	44037,27,60,138	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F633V	nsp2	0.000632	0.333333	1	1	T>G
ERR5749365	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	87964	0.001523	2147483647	43931,40935,79,2807	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749365	3037	PASS	C	T	25850	0.816364	58	2,26,12911,12705	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749365	3267	PASS	C	T	20338	0.96568	0	11,0,20317,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749365	4668	PASS	C	T	16928	0.970109	0	1,0,16913,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S650F	nsp3	0.002266	0.970109	2	1	C>T
ERR5749365	5388	PASS	C	A	7995	0.953346	2147483647	0,0,7990,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749365	5986	PASS	C	T	16178	0.972432	0	1,0,16169,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749365	6954	PASS	T	C	25285	0.827922	0	0,3,0,25157	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749365	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	36998	0.001081	126	17864,19094,40,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749365	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	16805	0.001428	0	16760,0,36,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749365	11287	PASS	GTCTGGTTTT	G	16809	0.997799	0	0,37,0,16772	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749365	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	37630	8.5E-4	2	22266,15310,18,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749365	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	10460	8.6E-4	0	10451,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749365	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	35439	0.001157	0	17705,17650,22,23	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749365	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	16516	0.004904	2147483647	16149,97,12,255	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749365	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	32152	7.78E-4	0	16121,16027,13,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749365	14408	PASS	C	T	32152	0.827942	6	1,4,16044,15854	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749365	14676	PASS	C	T	14382	0.785913	0	6,0,14318,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749365	15096	PASS	T	C	25806	0.967682	0	0,1,16,25782	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaT/aaC	N552	RdRp	0.941667	0.970182	1	1	T>C
ERR5749365	15279	PASS	C	T	26051	0.883958	0	5,0,25998,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749365	16176	PASS	T	C	24264	0.980424	0	0,0,12355,11900	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749365	17766	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13658	0.001538	0	13624,2,24,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V510	helicase	0.000768	0.920632	2	2	C>T
ERR5749365	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	27571	4.35E-4	0	27559,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749365	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	35261	0.002411	0	35144,3,90,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749365	20091	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	35194	5.97E-4	0	6,35167,0,21	HIGH	NONE	FRAME_SHIFT	ORF1ab	caa/Acaa	Q159T?	endoR	0.000368	0.051583	1	1	C>CA
ERR5749365	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30877	0.001004	0	30798,0,32,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749365	20844	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	52106	6.91E-4	7	21188,30811,11,27	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P62	MethTr	0.000293	0.905571	5	2	C>T
ERR5749365	21361	PASS	A	G	35045	0.958339	131	4,7,2,35004	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Aat/Gat	N235D	MethTr	0.001101	0.958339	1	1	A>G
ERR5749365	21764	PASS	ATACATG	A	16530	0.994737	22	87,1,16443,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749365	21990	PASS	TTTA	T	16540	0.998186	0	0,30,7,16503	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749365	23063	PASS	A	T	12495	0.867867	0	0,5,0,12427	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749365	23271	PASS	C	A	24012	0.913751	0	2,0,23988,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749365	23403	PASS	A	G	24006	0.966008	0	0,3,0,23981	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749365	23604	PASS	C	A	18391	0.919961	0	11,0,18341,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749365	23709	PASS	C	T	18372	0.938874	0	0,8,1,18331	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749365	23975	PASS	A	G	41309	0.745649	0	4,3,20637,20340	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ata/Gta	I805V	S	0.745649	0.745649	1	1	A>G
ERR5749365	24506	PASS	T	G	17594	0.973059	0	8,0,17579,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749365	24914	PASS	G	C	37684	0.958125	0	0,1,18757,18889	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749365	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	27302	4.76E-4	0	27289,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749365	26060	PASS	C	T	65613	0.800482	0	10,0,65117,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aCt/aTt	T223I	orf3a	0.000459	0.822477	2	2	C>T
ERR5749365	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	12757	0.001254	0	0,12739,0,16	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749365	27297	PASS	C	T	19510	0.91266	0	4,0,19465,0	LOW	SILENT	SYNONYMOUS_CODING	ORF6	atC/atT	I32	orf6	0.000978	0.91266	1	1	C>T
ERR5749365	27567	PASS	CTTTAGCACTCAA	C	21499	0.989953	122	189,6,21283,0	MODERATE	NONE	CODON_DELETION	ORF7a	agcactcaattt/	STQF60	orf7a	0.000449	0.998291	4	1	CTTTAGCACTCAA>C
ERR5749365	27567	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTTTAGCACTCAATTTGCT	C	21499	9.3E-4	0	189,6,20,0	MODERATE	NONE	CODON_DELETION	ORF7a	agcactcaatttgctttt/	STQFAF60	orf7a	0.000449	0.998291	4	1	CTTTAGCACTCAATTTGCT>C
ERR5749365	27741	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21498	0.001163	0	2,21427,0,26	LOW	SILENT	SYNONYMOUS_CODING	ORF7a	ctC/ctT	L116	orf7a	0.000363	0.954278	3	2	C>T
ERR5749365	27972	PASS	C	T	12498	0.894303	45	1,2,12411,38	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749365	28048	PASS	G	T	12472	0.91092	0	0,23,0,12446	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749365	28095	PASS	A	T	12484	0.945851	126	4,6,0,12455	HIGH	NONSENSE	STOP_GAINED	ORF8	Aaa/Taa	K68*	orf8	0.002672	0.967672	2	2	A>T
ERR5749365	28111	PASS	A	G	12484	0.975088	0	0,1,4,12477	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749365	28250	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TCTG	18678	0.002516	0	18633,1,47,0	MODERATE	NONE	CODON_INSERTION	ORF8	ttc/CTGttc	F120LF	orf8	0.000494	0.993968	5	3	T>TCTG
ERR5749365	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	18669	0.002571	0	18628,1,48,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749365	28270	PASS	TA	T	17596	0.999716	0	0,5,5,17586	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749365	28280	PASS	G	C	17599	0.914484	0	0,3,5,17571	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749365	28281	PASS	A	T	17599	0.920961	0	0,4,5,17566	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749365	28282	PASS	T	A	17601	0.949435	0	0,10,5,17584	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749365	28881	PASS	G	A	15114	0.776631	9	4,0,7496,7442	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749365	28882	PASS	G	A	15114	0.834193	0	3,2,7570,7400	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749365	28883	PASS	G	C	15114	0.945018	0	1,1,7574,7522	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749365	28977	PASS	C	T	7685	0.927001	0	0,2,1,7669	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749365	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	49198	8.94E-4	0	24692,24433,31,30	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749365	29686	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22100	0.001357	0	10999,11021,19,19	.	.	.	.	.	.	.	0.001045	0.802514	2	1	C>T
ERR5749366	241	PASS	C	T	10450	0.856842	0	1,1,5184,5216	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749366	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	10464	0.002294	0	10425,3,24,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749366	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10459	0.001339	0	9959,4,443,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749366	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	10459	0.001147	83	10446,1,9,3	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749366	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	10457	8.61E-4	0	10441,4,9,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749366	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	31673	7.89E-4	3	21170,10469,19,6	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749366	913	PASS	C	T	21184	0.91064	0	0,14,1,21146	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749366	1461	PASS	A	G	39646	0.905968	9	7,2,19582,19951	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K219R	nsp2	0.000518	0.90899	2	2	A>G
ERR5749366	1599	PASS	G	T	36755	0.955952	33	1,17,16533,20183	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGt/gTt	G265V	nsp2	0.001427	0.96468	2	1	G>T
ERR5749366	3037	PASS	C	T	18592	0.804808	81	1,31,9291,9134	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749366	3267	PASS	C	T	20537	0.964454	0	3,0,20518,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749366	3335	PASS	G	A	39686	0.867812	36	24,4,20374,19094	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E206K	nsp3	0.001289	0.891976	4	3	G>A
ERR5749366	4999	PASS	C	T	12044	0.935902	207	1,6,12026,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N760	nsp3	0.001692	0.947468	1	1	C>T
ERR5749366	5388	PASS	C	A	5006	0.955254	2147483647	0,0,5003,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749366	5986	PASS	C	T	12172	0.972642	2147483647	0,0,12165,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749366	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11559	0.001298	0	0,11435,0,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749366	6954	PASS	T	C	22971	0.820818	0	0,7,0,22820	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749366	8092	PASS	C	T	24909	0.063953	0	23134,0,1756,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ctC/ctT	L1791	nsp3	0.000539	0.063953	3	2	C>T
ERR5749366	9541	PASS	C	T	29106	0.950457	4	1,4,14287,14801	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ctC/ctT	L329	nsp4	0.000346	0.955771	2	2	C>T
ERR5749366	10165	PASS	C	T	16167	0.961898	263	4,8,16127,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y37	3Cpro	0.000632	0.976163	2	2	C>T
ERR5749366	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	19601	0.001531	0	19547,0,49,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749366	11287	PASS	GTCTGGTTTT	G	19599	0.997959	0	0,40,0,19559	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749366	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	36165	8.02E-4	0	22512,13600,20,11	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749366	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30585	0.001144	1	15275,15217,20,23	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749366	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12249	0.004735	2147483647	11943,99,7,195	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749366	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	23792	8.83E-4	0	11925,11860,11,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749366	14408	PASS	C	T	23792	0.833768	11	2,8,11858,11715	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749366	14676	PASS	C	T	13316	0.829979	0	3,0,13268,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749366	15279	PASS	C	T	22611	0.883464	0	4,0,22563,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749366	16176	PASS	T	C	19787	0.980088	4	3,1,8959,10813	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749366	17615	PASS	A	G	14458	0.912436	0	0,0,1,14429	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749366	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	22009	5.91E-4	0	21995,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749366	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28131	0.002168	0	28056,0,65,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749366	21302	PASS	C	T	28264	0.831128	0	0,46,0,28090	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCa/cTa	P215L	MethTr	0.001031	0.843069	1	1	C>T
ERR5749366	21304	PASS	C	A	28264	0.59988	0	0,1049,0,27194	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgc/Agc	R216S	MethTr	0.000411	0.605296	3	2	C>A
ERR5749366	21304	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	28264	9.55E-4	0	0,28237,0,27	HIGH	NONE	FRAME_SHIFT	ORF1ab	cgc/	R216	MethTr	0.000411	0.605296	3	2	CG>C
ERR5749366	21305	PASS	G	A	28264	0.679062	0	0,3,0,27743	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cGc/cAc	R216H	MethTr	0.000727	0.703943	1	1	G>A
ERR5749366	21375	PASS	G	A	28439	0.837758	1026	36,1,19,28251	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttG/ttA	L239	MethTr	0.002365	0.858793	2	2	G>A
ERR5749366	21727	PASS	C	T	11759	0.843949	137	2,4,11734,0	LOW	SILENT	SYNONYMOUS_CODING	S	ttC/ttT	F55	S	0.000896	0.878141	2	2	C>T
ERR5749366	21762	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTATACA	C	11754	0.001787	0	11733,0,21,0	MODERATE	NONE	CODON_DELETION	S	atacat/	IH68	S	0.001297	0.875707	2	2	CTATACA>C
ERR5749366	21764	PASS	ATACATG	A	11754	0.997022	0	35,0,11719,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749366	21990	PASS	TTTA	T	11759	0.998554	0	0,17,3,11739	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749366	23063	PASS	A	T	3692	0.857801	0	0,1,0,3674	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749366	23191	PASS	C	T	22353	0.973337	32	3,1,22328,2	LOW	SILENT	SYNONYMOUS_CODING	S	ttC/ttT	F543	S	0.000538	0.973337	2	2	C>T
ERR5749366	23271	PASS	C	A	22344	0.907313	0	4,0,22314,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749366	23403	PASS	A	G	22328	0.963588	0	0,2,0,22306	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749366	23604	PASS	C	A	14602	0.944597	0	6,0,14588,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749366	23709	PASS	C	T	14585	0.931025	0	0,6,1,14554	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749366	24506	PASS	T	G	18699	0.972619	0	7,0,18687,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749366	24914	PASS	G	C	33021	0.958572	0	0,1,16438,16556	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749366	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	24277	0.001977	93	16055,8161,54,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749366	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	22042	0.001497	311	21938,22,20,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749366	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	22006	7.27E-4	0	21990,0,16,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749366	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	22154	0.001354	1222	21843,125,73,78	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749366	26270	PASS	C	T	57175	0.930791	5	2,4,10678,46448	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	aCa/aTa	T9I	E	0.000586	0.930791	3	2	C>T
ERR5749366	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	11038	0.001903	0	1,11016,0,21	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749366	27643	PASS	C	T	21378	0.774301	24	6,1,21155,9	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Cct/Tct	P84S	orf7a	0.00166	0.858006	2	1	C>T
ERR5749366	27972	PASS	C	T	11021	0.898013	58	2,3,10913,57	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749366	28048	PASS	G	T	10970	0.923974	0	0,11,0,10951	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749366	28111	PASS	A	G	29631	0.978637	4	2,3,18645,10975	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749366	28250	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TCTG	18637	5.37E-4	0	18628,1,10,0	MODERATE	NONE	CODON_INSERTION	ORF8	ttc/CTGttc	F120LF	orf8	0.000494	0.993968	5	3	T>TCTG
ERR5749366	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	18633	6.98E-4	0	18623,1,13,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749366	28270	PASS	TA	T	36096	0.994681	447	186,6,18387,17517	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749366	28280	PASS	G	C	36013	0.935246	14	8,1,18432,17490	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749366	28281	PASS	A	T	36013	0.916669	25	21,5,18427,17501	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749366	28282	PASS	T	A	36014	0.909757	13	21,9,18383,17513	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749366	28881	PASS	G	A	17367	0.778718	12	5,0,8619,8509	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749366	28882	PASS	G	A	17367	0.833189	9	4,0,8704,8514	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749366	28883	PASS	G	C	17367	0.944377	0	1,0,8715,8638	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749366	28977	PASS	C	T	8844	0.923338	0	0,9,5,8813	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749366	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	31608	7.91E-4	90	22766,8792,4,23	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749366	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	45191	0.001151	0	22698,22412,33,33	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749367	241	PASS	C	T	6318	0.873061	0	0,0,3146,3144	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749367	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	11699	8.55E-4	0	11690,0,10,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749367	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	11699	6.84E-4	0	11667,0,8,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749367	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	11699	0.00171	0	11667,0,20,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749367	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	11706	0.001025	0	11680,14,12,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749367	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	11706	6.83E-4	0	11681,14,8,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749367	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20396	0.001373	0	0,20351,0,30	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749367	913	PASS	C	T	20397	0.911016	0	0,11,0,20367	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749367	1813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	19837	0.001462	0	0,19777,0,38	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcA	A336	nsp2	0.001022	0.152738	4	2	T>A
ERR5749367	2185	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	25014	5.2E-4	0	5,24996,0,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L462S?	nsp2	0.000441	0.963529	4	3	G>GT
ERR5749367	3037	PASS	C	T	19334	0.807541	67	0,22,9671,9490	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749367	3177	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	29293	0.001229	76	19512,9734,45,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cAt	P153H	nsp3	0.000773	0.96008	3	2	C>A
ERR5749367	3267	PASS	C	T	19557	0.96886	0	2,0,19543,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749367	4237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTA	T	36787	3.26E-4	0	18418,18358,6,6	HIGH	NONE	FRAME_SHIFT	ORF1ab	ata/	I508	nsp3	0.000302	0.918634	2	2	TTA>T
ERR5749367	4280	PASS	G	A	18428	0.847352	0	0,1,0,18309	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gta/Ata	V521I	nsp3	0.002822	0.896067	2	1	G>A
ERR5749367	5388	PASS	C	A	5411	0.955831	0	1,0,5406,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749367	5986	PASS	C	T	12867	0.978394	0	1,0,12862,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749367	6954	PASS	T	C	21206	0.817457	0	0,4,0,21098	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749367	7070	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	36038	9.71E-4	106	14725,21271,36,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggc/Tgc	G1451C	nsp3	0.000698	0.101434	3	1	G>T
ERR5749367	8084	PASS	G	A	23395	0.918059	0	11,0,23361,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E1789K	nsp3	0.000543	0.923413	4	2	G>A
ERR5749367	8084	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GA	23395	0.020004	0	22927,0,468,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctc/Actc	L1791T?	nsp3	0.000543	0.923413	4	2	G>GA
ERR5749367	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	21575	0.001576	0	21511,0,48,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749367	11199	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	42963	8.38E-4	0	21340,21429,21,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCc/gTc	A76V	nsp6	0.000309	0.056758	3	2	C>T
ERR5749367	11287	PASS	GTCTGGTTTT	G	21573	0.998239	0	0,38,2,21533	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749367	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	32611	0.001257	0	16288,16229,21,22	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749367	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	4198	0.005002	1228	4075,40,3,73	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749367	14408	PASS	C	T	8120	0.844089	0	1,1,4051,4018	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749367	14676	PASS	C	T	13274	0.816634	0	4,0,13230,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749367	15279	PASS	C	T	19952	0.886227	0	5,0,19922,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749367	16176	PASS	T	C	19836	0.979331	0	0,0,8476,11349	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749367	17615	PASS	A	G	16139	0.910217	0	0,0,1,16089	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749367	19343	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	19508	6.15E-4	0	19486,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F436	ExoN	0.000519	0.192257	7	2	CT>C
ERR5749367	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24753	0.001131	0	24706,0,29,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749367	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	32050	8.42E-4	0	31983,0,27,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749367	21764	PASS	ATACATG	A	13769	0.998039	0	27,0,13742,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749367	21990	PASS	TTTA	T	13775	0.99833	0	0,23,5,13747	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749367	23063	PASS	A	T	15071	0.857806	0	0,3,0,14990	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749367	23271	PASS	C	A	22071	0.941824	0	2,0,22054,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749367	23403	PASS	A	G	22063	0.96936	0	0,8,0,22037	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749367	23604	PASS	C	A	16568	0.943023	0	13,0,16549,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749367	23709	PASS	C	T	16551	0.939279	0	0,7,1,16518	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749367	23817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	30459	8.54E-4	0	13863,16552,14,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTt/cCt	L752P	S	0.000646	0.066832	1	1	T>C
ERR5749367	24506	PASS	T	G	18506	0.975089	0	10,0,18493,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749367	24914	PASS	G	C	42651	0.961079	3	1,0,21239,21383	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749367	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	28030	0.001498	53	19392,8579,48,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749367	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	10869	0.002392	465	10806,16,7,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749367	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	10832	0.001477	0	10816,0,16,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749367	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	13461	8.17E-4	0	0,13450,0,11	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749367	27972	PASS	C	T	9859	0.902221	20	1,1,9782,39	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749367	28048	PASS	G	T	9825	0.924886	0	0,5,0,9815	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749367	28111	PASS	A	G	31014	0.978107	14	3,6,21162,9825	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749367	28270	PASS	TA	T	41013	0.995416	416	186,9,20901,19924	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749367	28280	PASS	G	C	40935	0.935825	21	11,1,20943,19909	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749367	28281	PASS	A	T	40935	0.901136	25	23,6,20913,19907	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749367	28282	PASS	T	A	40939	0.918195	0	16,14,20890,19923	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749367	28881	PASS	G	A	14360	0.780362	12	5,0,7139,7051	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749367	28882	PASS	G	A	14360	0.827228	6	5,1,7204,7030	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749367	28883	PASS	G	C	14360	0.947006	6	0,2,7216,7133	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749367	28977	PASS	C	T	7314	0.91195	0	0,1,0,7271	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749367	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	40074	9.98E-4	210	32721,7266,7,38	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749367	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	65077	0.001106	0	32662,32299,47,45	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749368	241	PASS	C	T	44	0.886364	0	0,0,22,22	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749368	913	PASS	C	T	580	0.922414	2147483647	0,0,0,580	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749368	1862	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	759	0.013175	0	0,746,0,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Att	L353I	nsp2	0.000585	0.936867	4	2	C>A
ERR5749368	2498	PASS	G	T	311	0.07717	0	0,286,0,25	HIGH	NONSENSE	STOP_GAINED	ORF1ab	Gaa/Taa	E565*	nsp2	0.001031	0.07717	2	2	G>T
ERR5749368	3037	PASS	C	T	220	0.840909	0	0,0,110,109	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749368	3267	PASS	C	T	840	0.975	2147483647	0,0,839,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749368	4317	PASS	G	C	228	0.118421	0	0,201,0,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aGt/aCt	S533T	nsp3	0.001619	0.118421	2	1	G>C
ERR5749368	5388	PASS	C	A	79	0.949367	2147483647	0,0,79,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749368	5467	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	157	0.025478	0	76,75,3,3	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y916	nsp3	0.025478	0.860673	1	1	C>T
ERR5749368	5986	PASS	C	T	433	0.967667	2147483647	0,0,433,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749368	6696	PASS	C	CT	313	0.14377	0	0,268,0,45	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L1328S?	nsp3	0.000731	0.14377	4	2	C>CT
ERR5749368	6954	PASS	T	C	454	0.848018	2147483647	0,0,0,453	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749368	8602	PASS	G	T	250	0.056	0	0,236,0,14	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtG/gtT	V16	nsp4	0.000932	0.056	3	2	G>T
ERR5749368	8653	PASS	G	T	68	0.132353	0	58,0,10,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atT	M33I	nsp4	0.001328	0.132353	2	2	G>T
ERR5749368	10675	PASS	G	T	656	0.134146	0	0,560,0,96	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tgG/tgT	W207C	3Cpro	0.001625	0.134146	2	1	G>T
ERR5749368	10704	PASS	G	T	656	0.158537	0	0,547,0,109	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aGg/aTg	R217M	3Cpro	0.000771	0.158537	2	1	G>T
ERR5749368	11020	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5	1.0	2147483647	0,0,0,5	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ctC/ctT	L16	nsp6	0.00116	1	1	1	C>T
ERR5749368	14408	PASS	C	T	30	0.866667	0	0,0,15,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749368	14478	PASS	C	T	15	1.0	2147483647	0,0,0,15	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y346	RdRp	1	1	1	1	C>T
ERR5749368	14676	PASS	C	T	320	0.746875	0	1,0,318,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749368	15069	PASS	T	G	606	0.077558	0	275,275,28,28	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaT/aaG	N543K	RdRp	0.077558	0.077558	1	1	T>G
ERR5749368	15279	PASS	C	T	476	0.886555	2147483647	0,0,476,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749368	16176	PASS	T	C	577	0.974003	0	0,0,62,515	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749368	17081	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	578	0.019031	0	0,561,0,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGa/gTa	G282V	helicase	0.001926	0.120301	3	2	G>T
ERR5749368	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	2321	0.002154	0	2316,0,5,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749368	19067	PASS	A	G	812	0.076355	0	745,0,67,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cAa/cGa	Q343R	ExoN	0.004122	0.076355	1	1	A>G
ERR5749368	19092	PASS	T	C	812	0.078818	0	745,0,66,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taT/taC	Y351	ExoN	0.078818	0.078818	1	1	T>C
ERR5749368	20823	PASS	C	T	802	0.982544	0	0,0,638,164	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N55	MethTr	0.001138	0.982544	2	2	C>T
ERR5749368	21614	PASS	C	T	197	0.949239	2147483647	0,0,0,197	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L18F	S	0.001194	0.949239	2	2	C>T
ERR5749368	21764	PASS	ATACATG	A	884	0.996606	0	3,0,881,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749368	21990	PASS	TTTA	T	885	0.99887	0	0,1,1,883	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749368	23063	PASS	A	T	533	0.866792	2147483647	0,0,0,529	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749368	23271	PASS	C	A	383	0.921671	2147483647	0,0,383,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749368	23403	PASS	A	G	383	0.981723	2147483647	0,0,0,383	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749368	23604	PASS	C	A	536	0.938433	2147483647	0,0,536,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749368	23709	PASS	C	T	536	0.940298	2147483647	0,0,0,536	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749368	23712	PASS	A	G	536	0.958955	0	0,1,0,535	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aAt/aGt	N717S	S	0.000679	0.958955	3	2	A>G
ERR5749368	24506	PASS	T	G	580	0.984483	2147483647	0,0,580,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749368	24914	PASS	G	C	2251	0.957797	0	0,0,1119,1129	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749368	25395	PASS	G	T	3587	0.079175	0	3291,0,296,0	HIGH	MISSENSE	START_LOST	ORF3a	atG/atT	M1I	orf3a	0.001616	0.079175	2	1	G>T
ERR5749368	26193	PASS	G	A	1094	0.051188	0	0,1034,0,59	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	ccG/ccA	P267	orf3a	0.002649	0.051188	1	1	G>A
ERR5749368	26208	PASS	C	T	1094	0.068556	0	0,1010,0,82	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	agC/agT	S272	orf3a	0.000315	0.922222	2	2	C>T
ERR5749368	26425	PASS	CGTG	C	614	0.066775	0	0,573,0,41	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	E	cgtgtt/ctt	RV61L	E	0.066775	0.066775	1	1	CGTG>C
ERR5749368	27371	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1623	0.028343	0	0,1574,0,48	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF6	cCa/cTa	P57L	orf6	0.00148	0.066731	2	2	C>T
ERR5749368	27404	PASS	TTCTTTTCTTGGCACTGATAACACTCGCTACTTGTGAGCTTTATCACTACCAAGAGTG	T	1623	0.998768	0	0,2,0,1621	MODERATE	NONE	CODON_DELETION	ORF7a	cttttcttggcactgataacactcgctacttgtgagctttatcactaccaagagtgt/	LFLALITLATCELYHYQEC5	orf7a	0.001441	0.998768	2	2	TTCTTTTCTTGGCACTGATAACACTCGCTACTTGTGAGCTTTATCACTACCAAGAGTG>T
ERR5749368	27972	PASS	C	T	101	0.90099	0	0,0,99,1	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749368	28048	PASS	G	T	101	0.920792	2147483647	0,0,0,101	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749368	28111	PASS	A	G	3181	0.982395	0	2,0,3077,101	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749368	28270	PASS	TA	T	5999	0.995499	54	26,2,3046,2926	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749368	28280	PASS	G	C	5988	0.938544	3	2,0,3047,2922	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749368	28281	PASS	A	T	5988	0.920341	15	6,0,3047,2926	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749368	28282	PASS	T	A	5988	0.906313	0	4,3,3036,2924	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749368	28881	PASS	G	A	53	0.773585	0	0,0,25,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749368	28882	PASS	G	A	53	0.716981	0	0,0,26,25	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749368	28883	PASS	G	C	53	0.981132	0	0,0,26,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749368	28977	PASS	C	T	28	0.892857	2147483647	0,0,0,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749369	241	PASS	C	T	11534	0.857465	0	0,0,5732,5730	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749369	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	11067	0.006144	0	10988,10,68,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749369	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	11074	0.001716	0	10877,17,19,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749369	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	11074	0.004064	0	10877,17,45,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749369	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	11074	0.010204	0	10877,17,113,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749369	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	11075	0.001806	5	10013,27,724,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749369	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	11075	0.004063	0	11003,27,45,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749369	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	11075	0.003612	0	10998,28,40,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749369	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	11079	0.003249	0	11001,33,36,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749369	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATGGTTG	T	11079	7.22E-4	0	11001,33,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	atggttgag/	MVE85	leader	0.000587	0.476744	4	1	TATGGTTG>T
ERR5749369	520	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTT	G	11113	9.0E-4	0	11035,68,10,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttgag/gag	VE86E	leader	0.000583	0.051154	1	1	GGTT>G
ERR5749369	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	28567	8.4E-4	50	17475,11063,24,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749369	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	28567	5.95E-4	2	17383,11017,12,5	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749369	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	28567	0.004691	23	17383,11017,98,36	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749369	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTTG	A	28567	3.85E-4	1	17383,11017,6,5	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcatttgac/	KSFD141	leader	0.000303	0.999303	4	1	AAAGTCATTTG>A
ERR5749369	843	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34909	0.007505	0	17317,17271,148,149	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P13L	nsp2	0.000301	0.050923	4	2	C>T
ERR5749369	913	PASS	C	T	17494	0.902138	0	0,11,0,17444	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749369	2453	PASS	C	T	12951	0.724809	0	0,14,0,12716	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L550F	nsp2	0.00429	0.842201	2	2	C>T
ERR5749369	2509	PASS	C	T	12975	0.937418	135	4,3,0,12941	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P568	nsp2	0.001408	0.949382	1	1	C>T
ERR5749369	2702	PASS	T	G	93	0.129032	17	5,37,0,48	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F633V	nsp2	0.000632	0.333333	1	1	T>G
ERR5749369	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	19009	0.002788	0	5,17691,0,1290	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749369	3037	PASS	C	T	17061	0.82164	42	0,14,8532,8410	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749369	3267	PASS	C	T	18078	0.971014	0	2,0,18063,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749369	3877	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	18488	0.009303	0	13725,0,4751,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcG	A386	nsp3	0.000588	0.960227	2	1	T>G
ERR5749369	5192	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11207	0.004194	0	0,11141,0,56	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Ctg/Ttg	L825	nsp3	0.003789	0.912192	1	1	C>T
ERR5749369	5388	PASS	C	A	5539	0.952699	0	0,0,5530,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749369	5628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17063	0.009904	0	16873,0,186,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aTg	T970M	nsp3	0.000561	0.973644	3	2	C>T
ERR5749369	5944	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11671	0.002228	0	11630,3,28,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D1075	nsp3	0.002228	0.977177	1	1	C>T
ERR5749369	5986	PASS	C	T	11668	0.97686	0	1,0,11660,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749369	6954	PASS	T	C	20656	0.830993	0	0,2,1,20545	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749369	7070	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	37555	9.59E-4	115	16780,20726,37,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggc/Agc	G1451S	nsp3	0.000698	0.101434	3	1	G>A
ERR5749369	7113	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16832	0.001129	0	16785,6,24,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T1465I	nsp3	0.001129	0.920551	1	1	C>T
ERR5749369	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	24120	0.001493	79	14418,9666,36,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749369	10969	PASS	C	T	9706	0.918813	2147483647	0,0,0,9690	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F305	3Cpro	0.004039	0.921996	1	1	C>T
ERR5749369	11073	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TC	T	19962	7.51E-4	0	19945,2,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttc/	F34	nsp6	0.000385	0.092251	6	2	TC>T
ERR5749369	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19962	0.003807	0	19838,2,85,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749369	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	19955	0.001453	0	19908,0,40,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749369	11287	PASS	GTCTGGTTTT	G	19945	0.994184	0	0,116,0,19829	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749369	11671	PASS	C	T	20489	0.94436	131	8,4,20451,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	cgC/cgT	R233	nsp6	0.024564	0.94436	1	1	C>T
ERR5749369	11896	PASS	A	G	36100	0.98313	2	6,11,15598,20476	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caA/caG	Q18	nsp7	0.98313	0.98313	1	1	A>G
ERR5749369	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	18252	0.001205	0	18200,0,22,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749369	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	31069	0.001706	1	15509,15459,28,31	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749369	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	9130	0.004272	2205	8840,134,8,141	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749369	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	17578	0.002503	0	8815,8739,22,22	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749369	14408	PASS	C	T	17578	0.851234	3	2,4,8751,8660	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749369	14676	PASS	C	T	11861	0.805666	0	3,0,11830,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749369	15279	PASS	C	T	19278	0.891949	0	2,0,19259,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749369	16176	PASS	T	C	19064	0.981064	8	0,4,9003,10046	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749369	16508	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	21026	0.001046	0	20983,5,35,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGt/gTt	G91V	helicase	0.000561	0.074909	2	2	G>T
ERR5749369	17762	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12659	0.013587	0	12465,0,180,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A509V	helicase	0.000697	0.912542	2	2	C>T
ERR5749369	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	23749	0.001053	0	23724,0,25,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749369	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24945	0.002245	0	24856,0,57,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749369	20578	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	27519	8.72E-4	0	27458,0,55,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtg/Ttg	V320L	endoR	0.00085	0.958277	3	1	G>T
ERR5749369	21123	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	48061	3.33E-4	14	28074,19971,5,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F156	MethTr	0.000257	0.90982	5	2	GT>G
ERR5749369	21764	PASS	ATACATG	A	11821	0.996785	0	38,0,11783,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749369	21990	PASS	TTTA	T	11824	0.996955	0	0,36,3,11785	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749369	22290	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	20086	8.46E-4	0	0,20069,0,17	HIGH	NONE	FRAME_SHIFT	S	tta/	L244	S	0.000389	0.578006	2	2	CT>C
ERR5749369	23063	PASS	A	T	13404	0.85855	0	0,3,2,13317	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749369	23271	PASS	C	A	19402	0.920988	0	3,0,19378,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749369	23403	PASS	A	G	19393	0.966173	0	0,3,0,19373	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749369	23426	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTT	G	19414	5.67E-4	0	1,19402,0,11	HIGH	NONE	FRAME_SHIFT	S	gtt/	V622	S	0.000428	0.916192	4	2	GTT>G
ERR5749369	23522	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTA	G	14729	6.11E-4	0	14706,6,9,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	gaacatgtcaacaactcatatgagtgtgacatacccattggtgcaggtata/gta	EHVNNSYECDIPIGAGI654V	S	0.00053	0.959726	5	2	GAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTA>G
ERR5749369	23604	PASS	C	A	14715	0.93809	0	13,0,14693,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749369	23709	PASS	C	T	14711	0.925906	0	0,3,16,14664	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749369	24010	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATTTATTGAAGATCTAC	A	14886	8.06E-4	0	127,14744,0,12	HIGH	NONE	FRAME_SHIFT	S	attgaagatctacttttc/	IEDLLF818	S	0.000455	0.926398	4	2	ATTTATTGAAGATCTAC>A
ERR5749369	24506	PASS	T	G	16586	0.974255	0	8,0,16573,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749369	24914	PASS	G	C	36097	0.960911	0	0,1,17974,18091	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749369	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	14981	0.002203	436	14888,26,13,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749369	25912	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	14955	0.001337	0	18,14902,0,34	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Ggc/Tgc	G174C	orf3a	0.001337	0.979852	2	1	G>T
ERR5749369	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	40785	4.41E-4	0	6,40746,0,18	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749369	26526	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	11409	0.001665	0	1,11371,0,29	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Gca/Tca	A2S	M	0.001224	0.951192	3	1	G>T
ERR5749369	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	11829	0.001606	0	4,11799,0,19	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749369	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	11829	0.001353	0	4,11809,0,16	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749369	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	11827	0.006257	0	1,11743,0,74	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749369	27972	PASS	C	T	9447	0.908648	18	1,1,9349,59	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749369	28048	PASS	G	T	9406	0.915267	0	0,18,0,9381	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749369	28111	PASS	A	G	29286	0.977908	2	3,0,19857,9413	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749369	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	19844	7.56E-4	0	19827,8,15,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749369	28270	PASS	TA	T	38352	0.994837	380	191,14,19608,18546	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749369	28280	PASS	G	C	38282	0.936785	6	11,5,19656,18535	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749369	28281	PASS	A	T	38282	0.907581	19	27,10,19644,18525	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749369	28282	PASS	T	A	38283	0.913173	22	25,8,19622,18545	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749369	28881	PASS	G	A	12317	0.756597	9	3,0,6039,6101	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749369	28882	PASS	G	A	12316	0.823969	0	2,2,6111,6095	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749369	28883	PASS	G	C	12316	0.947061	0	0,0,6119,6184	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749369	28977	PASS	C	T	6195	0.925908	0	0,1,0,6175	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749369	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	55830	9.85E-4	0	28025,27714,32,32	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749370	241	PASS	C	T	20711	0.861813	1	2,4,10267,10369	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749370	292	PASS	C	T	10432	0.947949	0	0,3,0,10420	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N9	leader	0.939339	0.96124	1	1	C>T
ERR5749370	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	12591	0.003415	0	12534,1,43,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749370	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12587	0.001668	0	11715,1,793,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749370	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	12587	0.001033	0	12573,1,13,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749370	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	37240	3.76E-4	1	24608,12606,10,4	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749370	913	PASS	C	T	24607	0.919657	0	0,6,0,24568	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749370	1510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	24697	0.003401	0	0,24387,0,91	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G235	nsp2	0.002159	0.937304	1	1	T>C
ERR5749370	2618	PASS	A	G	45586	0.982166	0	3,0,45562,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Att/Gtt	I605V	nsp2	0.982166	0.982166	1	1	A>G
ERR5749370	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	90662	0.001268	2147483647	45210,42556,97,2545	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749370	3037	PASS	C	T	24672	0.812054	44	2,21,12330,12162	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749370	3267	PASS	C	T	23276	0.970742	0	1,0,23262,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749370	5388	PASS	C	A	7520	0.958511	2147483647	0,0,7515,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749370	5986	PASS	C	T	16037	0.976118	2147483647	0,0,16027,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749370	6954	PASS	T	C	28659	0.823581	0	0,2,0,28500	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749370	9430	PASS	C	T	18042	0.954329	0	0,2,7,18023	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I292	nsp4	0.001411	0.960894	1	1	C>T
ERR5749370	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	35301	5.95E-4	65	17210,18070,21,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749370	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	19550	0.001381	0	19493,4,42,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749370	11287	PASS	GTCTGGTTTT	G	19548	0.99821	0	0,34,1,19512	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749370	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	13863	0.003246	3183	13584,97,6,174	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749370	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	27015	5.92E-4	0	13566,13454,8,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749370	14408	PASS	C	T	27015	0.858708	7	2,6,13493,13349	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749370	14676	PASS	C	T	14854	0.758987	0	8,0,14798,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749370	15025	PASS	G	A	24028	0.946354	0	15,0,23951,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gca/Aca	A529T	RdRp	0.000933	0.946354	3	2	G>A
ERR5749370	15279	PASS	C	T	26521	0.895894	0	7,0,26473,2	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749370	16176	PASS	T	C	22576	0.983478	0	1,1,10645,11921	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749370	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	24911	4.82E-4	0	24899,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749370	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	35217	0.00159	0	35132,0,59,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749370	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	32076	9.04E-4	0	31989,0,67,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggA	G336	endoR	0.000719	0.968531	2	1	C>A
ERR5749370	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	38763	5.68E-4	0	19329,19424,10,12	HIGH	NONE	FRAME_SHIFT	S	ctt/Tctt	L5S?	S	0.000394	0.091869	4	1	G>GT
ERR5749370	21764	PASS	ATACATG	A	15637	0.99725	0	43,0,15594,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749370	21990	PASS	TTTA	T	15639	0.998338	0	0,26,4,15609	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749370	23063	PASS	A	T	12816	0.872893	0	0,1,0,12748	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749370	23271	PASS	C	A	25061	0.925941	0	2,0,25033,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749370	23403	PASS	A	G	25058	0.973661	2147483647	0,0,0,25045	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749370	23604	PASS	C	A	18006	0.940575	0	15,0,17980,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749370	23709	PASS	C	T	17984	0.945062	2147483647	0,0,0,17965	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749370	24506	PASS	T	G	20932	0.972339	0	9,0,20919,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749370	24914	PASS	G	C	36009	0.957844	0	1,1,17913,18056	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749370	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	28608	0.001258	50	19740,8811,40,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749370	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	30803	9.41E-4	362	30697,23,17,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749370	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	30765	5.85E-4	0	30747,0,18,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749370	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	30957	9.69E-4	1065	30503,191,154,80	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749370	27881	PASS	C	A	12986	0.975281	0	2,0,12984,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7b	caC/caA	H42Q	orf7b	0.001798	0.979167	2	2	C>A
ERR5749370	27972	PASS	C	T	13020	0.905146	0	0,0,12924,49	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749370	28048	PASS	G	T	12982	0.926206	0	0,9,2,12968	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749370	28111	PASS	A	G	33527	0.978077	1	4,4,20529,12982	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749370	28270	PASS	TA	T	39819	0.995203	500	190,3,20256,19372	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749370	28280	PASS	G	C	39738	0.940057	14	14,4,20289,19348	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749370	28281	PASS	A	T	39738	0.923071	51	37,7,20278,19353	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749370	28282	PASS	T	A	39739	0.910894	12	31,16,20246,19359	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749370	28881	PASS	G	A	17537	0.787478	9	4,0,8713,8644	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749370	28882	PASS	G	A	17536	0.838675	3	2,0,8781,8641	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749370	28883	PASS	G	C	17536	0.946111	0	1,1,8790,8728	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749370	28977	PASS	C	T	8936	0.932968	0	0,1,9,8910	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749370	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	49567	0.001231	0	24874,24603,38,35	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749370	29640	PASS	C	T	20819	0.955281	0	3,2,10585,10213	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF10	gCa/gTa	A28V	orf10	0.002681	0.955281	2	2	C>T
ERR5749370	29733	PASS	C	T	10600	0.915943	0	0,8,0,10575	.	.	.	.	.	.	.	0.001821	0.915943	2	1	C>T
ERR5749371	241	PASS	C	T	14183	0.864133	3	2,5,7055,7071	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749371	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	12736	9.42E-4	0	12726,1,12,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749371	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	12739	0.001177	0	12667,4,15,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749371	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	12739	0.003689	0	12667,4,47,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749371	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12729	0.002357	0	11648,5,956,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749371	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	12729	7.86E-4	0	12714,5,10,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749371	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	12729	7.86E-4	0	12705,6,10,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttatg/gtg	VM84V	leader	0.000554	0.991848	4	1	GTTA>G
ERR5749371	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	12730	0.001021	70	12705,7,10,3	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749371	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	32893	0.001307	39	20092,12744,38,5	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749371	913	PASS	C	T	20127	0.917822	0	0,9,0,20101	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749371	2305	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTAAATAAATTTTTGGCTTTGTGTGCTGACTCTATCATTATTGGTGGAGCTAAACTTAAAGC	G	14372	7.65E-4	0	14361,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtaaataaatttttggctttgtgtgctgactctatcattattggtggagctaaacttaaagccttg/	VNKFLALCADSIIIGGAKLKAL502	nsp2	0.000443	0.070409	4	3	GCTTGTAAATAAATTTTTGGCTTTGTGTGCTGACTCTATCATTATTGGTGGAGCTAAACTTAAAGC>G
ERR5749371	3037	PASS	C	T	19600	0.811071	60	0,20,9792,9654	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749371	3267	PASS	C	T	18949	0.973402	0	4,0,18935,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749371	4861	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	15811	6.32E-4	0	1,15801,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	agt/	S716	nsp3	0.000632	0.115789	2	1	TA>T
ERR5749371	5388	PASS	C	A	6909	0.966421	0	1,0,6902,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749371	5986	PASS	C	T	12121	0.975332	2147483647	0,0,12111,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749371	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11500	0.001478	0	2,11372,0,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749371	6954	PASS	T	C	21383	0.818594	0	0,2,0,21252	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749371	8123	PASS	C	T	23770	0.769962	0	2,0,23536,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Ttt	L1802F	nsp3	0.001144	0.778589	1	1	C>T
ERR5749371	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	30394	0.001546	134	15712,14635,47,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749371	10969	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20796	0.004039	0	0,20700,0,87	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F305	3Cpro	0.004039	0.921996	1	1	C>T
ERR5749371	11287	PASS	GTCTGGTTTT	G	19993	0.997949	0	0,40,0,19952	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749371	11455	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13866	0.00339	0	13798,2,49,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A161	nsp6	0.00147	0.968698	1	1	C>T
ERR5749371	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	18473	0.001191	0	18426,0,24,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749371	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	39242	0.001554	0	19594,19530,37,38	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749371	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	15714	0.004264	2147483647	15337,128,13,228	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749371	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	30549	0.001178	0	15320,15221,18,18	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749371	14408	PASS	C	T	30549	0.844381	2	4,6,15235,15056	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749371	14676	PASS	C	T	13396	0.704389	0	7,0,13325,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749371	15279	PASS	C	T	23114	0.87739	0	7,0,23070,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749371	16176	PASS	T	C	21813	0.980608	0	0,0,10696,11107	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749371	17615	PASS	A	G	14923	0.891242	0	0,0,1,14883	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749371	17626	PASS	C	T	14928	0.943931	0	0,11,0,14896	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cat/Tat	H464Y	helicase	0.001039	0.946125	2	2	C>T
ERR5749371	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	23633	7.19E-4	0	23616,0,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749371	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	22447	5.35E-4	0	0,22435,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749371	19296	PASS	G	A	18297	0.972946	310	2,9,18285,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttG/ttA	L419	ExoN	0.000586	0.977017	2	2	G>A
ERR5749371	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26591	0.002332	0	26507,2,67,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749371	20420	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	25757	5.05E-4	0	40,25703,0,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F268	endoR	0.000383	0.069626	2	1	AT>A
ERR5749371	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	29874	8.7E-4	0	14892,14956,13,13	HIGH	NONE	FRAME_SHIFT	S	ctt/Tctt	L5S?	S	0.000394	0.091869	4	1	G>GT
ERR5749371	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29845	0.001977	1	14589,14870,30,34	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749371	21764	PASS	ATACATG	A	12273	0.993808	0	75,0,12197,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749371	21817	PASS	A	G	12265	0.952711	2147483647	0,0,12247,0	LOW	SILENT	SYNONYMOUS_CODING	S	ccA/ccG	P85	S	0.000689	0.961354	3	2	A>G
ERR5749371	21990	PASS	TTTA	T	12280	0.998371	0	0,20,6,12254	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749371	23063	PASS	A	T	13497	0.874787	0	0,2,2,13436	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749371	23271	PASS	C	A	21642	0.916228	0	2,0,21616,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749371	23403	PASS	A	G	21628	0.969808	0	0,3,0,21612	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749371	23604	PASS	C	A	15313	0.952393	0	8,0,15295,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749371	23709	PASS	C	T	15300	0.94366	0	0,3,1,15279	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749371	24506	PASS	T	G	19420	0.97621	0	6,0,19411,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749371	24914	PASS	G	C	37642	0.956724	0	0,1,18747,18872	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749371	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	18138	0.001489	445	18058,13,12,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749371	25690	PASS	G	T	18106	0.976748	0	3,0,18090,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Ggc/Tgc	G100C	orf3a	0.971091	0.979849	1	1	G>T
ERR5749371	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	18106	6.08E-4	0	18095,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749371	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	G	12594	7.15E-4	0	2,12574,0,9	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/	ACLVGLMWLSYFIASF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT>G
ERR5749371	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	12594	6.35E-4	0	2,12574,0,8	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749371	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	12595	0.00135	0	2,12572,0,17	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749371	27513	PASS	C	T	21707	0.977565	0	2,0,21677,0	LOW	SILENT	SYNONYMOUS_CODING	ORF7a	taC/taT	Y40	orf7a	0.001863	0.982462	2	2	C>T
ERR5749371	27684	PASS	C	T	21644	0.894659	0	0,79,18,21456	LOW	SILENT	SYNONYMOUS_CODING	ORF7a	taC/taT	Y97	orf7a	0.000478	0.90411	2	2	C>T
ERR5749371	27972	PASS	C	T	10355	0.903332	0	0,0,10280,44	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749371	28048	PASS	G	T	10328	0.927963	0	0,11,0,10313	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749371	28111	PASS	A	G	30389	0.978611	0	3,2,20047,10327	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749371	28270	PASS	TA	T	38958	0.995457	415	177,7,19799,18982	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749371	28280	PASS	G	C	38889	0.939572	26	15,2,19836,18962	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749371	28281	PASS	A	T	38889	0.917946	15	16,5,19826,18960	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749371	28282	PASS	T	A	38891	0.911368	6	19,11,19791,18976	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749371	28881	PASS	G	A	18301	0.712912	45	15,0,8951,9007	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749371	28882	PASS	G	A	18301	0.818371	24	12,1,9142,8976	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749371	28883	PASS	G	C	18301	0.942845	0	1,1,9168,9121	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749371	28977	PASS	C	T	9334	0.934005	0	0,3,0,9319	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749371	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	36382	8.8E-4	181	27020,9293,1,33	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749371	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	53674	8.94E-4	0	26971,26619,33,30	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749371	29686	PASS	C	T	13525	0.802514	15	0,5,6754,6590	.	.	.	.	.	.	.	0.001045	0.802514	2	1	C>T
ERR5749371	29688	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	13541	0.004283	0	6708,6719,39,39	.	.	.	.	.	.	.	0.002374	0.664502	2	1	G>A
ERR5749372	241	PASS	C	T	10021	0.845425	0	0,0,4986,4983	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749372	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	9581	0.001461	0	9571,0,14,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749372	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	9573	0.002403	0	8888,0,655,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749372	556	PASS	C	T	9584	0.173414	2	14,7494,2,2045	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y97	leader	0.001497	0.173414	1	1	C>T
ERR5749372	560	PASS	C	T	9571	0.070839	0	1,8846,0,719	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgt/Tgt	R99C	leader	0.002097	0.070839	1	1	C>T
ERR5749372	913	PASS	C	T	17900	0.906313	0	0,8,0,17870	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749372	3037	PASS	C	T	21531	0.806094	78	2,33,10764,10571	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749372	3267	PASS	C	T	19019	0.969557	0	3,0,19011,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749372	4331	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29383	0.001191	7	12549,16750,13,28	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L538	nsp3	0.000987	0.928955	1	1	C>T
ERR5749372	5100	PASS	C	T	9814	0.071429	0	9069,0,732,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCa/tTa	S794L	nsp3	0.001443	0.071429	2	2	C>T
ERR5749372	5388	PASS	C	A	5773	0.95479	2147483647	0,0,5772,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749372	5986	PASS	C	T	14264	0.97343	0	3,0,14248,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749372	6954	PASS	T	C	20903	0.815194	0	0,2,1,20765	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749372	8950	PASS	C	T	33815	0.969185	2	1,3,16763,17023	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I132	nsp4	0.002808	0.982604	1	1	C>T
ERR5749372	8964	PASS	C	T	16784	0.981649	148	1,4,16766,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCa/tTa	S137L	nsp4	0.000553	0.981649	4	2	C>T
ERR5749372	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	28145	0.001528	104	15972,12130,43,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749372	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	17526	0.005078	0	17404,0,114,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749372	11287	PASS	GTCTGGTTTT	G	17519	0.998173	0	0,32,0,17487	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749372	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	35654	0.001206	5	21482,14112,23,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749372	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	18865	0.001325	0	18808,0,25,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749372	12513	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18864	0.010602	0	18653,0,201,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aTg	T141M	nsp8	0.000794	0.984064	2	2	C>T
ERR5749372	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26383	0.001251	0	13179,13131,21,21	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749372	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	14414	0.005828	2147483647	14002,132,6,266	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749372	14408	PASS	C	T	27861	0.833351	2	3,5,13902,13698	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749372	14676	PASS	C	T	11423	0.867635	0	2,0,11398,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749372	14688	PASS	C	T	11420	0.979772	2147483647	0,0,11409,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N416	RdRp	0.000534	0.979772	2	2	C>T
ERR5749372	15279	PASS	C	T	18534	0.890957	2147483647	0,0,18501,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749372	16176	PASS	T	C	17918	0.980411	0	1,0,9132,8775	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749372	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	31279	0.002206	0	31187,0,70,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749372	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	19422	9.78E-4	0	0,19400,0,19	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TA>T
ERR5749372	21234	PASS	C	T	33358	0.713622	0	22,0,33027,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A192	MethTr	0.000472	0.857572	5	2	C>T
ERR5749372	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	29332	0.023831	2144	14638,13908,0,699	HIGH	NONE	FRAME_SHIFT	S	ctt/Tctt	L5S?	S	0.000394	0.091869	4	1	G>GT
ERR5749372	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GTT	29332	0.002421	184	14638,13908,2,69	HIGH	NONE	FRAME_SHIFT	S	ctt/TTctt	L5F?	S	0.000394	0.091869	4	1	G>GTT
ERR5749372	21575	PASS	C	T	28341	0.8487	4	1,4,13387,14535	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749372	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	28329	0.003212	259	13622,14610,0,91	HIGH	NONE	FRAME_SHIFT	S	gtt/Tgtt	V6C?	S	0.000619	0.877942	3	2	C>CT
ERR5749372	21764	PASS	ATACATG	A	13535	0.996749	0	44,0,13491,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749372	21990	PASS	TTTA	T	13538	0.998079	0	0,26,4,13508	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749372	23063	PASS	A	T	13748	0.852488	0	0,5,0,13672	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749372	23271	PASS	C	A	18565	0.916186	33	1,1,18540,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749372	23403	PASS	A	G	18549	0.965712	0	0,1,0,18530	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749372	23604	PASS	C	A	16402	0.952506	0	12,0,16383,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749372	23709	PASS	C	T	16380	0.935959	0	0,5,2,16349	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749372	24010	PASS	A	G	30335	0.916532	3	0,2,14669,15632	LOW	SILENT	SYNONYMOUS_CODING	S	tcA/tcG	S816	S	0.000455	0.926398	4	2	A>G
ERR5749372	24506	PASS	T	G	16459	0.971383	0	5,0,16450,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749372	24914	PASS	G	C	35086	0.959215	0	1,1,17489,17570	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749372	25496	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	36785	0.001196	4	18015,18044,364,339	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aTa/aGa	I35R	orf3a	0.000369	0.96555	3	2	T>G
ERR5749372	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	19627	0.00163	228	19535,22,23,11	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749372	25844	PASS	C	T	19549	0.91043	0	0,6,0,19511	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aCt/aTt	T151I	orf3a	0.001226	0.938776	1	1	C>T
ERR5749372	27577	PASS	C	T	20074	0.858274	0	6,0,20012,0	HIGH	NONSENSE	STOP_GAINED	ORF7a	Caa/Taa	Q62*	orf7a	0.000614	0.952205	4	2	C>T
ERR5749372	27972	PASS	C	T	12875	0.901515	0	0,0,12757,81	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749372	28048	PASS	G	T	12797	0.910917	0	0,19,0,12773	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749372	28111	PASS	A	G	29583	0.976845	3	0,1,16760,12806	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749372	28270	PASS	TA	T	32301	0.994799	342	163,10,16536,15597	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749372	28280	PASS	G	C	32232	0.934785	2	9,6,16572,15577	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749372	28281	PASS	A	T	32232	0.915736	21	17,4,16572,15578	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749372	28282	PASS	T	A	32233	0.907517	5	15,9,16534,15592	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749372	28881	PASS	G	A	16291	0.764533	6	3,0,8091,7956	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749372	28882	PASS	G	A	16291	0.822172	9	4,0,8158,7962	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749372	28883	PASS	G	C	16291	0.943466	2	1,2,8172,8089	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749372	28977	PASS	C	T	8305	0.92342	2147483647	0,0,0,8294	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749372	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	55273	0.001285	0	27760,27413,41,41	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749373	241	PASS	C	T	13921	0.864737	0	0,0,6901,6941	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749373	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	9818	0.001732	0	9799,4,17,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749373	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	9818	0.001019	0	9744,3,10,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749373	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	9818	0.004583	0	9744,3,45,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749373	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTTGA	G	9818	0.00112	23	9744,3,10,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTTGA>G
ERR5749373	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	9805	0.001632	0	9010,8,670,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749373	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	9805	0.001836	0	9778,9,18,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749373	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	9807	0.001224	0	9777,12,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749373	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	9807	9.18E-4	0	9777,13,9,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749373	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	25620	4.68E-4	1	15783,9821,7,5	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749373	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	25620	0.001249	11	15758,9820,25,7	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749373	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15786	0.0019	0	0,15742,0,32	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749373	913	PASS	C	T	15787	0.906125	0	0,13,0,15741	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749373	1461	PASS	A	G	35266	0.900102	10	9,3,17458,17701	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K219R	nsp2	0.000518	0.90899	2	2	A>G
ERR5749373	1599	PASS	G	T	30773	0.959445	48	1,26,12823,17903	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGt/gTt	G265V	nsp2	0.001427	0.96468	2	1	G>T
ERR5749373	3037	PASS	C	T	16193	0.817514	57	0,19,8086,7979	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749373	3267	PASS	C	T	15383	0.970162	0	4,0,15365,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749373	3335	PASS	G	A	29837	0.883668	16	9,1,15305,14409	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E206K	nsp3	0.001289	0.891976	4	3	G>A
ERR5749373	4999	PASS	C	T	9898	0.93918	139	1,4,9887,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N760	nsp3	0.001692	0.947468	1	1	C>T
ERR5749373	5170	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	9881	8.1E-4	0	1,9872,0,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T819	nsp3	0.000565	0.894036	2	2	CCA>C
ERR5749373	5388	PASS	C	A	5318	0.959007	2147483647	0,0,5315,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749373	5986	PASS	C	T	10776	0.975687	2147483647	0,0,10770,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749373	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9748	0.001539	0	3,9616,0,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749373	6954	PASS	T	C	18428	0.808552	0	0,6,2,18333	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749373	9402	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	26466	4.53E-4	0	13241,13214,6,6	HIGH	NONE	FRAME_SHIFT	ORF1ab	ata/	I284	nsp4	0.000453	0.058824	2	2	CTA>C
ERR5749373	9541	PASS	C	T	26050	0.955317	0	2,2,12767,13263	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ctC/ctT	L329	nsp4	0.000346	0.955771	2	2	C>T
ERR5749373	10165	PASS	C	T	13846	0.964033	123	5,4,13744,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y37	3Cpro	0.000632	0.976163	2	2	C>T
ERR5749373	10702	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27248	0.04459	0	13263,12684,666,627	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D216	3Cpro	0.000396	0.098214	2	2	C>T
ERR5749373	11287	PASS	GTCTGGTTTT	G	14312	0.997065	0	0,42,0,14270	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749373	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	29210	8.56E-4	1	17219,11945,14,12	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749373	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25889	0.00112	0	12931,12888,17,16	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749373	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	9707	0.005563	2797	9451,88,2,160	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749373	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	18826	0.001115	0	9441,9374,11,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749373	14408	PASS	C	T	18826	0.850367	1	5,6,9390,9298	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749373	14676	PASS	C	T	10526	0.705206	0	2,0,10471,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749373	15279	PASS	C	T	17833	0.898951	0	1,0,17814,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749373	16176	PASS	T	C	15868	0.979077	2	3,1,8319,7535	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749373	17615	PASS	A	G	12195	0.892907	0	0,2,6,12148	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749373	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	19209	7.29E-4	0	19194,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749373	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25101	0.002032	0	25039,0,54,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749373	21302	PASS	C	T	24811	0.836484	0	0,33,1,24641	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCa/cTa	P215L	MethTr	0.001031	0.843069	1	1	C>T
ERR5749373	21304	PASS	C	A	24811	0.605296	0	0,870,1,23922	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgc/Agc	R216S	MethTr	0.000411	0.605296	3	2	C>A
ERR5749373	21305	PASS	G	A	24811	0.700979	0	0,0,1,24376	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cGc/cAc	R216H	MethTr	0.000727	0.703943	1	1	G>A
ERR5749373	21375	PASS	G	A	24950	0.839238	756	26,2,12,24820	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttG/ttA	L239	MethTr	0.002365	0.858793	2	2	G>A
ERR5749373	21727	PASS	C	T	10211	0.833121	252	3,8,10183,0	LOW	SILENT	SYNONYMOUS_CODING	S	ttC/ttT	F55	S	0.000896	0.878141	2	2	C>T
ERR5749373	21764	PASS	ATACATG	A	10199	0.996176	0	39,0,10160,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749373	21990	PASS	TTTA	T	10211	0.997062	0	0,30,11,10170	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749373	23063	PASS	A	T	3069	0.860541	0	0,1,1,3047	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749373	23191	PASS	C	T	16460	0.963123	0	1,0,16446,0	LOW	SILENT	SYNONYMOUS_CODING	S	ttC/ttT	F543	S	0.000538	0.973337	2	2	C>T
ERR5749373	23271	PASS	C	A	16458	0.913234	2147483647	0,0,16441,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749373	23403	PASS	A	G	16446	0.966861	0	0,1,0,16438	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749373	23604	PASS	C	A	12880	0.938276	0	4,0,12874,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749373	23709	PASS	C	T	12879	0.942464	0	0,7,3,12857	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749373	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	27334	4.76E-4	7	14446,12875,4,9	HIGH	NONE	FRAME_SHIFT	S	ttg/	L753	S	0.000334	0.080808	2	2	CT>C
ERR5749373	24506	PASS	T	G	14924	0.974538	0	9,0,14913,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749373	24914	PASS	G	C	27299	0.957105	0	1,1,13598,13672	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749373	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	20050	5.99E-4	0	20037,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749373	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	20230	0.001186	626	19883,174,104,52	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749373	26270	PASS	C	T	50073	0.918319	1	2,7,9112,40885	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	aCa/aTa	T9I	E	0.000586	0.930791	3	2	C>T
ERR5749373	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	9147	0.003061	0	0,9117,0,28	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749373	27643	PASS	C	T	18076	0.766707	0	2,0,17952,6	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Cct/Tct	P84S	orf7a	0.00166	0.858006	2	1	C>T
ERR5749373	27737	PASS	C	T	18183	0.817082	0	1,2330,8,15820	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	aCa/aTa	T115I	orf7a	0.001474	0.817082	2	2	C>T
ERR5749373	27972	PASS	C	T	9229	0.904865	0	0,0,9154,47	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749373	28048	PASS	G	T	9187	0.90824	0	0,16,0,9167	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749373	28111	PASS	A	G	24042	0.976167	0	6,4,14827,9194	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749373	28250	PASS	T	TG	14768	0.901882	0	1476,0,13318,1	HIGH	NONE	FRAME_SHIFT	ORF8	ttc/Gttc	F120V?	orf8	0.000494	0.993968	5	3	T>TG
ERR5749373	28250	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TCTG	14768	0.001287	0	1476,0,19,0	MODERATE	NONE	CODON_INSERTION	ORF8	ttc/CTGttc	F120LF	orf8	0.000494	0.993968	5	3	T>TCTG
ERR5749373	28253	PASS	CA	C	14766	0.903765	0	1421,0,13344,1	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749373	28270	PASS	TA	T	28881	0.996226	224	106,7,14644,14128	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749373	28280	PASS	G	C	28831	0.940966	2	3,1,14657,14117	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749373	28281	PASS	A	T	28831	0.908432	8	15,7,14646,14105	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749373	28282	PASS	T	A	28832	0.910204	0	7,7,14611,14123	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749373	28881	PASS	G	A	12572	0.708956	24	9,0,6149,6153	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749373	28882	PASS	G	A	12571	0.821017	4	4,1,6290,6146	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749373	28883	PASS	G	C	12571	0.936839	6	1,4,6305,6252	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749373	28977	PASS	C	T	6419	0.919458	0	0,1,0,6398	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749373	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	35418	0.001214	0	17794,17560,28,27	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749374	241	PASS	C	T	2449	0.864434	0	0,0,1224,1222	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749374	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	4986	0.012234	0	4926,0,61,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749374	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	4985	0.003009	0	4921,0,15,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749374	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	4985	0.008225	0	4921,0,41,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749374	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	4982	0.00281	0	4485,0,361,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749374	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	4982	0.004617	0	4959,0,23,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749374	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	4982	0.001204	0	4975,0,6,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749374	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	4981	0.003011	0	4960,0,15,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749374	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATGGTTG	T	4981	0.001405	0	4960,0,7,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	atggttgag/	MVE85	leader	0.000587	0.476744	4	1	TATGGTTG>T
ERR5749374	520	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTT	G	5030	0.001193	0	4975,49,6,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttgag/gag	VE86E	leader	0.000583	0.051154	1	1	GGTT>G
ERR5749374	656	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	5001	0.004599	0	4,4970,0,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gct/Cct	A131P	leader	0.001202	0.131429	1	1	G>C
ERR5749374	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	22625	9.28E-4	11	17601,4996,20,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749374	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	22624	4.86E-4	8	17125,4940,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749374	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	22624	0.023913	117	17125,4940,484,57	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749374	823	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17670	0.002264	0	17565,50,46,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V6	nsp2	0.001213	0.901722	1	1	C>T
ERR5749374	843	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	35182	8.53E-4	8	17592,17531,17,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cAt	P13H	nsp2	0.000301	0.050923	4	2	C>A
ERR5749374	913	PASS	C	T	17622	0.917036	0	0,5,0,17560	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749374	2185	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	18986	4.74E-4	0	1,18976,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L462S?	nsp2	0.000441	0.963529	4	3	G>GT
ERR5749374	3037	PASS	C	T	14961	0.820533	39	0,13,7456,7364	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749374	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	7559	0.002381	517	2,7537,18,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749374	3177	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	26308	0.001292	49	18727,7537,42,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cAt	P153H	nsp3	0.000773	0.96008	3	2	C>A
ERR5749374	3267	PASS	C	T	18767	0.973837	0	3,0,18760,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749374	3671	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	21739	9.66E-4	0	10849,10758,11,12	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E318K	nsp3	0.000351	0.0625	6	2	G>A
ERR5749374	4423	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14280	0.001401	0	14253,2,22,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	cgC/cgT	R568	nsp3	0.00063	0.953796	2	2	C>T
ERR5749374	4423	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	14280	6.3E-4	0	14269,2,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K569	nsp3	0.00063	0.953796	2	2	CA>C
ERR5749374	4529	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTTTAC	T	14246	5.62E-4	0	0,14238,0,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	tacttt/	YF605	nsp3	0.000527	0.402778	3	1	TTTTAC>T
ERR5749374	4578	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTAACGATC	T	14275	0.001121	0	0,14259,0,16	HIGH	NONE	FRAME_SHIFT	ORF1ab	aacgatctaaat/	NDLN621	nsp3	0.000519	0.082979	2	2	TTAACGATC>T
ERR5749374	5388	PASS	C	A	4221	0.960673	2147483647	0,0,4217,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749374	5986	PASS	C	T	12318	0.973616	0	1,0,12302,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749374	6286	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	21863	5.49E-4	0	21851,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tgg/	W1190	nsp3	0.000549	0.949782	2	2	CT>C
ERR5749374	6335	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	21855	9.61E-4	0	21799,0,23,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tcg/Ccg	S1206P	nsp3	0.000961	0.949947	2	1	T>C
ERR5749374	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11822	0.001269	0	15,11672,0,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749374	6954	PASS	T	C	20119	0.810577	0	0,3,0,20000	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749374	7070	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	25523	0.004584	797	5237,20153,117,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggc/Cgc	G1451R	nsp3	0.000698	0.101434	3	1	G>C
ERR5749374	7564	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	14448	6.92E-4	0	0,14438,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/tTat	Y1617L?	nsp3	0.000586	0.056194	4	2	C>CT
ERR5749374	7735	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22479	0.00218	0	22416,0,49,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I1672	nsp3	0.000658	0.954659	3	2	C>T
ERR5749374	8151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	41155	7.05E-4	0	20189,20541,17,19	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gTc/gCc	V1811A	nsp3	0.00055	0.34	2	1	T>C
ERR5749374	8950	PASS	C	T	30014	0.978077	15	0,4,17950,12047	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I132	nsp4	0.002808	0.982604	1	1	C>T
ERR5749374	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	13150	6.08E-4	2	11590,1552,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749374	10842	PASS	A	G	1783	0.150308	0	1487,0,296,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gAt/gGt	D263G	3Cpro	0.150308	0.150308	1	1	A>G
ERR5749374	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	23157	0.002202	0	23074,0,67,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749374	11287	PASS	GTCTGGTTTT	G	23156	0.993436	0	0,152,0,23004	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749374	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	32886	0.001125	42	23592,9216,39,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749374	11750	PASS	C	T	45876	0.689576	45	2,19,23498,20142	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L260F	nsp6	0.001019	0.70989	2	1	C>T
ERR5749374	11750	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	G	45876	0.003684	7	2,19,78,2087	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Gtc	L260V	nsp6	0.001019	0.70989	2	1	C>G
ERR5749374	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	17312	0.001617	0	17252,0,29,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749374	13115	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15507	0.001806	0	15466,0,33,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L31	nsp10	0.001806	0.922167	1	1	C>T
ERR5749374	13308	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	15514	0.004512	0	8,15416,0,72	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K95R	nsp10	0.001976	0.928707	2	1	A>G
ERR5749374	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	5185	0.001543	0	2600,2582,4,4	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749374	14408	PASS	C	T	5185	0.848987	6	1,4,2590,2559	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749374	14676	PASS	C	T	11607	0.712673	0	6,0,11545,6	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749374	15279	PASS	C	T	16533	0.883869	0	1,0,16513,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749374	16176	PASS	T	C	12709	0.978362	4	1,0,4113,8589	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749374	16573	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GACTGGACAAATGCTGGTGATTACATTTT	G	25132	5.97E-4	0	25117,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gactggacaaatgctggtgattacatttta/	DWTNAGDYIL113	helicase	0.000597	0.156477	4	2	GACTGGACAAATGCTGGTGATTACATTTT>G
ERR5749374	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	20344	0.001671	0	20310,0,34,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749374	17181	PASS	T	C	12149	0.988312	0	8,0,12135,2	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaT/gaC	D315	helicase	0.986595	0.991193	1	1	T>C
ERR5749374	18504	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	31816	9.11E-4	0	13,31246,0,505	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K155N	ExoN	0.000518	0.094148	4	3	A>C
ERR5749374	18576	PASS	C	T	31984	0.849612	0	0,5,0,31843	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D179	ExoN	0.005404	0.876866	2	2	C>T
ERR5749374	18642	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AGGACCTG	A	60370	4.64E-4	91	28344,31998,28,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggacctgag/	GPE202	ExoN	0.000464	0.078253	3	2	AGGACCTG>A
ERR5749374	18747	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	28371	9.16E-4	0	28339,7,26,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tataat/	YN237	ExoN	0.000375	0.982946	4	2	CTA>C
ERR5749374	18984	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTTGTTAAAGCTGCATTATTAGCAGACA	G	28655	4.19E-4	0	28643,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttgttaaagctgcattattagcagacaaa/	VVKAALLADK316	ExoN	0.000419	0.950929	5	2	GGTTGTTAAAGCTGCATTATTAGCAGACA>G
ERR5749374	19011	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28655	0.001012	0	28600,0,30,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D324	ExoN	0.000408	0.975746	4	2	C>T
ERR5749374	19011	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	28655	8.03E-4	0	28632,0,23,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K325	ExoN	0.000408	0.975746	4	2	CA>C
ERR5749374	19034	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTGG	T	28654	3.84E-4	0	28643,0,11,0	MODERATE	NONE	CODON_DELETION	ORF1ab	ggt/	G333	ExoN	0.000384	0.060908	2	2	TTGG>T
ERR5749374	19299	PASS	T	C	18228	0.987656	0	5,0,18216,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taT/taC	Y420	ExoN	0.001065	0.987656	2	2	T>C
ERR5749374	19343	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTTTTGTTAAT	C	18228	8.23E-4	0	18209,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tttgttaattta/	FVNL436	ExoN	0.000519	0.192257	7	2	CTTTTGTTAAT>C
ERR5749374	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15891	0.003272	0	15812,0,56,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749374	20420	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	31316	4.79E-4	0	168,31121,0,15	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F268	endoR	0.000383	0.069626	2	1	AT>A
ERR5749374	20420	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATT	A	31316	3.83E-4	0	168,31121,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F268	endoR	0.000383	0.069626	2	1	ATT>A
ERR5749374	21123	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	54532	3.67E-4	4	29896,24616,9,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F156	MethTr	0.000257	0.90982	5	2	GT>G
ERR5749374	21234	PASS	C	T	29882	0.620039	0	32,0,29385,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A192	MethTr	0.000472	0.857572	5	2	C>T
ERR5749374	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	31190	5.45E-4	0	15575,15598,8,9	HIGH	NONE	FRAME_SHIFT	S	ctt/Tctt	L5S?	S	0.000394	0.091869	4	1	G>GT
ERR5749374	21657	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TCA	T	15659	7.02E-4	0	0,15647,0,11	HIGH	NONE	FRAME_SHIFT	S	acacgt/	TR33	S	0.000702	0.06812	2	2	TCA>T
ERR5749374	21764	PASS	ATACATG	A	13518	0.997929	0	28,0,13490,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749374	21817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	13518	7.4E-4	0	13507,1,10,0	HIGH	NONE	FRAME_SHIFT	S	ttt/	F86	S	0.000689	0.961354	3	2	AT>A
ERR5749374	21990	PASS	TTTA	T	13526	0.995342	0	0,63,8,13455	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749374	22290	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	20873	5.27E-4	0	7,20855,0,11	HIGH	NONE	FRAME_SHIFT	S	tta/	L244	S	0.000389	0.578006	2	2	CT>C
ERR5749374	22293	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	30758	8.45E-4	41	9886,20843,0,26	HIGH	NONE	FRAME_SHIFT	S	tta/	L244	S	0.000308	0.160511	4	1	TA>T
ERR5749374	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	18327	0.001419	0	0,18285,0,26	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749374	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	32739	0.0011	10	14380,18299,21,15	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749374	23063	PASS	A	T	14384	0.858593	0	0,2,0,14302	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749374	23271	PASS	C	A	22174	0.900514	27	1,1,22122,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749374	23403	PASS	A	G	22143	0.96211	0	0,4,0,22113	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749374	23541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATG	A	14658	0.00191	0	14627,3,28,0	HIGH	NONE	FRAME_SHIFT	S	tatgag/	YE660	S	0.000911	0.950734	4	2	ATG>A
ERR5749374	23604	PASS	C	A	14651	0.944441	0	8,0,14630,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749374	23709	PASS	C	T	14635	0.93905	0	0,7,0,14612	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749374	24127	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	21404	0.001355	10	11807,9569,21,8	HIGH	NONE	FRAME_SHIFT	S	aac/	N856	S	0.000324	0.111888	4	1	TA>T
ERR5749374	24506	PASS	T	G	15087	0.973686	0	9,0,15074,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749374	24914	PASS	G	C	39301	0.958271	6	0,3,19582,19683	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749374	25531	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATTG	A	21130	4.73E-4	0	9,21104,0,10	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF3a	gttggc/ggc	VG48G	orf3a	0.000473	0.975891	5	2	ATTG>A
ERR5749374	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	5210	0.005182	549	5149,14,2,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749374	25844	PASS	C	T	5162	0.919992	0	0,2,0,5151	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aCt/aTt	T151I	orf3a	0.001226	0.938776	1	1	C>T
ERR5749374	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	33368	8.69E-4	0	2,33337,0,29	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749374	26416	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	21896	4.57E-4	27	11044,11075,0,10	HIGH	NONE	FRAME_SHIFT	E	tac/	Y59	E	0.000457	0.913418	2	2	GT>G
ERR5749374	26681	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12172	0.001643	0	11970,180,20,0	LOW	SILENT	SYNONYMOUS_CODING	M	ttC/ttT	F53	M	0.001297	0.074505	1	1	C>T
ERR5749374	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	11991	0.001001	0	3,11970,0,12	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749374	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	11991	9.17E-4	0	3,11977,0,11	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749374	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	11989	0.005005	0	1,11928,0,60	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749374	27552	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATTTGCACTGACTTGCTTTAGCACTCAATTTGCTTTTGCTTGTCCTGACGGCGTAAAACACGTCTATCAGTTACGTGCCAGATCAG	A	19634	0.001273	0	19547,62,25,0	HIGH	NONE	FRAME_SHIFT	ORF7a	gcactgacttgctttagcactcaatttgcttttgcttgtcctgacggcgtaaaacacgtctatcagttacgtgccagatcagtttca/	ALTCFSTQFAFACPDGVKHVYQLRARSVS55	orf7a	0.000563	0.985801	6	1	ATTTGCACTGACTTGCTTTAGCACTCAATTTGCTTTTGCTTGTCCTGACGGCGTAAAACACGTCTATCAGTTACGTGCCAGATCAG>A
ERR5749374	27577	PASS	C	T	19480	0.802875	2147483647	0,0,19259,0	HIGH	NONSENSE	STOP_GAINED	ORF7a	Caa/Taa	Q62*	orf7a	0.000614	0.952205	4	2	C>T
ERR5749374	27972	PASS	C	T	7741	0.893683	18	1,1,7662,51	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749374	27996	PASS	G	A	15358	0.077158	0	7036,7041,630,631	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	Gac/Aac	D35N	orf8	0.00609	0.077158	2	1	G>A
ERR5749374	28048	PASS	G	T	7690	0.922367	0	0,9,0,7673	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749374	28111	PASS	A	G	31675	0.9785	13	1,3,23966,7688	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749374	28237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTGT	G	23976	7.09E-4	0	23957,3,17,0	MODERATE	NONE	CODON_DELETION	ORF8	gtt/	V117	orf8	0.000442	0.966707	4	2	GTGT>G
ERR5749374	28239	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTGT	G	23979	4.17E-4	0	23963,6,10,0	HIGH	NONE	FRAME_SHIFT	ORF8	gtttta/	VL117	orf8	0.000417	0.984998	9	2	GTTGT>G
ERR5749374	28250	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TCTG	23967	6.26E-4	0	23947,6,15,0	MODERATE	NONE	CODON_INSERTION	ORF8	ttc/CTGttc	F120LF	orf8	0.000494	0.993968	5	3	T>TCTG
ERR5749374	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23965	0.001085	0	23868,7,26,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749374	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	23963	6.26E-4	0	23943,7,15,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749374	28270	PASS	TA	T	46498	0.995032	528	228,9,23675,22592	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749374	28280	PASS	G	C	46410	0.935941	20	22,7,23744,22551	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749374	28281	PASS	A	T	46410	0.91254	53	38,7,23732,22570	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749374	28282	PASS	T	A	46415	0.911882	7	27,16,23673,22579	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749374	28371	PASS	G	A	23976	0.072114	0	1,21985,0,1974	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGt/aAt	S33N	N	0.072114	0.072114	1	1	G>A
ERR5749374	28406	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTACCCAATA	T	23989	0.001501	0	13,23940,0,36	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	N	ttacccaataat/tat	LPNN45Y	N	0.00043	0.921074	3	2	TTACCCAATA>T
ERR5749374	28407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TACCCAATA	T	23992	9.17E-4	0	13,23957,0,22	HIGH	NONE	FRAME_SHIFT	N	cccaataat/	PNN46	N	0.000382	0.179673	1	1	TACCCAATA>T
ERR5749374	28881	PASS	G	A	11041	0.713522	39	13,0,5375,5439	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749374	28882	PASS	G	A	11036	0.818956	15	6,0,5510,5416	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749374	28883	PASS	G	C	11036	0.941102	0	2,1,5521,5504	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749374	28977	PASS	C	T	5632	0.929155	0	0,2,0,5621	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749374	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	63753	0.001208	0	31998,31633,49,46	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749374	29192	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTTG	T	64020	3.91E-4	0	32043,31944,12,13	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	N	tttgcc/tcc	FA307S	N	0.000391	0.940667	2	2	TTTG>T
ERR5749374	29867	PASS	T	A	10	1.0	2147483647	0,0,0,10	.	.	.	.	.	.	.	1	1	1	1	T>A
ERR5749375	241	PASS	C	T	3141	0.852276	3	0,2,1562,1562	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749375	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	9692	0.002373	0	9648,0,23,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749375	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	9692	0.00196	0	9648,0,19,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749375	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	9684	0.001859	0	8977,0,639,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749375	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	9684	0.001446	0	9670,0,14,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749375	656	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	9712	0.001544	0	2,9676,0,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gct/Cct	A131P	leader	0.001202	0.131429	1	1	G>C
ERR5749375	657	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9712	0.002677	0	2,9682,0,28	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A131V	leader	0.001202	0.365979	3	1	C>T
ERR5749375	673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	26292	5.71E-4	64	16580,9697,0,15	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggc/	G137	leader	0.000454	0.602236	3	2	CG>C
ERR5749375	676	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26292	8.75E-4	2	16560,9672,14,11	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G137	leader	0.000799	0.919273	2	1	C>T
ERR5749375	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	26292	5.71E-4	2	16564,9708,11,4	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749375	913	PASS	C	T	16570	0.917381	0	0,20,0,16528	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749375	1461	PASS	A	G	35383	0.905689	2	5,3,17531,17770	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K219R	nsp2	0.000518	0.90899	2	2	A>G
ERR5749375	1599	PASS	G	T	37005	0.96468	6	5,10,19005,17950	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGt/gTt	G265V	nsp2	0.001427	0.96468	2	1	G>T
ERR5749375	3037	PASS	C	T	15675	0.814545	45	0,15,7834,7712	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749375	3267	PASS	C	T	17468	0.972063	0	3,0,17458,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749375	3335	PASS	G	A	33974	0.891976	20	8,0,17400,16448	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E206K	nsp3	0.001289	0.891976	4	3	G>A
ERR5749375	3787	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10253	0.003219	0	7,10207,0,37	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y356	nsp3	0.002354	0.956541	1	1	C>T
ERR5749375	4237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTA	T	32962	3.94E-4	0	16489,16460,7,6	HIGH	NONE	FRAME_SHIFT	ORF1ab	ata/	I508	nsp3	0.000302	0.918634	2	2	TTA>T
ERR5749375	4255	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	32992	0.001121	0	16464,16453,19,19	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccG/ccA	P512	nsp3	0.001102	0.871853	2	1	G>A
ERR5749375	4999	PASS	C	T	10527	0.947468	140	0,4,10515,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N760	nsp3	0.001692	0.947468	1	1	C>T
ERR5749375	5170	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	10503	9.52E-4	0	0,10493,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T819	nsp3	0.000565	0.894036	2	2	CCA>C
ERR5749375	5388	PASS	C	A	4492	0.963045	2147483647	0,0,4492,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749375	5986	PASS	C	T	11831	0.976587	0	1,0,11826,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749375	6954	PASS	T	C	19788	0.828179	0	0,8,0,19690	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749375	6990	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	19836	5.04E-4	0	0,19826,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L1425	nsp3	0.000504	0.101156	4	2	CT>C
ERR5749375	9541	PASS	C	T	19286	0.955771	0	2,0,13704,5570	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ctC/ctT	L329	nsp4	0.000346	0.955771	2	2	C>T
ERR5749375	10165	PASS	C	T	17683	0.966917	96	9,3,17635,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y37	3Cpro	0.000632	0.976163	2	2	C>T
ERR5749375	11075	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TTC	22005	7.27E-4	0	21988,1,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/ttCTt	F35F?	nsp6	0.000555	0.885796	4	2	T>TTC
ERR5749375	11199	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	43827	7.76E-4	0	21753,21888,19,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCc/gTc	A76V	nsp6	0.000309	0.056758	3	2	C>T
ERR5749375	11287	PASS	GTCTGGTTTT	G	21993	0.998272	0	0,38,0,21955	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749375	11750	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	39370	0.00127	0	20014,19242,38,35	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L260F	nsp6	0.001019	0.70989	2	1	C>T
ERR5749375	11824	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20101	0.001741	0	0,20053,0,37	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I284	nsp6	0.000465	0.922016	2	2	C>T
ERR5749375	12125	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	18475	0.001353	0	11,18382,0,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y12H	nsp8	0.000847	0.113436	1	1	T>C
ERR5749375	12357	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18700	0.001711	0	4,18639,0,34	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T89I	nsp8	0.000909	0.956941	3	2	C>T
ERR5749375	12459	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	36722	0.001008	3	17991,18687,16,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T123I	nsp8	0.000658	0.986093	1	1	C>T
ERR5749375	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	18012	0.00111	0	17957,0,22,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749375	12961	PASS	A	G	10679	0.904485	0	0,115,0,10554	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaA/aaG	K92	nsp9	0.00128	0.923934	1	1	A>G
ERR5749375	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29135	9.61E-4	0	14552,14514,14,15	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749375	14408	PASS	C	T	7625	0.844066	0	4,4,3806,3766	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749375	14676	PASS	C	T	11205	0.83079	0	5,0,11170,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749375	15279	PASS	C	T	17080	0.888525	0	2,0,17053,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749375	16176	PASS	T	C	16891	0.982476	0	2,3,6810,10066	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749375	16939	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	18764	9.59E-4	0	18453,0,300,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tta/Gta	L235V	helicase	0.000959	0.959205	2	2	T>G
ERR5749375	17615	PASS	A	G	14778	0.905806	2147483647	0,0,0,14736	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749375	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	24395	0.001148	0	24367,0,28,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749375	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	22523	5.33E-4	0	0,22511,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749375	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18367	0.003376	0	18289,0,68,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749375	21234	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29625	9.45E-4	0	29522,0,45,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A192	MethTr	0.000472	0.857572	5	2	C>T
ERR5749375	21302	PASS	C	T	29512	0.842268	0	0,31,0,29349	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCa/cTa	P215L	MethTr	0.001031	0.843069	1	1	C>T
ERR5749375	21304	PASS	C	A	29513	0.597669	0	0,1094,0,28406	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgc/Agc	R216S	MethTr	0.000411	0.605296	3	2	C>A
ERR5749375	21305	PASS	G	A	29513	0.699183	0	0,2,0,28984	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cGc/cAc	R216H	MethTr	0.000727	0.703943	1	1	G>A
ERR5749375	21375	PASS	G	A	29685	0.84093	480	18,2,38,29520	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttG/ttA	L239	MethTr	0.002365	0.858793	2	2	G>A
ERR5749375	21727	PASS	C	T	12530	0.868795	404	0,12,12503,0	LOW	SILENT	SYNONYMOUS_CODING	S	ttC/ttT	F55	S	0.000896	0.878141	2	2	C>T
ERR5749375	21732	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	12530	7.18E-4	0	12509,12,9,0	HIGH	NONE	FRAME_SHIFT	S	ttc/	F58	S	0.000576	0.076745	4	2	CT>C
ERR5749375	21764	PASS	ATACATG	A	12516	0.997283	0	34,0,12482,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749375	21990	PASS	TTTA	T	12523	0.997445	0	0,32,5,12486	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749375	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19713	0.001065	4	2866,16818,1,20	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749375	23063	PASS	A	T	2860	0.870629	2147483647	0,0,0,2844	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749375	23191	PASS	C	T	19923	0.965517	0	1,0,19906,0	LOW	SILENT	SYNONYMOUS_CODING	S	ttC/ttT	F543	S	0.000538	0.973337	2	2	C>T
ERR5749375	23271	PASS	C	A	19915	0.913984	0	1,0,19891,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749375	23403	PASS	A	G	19908	0.968656	0	0,2,0,19894	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749375	23604	PASS	C	A	15427	0.941855	0	15,0,15399,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749375	23709	PASS	C	T	15408	0.944834	0	0,3,1,15390	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749375	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	28301	5.65E-4	11	12857,15428,11,5	HIGH	NONE	FRAME_SHIFT	S	ttg/	L753	S	0.000334	0.080808	2	2	CT>C
ERR5749375	24506	PASS	T	G	17580	0.975142	0	5,0,17572,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749375	24914	PASS	G	C	39299	0.960686	0	0,0,19575,19696	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749375	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	11593	0.002588	604	11508,32,4,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749375	26270	PASS	C	T	49264	0.925422	1	2,6,10051,39170	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	aCa/aTa	T9I	E	0.000586	0.930791	3	2	C>T
ERR5749375	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	12790	0.001095	0	0,12772,0,14	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749375	27643	PASS	C	T	23422	0.776663	0	2,0,23241,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Cct/Tct	P84S	orf7a	0.00166	0.858006	2	1	C>T
ERR5749375	27741	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	23466	7.24E-4	0	3,23444,0,17	HIGH	NONE	FRAME_SHIFT	ORF7a	aga/	R118	orf7a	0.000363	0.954278	3	2	CA>C
ERR5749375	27972	PASS	C	T	11476	0.912949	87	5,5,11366,65	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749375	28048	PASS	G	T	11412	0.915615	0	0,12,0,11396	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749375	28057	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11417	0.001401	0	0,11394,0,19	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	gCa/gTa	A55V	orf8	0.001401	0.051498	1	1	C>T
ERR5749375	28111	PASS	A	G	31005	0.9801	8	0,2,19584,11415	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749375	28270	PASS	TA	T	38045	0.996057	336	152,8,19357,18538	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749375	28280	PASS	G	C	37989	0.939798	21	11,1,19381,18523	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749375	28281	PASS	A	T	37989	0.917134	27	22,5,19378,18526	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749375	28282	PASS	T	A	37990	0.912872	8	20,11,19328,18535	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749375	28881	PASS	G	A	17404	0.786026	24	9,0,8638,8558	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749375	28882	PASS	G	A	17404	0.833946	11	7,1,8713,8508	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749375	28883	PASS	G	C	17404	0.944725	2	3,1,8738,8649	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749375	28977	PASS	C	T	8841	0.928854	0	0,3,1,8827	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749375	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	59677	0.001257	0	29939,29634,45,44	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749376	241	PASS	C	T	7695	0.869526	3	0,2,3817,3848	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749376	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	12693	0.003466	0	12643,10,44,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749376	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	12698	0.001496	0	12524,15,19,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749376	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	12698	0.001811	0	12524,15,23,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749376	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	12698	0.00882	0	12524,15,112,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749376	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12711	0.002045	7	11501,34,933,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749376	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	12711	0.001573	0	12656,35,20,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749376	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	12711	7.08E-4	0	12648,32,9,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttatg/gtg	VM84V	leader	0.000554	0.991848	4	1	GTTA>G
ERR5749376	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	12711	9.44E-4	0	12648,32,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749376	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	12710	7.08E-4	0	12648,37,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TA>T
ERR5749376	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	12710	9.44E-4	0	12648,37,12,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749376	657	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12715	0.001416	0	5,12691,0,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A131V	leader	0.001202	0.365979	3	1	C>T
ERR5749376	676	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	37732	9.28E-4	85	25005,12632,9,33	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G137	leader	0.000799	0.919273	2	1	C>T
ERR5749376	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	37728	5.83E-4	26	24998,12698,21,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749376	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	37730	3.71E-4	1	24885,12679,10,4	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749376	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	37730	0.003578	69	24885,12679,117,18	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749376	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25009	0.001	0	1,24953,0,28	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749376	913	PASS	C	T	25010	0.912955	0	0,14,1,24958	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749376	1510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	23630	0.002624	0	0,23365,0,68	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G235	nsp2	0.002159	0.937304	1	1	T>C
ERR5749376	2453	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17478	0.005321	0	1,17346,0,124	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L550F	nsp2	0.00429	0.842201	2	2	C>T
ERR5749376	2702	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	44247	8.14E-4	2196	43940,54,71,102	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F633V	nsp2	0.000632	0.333333	1	1	T>G
ERR5749376	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	87792	0.001412	2147483647	43799,40965,86,2706	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749376	3037	PASS	C	T	21899	0.808667	47	1,19,10935,10781	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749376	3267	PASS	C	T	23855	0.967009	0	2,0,23833,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749376	3575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	15903	7.55E-4	0	15892,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/ttTa	L287F?	nsp3	0.000594	0.059126	3	1	G>GT
ERR5749376	5388	PASS	C	A	7688	0.958247	0	1,0,7680,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749376	5986	PASS	C	T	14799	0.97662	2147483647	0,0,14786,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749376	6954	PASS	T	C	27042	0.816101	0	0,1,1,26899	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749376	7070	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	48664	7.4E-4	90	21475,27134,35,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggc/Agc	G1451S	nsp3	0.000698	0.101434	3	1	G>A
ERR5749376	7564	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	18779	0.001172	0	0,18754,0,22	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/	Y1617	nsp3	0.000586	0.056194	4	2	CT>C
ERR5749376	8669	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	27758	9.73E-4	0	27724,0,27,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F39L	nsp4	0.000973	0.22449	1	1	T>C
ERR5749376	10595	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	21789	9.64E-4	0	13,21715,0,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F181L	3Cpro	0.000964	0.076408	1	1	T>C
ERR5749376	11071	PASS	G	GT	23308	0.087481	0	20624,6,2039,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttc/ttTc	F34F?	nsp6	0.001292	0.087481	5	3	G>GT
ERR5749376	11071	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GTT	23308	0.021194	0	20624,6,494,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttc/ttTTc	F34F?	nsp6	0.001292	0.087481	5	3	G>GTT
ERR5749376	11071	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GTTT	23308	0.004677	0	20624,6,109,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_INSERTION	ORF1ab	ttc/ttTTTc	F34FF	nsp6	0.001292	0.087481	5	3	G>GTTT
ERR5749376	11071	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	23308	0.001459	0	23231,6,48,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L33F	nsp6	0.001292	0.087481	5	3	G>T
ERR5749376	11073	PASS	TC	T	23306	0.092251	0	21148,6,2150,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttc/	F34	nsp6	0.000385	0.092251	6	2	TC>T
ERR5749376	11074	PASS	C	CT	23306	0.092637	0	20622,6,2159,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CT
ERR5749376	11074	PASS	C	T	23306	0.820432	193	9,6,20969,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749376	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	23306	0.01712	0	20622,6,399,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749376	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTTT	23306	0.003819	0	20622,6,89,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_INSERTION	ORF1ab	ttg/ttTTTg	L37FL	nsp6	0.000965	0.945355	5	2	C>CTTT
ERR5749376	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	23148	0.001901	0	22807,0,325,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749376	11104	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	23083	0.0013	0	22666,0,39,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccT/ccC	P44	nsp6	0.000866	0.675414	2	1	T>C
ERR5749376	11287	PASS	GTCTGGTTTT	G	23287	0.996608	24	1,77,0,23208	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749376	12459	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	50134	6.58E-4	10	22134,27957,10,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T123I	nsp8	0.000658	0.986093	1	1	C>T
ERR5749376	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	36538	0.001341	0	18251,18182,27,27	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749376	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	17272	0.004111	2147483647	16853,140,12,261	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749376	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	33577	0.001698	3	16820,16718,32,25	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749376	14408	PASS	C	T	33577	0.843286	1	5,6,16737,16577	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749376	14676	PASS	C	T	15539	0.718064	0	2,0,15465,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749376	15279	PASS	C	T	25970	0.869349	0	1,0,25923,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749376	16176	PASS	T	C	23612	0.981916	3	1,0,11008,12594	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749376	16468	PASS	C	T	38498	0.97283	1	6,3,27465,11005	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ccc/Tcc	P78S	helicase	0.001077	0.977186	1	1	C>T
ERR5749376	16508	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	27488	0.001055	0	27422,9,57,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGt/gTt	G91V	helicase	0.000561	0.074909	2	2	G>T
ERR5749376	17615	PASS	A	G	17856	0.899306	0	0,3,9,17786	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749376	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	28168	7.1E-4	0	28146,0,20,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749376	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	29412	4.76E-4	0	0,29398,0,14	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749376	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	32322	0.002104	0	32223,0,69,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749376	21764	PASS	ATACATG	A	14776	0.997158	0	42,0,14734,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749376	21990	PASS	TTTA	T	14788	0.996416	0	0,53,9,14726	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749376	21994	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTAC	T	41026	3.41E-4	62	26247,14763,0,14	MODERATE	NONE	CODON_DELETION	S	tac/	Y145	S	0.000341	0.347498	1	1	TTAC>T
ERR5749376	23063	PASS	A	T	16588	0.862973	0	0,3,1,16495	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749376	23271	PASS	C	A	27094	0.918211	0	3,0,27063,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749376	23403	PASS	A	G	27085	0.9681	0	0,1,0,27058	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749376	23604	PASS	C	A	18432	0.934353	0	17,0,18402,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749376	23709	PASS	C	T	18421	0.939254	0	0,4,7,18377	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749376	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	38692	0.001344	4	20206,18404,31,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L752F	S	0.000334	0.080808	2	2	C>T
ERR5749376	24010	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATTTATTGAAGATCTAC	A	20377	4.91E-4	0	161,20207,0,10	HIGH	NONE	FRAME_SHIFT	S	attgaagatctacttttc/	IEDLLF818	S	0.000455	0.926398	4	2	ATTTATTGAAGATCTAC>A
ERR5749376	24127	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TTTTTG	34794	3.74E-4	29	14565,20229,0,13	HIGH	NONE	FRAME_SHIFT+STOP_GAINED	S	aac/TTTTGaac	N856F*?	S	0.000324	0.111888	4	1	T>TTTTTG
ERR5749376	24506	PASS	T	G	22974	0.974754	0	6,0,22963,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749376	24914	PASS	G	C	43644	0.958368	0	1,2,21743,21871	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749376	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	29678	0.001584	83	20107,9504,59,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749376	25350	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20326	0.001132	0	20296,0,23,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCa/cTa	P1263L	S	0.000626	0.97904	4	2	C>T
ERR5749376	25603	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20340	0.001967	0	14,20280,0,42	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	Cta/Tta	L71	orf3a	0.001967	0.924436	1	1	C>T
ERR5749376	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	23251	0.001032	0	23227,0,24,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749376	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	54741	7.49E-4	0	2,54694,0,41	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749376	26159	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTAATCCAG	T	54745	3.11E-4	0	2,54726,0,17	HIGH	NONE	FRAME_SHIFT	ORF3a	ccagtaatg/	PVM258	orf3a	0.000311	0.053032	2	2	TTAATCCAG>T
ERR5749376	26526	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	12838	0.00148	0	4,12793,0,28	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Gca/Tca	A2S	M	0.001224	0.951192	3	1	G>T
ERR5749376	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	14106	8.51E-4	0	9,14072,0,12	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749376	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	14106	0.001276	0	8,14080,0,18	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749376	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	14106	0.003615	0	5,14046,0,51	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749376	27382	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	22014	0.001317	0	105,21803,0,33	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF6	Gat/Cat	D61H	orf6	0.001236	0.927964	2	2	G>C
ERR5749376	27383	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	22014	0.001454	0	104,21842,0,48	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF6	gAt/gTt	D61V	orf6	0.001454	0.928985	1	1	A>T
ERR5749376	27384	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	22015	0.00159	0	103,21800,0,54	LOW	SILENT	SYNONYMOUS_CODING	ORF6	gaT/gaC	D61	orf6	0.00154	0.931035	3	3	T>C
ERR5749376	27390	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	22107	0.001176	0	189,21861,0,48	.	.	.	.	.	.	.	0.001176	0.885357	1	1	G>T
ERR5749376	27532	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27469	0.001165	0	27415,6,32,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Cat/Tat	H47Y	orf7a	0.001165	0.982473	2	1	C>T
ERR5749376	27641	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27311	0.003625	0	27141,9,105,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	tCa/tTa	S83L	orf7a	0.000983	0.911213	2	2	C>T
ERR5749376	27972	PASS	C	T	14063	0.896679	51	3,3,13910,94	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749376	28048	PASS	G	T	13965	0.925385	0	0,20,0,13938	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749376	28111	PASS	A	G	35735	0.976801	1	4,4,21735,13979	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749376	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	21732	5.06E-4	0	21721,7,11,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749376	28270	PASS	TA	T	42132	0.994565	493	226,12,21453,20450	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749376	28271	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AA	A	42130	5.93E-4	71	21641,20463,25,0	.	.	.	.	.	.	.	0.000482	0.924941	3	2	AA>A
ERR5749376	28280	PASS	G	C	42057	0.938346	37	22,3,21519,20433	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749376	28281	PASS	A	T	42057	0.917612	22	28,10,21514,20427	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749376	28282	PASS	T	A	42057	0.913689	12	31,16,21466,20439	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749376	28407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TACCCAATA	T	21770	5.51E-4	0	15,21744,0,12	HIGH	NONE	FRAME_SHIFT	N	cccaataat/	PNN46	N	0.000382	0.179673	1	1	TACCCAATA>T
ERR5749376	28881	PASS	G	A	20177	0.746047	14	10,2,9915,9921	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749376	28882	PASS	G	A	20176	0.829946	6	5,1,10083,9905	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749376	28883	PASS	G	C	20176	0.943002	0	3,3,10100,10046	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749376	28977	PASS	C	T	10295	0.930063	0	0,0,3,10261	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749376	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	40906	9.05E-4	140	30602,10211,6,33	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749376	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	60803	0.001102	0	30532,30170,44,41	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749377	71	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4930	0.002637	0	4912,0,13,0	.	.	.	.	.	.	.	0.002088	0.926791	2	1	C>T
ERR5749377	241	PASS	C	T	9194	0.857842	0	0,0,4572,4586	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749377	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	8144	0.001351	0	7578,0,555,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749377	553	PASS	G	A	8149	0.830163	0	0,0,4,8075	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caG/caA	Q96	leader	0.002322	0.830163	2	2	G>A
ERR5749377	913	PASS	C	T	22719	0.919715	0	0,13,2,22679	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749377	1108	PASS	C	T	13136	0.964297	0	1,0,13127,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I101	nsp2	0.002075	0.964297	1	1	C>T
ERR5749377	1510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	19738	0.00304	0	2,19521,0,64	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G235	nsp2	0.002159	0.937304	1	1	T>C
ERR5749377	1813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	20006	0.0013	0	0,19945,0,28	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcA	A336	nsp2	0.001022	0.152738	4	2	T>A
ERR5749377	3037	PASS	C	T	18548	0.828553	54	0,18,9255,9167	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749377	3114	PASS	G	A	9319	0.941088	0	0,1,0,9307	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGt/gAt	G132D	nsp3	0.028302	0.941088	2	1	G>A
ERR5749377	3267	PASS	C	T	22460	0.972084	0	2,0,22452,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749377	5388	PASS	C	A	5673	0.960515	2147483647	0,0,5671,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749377	5986	PASS	C	T	14053	0.976802	0	1,0,14039,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749377	6954	PASS	T	C	24379	0.83211	0	0,12,2,24268	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749377	7067	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	39425	7.86E-4	102	14948,24421,32,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E1450K	nsp3	0.000274	0.059217	5	3	G>A
ERR5749377	7740	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	22760	0.001054	0	22732,0,27,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gAt/gGt	D1674G	nsp3	0.000834	0.078818	3	2	A>G
ERR5749377	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	21683	6.0E-4	18	14716,6955,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749377	11287	PASS	GTCTGGTTTT	G	22899	0.998297	0	0,38,0,22860	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749377	12125	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	17710	0.001242	0	7,17639,0,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y12H	nsp8	0.000847	0.113436	1	1	T>C
ERR5749377	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	32529	0.001752	1	16239,16188,29,32	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749377	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	14997	0.004201	2147483647	14694,85,9,197	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749377	14408	PASS	C	T	29264	0.848585	0	4,3,14611,14481	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749377	14676	PASS	C	T	13970	0.748819	0	10,0,13915,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749377	15279	PASS	C	T	21642	0.895158	0	3,0,21614,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749377	16176	PASS	T	C	18248	0.983889	7	2,0,7417,10824	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749377	17615	PASS	A	G	13100	0.909084	2147483647	0,0,0,13071	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749377	17750	PASS	C	T	13855	0.881487	38	1,1,13835,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A505V	helicase	0.001509	0.881487	2	1	C>T
ERR5749377	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	23904	5.44E-4	0	23891,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749377	19079	PASS	A	G	28458	0.96609	0	4,0,28441,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gAa/gGa	E347G	ExoN	0.001121	0.967175	2	1	A>G
ERR5749377	19854	PASS	C	T	21745	0.960911	306	9,4,0,21706	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D78	endoR	0.950322	0.965654	1	1	C>T
ERR5749377	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22157	0.00158	0	22104,0,37,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749377	20397	PASS	G	A	32205	0.171868	1	17,25709,3,6239	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaG/aaA	K259	endoR	0.171868	0.171868	1	1	G>A
ERR5749377	20578	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	36432	0.001235	0	36329,0,98,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtg/Ttg	V320L	endoR	0.00085	0.958277	3	1	G>T
ERR5749377	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	36426	8.51E-4	0	36339,0,34,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749377	21621	PASS	C	T	18311	0.944623	0	0,5,0,18285	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCc/aTc	T20I	S	0.00148	0.944623	2	2	C>T
ERR5749377	21764	PASS	ATACATG	A	13965	0.997494	0	35,0,13929,1	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749377	21777	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	13965	0.039098	0	13379,1,574,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gGg/gAg	G72E	S	0.039098	0.058595	2	1	G>A
ERR5749377	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	13965	0.001074	0	13949,1,15,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749377	21976	PASS	T	C	13975	0.977603	358	11,1,1,13955	LOW	SILENT	SYNONYMOUS_CODING	S	gaT/gaC	D138	S	0.000856	0.977603	2	2	T>C
ERR5749377	21990	PASS	TTTA	T	13974	0.998783	0	0,17,11,13946	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749377	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	32341	9.59E-4	0	14831,17463,15,16	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749377	23042	PASS	T	C	14789	0.900602	0	0,2,3,14754	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Cca	S494P	S	0.030769	0.900602	1	1	T>C
ERR5749377	23063	PASS	A	T	14822	0.838213	0	0,6,0,14736	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749377	23271	PASS	C	A	23700	0.925738	0	3,0,23677,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749377	23403	PASS	A	G	23692	0.973451	0	0,3,0,23681	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749377	23604	PASS	C	A	16483	0.944852	0	6,0,16471,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749377	23709	PASS	C	T	16470	0.945477	0	0,3,0,16445	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749377	24237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13039	0.001611	0	13004,0,26,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gTt	A892V	S	0.001242	0.889739	1	1	C>T
ERR5749377	24506	PASS	T	G	18577	0.974323	0	5,0,18568,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749377	24914	PASS	G	C	37715	0.95983	0	0,0,18784,18907	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749377	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	26779	0.001942	63	19643,7071,59,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749377	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	15884	9.44E-4	0	15869,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749377	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	13418	7.45E-4	0	0,13408,0,10	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749377	27676	PASS	G	T	22963	0.877803	0	0,107,2,22838	HIGH	NONSENSE	STOP_GAINED	ORF7a	Gaa/Taa	E95*	orf7a	0.000609	0.877803	2	2	G>T
ERR5749377	27972	PASS	C	T	12166	0.899145	23	0,1,12073,55	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749377	28048	PASS	G	T	12123	0.926256	0	0,17,0,12102	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749377	28111	PASS	A	G	35027	0.980301	0	8,4,22885,12118	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749377	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22892	0.001485	0	22819,4,35,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749377	28270	PASS	TA	T	44582	0.995581	471	197,7,22634,21751	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749377	28280	PASS	G	C	44503	0.93951	32	20,3,22671,21726	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749377	28281	PASS	A	T	44503	0.917489	49	38,8,22649,21733	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749377	28282	PASS	T	A	44504	0.914884	8	30,19,22611,21738	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749377	28881	PASS	G	A	17324	0.773089	12	5,0,8556,8559	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749377	28882	PASS	G	A	17323	0.837153	11	9,2,8641,8524	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749377	28883	PASS	G	C	17323	0.945564	0	0,0,8667,8643	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749377	28977	PASS	C	T	8795	0.921433	2147483647	0,0,0,8781	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749377	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	63568	0.001432	0	31883,31555,57,57	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749377	29302	PASS	T	C	31980	0.934178	328	10,8,1,31919	LOW	SILENT	SYNONYMOUS_CODING	N	gaT/gaC	D343	N	0.013749	0.934178	1	1	T>C
ERR5749377	29779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	10345	0.002223	0	0,10314,0,31	.	.	.	.	.	.	.	0.001489	0.975228	1	1	G>T
ERR5749378	239	PASS	T	C	48	0.25	0	17,16,7,7	.	.	.	.	.	.	.	0.000495	0.25	4	1	T>C
ERR5749378	241	PASS	C	T	49	0.857143	0	0,0,24,25	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749378	379	PASS	C	A	130	0.876923	0	0,0,105,25	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtA	V38	leader	0.847169	0.944238	2	1	C>A
ERR5749378	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	631	0.038035	16	502,105,24,0	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749378	913	PASS	C	T	526	0.908745	2147483647	0,0,0,526	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749378	3037	PASS	C	T	276	0.869565	0	0,0,138,137	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749378	3045	PASS	C	T	276	0.07971	0	125,125,13,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCa/cTa	P109L	nsp3	0.001332	0.07971	2	2	C>T
ERR5749378	3267	PASS	C	T	404	0.970297	2147483647	0,0,404,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749378	3340	PASS	G	T	803	0.845579	0	31,31,372,369	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtG/gtT	V207	nsp3	0.000712	0.845579	3	2	G>T
ERR5749378	3802	PASS	T	TA	405	0.064198	18	70,309,0,26	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/aaAt	N363K?	nsp3	0.000554	0.064198	4	2	T>TA
ERR5749378	3811	PASS	C	T	405	0.920988	0	0,0,70,335	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ctC/ctT	L364	nsp3	0.002015	0.946635	1	1	C>T
ERR5749378	5388	PASS	C	A	104	0.923077	2147483647	0,0,104,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749378	5501	PASS	A	G	102	0.941176	2147483647	0,0,0,102	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Aga/Gga	R928G	nsp3	0.924621	0.941176	1	1	A>G
ERR5749378	5986	PASS	C	T	624	0.972756	2147483647	0,0,624,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749378	6954	PASS	T	C	624	0.807692	2147483647	0,0,0,623	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749378	9006	PASS	T	G	1729	0.052053	0	1636,0,92,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gTt/gGt	V151G	nsp4	0.001514	0.052053	1	1	T>G
ERR5749378	10595	PASS	T	C	746	0.076408	0	0,681,0,65	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F181L	3Cpro	0.000964	0.076408	1	1	T>C
ERR5749378	11074	PASS	CT	C	1999	0.057029	0	1884,0,114,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000965	0.945355	5	2	CT>C
ERR5749378	11075	PASS	T	C	1999	0.077039	0	1705,0,178,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F35L	nsp6	0.000555	0.885796	4	2	T>C
ERR5749378	11287	PASS	GTCTGGTTTT	G	1996	0.996994	0	0,5,0,1990	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749378	12756	PASS	C	T	1226	0.798532	0	0,0,222,1004	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T24I	nsp9	0.000889	0.877514	1	1	C>T
ERR5749378	13498	PASS	A	G	1151	0.94179	0	3,2,574,570	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Aca/Gca	T20A	RdRp	0.001341	0.952048	1	1	A>G
ERR5749378	13787	PASS	G	C	244	0.07377	0	112,112,10,10	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cGt/cCt	R116P	RdRp	0.07377	0.07377	1	1	G>C
ERR5749378	14098	PASS	G	T	1087	0.065317	0	1008,8,71,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggt/Tgt	G220C	RdRp	0.000806	0.065317	4	2	G>T
ERR5749378	14216	PASS	C	T	1079	0.962929	2147483647	0,0,0,1079	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T259I	RdRp	0.006249	0.962929	1	1	C>T
ERR5749378	14408	PASS	C	T	60	0.85	0	0,0,29,29	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749378	14676	PASS	C	T	388	0.770619	2147483647	0,0,387,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749378	15096	PASS	T	C	381	0.965879	0	0,0,9,371	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaT/aaC	N552	RdRp	0.941667	0.970182	1	1	T>C
ERR5749378	15279	PASS	C	T	566	0.883392	2147483647	0,0,566,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749378	16176	PASS	T	C	666	0.974474	0	0,0,73,593	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749378	16523	PASS	C	T	2322	0.056848	0	2184,0,137,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T96I	helicase	0.001196	0.056848	2	1	C>T
ERR5749378	18256	PASS	T	C	417	0.057554	0	0,393,0,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F73L	ExoN	0.057554	0.057554	1	1	T>C
ERR5749378	19983	PASS	C	CT	244	0.065574	0	228,0,16,0	HIGH	NONE	FRAME_SHIFT+STOP_GAINED	ORF1ab	gat/Tgat	D124*?	endoR	0.000884	0.981982	5	2	C>CT
ERR5749378	21764	PASS	ATACATG	A	1054	0.997154	0	3,0,1051,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749378	21990	PASS	TTTA	T	1054	1.0	2147483647	0,0,0,1054	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749378	23063	PASS	A	T	1379	0.870921	2147483647	0,0,0,1373	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749378	23271	PASS	C	A	711	0.918425	2147483647	0,0,711,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749378	23403	PASS	A	G	711	0.981716	2147483647	0,0,0,711	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749378	23604	PASS	C	A	981	0.955148	0	2,0,979,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749378	23709	PASS	C	T	976	0.954918	2147483647	0,0,0,974	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749378	24506	PASS	T	G	934	0.973233	0	1,0,933,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749378	24914	PASS	G	C	12989	0.960659	0	0,0,6474,6509	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749378	26493	PASS	G	GT	664	0.069277	0	0,618,0,46	.	.	.	.	.	.	.	0.001082	0.069277	3	1	G>GT
ERR5749378	27972	PASS	C	T	220	0.868182	0	0,0,219,1	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749378	28048	PASS	G	T	221	0.932127	2147483647	0,0,0,221	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749378	28095	PASS	A	T	221	0.963801	2147483647	0,0,0,221	HIGH	NONSENSE	STOP_GAINED	ORF8	Aaa/Taa	K68*	orf8	0.002672	0.967672	2	2	A>T
ERR5749378	28111	PASS	A	G	3757	0.982965	0	0,0,3536,221	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749378	28270	PASS	TA	T	6878	0.995493	62	29,2,3497,3350	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749378	28280	PASS	G	C	6863	0.93516	3	2,0,3500,3349	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749378	28281	PASS	A	T	6863	0.914323	0	4,4,3495,3347	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749378	28282	PASS	T	A	6864	0.908217	2	3,1,3497,3351	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749378	28498	PASS	C	T	3095	0.95832	2147483647	0,0,3089,0	LOW	SILENT	SYNONYMOUS_CODING	N	aaC/aaT	N75	N	0.953211	0.95832	1	1	C>T
ERR5749378	28674	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3095	0.00517	0	0,3075,0,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gCa/gTa	A134V	N	0.001338	0.958634	1	1	C>T
ERR5749378	28881	PASS	G	A	112	0.848214	0	0,0,56,56	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749378	28882	PASS	G	A	112	0.866071	0	0,0,56,56	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749378	28883	PASS	G	C	112	0.991071	0	0,0,56,56	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749378	28977	PASS	C	T	56	0.982143	2147483647	0,0,0,56	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749379	241	PASS	C	T	7654	0.865822	4	1,4,3807,3812	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749379	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	7969	0.002259	0	7950,3,18,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749379	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	7968	0.002385	0	7906,3,19,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749379	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	7968	0.003514	0	7906,3,28,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749379	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	7966	0.002385	0	7269,8,580,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749379	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	7966	0.002887	0	7934,8,23,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749379	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	7964	0.001507	0	7941,8,12,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749379	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	28046	4.99E-4	4	20056,7975,12,2	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749379	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	28045	3.92E-4	13	20007,7968,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749379	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	28045	0.001925	11	20007,7968,45,9	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749379	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20060	0.001097	0	0,20012,0,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749379	913	PASS	C	T	20060	0.922233	0	0,6,0,20024	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749379	2948	PASS	A	T	9883	0.630881	0	1,0,9765,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Att/Ttt	I77F	nsp3	0.630881	0.630881	1	1	A>T
ERR5749379	3037	PASS	C	T	19605	0.802244	60	0,20,9806,9650	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749379	3164	PASS	G	A	9911	0.970235	758	26,1,0,9880	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gct/Act	A149T	nsp3	0.962341	0.970235	1	1	G>A
ERR5749379	3177	PASS	C	T	26368	0.896807	7	5,0,16471,9871	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P153L	nsp3	0.000773	0.96008	3	2	C>T
ERR5749379	3267	PASS	C	T	16482	0.970999	2147483647	0,0,16466,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749379	5388	PASS	C	A	6185	0.957478	2147483647	0,0,6181,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749379	5986	PASS	C	T	3452	0.975377	2147483647	0,0,3449,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749379	6266	PASS	G	A	22342	0.949825	146	1,4,22331,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gcc/Acc	A1183T	nsp3	0.000676	0.950772	2	2	G>A
ERR5749379	6954	PASS	T	C	21239	0.823579	0	0,1,3,21127	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749379	7067	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	38926	4.11E-4	55	17594,21314,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gaa/	E1450	nsp3	0.000274	0.059217	5	3	GA>G
ERR5749379	7735	PASS	C	T	21967	0.954659	0	1,0,21935,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I1672	nsp3	0.000658	0.954659	3	2	C>T
ERR5749379	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	28091	6.41E-4	48	15039,13034,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749379	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	18512	0.00135	0	18461,0,42,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749379	11287	PASS	GTCTGGTTTT	G	18511	0.997029	25	1,55,0,18456	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749379	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	33682	0.001009	0	16825,16779,17,18	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749379	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	14577	0.004116	2147483647	14238,132,4,199	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749379	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	28337	0.001659	0	14208,14101,24,23	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749379	14408	PASS	C	T	28337	0.842044	1	5,6,14145,13950	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749379	14676	PASS	C	T	11899	0.774771	0	2,0,11866,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749379	15279	PASS	C	T	19865	0.900126	0	3,0,19837,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749379	16176	PASS	T	C	17613	0.979958	0	0,0,8155,9448	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749379	17750	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11915	0.002182	0	11875,1,30,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A505V	helicase	0.001509	0.881487	2	1	C>T
ERR5749379	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	21133	7.57E-4	0	21117,0,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749379	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30852	0.001621	0	30780,0,56,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749379	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29960	0.001135	1	14681,14940,19,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749379	21764	PASS	ATACATG	A	13733	0.997233	0	38,0,13695,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749379	21990	PASS	TTTA	T	13737	0.997307	0	0,37,2,13698	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749379	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27942	9.66E-4	2	13462,14421,15,12	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749379	23063	PASS	A	T	13480	0.869362	0	0,2,8,13392	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749379	23271	PASS	C	A	20852	0.921111	0	2,0,20832,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749379	23403	PASS	A	G	20843	0.974188	0	0,5,0,20830	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749379	23604	PASS	C	A	16096	0.944085	0	20,0,16066,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749379	23709	PASS	C	T	16078	0.9462	0	0,7,4,16043	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749379	23817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	31835	8.8E-4	0	15712,16078,15,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTt/cCt	L752P	S	0.000646	0.066832	1	1	T>C
ERR5749379	24127	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	28560	7.35E-4	1	12824,15723,8,13	HIGH	NONE	FRAME_SHIFT	S	aac/	N856	S	0.000324	0.111888	4	1	TA>T
ERR5749379	24506	PASS	T	G	16463	0.975339	0	7,0,16450,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749379	24914	PASS	G	C	33362	0.959805	0	0,0,16610,16718	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749379	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	20240	0.001482	495	20149,17,11,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749379	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	52507	3.24E-4	0	2,52484,0,17	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749379	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	12696	8.66E-4	0	6,12671,0,11	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749379	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	12697	0.003623	0	3,12639,0,46	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749379	27972	PASS	C	T	13056	0.910463	19	1,1,12943,74	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749379	28048	PASS	G	T	12992	0.917411	0	0,20,0,12966	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749379	28111	PASS	A	G	30881	0.979049	0	2,2,17867,12997	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749379	28270	PASS	TA	T	34480	0.995273	401	166,5,17640,16677	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749379	28280	PASS	G	C	34401	0.936397	14	6,0,17669,16655	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749379	28281	PASS	A	T	34402	0.917999	17	17,5,17656,16654	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749379	28282	PASS	T	A	34403	0.910153	0	18,18,17607,16657	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749379	28881	PASS	G	A	17310	0.762507	12	11,3,8538,8513	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749379	28882	PASS	G	A	17307	0.831744	15	6,0,8631,8498	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749379	28883	PASS	G	C	17307	0.944936	3	0,1,8659,8633	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749379	28977	PASS	C	T	8838	0.929396	0	0,3,1,8816	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749379	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	36785	0.001142	222	27918,8787,3,42	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749379	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	55477	7.21E-4	0	27864,27541,26,25	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749379	29584	PASS	T	C	20394	0.957929	3	0,1,10837,9529	LOW	SILENT	SYNONYMOUS_CODING	ORF10	ttT/ttC	F9	orf10	0.957929	0.957929	1	1	T>C
ERR5749380	241	PASS	C	T	1094	0.840037	0	0,0,545,537	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749380	442	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	4265	0.001641	0	4258,0,7,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/	V60	leader	0.001641	0.297974	2	2	CG>C
ERR5749380	478	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	4263	0.001407	0	4257,0,6,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K72	leader	0.000799	0.109934	2	2	CA>C
ERR5749380	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	4254	0.005877	0	4231,0,25,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749380	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	4309	0.006498	0	4212,55,28,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749380	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTTGA	G	4309	0.003249	0	4212,55,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTTGA>G
ERR5749380	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	4339	0.002074	0	4240,90,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749380	597	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	4264	0.00258	0	0,4253,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggc/	G112	leader	0.000983	0.333333	2	2	TG>T
ERR5749380	673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	10328	0.008424	153	6048,4193,14,73	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggc/	G137	leader	0.000454	0.602236	3	2	CG>C
ERR5749380	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	10328	0.007262	116	5991,4260,71,4	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749380	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6057	0.002642	0	0,6029,0,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749380	913	PASS	C	T	6058	0.909376	0	0,9,0,6033	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749380	1230	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AGT	A	7319	0.002323	0	0,7302,0,17	HIGH	NONE	FRAME_SHIFT	ORF1ab	tgtgat/	CD143	nsp2	0.00129	0.969658	2	2	AGT>A
ERR5749380	1426	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8187	0.002931	0	8153,0,28,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y207	nsp2	0.002931	0.892537	1	1	C>T
ERR5749380	1694	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	9739	0.001643	0	9717,0,17,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Ttg/Ctg	L297	nsp2	0.001643	0.974382	1	1	T>C
ERR5749380	1846	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATC	A	9738	0.001438	0	0,9724,0,14	HIGH	NONE	FRAME_SHIFT	ORF1ab	tca/	S348	nsp2	0.001438	0.945471	2	2	ATC>A
ERR5749380	1862	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	9739	0.001951	0	0,9720,0,19	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/	Y354	nsp2	0.000585	0.936867	4	2	CT>C
ERR5749380	2185	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	4604	0.002172	0	5,4589,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F461	nsp2	0.000441	0.963529	4	3	GT>G
ERR5749380	3037	PASS	C	T	6872	0.821013	18	0,6,3434,3392	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749380	3267	PASS	C	T	6909	0.973802	2147483647	0,0,6907,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749380	3575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	3031	0.004619	0	3018,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L287	nsp3	0.000594	0.059126	3	1	GT>G
ERR5749380	3787	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3034	0.003626	0	2,3020,0,11	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y356	nsp3	0.002354	0.956541	1	1	C>T
ERR5749380	3832	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	2373	0.00295	0	2366,0,7,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L373	nsp3	0.000689	0.327273	4	2	CT>C
ERR5749380	3961	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	2364	0.003807	0	2354,1,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K415	nsp3	0.000417	0.869983	2	2	CA>C
ERR5749380	4832	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTAGGTA	C	15860	0.001513	0	7926,7914,12,12	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtatagaa/gaa	GIE706E	nsp3	0.000542	0.727166	3	2	CTAGGTA>C
ERR5749380	5100	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	5658	0.003181	0	5640,0,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tca/	S794	nsp3	0.001443	0.071429	2	2	CA>C
ERR5749380	5388	PASS	C	A	1842	0.962541	2147483647	0,0,1841,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749380	5986	PASS	C	T	5057	0.97192	0	1,0,5038,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749380	6031	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5056	0.00356	0	5013,0,21,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N1104	nsp3	0.00356	0.908294	1	1	C>T
ERR5749380	6310	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7622	0.00551	0	7571,0,43,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	agC/agT	S1197	nsp3	0.00099	0.94715	2	2	C>T
ERR5749380	6762	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	13520	0.002145	19	7868,5614,30,8	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aAt	T1348N	nsp3	0.001474	0.966761	2	1	C>A
ERR5749380	6936	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15694	0.00274	0	7727,7652,22,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S1406F	nsp3	0.000553	0.91447	2	2	C>T
ERR5749380	6954	PASS	T	C	7874	0.790069	0	0,1,0,7819	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749380	7058	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	7896	0.003293	0	0,7837,0,32	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggt/Agt	G1447S	nsp3	0.000616	0.910617	2	2	G>A
ERR5749380	8603	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	3836	0.002607	0	0,3820,0,10	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Atc	F17I	nsp4	0.002607	0.974959	2	1	T>A
ERR5749380	8950	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9616	0.002808	22	7792,1795,27,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I132	nsp4	0.002808	0.982604	1	1	C>T
ERR5749380	9198	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	7821	0.003197	0	0,7796,0,25	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F216	nsp4	0.000543	0.93476	4	2	CT>C
ERR5749380	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	9115	0.005376	17	8290,776,49,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749380	10189	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11388	0.002547	0	11357,0,29,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acC/acT	T45	3Cpro	0.000675	0.074883	2	2	C>T
ERR5749380	10193	PASS	G	A	11387	0.855888	0	2,0,11371,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E47K	3Cpro	0.000774	0.869819	2	2	G>A
ERR5749380	10195	PASS	A	T	11387	0.965048	0	5,0,11378,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gaA/gaT	E47D	3Cpro	0.951998	0.969772	1	1	A>T
ERR5749380	10244	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAT	C	11383	0.001845	0	11362,0,21,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cataat/	HN64	3Cpro	0.001845	0.074194	2	2	CAT>C
ERR5749380	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	14348	0.002648	0	14008,0,38,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749380	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14348	0.004042	0	14269,0,62,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749380	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	14345	0.00474	0	14258,0,81,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749380	11220	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	27781	0.001584	53	13442,14227,7,39	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTg/aCg	M83T	nsp6	0.000767	0.057907	2	2	T>C
ERR5749380	11235	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14335	0.002721	0	0,14288,0,40	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A88V	nsp6	0.000512	0.942208	2	2	C>T
ERR5749380	11287	PASS	GTCTGGTTTT	G	14339	0.99721	0	0,40,0,14299	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749380	11991	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	16510	0.003937	0	16434,0,69,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gAa/gGa	E50G	nsp7	0.003937	0.05063	1	1	A>G
ERR5749380	12024	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16506	0.002605	0	16431,0,45,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCc/tTc	S61F	nsp7	0.002605	0.052021	1	1	C>T
ERR5749380	12741	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12942	0.002318	168	3537,9370,30,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T19I	nsp9	0.000486	0.962552	2	2	C>T
ERR5749380	13208	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AATAT	A	23736	0.001011	0	11862,11853,12,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	aatatg/	NM62	nsp10	0.000407	0.953357	4	2	AATAT>A
ERR5749380	13384	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	6784	0.003243	0	6762,0,22,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggt/	G121	nsp10	0.000578	0.056161	3	3	CG>C
ERR5749380	13458	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6784	0.002064	0	6767,0,14,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCg/tTg	S6L	nsp11	0.001017	0.058608	4	2	C>T
ERR5749380	13468	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6782	0.002064	0	6752,0,20,0	LOW	SILENT	SPLICE_SITE_REGION+SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N9	RdRp	0.000713	0.076498	2	2	C>T
ERR5749380	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13548	0.002879	0	6753,6736,22,22	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749380	13995	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	8294	0.002411	0	8271,0,20,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcC	A185	RdRp	0.000877	0.050235	2	2	T>C
ERR5749380	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	6221	0.004019	1658	6054,65,2,97	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749380	14408	PASS	C	T	12056	0.843563	0	3,3,6014,5958	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749380	14676	PASS	C	T	4470	0.758389	0	3,0,4454,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749380	15042	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	4538	0.002424	0	4520,0,13,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaT/aaC	N534	RdRp	0.002424	0.901818	2	2	T>C
ERR5749380	15279	PASS	C	T	6886	0.889486	2147483647	0,0,6874,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749380	15620	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	12395	0.001694	0	12328,0,24,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cTt/cCt	L727P	RdRp	0.001388	0.088584	1	1	T>C
ERR5749380	15652	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAC	G	12393	0.002421	0	12363,0,30,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T739	RdRp	0.000691	0.935936	2	2	GAC>G
ERR5749380	15654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12393	0.001856	0	12328,0,25,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D738	RdRp	0.001856	0.060658	2	2	C>T
ERR5749380	16176	PASS	T	C	6985	0.979528	0	0,0,2166,4817	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749380	16792	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CGT	C	23200	0.001121	86	10721,12453,26,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gta/	V187	helicase	0.000335	0.072562	5	2	CGT>C
ERR5749380	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	10747	0.00121	0	10734,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749380	17602	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	10258	0.002047	59	9848,10176,0,21	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/	Y457	helicase	0.001035	0.156682	1	1	GT>G
ERR5749380	17717	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GC	G	16629	5.41E-4	37	6409,10211,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggc/	G494	helicase	0.000541	0.057143	2	2	GC>G
ERR5749380	17762	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTG	C	6418	0.002805	0	6400,4,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtc/	V510	helicase	0.000697	0.912542	2	2	CTG>C
ERR5749380	18029	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11774	0.001444	44	5354,6394,0,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCa/gTa	A598V	helicase	0.001444	0.063613	1	1	C>T
ERR5749380	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	20920	6.21E-4	0	20907,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749380	18747	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	20917	0.004016	0	20833,0,84,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tataat/	YN237	ExoN	0.000375	0.982946	4	2	CTA>C
ERR5749380	18756	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	20913	0.002056	0	20856,0,57,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccG/ccT	P239	ExoN	0.000392	0.942688	3	2	G>T
ERR5749380	19023	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	4870	0.002259	0	4851,0,14,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtT/gtC	V328	ExoN	0.001259	0.951351	2	1	T>C
ERR5749380	19269	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13237	0.001435	63	8362,4847,2,19	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N410	ExoN	0.000773	0.954777	2	2	C>T
ERR5749380	20233	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17850	0.002801	0	17792,1,52,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ccc/Tcc	P205S	endoR	0.000964	0.980008	2	1	C>T
ERR5749380	20445	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	17984	0.001446	0	145,17813,0,26	HIGH	NONE	FRAME_SHIFT	ORF1ab	aac/aaAc	N277K?	endoR	0.000518	0.059736	4	2	T>TA
ERR5749380	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	10422	0.002399	0	0,10397,0,25	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TA>T
ERR5749380	21304	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	11417	0.001226	0	15,11388,0,14	HIGH	NONE	FRAME_SHIFT	ORF1ab	cgc/	R216	MethTr	0.000411	0.605296	3	2	CG>C
ERR5749380	21727	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6962	0.003447	0	6926,8,25,0	LOW	SILENT	SYNONYMOUS_CODING	S	ttC/ttT	F55	S	0.000896	0.878141	2	2	C>T
ERR5749380	21764	PASS	ATACATG	A	6954	0.989215	0	75,0,6879,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749380	21990	PASS	TTTA	T	6954	0.989215	0	0,75,0,6879	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749380	22323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17381	0.001151	29	5188,12166,0,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCt/tTt	S254F	S	0.000812	0.978946	3	2	C>T
ERR5749380	22690	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	13599	0.0025	0	13439,65,42,0	LOW	SILENT	SYNONYMOUS_CODING	S	acT/acC	T376	S	0.000815	0.051311	2	1	T>C
ERR5749380	23063	PASS	A	T	8472	0.859537	0	0,3,0,8421	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749380	23191	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8425	0.00273	0	8380,0,23,0	LOW	SILENT	SYNONYMOUS_CODING	S	ttC/ttT	F543	S	0.000538	0.973337	2	2	C>T
ERR5749380	23271	PASS	C	A	8422	0.908692	0	1,0,8415,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749380	23277	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8422	0.002137	0	8388,0,23,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCt/aTt	T572I	S	0.001007	0.74768	1	1	C>T
ERR5749380	23403	PASS	A	G	8418	0.96947	2147483647	0,0,0,8414	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749380	23481	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16311	0.002207	123	7828,8419,39,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCt/tTt	S640F	S	0.001098	0.964516	1	1	C>T
ERR5749380	23522	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTT	G	7886	0.003043	0	7862,0,24,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	gaacatgtcaacaactcatatgagtgtgacatacccattggtgcaggtatatgcgctagttat/gat	EHVNNSYECDIPIGAGICASY654D	S	0.00053	0.959726	5	2	GAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTT>G
ERR5749380	23604	PASS	C	A	7886	0.936216	0	7,0,7871,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749380	23709	PASS	C	T	7896	0.932624	0	0,2,24,7861	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749380	23758	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7885	0.001776	0	0,7854,0,14	LOW	SILENT	SYNONYMOUS_CODING	S	acC/acT	T732	S	0.001489	0.964055	1	1	C>T
ERR5749380	23766	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7885	0.001902	0	0,7867,0,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCa/tTa	S735L	S	0.001668	0.163547	1	1	C>T
ERR5749380	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	10406	0.002018	129	2500,7885,21,0	HIGH	NONE	FRAME_SHIFT	S	ttg/	L753	S	0.000334	0.080808	2	2	CT>C
ERR5749380	24382	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	5697	0.002984	0	0,5678,0,19	LOW	SILENT	SYNONYMOUS_CODING	S	tcC/tcA	S940	S	0.002118	0.920404	2	1	C>A
ERR5749380	24506	PASS	T	G	9915	0.974483	0	1,0,9909,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749380	24794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	16192	0.001791	0	16155,0,32,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gct/Tct	A1078S	S	0.001791	0.957884	1	1	G>T
ERR5749380	24914	PASS	G	C	32203	0.958141	0	0,0,16039,16136	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749380	25350	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	16885	0.003139	0	16832,0,53,0	HIGH	NONE	FRAME_SHIFT	S	cca/	P1263	S	0.000626	0.97904	4	2	CA>C
ERR5749380	25555	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	16878	0.00154	0	0,16852,0,26	HIGH	NONE	FRAME_SHIFT	ORF3a	ttt/	F56	orf3a	0.000552	0.900573	5	2	GT>G
ERR5749380	25571	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16881	0.002014	0	0,16844,0,34	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	tCc/tTc	S60F	orf3a	0.001558	0.922217	1	1	C>T
ERR5749380	25587	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	16882	0.002902	0	0,16811,0,49	HIGH	NONE	FRAME_SHIFT	ORF3a	aag/	K67	orf3a	0.000598	0.813206	6	2	CA>C
ERR5749380	25587	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAAA	C	16882	0.001303	0	0,16811,0,22	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF3a	aaaaag/aag	KK66K	orf3a	0.000598	0.813206	6	2	CAAA>C
ERR5749380	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	1627	0.010449	264	1578,22,1,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749380	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	17242	5.22E-4	0	0,17233,0,9	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749380	26159	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTAATCCAG	T	17242	0.002378	0	0,17201,0,41	HIGH	NONE	FRAME_SHIFT	ORF3a	ccagtaatg/	PVM258	orf3a	0.000311	0.053032	2	2	TTAATCCAG>T
ERR5749380	26256	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23167	9.5E-4	18	5883,17247,11,11	LOW	SILENT	SYNONYMOUS_CODING	E	ttC/ttT	F4	E	0.000748	0.969561	2	2	C>T
ERR5749380	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	G	7261	0.002066	0	0,7234,0,15	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/	ACLVGLMWLSYFIASF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT>G
ERR5749380	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTT	G	7261	0.00179	0	0,7234,0,13	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/	ACLVGLMWLSYFIASF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTT>G
ERR5749380	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	7261	0.001928	0	0,7247,0,14	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749380	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	7261	0.011293	0	0,7172,0,82	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749380	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	G	7261	9.64E-4	0	0,7172,0,7	HIGH	NONE	FRAME_SHIFT	M	cttgtaggcttgatgtggctcagctacttcattgcttctttc/	LVGLMWLSYFIASF87	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT>G
ERR5749380	26801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	G	7264	0.002753	0	0,7051,0,20	LOW	SILENT	SYNONYMOUS_CODING	M	ctC/ctG	L93	M	0.002753	0.954545	3	1	C>G
ERR5749380	26907	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20929	0.001625	0	20880,3,34,0	LOW	SILENT	SYNONYMOUS_CODING	M	Ctg/Ttg	L129	M	0.000817	0.976032	1	1	C>T
ERR5749380	27371	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13596	0.001912	0	27,13515,0,31	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF6	cCa/cTa	P57L	orf6	0.00148	0.066731	2	2	C>T
ERR5749380	27493	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26769	0.001121	77	13166,13562,1,31	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Cct/Tct	P34S	orf7a	0.000794	0.971493	2	1	C>T
ERR5749380	27494	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	26769	6.72E-4	42	13156,13595,17,1	HIGH	NONE	FRAME_SHIFT	ORF7a	tgc/	C35	orf7a	0.000672	0.961447	2	2	CT>C
ERR5749380	27604	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	13172	0.001063	0	13158,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF7a	gta/gtTa	V71V?	orf7a	0.001008	0.967671	3	2	G>GT
ERR5749380	27641	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	13160	0.001292	0	13144,0,17,0	HIGH	NONE	FRAME_SHIFT	ORF7a	tca/	S83	orf7a	0.000983	0.911213	2	2	CA>C
ERR5749380	27793	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTTTA	T	13177	0.002125	0	1,13148,0,28	HIGH	NONE	FRAME_SHIFT	ORF7b	ttttta/	FL13	orf7b	0.002125	0.99633	2	1	TTTTA>T
ERR5749380	27972	PASS	C	T	3711	0.900835	0	0,0,3662,34	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749380	28048	PASS	G	T	3680	0.933967	0	0,4,0,3674	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749380	28111	PASS	A	G	21907	0.977907	0	2,0,18218,3674	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749380	28250	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TCTG	18208	9.34E-4	0	18191,0,17,0	MODERATE	NONE	CODON_INSERTION	ORF8	ttc/CTGttc	F120LF	orf8	0.000494	0.993968	5	3	T>TCTG
ERR5749380	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	18200	9.34E-4	0	18187,0,17,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749380	28270	PASS	TA	T	35218	0.994435	492	198,5,17956,17066	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749380	28280	PASS	G	C	35153	0.937502	27	13,1,18012,17027	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749380	28281	PASS	A	T	35153	0.911302	27	20,4,18003,17039	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749380	28282	PASS	T	A	35154	0.908261	3	31,24,17978,17049	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749380	28651	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	14359	0.002437	0	0,14324,0,35	HIGH	NONE	FRAME_SHIFT	N	aaa/	K127	N	0.000502	0.918117	3	2	CA>C
ERR5749380	28881	PASS	G	A	3167	0.730976	0	0,0,1548,1564	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749380	28882	PASS	G	A	3167	0.819703	0	1,0,1573,1553	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749380	28883	PASS	G	C	3167	0.937796	0	1,1,1578,1586	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749380	28977	PASS	C	T	1623	0.932224	0	0,0,2,1620	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749380	29077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9803	0.002142	0	9759,0,22,0	LOW	SILENT	SYNONYMOUS_CODING	N	taC/taT	Y268	N	0.000408	0.88565	3	2	C>T
ERR5749380	29386	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	5078	0.001378	0	5071,0,7,0	HIGH	NONE	FRAME_SHIFT	N	aag/aaAg	K373K?	N	0.000887	0.899197	4	2	C>CA
ERR5749380	29443	PASS	A	T	5076	0.877069	0	8,0,5066,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	caA/caT	Q390H	N	0.877069	0.877069	1	1	A>T
ERR5749381	241	PASS	C	T	11227	0.867106	0	0,0,5583,5591	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749381	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	12458	0.001686	0	12437,4,21,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749381	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	12462	0.00321	0	12399,8,40,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749381	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12467	0.001845	1	11523,19,824,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749381	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	12466	0.001043	0	12433,19,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749381	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	12463	8.83E-4	0	12428,19,11,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749381	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	33386	0.001258	22	20884,12447,35,7	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749381	913	PASS	C	T	20913	0.887295	0	0,10,0,20863	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749381	3037	PASS	C	T	20973	0.803652	47	2,22,10483,10293	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749381	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10582	0.001701	482	4,10552,18,5	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749381	3267	PASS	C	T	20438	0.972404	0	3,0,20425,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749381	5077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	14010	0.001428	0	13944,0,21,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtT/gtC	V786	nsp3	0.001393	0.168205	1	1	T>C
ERR5749381	5388	PASS	C	A	5993	0.95695	2147483647	0,0,5991,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749381	5986	PASS	C	T	13465	0.975938	0	1,0,13457,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749381	6432	PASS	C	T	22465	0.931716	0	0,8,4,22421	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCc/aTc	T1238I	nsp3	0.931716	0.936031	1	1	C>T
ERR5749381	6813	PASS	C	T	35296	0.223425	30	16778,10203,5306,2957	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T1365I	nsp3	0.001082	0.95799	2	1	C>T
ERR5749381	6954	PASS	T	C	22025	0.80336	0	0,6,5,21864	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749381	7070	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	38832	0.002395	338	16603,22114,97,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggc/Agc	G1451S	nsp3	0.000698	0.101434	3	1	G>A
ERR5749381	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	28731	0.001114	64	17799,10900,32,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749381	10323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	19447	0.001748	0	0,19346,0,37	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749381	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	23156	0.001425	0	23078,0,57,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749381	11104	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	23149	0.001166	0	23051,0,30,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccT/ccC	P44	nsp6	0.000866	0.675414	2	1	T>C
ERR5749381	11287	PASS	GTCTGGTTTT	G	23151	0.996458	0	0,82,0,23069	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749381	12459	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	45095	0.001331	1	22278,22738,29,33	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T123I	nsp8	0.000658	0.986093	1	1	C>T
ERR5749381	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	22314	9.86E-4	0	22263,0,22,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749381	12513	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22314	0.001031	0	22283,0,23,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aTg	T141M	nsp8	0.000794	0.984064	2	2	C>T
ERR5749381	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	39752	0.001107	0	19858,19778,24,24	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749381	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	15276	0.005368	2147483647	14856,149,5,264	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749381	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	29555	7.44E-4	0	14841,14716,12,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749381	14408	PASS	C	T	29555	0.843681	12	3,10,14773,14555	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749381	14676	PASS	C	T	14958	0.809199	0	4,0,14925,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749381	15279	PASS	C	T	23949	0.903462	0	4,0,23921,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749381	15983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	12177	8.21E-4	0	12168,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T850	RdRp	0.000701	0.338235	2	1	TA>T
ERR5749381	16176	PASS	T	C	22774	0.977035	2	0,2,10573,12188	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749381	16391	PASS	C	T	10579	0.732678	2147483647	0,0,0,10551	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A52V	helicase	0.71923	0.732678	1	1	C>T
ERR5749381	17615	PASS	A	G	17502	0.892012	0	0,0,5,17437	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749381	18032	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27798	0.001259	4	13587,14166,22,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T599I	helicase	0.000604	0.973948	2	2	C>T
ERR5749381	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	28032	4.64E-4	0	28019,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749381	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25129	0.00386	0	25006,0,100,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749381	20091	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	25077	6.78E-4	0	1,25059,0,17	HIGH	NONE	FRAME_SHIFT	ORF1ab	caa/Acaa	Q159T?	endoR	0.000368	0.051583	1	1	C>CA
ERR5749381	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	22548	0.00102	0	0,22525,0,23	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TA>T
ERR5749381	21305	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	28721	8.36E-4	0	0,28648,0,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cGc/cAc	R216H	MethTr	0.000727	0.703943	1	1	G>A
ERR5749381	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	32903	0.002127	7	16093,16369,37,50	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749381	21764	PASS	ATACATG	A	14019	0.995363	0	63,0,13954,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749381	21990	PASS	TTTA	T	14031	0.997363	0	0,37,11,13983	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749381	22227	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22799	0.01	0	0,22447,0,276	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gTt	A222V	S	0.000419	0.824305	2	2	C>T
ERR5749381	22290	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	22809	5.7E-4	0	3,22793,0,13	HIGH	NONE	FRAME_SHIFT	S	tta/	L244	S	0.000389	0.578006	2	2	CT>C
ERR5749381	23063	PASS	A	T	15827	0.84716	0	0,7,4,15724	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749381	23271	PASS	C	A	24240	0.929909	0	3,0,24220,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749381	23403	PASS	A	G	24234	0.964719	0	0,1,0,24219	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749381	23604	PASS	C	A	17077	0.94437	0	5,0,17064,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749381	23709	PASS	C	T	17054	0.937024	0	0,6,3,17021	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749381	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	32459	6.47E-4	0	15374,17064,9,12	HIGH	NONE	FRAME_SHIFT	S	ttg/	L753	S	0.000334	0.080808	2	2	CT>C
ERR5749381	24010	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATTTATTGAAGATCTAC	A	15459	5.82E-4	0	113,15341,0,9	HIGH	NONE	FRAME_SHIFT	S	attgaagatctacttttc/	IEDLLF818	S	0.000455	0.926398	4	2	ATTTATTGAAGATCTAC>A
ERR5749381	24506	PASS	T	G	21698	0.975343	0	8,0,21686,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749381	24914	PASS	G	C	43880	0.956609	0	0,1,21888,21956	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749381	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	13084	0.001681	393	13030,13,7,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749381	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	13229	0.002041	1075	13028,74,48,67	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749381	26526	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	14009	0.00157	0	4,13967,0,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Gca/Aca	A2T	M	0.001224	0.951192	3	1	G>A
ERR5749381	26606	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14017	0.001284	0	13986,0,20,0	LOW	SILENT	SYNONYMOUS_CODING	M	ttC/ttT	F28	M	0.001284	0.951495	1	1	C>T
ERR5749381	26730	PASS	G	C	27722	0.91422	11	6,1,13806,13854	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Gtt/Ctt	V70L	M	0.000371	0.919543	3	2	G>C
ERR5749381	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	14009	0.00207	0	6,13965,0,29	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749381	27476	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	44512	7.19E-4	0	23657,20786,17,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	aCa/aTa	T28I	orf7a	0.000547	0.22827	4	2	C>T
ERR5749381	27972	PASS	C	T	10435	0.900719	35	2,2,10323,71	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749381	28048	PASS	G	T	10358	0.90056	0	0,22,0,10326	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749381	28111	PASS	A	G	33361	0.977878	4	4,0,22974,10372	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749381	28270	PASS	TA	T	44027	0.994776	435	218,15,22684,21113	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749381	28280	PASS	G	C	43938	0.936979	13	10,2,22754,21108	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749381	28281	PASS	A	T	43938	0.911603	8	30,18,22730,21079	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749381	28282	PASS	T	A	43945	0.901673	0	17,17,22668,21113	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749381	28881	PASS	G	A	16918	0.768294	5	7,12,8412,8249	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749381	28881	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGGGAACTTCTCCTGCTAGAATGGCTGGCAATGGCGGTGATGCTGCTCTTGCTTTGCTGCTGCT	G	16916	7.09E-4	36	8502,8404,0,12	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	N	aggggaacttctcctgctagaatggctggcaatggcggtgatgctgctcttgctttgctgctgctt/agt	RGTSPARMAGNGGDAALALLLL203S	N	0.000709	0.947368	4	2	GGGGAACTTCTCCTGCTAGAATGGCTGGCAATGGCGGTGATGCTGCTCTTGCTTTGCTGCTGCT>G
ERR5749381	28882	PASS	G	A	16916	0.821116	9	4,0,8487,8229	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749381	28883	PASS	G	C	16916	0.942776	3	0,1,8495,8389	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749381	28977	PASS	C	T	8619	0.909618	2147483647	0,0,0,8597	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749381	29109	PASS	C	A	31013	0.940186	0	16,0,30988,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	cCa/cAa	P279Q	N	0.004059	0.940585	2	2	C>A
ERR5749381	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	61554	0.001202	0	30916,30528,45,44	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749381	29686	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18418	0.001357	0	9186,9177,14,14	.	.	.	.	.	.	.	0.001045	0.802514	2	1	C>T
ERR5749382	241	PASS	C	T	38	0.921053	0	0,0,19,19	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749382	514	PASS	TGTTATG	T	228	0.061404	0	214,0,14,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749382	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	2158	0.016219	13	1895,228,35,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749382	913	PASS	C	T	1929	0.906169	2147483647	0,0,0,1924	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749382	1960	PASS	C	T	2109	0.105737	0	1875,0,233,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A385	nsp2	0.001414	0.105737	2	1	C>T
ERR5749382	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	7627	0.001967	674	3803,3543,6,250	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749382	2862	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4324	0.009944	19	487,3793,0,43	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T48I	nsp3	0.000547	0.850688	4	2	C>T
ERR5749382	3037	PASS	C	T	970	0.806186	0	0,0,485,477	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749382	3267	PASS	C	T	2537	0.973591	2147483647	0,0,2536,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749382	4206	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	851	0.017626	0	836,0,15,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCg/gTg	A496V	nsp3	0.003069	0.879444	1	1	C>T
ERR5749382	5388	PASS	C	A	347	0.956772	2147483647	0,0,347,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749382	5986	PASS	C	T	1608	0.982587	0	1,0,1607,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749382	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	1314	0.023592	0	0,1281,0,31	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L1328S?	nsp3	0.000731	0.14377	4	2	C>CT
ERR5749382	6954	PASS	T	C	2608	0.812883	0	0,1,0,2590	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749382	7674	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4126	0.019147	0	4044,0,79,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCg/gTg	A1652V	nsp3	0.000682	0.109264	3	2	C>T
ERR5749382	10386	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	7619	0.001575	8	3728,3879,3,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	tca/	S113	3Cpro	0.000642	0.160456	4	2	CT>C
ERR5749382	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	8056	0.017502	0	7576,0,141,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749382	11152	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8036	0.020159	0	7853,0,164,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V60	nsp6	0.000678	0.974465	2	2	C>T
ERR5749382	11287	PASS	GTCTGGTTTT	G	8051	0.999255	0	0,6,0,8045	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749382	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4641	0.003448	0	2313,2305,8,8	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749382	14120	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3672	0.009532	0	1812,1808,25,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCa/cTa	P227L	RdRp	0.00121	0.786944	2	2	C>T
ERR5749382	14408	PASS	C	T	42	0.833333	0	0,0,21,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749382	14676	PASS	C	T	1251	0.76259	0	2,0,1242,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749382	15025	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	1064	0.009398	0	1053,0,10,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gca/Aca	A529T	RdRp	0.000933	0.946354	3	2	G>A
ERR5749382	15279	PASS	C	T	1619	0.896232	2147483647	0,0,1618,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749382	15493	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	1619	0.019765	0	0,1587,0,32	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gcc/Ccc	A685P	RdRp	0.001408	0.076816	3	2	G>C
ERR5749382	15654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	G	3118	0.010584	0	3077,0,38,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gaC/gaG	D738E	RdRp	0.001856	0.060658	2	2	C>G
ERR5749382	16176	PASS	T	C	1304	0.980828	0	0,0,176,1125	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749382	17615	PASS	A	G	1582	0.886852	0	0,1,0,1577	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749382	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3749	0.018405	0	1794,1826,38,41	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749382	21658	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1894	0.008448	0	0,1873,0,17	LOW	SILENT	SYNONYMOUS_CODING	S	ttC/ttT	F32	S	0.001649	0.937508	2	2	C>T
ERR5749382	21764	PASS	ATACATG	A	2515	0.998807	0	3,0,2512,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749382	21990	PASS	TTTA	T	2517	0.992451	0	0,19,1,2497	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749382	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	7539	0.00199	0	0,7517,0,15	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749382	23063	PASS	A	T	2050	0.852195	0	0,1,0,2039	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749382	23271	PASS	C	A	2900	0.920345	0	2,0,2897,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749382	23403	PASS	A	G	2900	0.965862	2147483647	0,0,0,2899	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749382	23418	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	2901	0.01172	0	0,2862,0,37	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAa/gTa	E619V	S	0.01172	0.91844	1	1	A>T
ERR5749382	23593	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	2599	0.027703	0	2525,0,74,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	caG/caC	Q677H	S	0.021779	0.924148	3	2	G>C
ERR5749382	23604	PASS	C	A	2599	0.95075	0	6,0,2591,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749382	23709	PASS	C	T	2598	0.943803	0	0,1,0,2593	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749382	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	3062	0.009798	17	464,2568,0,30	HIGH	NONE	FRAME_SHIFT	S	ttg/	L753	S	0.000334	0.080808	2	2	CT>C
ERR5749382	24506	PASS	T	G	3339	0.974543	0	2,0,3337,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749382	24914	PASS	G	C	8646	0.948647	0	0,0,4313,4326	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749382	26907	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8820	0.0161	0	8674,0,145,0	LOW	SILENT	SYNONYMOUS_CODING	M	Ctg/Ttg	L129	M	0.000817	0.976032	1	1	C>T
ERR5749382	27312	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	5392	0.003153	0	5375,0,17,0	HIGH	NONE	FRAME_SHIFT	ORF6	aat/	N39	orf6	0.000911	0.088458	4	2	TA>T
ERR5749382	27577	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAATTTGCTTTTGCTTGTCCTGACGGCGTAAAACACGTCTATCAGTTACGTGCCAGATCAGTTTCACCT	C	5210	0.010749	0	5154,0,56,0	HIGH	NONE	FRAME_SHIFT	ORF7a	tttgcttttgcttgtcctgacggcgtaaaacacgtctatcagttacgtgccagatcagtttcacctaaa/	FAFACPDGVKHVYQLRARSVSPK63	orf7a	0.000614	0.952205	4	2	CAATTTGCTTTTGCTTGTCCTGACGGCGTAAAACACGTCTATCAGTTACGTGCCAGATCAGTTTCACCT>C
ERR5749382	27746	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	5209	0.01363	0	0,5120,0,77	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	aGa/aAa	R118K	orf7a	0.000528	0.94095	3	2	G>A
ERR5749382	28881	PASS	G	A	602	0.749169	0	0,0,290,295	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749382	28882	PASS	G	A	602	0.822259	0	0,0,299,297	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749382	28883	PASS	G	C	602	0.943522	0	0,0,299,302	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749382	28977	PASS	C	T	309	0.961165	2147483647	0,0,0,309	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749382	29386	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	1304	0.013037	0	1287,0,17,0	HIGH	NONE	FRAME_SHIFT	N	aag/	K373	N	0.000887	0.899197	4	2	CAA>C
ERR5749382	29451	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1303	0.007675	0	1293,0,10,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aCt/aTt	T393I	N	0.007675	0.757685	2	2	C>T
ERR5749383	241	PASS	C	T	238	0.831933	0	0,0,119,118	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749383	823	PASS	C	T	1974	0.901722	0	1,0,1968,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V6	nsp2	0.001213	0.901722	1	1	C>T
ERR5749383	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1977	0.00607	0	0,1962,0,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749383	913	PASS	C	T	1977	0.91047	0	0,2,0,1974	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749383	1813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	8208	0.004386	0	0,8165,0,37	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcA	A336	nsp2	0.001022	0.152738	4	2	T>A
ERR5749383	3037	PASS	C	T	3400	0.813824	9	0,3,1698,1668	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749383	3267	PASS	C	T	1837	0.972237	2147483647	0,0,1836,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749383	4331	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5354	0.002428	18	1686,3647,0,13	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L538	nsp3	0.000987	0.928955	1	1	C>T
ERR5749383	5388	PASS	C	A	1309	0.957983	2147483647	0,0,1308,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749383	5628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	2146	0.00233	0	2141,0,5,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acg/	T970	nsp3	0.000561	0.973644	3	2	CG>C
ERR5749383	5986	PASS	C	T	4582	0.973592	2147483647	0,0,4581,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749383	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	4515	0.012846	0	0,4457,0,58	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L1328S?	nsp3	0.000731	0.14377	4	2	C>CT
ERR5749383	6954	PASS	T	C	7303	0.80063	0	0,1,0,7255	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749383	7674	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9298	0.001828	0	9277,1,17,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCg/gTg	A1652V	nsp3	0.000682	0.109264	3	2	C>T
ERR5749383	8043	PASS	C	T	3498	0.946827	0	1,0,3494,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A1775V	nsp3	0.001071	0.946827	1	1	C>T
ERR5749383	8950	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7740	0.002972	11	6785,929,25,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I132	nsp4	0.002808	0.982604	1	1	C>T
ERR5749383	8964	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	6810	0.006902	0	6763,0,47,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K138	nsp4	0.000553	0.981649	4	2	CA>C
ERR5749383	9430	PASS	C	T	179	0.960894	2147483647	0,0,0,179	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I292	nsp4	0.001411	0.960894	1	1	C>T
ERR5749383	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	5501	0.004181	0	5299,179,23,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749383	10138	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11469	0.001482	16	9891,1556,11,6	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N28	3Cpro	0.000458	0.983567	3	3	C>T
ERR5749383	10386	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13612	0.00169	135	3680,9905,24,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T111I	3Cpro	0.000642	0.160456	4	2	C>T
ERR5749383	10386	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	13612	7.35E-4	15	3699,9903,6,4	HIGH	NONE	FRAME_SHIFT	ORF1ab	tca/	S113	3Cpro	0.000642	0.160456	4	2	CT>C
ERR5749383	11287	PASS	GTCTGGTTTT	G	10087	0.999108	0	0,9,0,10078	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749383	11674	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	2579	0.006592	0	2562,0,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F235	nsp6	0.00054	0.985782	3	2	CT>C
ERR5749383	11767	PASS	C	T	5120	0.854102	3	0,2,2548,2556	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	agC/agT	S265	nsp6	0.000949	0.854102	1	1	C>T
ERR5749383	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6378	0.002195	0	3180,3173,8,8	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749383	14408	PASS	C	T	751	0.840213	0	0,0,377,369	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749383	14676	PASS	C	T	1412	0.786827	2147483647	0,0,1409,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749383	15279	PASS	C	T	3085	0.905673	2147483647	0,0,3084,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749383	15371	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	6155	0.002924	1	3069,3060,12,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aAg	T644K	RdRp	0.00056	0.786959	4	2	C>A
ERR5749383	15396	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	3076	0.001625	0	0,3071,0,5	HIGH	NONE	FRAME_SHIFT	ORF1ab	tataga/	YR653	RdRp	0.000524	0.116667	1	1	CTA>C
ERR5749383	15654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7829	0.002682	0	7799,0,23,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D738	RdRp	0.001856	0.060658	2	2	C>T
ERR5749383	15983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	1554	0.006435	0	1546,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T850	RdRp	0.000701	0.338235	2	1	TA>T
ERR5749383	16176	PASS	T	C	2818	0.97445	3	1,0,1259,1557	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749383	17615	PASS	A	G	5428	0.903832	2147483647	0,0,0,5414	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749383	18658	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	18745	6.94E-4	0	18729,3,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tgt/	C207	ExoN	0.000507	0.115741	3	2	TG>T
ERR5749383	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	18742	9.07E-4	0	18725,0,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749383	19114	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	10519	0.004848	1	5217,5232,30,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Aaa/Gaa	K359E	ExoN	0.00119	0.098958	2	2	A>G
ERR5749383	19293	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	7396	0.002704	0	7373,0,20,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	agT/agC	S418	ExoN	0.002704	0.060409	2	2	T>C
ERR5749383	19328	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	7396	0.003786	0	7368,0,28,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F431	ExoN	0.000459	0.937906	4	2	CT>C
ERR5749383	20951	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	G	4168	0.002639	0	4152,0,11,0	HIGH	NONSENSE	STOP_GAINED	ORF1ab	tCa/tGa	S98*	MethTr	0.000431	0.138667	3	3	C>G
ERR5749383	21304	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	13996	0.001358	0	0,13953,0,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgc/Agc	R216S	MethTr	0.000411	0.605296	3	2	C>A
ERR5749383	21334	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	14016	0.005066	0	0,13937,0,72	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gca/Aca	A226T	MethTr	0.000897	0.077475	3	1	G>A
ERR5749383	21764	PASS	ATACATG	A	6330	0.995735	0	27,0,6303,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749383	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	6330	0.001738	0	6319,0,11,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749383	21854	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	12634	0.002216	0	6294,6285,15,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tct/Cct	S98P	S	0.00132	0.05283	1	1	T>C
ERR5749383	21990	PASS	TTTA	T	6331	0.998894	0	0,7,0,6324	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749383	22290	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	8017	0.003617	0	0,7988,0,29	HIGH	NONE	FRAME_SHIFT	S	tta/	L244	S	0.000389	0.578006	2	2	CT>C
ERR5749383	22323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	13555	8.12E-4	42	5529,8015,11,0	HIGH	NONE	FRAME_SHIFT	S	tct/	S255	S	0.000812	0.978946	3	2	CT>C
ERR5749383	22384	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	5540	0.002347	0	5523,0,13,0	LOW	SILENT	SYNONYMOUS_CODING	S	acT/acC	T274	S	0.001609	0.118834	1	1	T>C
ERR5749383	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	12430	0.001448	0	0,12404,0,18	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749383	23063	PASS	A	T	5903	0.863629	0	0,2,0,5877	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749383	23271	PASS	C	A	1914	0.925287	2147483647	0,0,1913,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749383	23403	PASS	A	G	1914	0.970742	2147483647	0,0,0,1914	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749383	23604	PASS	C	A	6287	0.941626	0	7,0,6276,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749383	23709	PASS	C	T	6275	0.941833	0	0,2,0,6267	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749383	24506	PASS	T	G	5767	0.97295	0	3,0,5764,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749383	24914	PASS	G	C	16600	0.963916	0	1,1,8279,8311	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749383	25587	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	13977	0.002146	0	0,13947,0,30	HIGH	NONE	FRAME_SHIFT	ORF3a	aag/	K67	orf3a	0.000598	0.813206	6	2	CA>C
ERR5749383	26156	PASS	T	C	11608	0.924104	0	0,1,0,11586	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	gTt/gCt	V255A	orf3a	0.001058	0.924104	2	2	T>C
ERR5749383	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	11609	0.002067	0	0,11562,0,29	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	gtT/gtC	V255	orf3a	0.000249	0.122153	5	2	T>C
ERR5749383	26208	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	11644	0.00146	0	0,11627,0,17	HIGH	NONE	FRAME_SHIFT	ORF3a	gtg/	V273	orf3a	0.000315	0.922222	2	2	CG>C
ERR5749383	26493	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	2541	0.004329	0	0,2530,0,11	.	.	.	.	.	.	.	0.001082	0.069277	3	1	G>GT
ERR5749383	27312	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	10711	0.004761	0	10661,0,51,0	HIGH	NONE	FRAME_SHIFT	ORF6	aat/aaAt	N39K?	orf6	0.000911	0.088458	4	2	T>TA
ERR5749383	27506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	20914	0.001148	77	10189,10689,1,31	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	gGa/gTa	G38V	orf7a	0.000715	0.985435	4	2	G>T
ERR5749383	27513	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10198	0.001863	0	10167,4,19,0	LOW	SILENT	SYNONYMOUS_CODING	ORF7a	taC/taT	Y40	orf7a	0.001863	0.982462	2	2	C>T
ERR5749383	27527	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10198	0.002451	0	10164,4,27,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	cCa/cTa	P45L	orf7a	0.001708	0.973593	1	1	C>T
ERR5749383	27641	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10178	0.002653	0	10136,0,31,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	tCa/tTa	S83L	orf7a	0.000983	0.911213	2	2	C>T
ERR5749383	27807	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10195	0.001667	0	1,10165,0,19	LOW	SILENT	SYNONYMOUS_CODING	ORF7b	Cta/Tta	L18	orf7b	0.000505	0.965257	2	2	C>T
ERR5749383	27816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	12146	0.001811	14	1952,10172,0,22	HIGH	NONE	FRAME_SHIFT	ORF7b	tta/	L22	orf7b	0.000423	0.053007	1	1	GT>G
ERR5749383	27972	PASS	C	T	1956	0.902352	0	0,0,1947,5	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749383	28048	PASS	G	T	1951	0.927217	0	0,1,0,1949	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749383	28111	PASS	A	G	11263	0.980467	0	0,0,9309,1949	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749383	28192	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	9311	0.001933	0	9287,0,18,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	gTg/gCg	V100A	orf8	0.001134	0.980889	2	1	T>C
ERR5749383	28270	PASS	TA	T	18025	0.99534	209	83,2,9197,8744	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749383	28280	PASS	G	C	17990	0.93035	9	4,0,9217,8741	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749383	28281	PASS	A	T	17990	0.918733	7	13,6,9210,8737	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749383	28282	PASS	T	A	17991	0.911456	2	6,3,9204,8745	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749383	28292	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	18536	0.001025	0	9233,9285,9,10	HIGH	NONE	FRAME_SHIFT	N	aat/	N8	N	0.000304	0.055324	4	2	CA>C
ERR5749383	28881	PASS	G	A	666	0.74024	0	0,0,327,327	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749383	28882	PASS	G	A	666	0.83033	0	0,0,334,328	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749383	28883	PASS	G	C	666	0.932432	0	0,0,334,330	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749383	28977	PASS	C	T	339	0.914454	2147483647	0,0,0,339	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749383	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	20165	0.001091	0	10116,9990,13,13	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749383	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	20165	0.001389	84	10116,9990,29,0	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccT	P302	N	0.000713	0.913732	2	1	G>T
ERR5749383	29778	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGA	G	3042	0.001972	0	0,3036,0,6	.	.	.	.	.	.	.	0.001972	0.38	2	1	GGA>G
ERR5749384	199	PASS	G	T	1005	0.764179	0	9,0,995,0	.	.	.	.	.	.	.	0.615385	0.766141	1	1	G>T
ERR5749384	241	PASS	C	T	2007	0.854509	0	0,0,999,997	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749384	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	5350	0.003551	0	5332,0,19,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749384	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	5346	0.003554	0	5327,0,19,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749384	913	PASS	C	T	6680	0.913174	0	0,3,0,6670	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749384	2453	PASS	C	T	8294	0.753677	0	0,7,0,8193	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L550F	nsp2	0.00429	0.842201	2	2	C>T
ERR5749384	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	28459	0.001441	2534	14206,13218,20,933	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749384	3037	PASS	C	T	9101	0.814746	14	1,7,4546,4470	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749384	3267	PASS	C	T	7108	0.972848	0	1,0,7105,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749384	3877	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	5856	0.004781	0	4862,0,993,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcG	A386	nsp3	0.000588	0.960227	2	1	T>G
ERR5749384	4861	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	9288	8.61E-4	0	0,9280,0,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	agt/	S716	nsp3	0.000632	0.115789	2	1	TA>T
ERR5749384	5388	PASS	C	A	3089	0.960505	2147483647	0,0,3088,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749384	5986	PASS	C	T	7617	0.971905	0	2,0,7612,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749384	6500	PASS	C	T	17439	0.427146	32	4398,5314,3295,4426	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cca/Tca	P1261S	nsp3	0.427146	0.427146	1	1	C>T
ERR5749384	6954	PASS	T	C	12657	0.815596	0	0,1,0,12571	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749384	7070	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	17106	0.009003	933	4251,12688,157,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggc/Agc	G1451S	nsp3	0.000698	0.101434	3	1	G>A
ERR5749384	8964	PASS	C	T	10565	0.422527	0	6016,0,4544,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCa/tTa	S137L	nsp4	0.000553	0.981649	4	2	C>T
ERR5749384	9532	PASS	C	T	9806	0.966959	0	1,0,8719,1083	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F326	nsp4	0.000899	0.966959	1	1	C>T
ERR5749384	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	9806	0.001122	2	8712,1083,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749384	11075	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TC	14641	0.001025	0	14626,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/tCtt	F35S?	nsp6	0.000555	0.885796	4	2	T>TC
ERR5749384	11287	PASS	GTCTGGTTTT	G	14633	0.99836	0	0,24,0,14609	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749384	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	15993	0.001125	0	9174,6782,12,10	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749384	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	11694	0.001539	0	11665,0,18,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749384	13468	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	8223	0.001094	0	8214,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggg/	G10	nsp11	0.000713	0.076498	2	2	CG>C
ERR5749384	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16414	0.002681	0	8188,8163,25,25	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749384	14168	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	8683	8.06E-4	0	0,8676,0,7	HIGH	NONE	FRAME_SHIFT	ORF1ab	atatta/	IL244	RdRp	0.000479	0.314961	1	1	CTA>C
ERR5749384	14408	PASS	C	T	2382	0.856843	0	0,0,1190,1175	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749384	14676	PASS	C	T	5138	0.810627	0	3,0,5129,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749384	15279	PASS	C	T	8968	0.893845	0	2,0,8953,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749384	15720	PASS	C	T	11572	0.91177	0	0,7,0,11527	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D760	RdRp	0.001002	0.917823	1	1	C>T
ERR5749384	16176	PASS	T	C	9160	0.979694	0	0,0,4173,4980	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749384	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	19568	0.001533	0	19538,0,30,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749384	18897	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	19571	4.6E-4	0	3,19559,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/	V287	ExoN	0.00046	0.060685	3	3	TG>T
ERR5749384	19320	PASS	C	T	11299	0.945128	0	3,0,11281,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H427	ExoN	0.004154	0.957053	2	2	C>T
ERR5749384	19343	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	11298	7.08E-4	0	11290,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F436	ExoN	0.000519	0.192257	7	2	CT>C
ERR5749384	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9490	0.00411	0	9446,0,40,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749384	21764	PASS	ATACATG	A	8704	0.996094	0	34,0,8670,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749384	21990	PASS	TTTA	T	8705	0.998621	0	0,12,1,8692	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749384	23063	PASS	A	T	9846	0.854966	0	0,2,0,9798	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749384	23271	PASS	C	A	7729	0.921335	0	1,0,7718,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749384	23403	PASS	A	G	7726	0.964665	0	0,12,0,7709	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749384	23604	PASS	C	A	9458	0.941425	0	12,0,9446,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749384	23709	PASS	C	T	9445	0.942403	2147483647	0,0,0,9433	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749384	24506	PASS	T	G	11054	0.975122	0	4,0,11044,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749384	24914	PASS	G	C	27081	0.955762	0	0,1,13483,13576	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749384	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	3729	0.003754	353	3692,15,0,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749384	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	8091	0.001236	0	0,8081,0,10	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749384	27972	PASS	C	T	5186	0.90108	40	2,2,5146,18	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749384	28048	PASS	G	T	5170	0.9147	0	0,6,0,5159	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749384	28111	PASS	A	G	18893	0.977558	0	3,1,13698,5181	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749384	28270	PASS	TA	T	26494	0.995206	310	128,4,13530,12837	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749384	28280	PASS	G	C	26439	0.941564	6	5,1,13567,12826	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749384	28281	PASS	A	T	26439	0.908242	14	12,3,13558,12827	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749384	28282	PASS	T	A	26441	0.906206	4	12,7,13522,12831	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749384	28292	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	27253	5.87E-4	0	13583,13640,8,8	HIGH	NONE	FRAME_SHIFT	N	aat/	N8	N	0.000304	0.055324	4	2	CAA>C
ERR5749384	28396	PASS	G	A	13723	0.93449	246	8,3,2,13690	LOW	SILENT	SYNONYMOUS_CODING	N	cgG/cgA	R41	N	0.000496	0.946059	5	2	G>A
ERR5749384	28881	PASS	G	A	4222	0.776646	0	1,1,2100,2069	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749384	28882	PASS	G	A	4222	0.810516	2	3,1,2111,2060	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749384	28883	PASS	G	C	4222	0.933207	3	0,1,2118,2096	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749384	28977	PASS	C	T	2151	0.928405	2147483647	0,0,0,2147	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749384	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	37885	9.5E-4	0	19040,18794,23,21	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749384	29779	PASS	G	T	5156	0.962762	2147483647	0,0,0,5156	.	.	.	.	.	.	.	0.001489	0.975228	1	1	G>T
ERR5749385	241	PASS	C	T	24	0.916667	0	0,0,12,12	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749385	913	PASS	C	T	157	0.936306	2147483647	0,0,0,157	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749385	1735	PASS	TG	T	675	0.062222	0	633,0,42,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtg/	V311	nsp2	0.002028	0.062222	1	1	TG>T
ERR5749385	2453	PASS	C	T	276	0.735507	2147483647	0,0,0,272	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L550F	nsp2	0.00429	0.842201	2	2	C>T
ERR5749385	3037	PASS	C	T	219	0.826484	0	0,0,110,109	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749385	3122	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	110	0.045455	0	0,104,0,6	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gat/Cat	D135H	nsp3	0.045455	0.053719	1	1	G>C
ERR5749385	3267	PASS	C	T	169	0.982249	2147483647	0,0,169,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749385	5388	PASS	C	A	58	0.931035	2147483647	0,0,58,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749385	5986	PASS	C	T	354	0.971751	2147483647	0,0,354,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749385	6347	PASS	C	T	213	0.070423	0	196,0,17,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Ctg/Ttg	L1210	nsp3	0.070423	0.070423	1	1	C>T
ERR5749385	6696	PASS	C	CT	335	0.053731	0	0,317,0,18	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L1328S?	nsp3	0.000731	0.14377	4	2	C>CT
ERR5749385	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	335	0.008955	0	0,332,0,3	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F1327	nsp3	0.000731	0.14377	4	2	CT>C
ERR5749385	6954	PASS	T	C	346	0.83237	2147483647	0,0,0,346	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749385	6990	PASS	C	T	346	0.101156	0	0,303,0,38	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S1424F	nsp3	0.000504	0.101156	4	2	C>T
ERR5749385	9985	PASS	C	G	253	0.079051	0	116,115,11,11	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gaC/gaG	D477E	nsp4	0.079051	0.079051	1	1	C>G
ERR5749385	11074	PASS	C	CT	1268	0.055994	0	1194,0,71,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CT
ERR5749385	11287	PASS	GTCTGGTTTT	G	1267	1.0	2147483647	0,0,0,1267	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749385	14097	PASS	C	T	270	0.981481	2147483647	0,0,270,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F219	RdRp	0.000613	0.981481	2	2	C>T
ERR5749385	14408	PASS	C	T	66	0.833333	0	0,0,33,32	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749385	14676	PASS	C	T	40	0.825	2147483647	0,0,39,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749385	15023	PASS	T	A	177	0.073446	0	162,0,15,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTc/tAc	F528Y	RdRp	0.001017	0.073446	2	2	T>A
ERR5749385	15071	PASS	T	A	352	0.0625	0	161,163,14,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cTt/cAt	L544H	RdRp	0.000813	0.0625	2	2	T>A
ERR5749385	15279	PASS	C	T	144	0.909722	2147483647	0,0,144,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749385	16176	PASS	T	C	112	0.964286	0	0,0,44,68	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749385	20481	PASS	A	G	1711	0.964348	2147483647	0,0,0,1707	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcA/tcG	S287	endoR	0.001272	0.966106	1	1	A>G
ERR5749385	20507	PASS	AT	A	1725	0.062609	0	14,1603,0,108	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L297	endoR	0.000629	0.062609	1	1	AT>A
ERR5749385	21764	PASS	ATACATG	A	531	1.0	2147483647	0,0,531,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749385	21990	PASS	TTTA	T	531	0.998117	0	0,1,0,530	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749385	23063	PASS	A	T	522	0.83908	2147483647	0,0,0,521	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749385	23271	PASS	C	A	86	0.953488	2147483647	0,0,86,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749385	23403	PASS	A	G	86	0.976744	2147483647	0,0,0,86	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749385	23604	PASS	C	A	364	0.961538	2147483647	0,0,364,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749385	23709	PASS	C	T	363	0.939394	2147483647	0,0,0,363	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749385	23817	PASS	T	C	404	0.066832	10	40,336,0,28	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTt/cCt	L752P	S	0.000646	0.066832	1	1	T>C
ERR5749385	24506	PASS	T	G	349	0.965616	2147483647	0,0,349,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749385	24914	PASS	G	C	2578	0.95578	0	0,0,1285,1293	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749385	25967	PASS	A	G	1043	0.059444	5	950,31,62,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aAa/aGa	K192R	orf3a	0.059444	0.059444	1	1	A>G
ERR5749385	26895	PASS	C	T	1752	0.962329	2147483647	0,0,1750,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Cat/Tat	H125Y	M	0.000874	0.97046	1	1	C>T
ERR5749385	27461	PASS	G	T	1264	0.969146	2147483647	0,0,0,1264	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	tGt/tTt	C23F	orf7a	0.002221	0.974441	1	1	G>T
ERR5749385	27972	PASS	C	T	83	0.939759	0	0,0,81,2	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749385	28048	PASS	G	T	81	0.925926	2147483647	0,0,0,81	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749385	28111	PASS	A	G	1858	0.981163	0	2,0,1771,82	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749385	28245	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	1775	0.028732	0	1722,0,53,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	Tta/Cta	L118	orf8	0.019165	0.950471	2	2	T>C
ERR5749385	28270	PASS	TA	T	3426	0.997081	29	11,0,1753,1663	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749385	28280	PASS	G	C	3423	0.943325	0	1,0,1754,1660	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749385	28281	PASS	A	T	3423	0.912065	4	4,1,1751,1662	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749385	28282	PASS	T	A	3424	0.912675	0	2,1,1746,1664	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749385	28292	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	3528	0.001701	0	1756,1766,3,3	HIGH	NONE	FRAME_SHIFT	N	aat/	N8	N	0.000304	0.055324	4	2	CA>C
ERR5749385	28881	PASS	G	A	69	0.782609	0	0,0,34,34	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749385	28882	PASS	G	A	69	0.753623	0	0,0,34,31	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749385	28883	PASS	G	C	69	0.913043	0	0,0,34,34	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749385	28977	PASS	C	T	35	0.971429	2147483647	0,0,0,35	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749385	29384	PASS	G	A	212	0.099057	0	191,0,21,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gac/Aac	D371N	N	0.009923	0.099057	2	2	G>A
ERR5749385	29386	PASS	C	A	212	0.891509	2147483647	0,0,211,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaC/gaA	D371E	N	0.000887	0.899197	4	2	C>A
ERR5749386	241	PASS	C	T	5437	0.860033	0	0,0,2705,2710	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749386	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	9671	8.27E-4	0	9661,0,8,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749386	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	9671	0.002068	0	9643,0,20,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749386	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	9667	0.001552	0	8928,3,681,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749386	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	9667	9.31E-4	0	9655,3,9,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749386	676	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28850	8.67E-4	28	19143,9657,11,19	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G137	leader	0.000799	0.919273	2	1	C>T
ERR5749386	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	28850	8.32E-4	4	19146,9677,14,10	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749386	913	PASS	C	T	19144	0.909632	0	0,17,0,19090	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749386	1510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	18424	0.00304	0	0,18196,0,63	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G235	nsp2	0.002159	0.937304	1	1	T>C
ERR5749386	3037	PASS	C	T	16564	0.808802	45	0,15,8268,8164	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749386	3177	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	26510	0.001132	27	18127,8342,33,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cAt	P153H	nsp3	0.000773	0.96008	3	2	C>A
ERR5749386	3267	PASS	C	T	18161	0.968779	0	1,0,18153,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749386	5170	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	10520	7.6E-4	0	1,10511,0,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T819	nsp3	0.000565	0.894036	2	2	CCA>C
ERR5749386	5388	PASS	C	A	5395	0.959963	2147483647	0,0,5390,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749386	5986	PASS	C	T	11556	0.972568	2147483647	0,0,11547,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749386	6954	PASS	T	C	19288	0.811385	0	0,3,0,19176	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749386	7926	PASS	C	T	19899	0.965124	0	0,2,0,19884	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCa/gTa	A1736V	nsp3	0.000531	0.97019	5	2	C>T
ERR5749386	10533	PASS	G	T	16226	0.911315	0	15,0,15914,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tGt/tTt	C160F	3Cpro	0.000835	0.917216	4	2	G>T
ERR5749386	10533	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	16226	0.003266	0	16158,0,53,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tac/tTac	Y161L?	3Cpro	0.000835	0.917216	4	2	G>GT
ERR5749386	10789	PASS	C	T	4592	0.944686	2147483647	0,0,4587,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D245	3Cpro	0.001434	0.956641	1	1	C>T
ERR5749386	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	19042	0.002048	0	18973,0,63,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749386	11287	PASS	GTCTGGTTTT	G	19041	0.997847	0	0,38,0,19000	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749386	12513	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18198	0.001319	0	18171,0,24,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aTg	T141M	nsp8	0.000794	0.984064	2	2	C>T
ERR5749386	12970	PASS	C	T	13532	0.861883	0	0,4,0,13497	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N95	nsp9	0.8352	0.861883	1	1	C>T
ERR5749386	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	31996	0.001219	0	15974,15942,21,21	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749386	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	4261	0.004224	1027	4154,44,2,60	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749386	14408	PASS	C	T	8273	0.863774	0	3,3,4123,4104	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749386	14676	PASS	C	T	11891	0.776806	0	9,0,11834,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749386	14913	PASS	C	T	17414	0.981624	266	4,8,17382,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N491	RdRp	0.011397	0.981624	1	1	C>T
ERR5749386	15246	PASS	A	T	30	0.633333	5	1,8,0,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttA/ttT	L602F	RdRp	0.001432	0.633333	1	1	A>T
ERR5749386	15279	PASS	C	T	19099	0.900937	0	3,0,19077,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749386	16176	PASS	T	C	17716	0.981881	6	2,0,8006,9703	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749386	16647	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	19550	0.001074	0	0,19433,0,22	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acG/acA	T137	helicase	0.000746	0.885245	2	1	G>A
ERR5749386	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24532	0.001671	0	24471,0,45,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749386	21764	PASS	ATACATG	A	11800	0.997712	0	27,0,11773,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749386	21974	PASS	G	T	11804	0.925534	156	5,6,0,11786	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gat/Tat	D138Y	S	0.001167	0.928915	2	2	G>T
ERR5749386	21990	PASS	TTTA	T	11807	0.99712	0	0,34,5,11768	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749386	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27050	0.001146	1	13562,13442,15,17	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749386	23063	PASS	A	T	13558	0.868122	0	0,4,0,13506	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749386	23271	PASS	C	A	20395	0.921255	0	3,0,20373,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749386	23403	PASS	A	G	20386	0.972874	0	0,3,2,20364	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749386	23604	PASS	C	A	14926	0.944794	0	14,0,14901,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749386	23709	PASS	C	T	14913	0.940455	0	0,3,2,14884	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749386	24506	PASS	T	G	16443	0.972572	0	4,0,16436,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749386	24914	PASS	G	C	35617	0.959991	0	0,1,17740,17857	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749386	25138	PASS	T	C	6458	0.894395	0	2,0,6445,0	LOW	SILENT	SYNONYMOUS_CODING	S	aaT/aaC	N1192	S	0.001865	0.901453	2	2	T>C
ERR5749386	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	23054	0.001822	83	16527,6458,59,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749386	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	13417	0.001789	386	13359,14,8,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749386	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	12091	0.001654	0	0,12069,0,20	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749386	27915	PASS	G	A	10289	0.952085	0	3,0,10283,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	Gga/Aga	G8R	orf8	0.949134	0.95909	1	1	G>A
ERR5749386	27972	PASS	C	T	10330	0.885963	93	4,5,10231,51	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749386	28048	PASS	G	T	10284	0.91375	0	0,13,0,10262	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749386	28111	PASS	A	G	27168	0.980124	7	5,0,16867,10292	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749386	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16852	0.001246	0	16783,2,22,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749386	28270	PASS	TA	T	32687	0.995166	398	159,4,16642,15887	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749386	28280	PASS	G	C	32625	0.938299	9	6,1,16683,15859	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749386	28281	PASS	A	T	32625	0.921625	36	28,6,16669,15871	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749386	28282	PASS	T	A	32627	0.908603	11	21,10,16633,15883	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749386	28881	PASS	G	A	15291	0.777385	9	4,0,7589,7527	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749386	28882	PASS	G	A	15290	0.825768	6	5,1,7659,7481	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749386	28883	PASS	G	C	15292	0.943696	6	0,2,7666,7608	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749386	28977	PASS	C	T	7777	0.929922	0	0,2,0,7765	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749386	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	35863	8.37E-4	113	28053,7744,6,25	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749386	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	55725	0.001023	2	27984,27643,38,32	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749386	29449	PASS	G	T	8852	0.949277	0	6,0,8836,0	LOW	SILENT	SYNONYMOUS_CODING	N	gtG/gtT	V392	N	0.949277	0.949277	1	1	G>T
ERR5749387	239	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTC	T	27315	6.59E-4	0	13574,13720,9,9	.	.	.	.	.	.	.	0.000495	0.25	4	1	TTC>T
ERR5749387	241	PASS	C	T	27311	0.856505	0	2,2,13541,13624	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749387	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	16775	0.006796	0	16660,3,114,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749387	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	16777	0.001967	0	16498,5,33,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749387	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	16777	0.002861	0	16498,5,48,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749387	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	16777	0.01055	0	16498,5,177,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749387	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTTGA	G	16777	6.56E-4	0	16498,5,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTTGA>G
ERR5749387	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	16776	0.00304	1	15083,17,1204,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749387	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	16776	0.005603	10	16665,16,93,1	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749387	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	16778	0.001371	0	16701,19,23,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttatg/gtg	VM84V	leader	0.000554	0.991848	4	1	GTTA>G
ERR5749387	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	16778	0.001609	0	16701,19,27,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749387	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	16780	0.002801	11	16673,24,46,1	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749387	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATGGTTG	T	16780	0.001609	0	16673,24,27,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	atggttgag/	MVE85	leader	0.000587	0.476744	4	1	TATGGTTG>T
ERR5749387	520	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTT	G	16847	0.001009	24	16740,90,15,2	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttgag/gag	VE86E	leader	0.000583	0.051154	1	1	GGTT>G
ERR5749387	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	42854	0.001447	20	25995,16786,48,14	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749387	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	42854	7.23E-4	2	25863,16714,17,14	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749387	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	42854	0.005414	21	25863,16714,161,71	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749387	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTTG	A	42854	3.03E-4	1	25863,16714,7,6	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcatttgac/	KSFD141	leader	0.000303	0.999303	4	1	AAAGTCATTTG>A
ERR5749387	913	PASS	C	T	26028	0.920662	0	0,11,0,25979	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749387	1573	PASS	A	G	61	0.213115	122	0,43,13,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acA/acG	T256	nsp2	0.001231	0.75	1	1	A>G
ERR5749387	2702	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	49511	7.27E-4	2526	49142,85,69,120	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F633V	nsp2	0.000632	0.333333	1	1	T>G
ERR5749387	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	98193	9.88E-4	2147483647	49002,46104,80,2756	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749387	3037	PASS	C	T	27422	0.809861	86	2,36,13677,13478	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749387	3095	PASS	T	C	13816	0.955124	0	0,3,0,13803	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tca/Cca	S126P	nsp3	0.937591	0.970297	1	1	T>C
ERR5749387	3177	PASS	C	T	36642	0.899514	13	3,7,22787,13794	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P153L	nsp3	0.000773	0.96008	3	2	C>T
ERR5749387	3267	PASS	C	T	22810	0.969925	2147483647	0,0,22795,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749387	4578	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTAACGATC	T	17622	8.51E-4	0	0,17607,0,15	HIGH	NONE	FRAME_SHIFT	ORF1ab	aacgatctaaat/	NDLN621	nsp3	0.000519	0.082979	2	2	TTAACGATC>T
ERR5749387	5388	PASS	C	A	6625	0.954868	2147483647	0,0,6622,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749387	5986	PASS	C	T	16362	0.975553	0	2,0,16351,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749387	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16106	0.001428	0	10,15908,0,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749387	6954	PASS	T	C	29240	0.824077	0	0,9,7,29082	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749387	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	38098	8.92E-4	121	16666,21398,34,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749387	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	16896	0.001361	0	16826,3,40,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749387	11287	PASS	GTCTGGTTTT	G	16892	0.99485	45	2,87,0,16805	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749387	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	39254	8.66E-4	7	24204,14990,20,19	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749387	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	16282	0.001106	0	16252,0,19,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749387	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	35881	0.001282	1	17906,17873,27,29	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749387	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	16303	0.004662	2147483647	15890,156,6,246	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749387	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	31633	0.002972	2	15834,15729,50,44	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749387	14408	PASS	C	T	31633	0.837227	6	1,4,15753,15586	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749387	14676	PASS	C	T	15690	0.81007	0	6,0,15650,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749387	15279	PASS	C	T	26387	0.89582	0	1,0,26356,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749387	15960	PASS	C	T	11340	0.792945	0	4,0,11284,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A840	RdRp	0.001581	0.81574	1	1	C>T
ERR5749387	16176	PASS	T	C	22023	0.9827	0	0,0,10657,11356	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749387	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	28754	5.22E-4	0	28739,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749387	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	36533	0.00156	0	36434,2,63,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749387	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	39966	8.01E-4	0	19603,19921,20,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749387	21764	PASS	ATACATG	A	17873	0.996923	0	55,0,17818,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749387	21990	PASS	TTTA	T	17881	0.997819	0	0,39,5,17837	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749387	22290	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	24948	4.81E-4	0	7,24929,0,12	HIGH	NONE	FRAME_SHIFT	S	tta/	L244	S	0.000389	0.578006	2	2	CT>C
ERR5749387	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29947	9.35E-4	4	12286,17589,15,15	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749387	23063	PASS	A	T	12320	0.872727	0	0,3,3,12259	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749387	23271	PASS	C	A	24596	0.918117	0	3,0,24561,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749387	23403	PASS	A	G	24580	0.971481	0	0,2,0,24555	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749387	23604	PASS	C	A	18805	0.925073	0	9,0,18781,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749387	23709	PASS	C	T	18803	0.943307	0	0,7,14,18766	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749387	24010	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATTTATTGAAGATCTAC	A	23490	5.11E-4	0	189,23289,0,12	HIGH	NONE	FRAME_SHIFT	S	attgaagatctacttttc/	IEDLLF818	S	0.000455	0.926398	4	2	ATTTATTGAAGATCTAC>A
ERR5749387	24127	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TTTG	37198	4.57E-4	32	13879,23319,0,17	MODERATE	NONE	CODON_INSERTION	S	aac/TTGaac	N856LN	S	0.000324	0.111888	4	1	T>TTTG
ERR5749387	24127	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	37198	8.06E-4	0	13857,23337,12,18	HIGH	NONE	FRAME_SHIFT	S	aac/	N856	S	0.000324	0.111888	4	1	TA>T
ERR5749387	24432	PASS	A	T	33973	0.935743	21	10,0,20082,13864	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cAa/cTa	Q957L	S	0.935743	0.949489	1	1	A>T
ERR5749387	24506	PASS	T	G	20091	0.976557	0	8,0,20078,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749387	24914	PASS	G	C	33608	0.962122	3	1,0,16743,16831	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749387	25495	PASS	A	G	40094	0.911134	1	3,2,19910,20135	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Ata/Gta	I35V	orf3a	0.000735	0.911134	2	1	A>G
ERR5749387	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	33334	5.7E-4	0	33313,2,19,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749387	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	33589	0.001221	1521	33066,240,139,109	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749387	26013	PASS	C	T	71053	0.9696	0	11,0,71000,0	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	ttC/ttT	F207	orf3a	0.000839	0.974528	1	1	C>T
ERR5749387	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	70938	8.6E-4	0	5,70870,0,61	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749387	26395	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	28768	7.65E-4	2237	14483,13505,5,756	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	Ctt/Att	L51I	E	0.000707	0.745829	2	1	C>A
ERR5749387	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	11312	0.001149	0	4,11278,0,13	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749387	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTTT	G	11312	0.001326	0	4,11278,0,15	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgtttgcg/gcg	ACLVGLMWLSYFIASFRLFA85A	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTTT>G
ERR5749387	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	11313	0.001679	0	4,11289,0,19	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749387	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	11313	0.007513	0	3,11214,0,85	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749387	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	G	11313	7.96E-4	0	3,11214,0,9	HIGH	NONE	FRAME_SHIFT	M	cttgtaggcttgatgtggctcagctacttcattgcttctttc/	LVGLMWLSYFIASF87	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT>G
ERR5749387	27972	PASS	C	T	11791	0.898312	0	0,0,11684,73	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749387	28001	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	23431	0.00111	0	11680,11705,16,15	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ccG/ccA	P36	orf8	0.00085	0.830607	2	1	G>A
ERR5749387	28048	PASS	G	T	11745	0.930864	0	0,9,2,11725	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749387	28111	PASS	A	G	32524	0.978508	1	6,2,20765,11745	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749387	28237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTGT	G	20765	5.78E-4	0	20753,0,12,0	MODERATE	NONE	CODON_DELETION	ORF8	gtt/	V117	orf8	0.000442	0.966707	4	2	GTGT>G
ERR5749387	28270	PASS	TA	T	40334	0.995463	445	184,6,20509,19642	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749387	28280	PASS	G	C	40265	0.937986	9	8,2,20553,19621	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749387	28281	PASS	A	T	40265	0.918465	34	23,4,20542,19623	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749387	28282	PASS	T	A	40267	0.912112	10	22,11,20493,19635	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749387	28406	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTACCCAATA	T	20800	9.62E-4	0	34,20741,0,20	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	N	ttacccaataat/tat	LPNN45Y	N	0.00043	0.921074	3	2	TTACCCAATA>T
ERR5749387	28407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TACCCAATA	T	20801	6.25E-4	0	34,20753,0,13	HIGH	NONE	FRAME_SHIFT	N	cccaataat/	PNN46	N	0.000382	0.179673	1	1	TACCCAATA>T
ERR5749387	28881	PASS	G	A	20448	0.673513	189	96,1,11979,7723	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749387	28882	PASS	G	A	20444	0.75362	143	69,0,12369,7682	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749387	28883	PASS	G	C	20444	0.915819	8	10,2,12615,7801	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749387	28977	PASS	C	T	7994	0.929947	0	0,1,13,7961	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749387	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	52080	0.001306	0	27898,24070,40,37	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749387	29524	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	25956	0.001002	984	10963,14223,1,411	LOW	SILENT	SYNONYMOUS_CODING	N	acT/acA	T417	N	0.001002	0.932604	2	1	T>A
ERR5749387	29542	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	26272	9.9E-4	917	10956,14848,1,397	.	.	.	.	.	.	.	0.00099	0.957487	2	1	A>C
ERR5749387	29749	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	15082	0.00126	0	0,14797,0,224	.	.	.	.	.	.	.	0.00126	0.997197	2	1	A>C
ERR5749388	241	PASS	C	T	17394	0.874612	3	0,2,8645,8693	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749388	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	12915	0.001858	0	12886,8,24,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749388	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	12918	9.29E-4	0	12826,9,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749388	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	12918	0.001548	0	12826,9,20,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749388	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	12918	0.003561	31	12826,9,44,2	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749388	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12919	0.001471	0	11949,14,821,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749388	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	12919	0.001626	15	12883,15,20,1	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749388	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	12919	6.97E-4	0	12880,16,9,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttatg/gtg	VM84V	leader	0.000554	0.991848	4	1	GTTA>G
ERR5749388	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	12919	8.51E-4	0	12880,16,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749388	520	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTT	G	12933	6.19E-4	0	12894,31,8,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttgag/gag	VE86E	leader	0.000583	0.051154	1	1	GGTT>G
ERR5749388	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	34405	3.49E-4	1	21474,12918,7,5	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749388	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	34403	0.001105	1	21448,12908,25,13	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749388	913	PASS	C	T	21469	0.910336	0	0,13,0,21420	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749388	3037	PASS	C	T	22873	0.814716	63	0,21,11426,11262	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749388	3267	PASS	C	T	21121	0.972113	0	2,0,21111,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749388	4764	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	17318	0.002137	0	17280,0,37,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cAt/cGt	H682R	nsp3	0.000673	0.93404	4	2	A>G
ERR5749388	5170	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	12385	7.27E-4	0	7,12369,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T819	nsp3	0.000565	0.894036	2	2	CCA>C
ERR5749388	5388	PASS	C	A	8269	0.955013	2147483647	0,0,8259,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749388	5986	PASS	C	T	14226	0.977154	0	2,0,14217,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749388	6954	PASS	T	C	23112	0.809579	0	0,5,3,22965	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749388	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	34322	0.001661	159	17855,16410,57,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749388	10138	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26271	0.001066	0	19290,6946,21,7	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N28	3Cpro	0.000458	0.983567	3	3	C>T
ERR5749388	11082	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	19788	6.57E-4	0	19787,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000427	0.179468	2	1	TG>T
ERR5749388	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	19788	0.00187	0	19713,0,56,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749388	11287	PASS	GTCTGGTTTT	G	19784	0.996816	0	0,63,1,19720	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749388	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	38896	8.23E-4	0	22565,16269,19,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749388	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	12637	6.33E-4	0	12630,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749388	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	31965	9.07E-4	0	15969,15921,17,18	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749388	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	13692	0.003579	2147483647	13344,125,6,209	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749388	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	26565	8.28E-4	0	13322,13237,11,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749388	14408	PASS	C	T	26565	0.845398	5	5,9,13266,13114	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749388	14676	PASS	C	T	13588	0.745879	0	10,0,13528,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749388	15279	PASS	C	T	23330	0.896614	0	2,0,23308,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749388	16176	PASS	T	C	22625	0.980818	3	0,1,11845,10766	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749388	19363	PASS	T	C	21668	0.959526	0	3,0,21645,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Tta/Cta	L442	ExoN	0.959526	0.959526	1	1	T>C
ERR5749388	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34520	0.002549	0	34400,0,94,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749388	20031	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34475	0.005221	0	34184,0,200,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A137	endoR	0.005221	0.880489	1	1	C>T
ERR5749388	21724	PASS	G	T	14052	0.911899	33	5,1,14035,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	ttG/ttT	L54F	S	0.000586	0.911899	2	2	G>T
ERR5749388	21764	PASS	ATACATG	A	14049	0.996655	0	47,0,14002,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749388	21990	PASS	TTTA	T	14053	0.998577	0	0,20,2,14031	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749388	23063	PASS	A	T	13714	0.873706	0	0,3,0,13656	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749388	23271	PASS	C	A	22183	0.914709	0	2,0,22147,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749388	23403	PASS	A	G	22176	0.96379	0	0,1,0,22155	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749388	23604	PASS	C	A	17374	0.958731	0	9,0,17356,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749388	23709	PASS	C	T	17370	0.944502	0	0,3,9,17333	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749388	24506	PASS	T	G	19049	0.976219	0	7,0,19038,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749388	24914	PASS	G	C	40049	0.961497	0	0,1,19952,20068	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749388	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	25044	4.79E-4	0	25032,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749388	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	25221	0.001189	1102	24839,155,121,79	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749388	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	57018	2.63E-4	0	0,57003,0,15	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749388	26645	PASS	C	T	13178	0.828654	0	1,0,13122,0	LOW	SILENT	SYNONYMOUS_CODING	M	aaC/aaT	N41	M	0.00097	0.828654	2	2	C>T
ERR5749388	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	13179	9.86E-4	0	2,13157,0,13	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749388	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	13178	0.002277	0	0,13141,0,30	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749388	27793	PASS	TTTTAGCC	T	21252	0.99633	0	0,78,2,21172	HIGH	NONE	FRAME_SHIFT	ORF7b	ttagccttt/	LAF14	orf7b	0.002125	0.99633	2	1	TTTTAGCC>T
ERR5749388	28048	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	5	1.0	2147483647	0,0,0,5	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749388	28111	PASS	A	G	19704	0.977974	0	2,0,19690,5	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749388	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	19676	6.1E-4	0	19667,2,12,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749388	28270	PASS	TA	T	38170	0.995599	327	160,11,19459,18543	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749388	28280	PASS	G	C	38095	0.936973	5	6,2,19494,18524	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749388	28281	PASS	A	T	38095	0.923087	15	22,9,19487,18523	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749388	28282	PASS	T	A	38099	0.911572	2	11,14,19441,18535	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749388	28406	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTACCCAATA	T	19712	5.58E-4	0	11,19690,0,11	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	N	ttacccaataat/tat	LPNN45Y	N	0.00043	0.921074	3	2	TTACCCAATA>T
ERR5749388	28881	PASS	G	A	17423	0.734087	21	12,2,8552,8584	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749388	28882	PASS	G	A	17421	0.830148	16	9,1,8685,8582	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749388	28883	PASS	G	C	17421	0.942598	3	2,0,8704,8696	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749388	28977	PASS	C	T	8852	0.935382	0	0,2,1,8826	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749388	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	54777	9.86E-4	0	27525,27170,35,33	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749389	71	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2101	0.015231	0	2068,0,32,0	.	.	.	.	.	.	.	0.002088	0.926791	2	1	C>T
ERR5749389	241	PASS	C	T	3255	0.867588	0	1,1,1621,1622	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749389	367	PASS	C	A	21683	0.909053	0	1,0,20042,1632	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcA	S34	leader	0.002556	0.909053	2	2	C>A
ERR5749389	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	20013	4.5E-4	0	19973,6,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749389	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	20013	7.99E-4	0	19973,6,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749389	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	19999	0.0022	2	18296,14,1610,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749389	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	19999	0.0014	0	19957,14,28,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749389	676	PASS	C	T	43096	0.919273	13	0,4,23038,20006	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G137	leader	0.000799	0.919273	2	1	C>T
ERR5749389	680	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	43096	9.05E-4	33	22999,20026,33,8	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gat/Aat	D139N	leader	0.000661	0.166667	3	2	G>A
ERR5749389	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	43096	8.12E-4	3	23023,20038,21,14	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749389	913	PASS	C	T	23030	0.918932	0	0,5,0,23000	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749389	1357	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	20268	4.93E-4	0	20258,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/	V185	nsp2	0.000493	0.077966	3	2	TG>T
ERR5749389	3037	PASS	C	T	14226	0.816603	39	0,13,7106,6996	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749389	3267	PASS	C	T	23250	0.970538	0	3,0,23233,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749389	3832	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	8656	0.001271	0	8645,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L373	nsp3	0.000689	0.327273	4	2	CT>C
ERR5749389	5388	PASS	C	A	4078	0.963462	2147483647	0,0,4076,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749389	5986	PASS	C	T	11512	0.976025	0	1,0,11508,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749389	6954	PASS	T	C	21536	0.830006	0	0,2,0,21435	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749389	10228	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAT	C	18760	5.33E-4	0	18750,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	att/	I59	3Cpro	0.000533	0.961998	2	2	CAT>C
ERR5749389	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	27204	0.001948	0	26487,3,53,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749389	11287	PASS	GTCTGGTTTT	G	27186	0.997867	0	0,57,0,27128	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749389	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	34605	0.001185	0	25810,8727,31,11	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749389	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	18340	0.001254	0	18296,0,23,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749389	13459	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	20206	7.42E-4	0	20192,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/ttTa	L8F?	nsp11	0.000691	0.060726	5	2	G>GT
ERR5749389	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	40360	0.001586	0	20152,20089,36,36	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749389	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	8888	0.00495	2564	8646,88,3,150	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749389	14408	PASS	C	T	17197	0.846078	3	0,1,8601,8492	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749389	14676	PASS	C	T	15274	0.795862	0	7,0,15233,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749389	15279	PASS	C	T	19019	0.889058	2147483647	0,0,18983,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749389	15983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	13738	0.001165	0	13724,0,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T850	RdRp	0.000701	0.338235	2	1	TA>T
ERR5749389	16176	PASS	T	C	18374	0.979972	0	0,0,4582,13785	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749389	17762	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTG	C	12919	6.97E-4	0	12910,7,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtc/	V510	helicase	0.000697	0.912542	2	2	CTG>C
ERR5749389	17799	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	12919	0.001548	0	12884,0,24,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtA/gtG	V521	helicase	0.001548	0.98027	1	1	A>G
ERR5749389	18681	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29240	0.028796	0	28288,0,943,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A214	ExoN	0.028796	0.923661	1	1	C>T
ERR5749389	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	29240	7.52E-4	0	29218,0,22,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749389	21660	PASS	C	T	16330	0.108941	0	6,14416,0,1904	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T33I	S	0.008721	0.937304	1	1	C>T
ERR5749389	21764	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATACATG	A	7	1.0	2147483647	0,0,7,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749389	21990	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTTA	T	7	0.714286	13	0,2,5,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749389	21991	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTA	T	12510	8.79E-4	0	20,12477,0,11	HIGH	NONE	FRAME_SHIFT	S	tat/	Y144	S	0.00078	0.991378	2	1	TTA>T
ERR5749389	23063	PASS	A	T	14904	0.874262	2147483647	0,0,0,14837	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749389	23271	PASS	C	A	28008	0.918238	0	2,0,27975,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749389	23403	PASS	A	G	27999	0.966642	0	0,6,0,27962	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749389	23604	PASS	C	A	14560	0.940728	0	17,0,14539,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749389	23635	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14547	0.004537	0	14464,0,72,0	LOW	SILENT	SYNONYMOUS_CODING	S	tcC/tcT	S691	S	0.002385	0.958978	1	1	C>T
ERR5749389	23709	PASS	C	T	14538	0.93658	0	0,1,0,14522	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749389	23780	PASS	A	G	14566	0.967596	0	0,8,0,14549	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Atg/Gtg	M740V	S	0.002014	0.967596	3	2	A>G
ERR5749389	23817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	25264	0.001227	8	10689,14540,9,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTt/cCt	L752P	S	0.000646	0.066832	1	1	T>C
ERR5749389	24444	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	19237	8.32E-4	0	19218,3,16,0	HIGH	NONE	FRAME_SHIFT	S	acg/	T961	S	0.000832	0.063732	2	2	CG>C
ERR5749389	24506	PASS	T	G	19232	0.977121	0	3,0,19226,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749389	24794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	23626	0.009947	0	23366,0,249,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gct/Tct	A1078S	S	0.001791	0.957884	1	1	G>T
ERR5749389	24914	PASS	G	C	46911	0.959604	0	0,0,23383,23494	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749389	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	5537	0.003793	401	5495,11,4,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749389	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	5508	0.001816	0	5498,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749389	26280	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	44378	7.89E-4	23	14625,29666,5,36	LOW	SILENT	SYNONYMOUS_CODING	E	ttA/ttG	L12	E	0.000789	0.06713	2	2	A>G
ERR5749389	27312	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	20856	0.001007	0	20835,0,21,0	HIGH	NONE	FRAME_SHIFT	ORF6	aat/aaAt	N39K?	orf6	0.000911	0.088458	4	2	T>TA
ERR5749389	27741	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	22189	5.41E-4	0	0,22176,0,12	HIGH	NONE	FRAME_SHIFT	ORF7a	aaaaga/	KR117	orf7a	0.000363	0.954278	3	2	CAA>C
ERR5749389	27972	PASS	C	T	7975	0.902947	0	1,0,7913,33	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749389	28048	PASS	G	T	7946	0.918827	0	0,9,0,7929	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749389	28111	PASS	A	G	36992	0.979806	0	6,1,29025,7952	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749389	28270	PASS	TA	T	56255	0.995343	615	263,10,28658,27335	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749389	28280	PASS	G	C	56144	0.937999	19	10,1,28710,27321	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749389	28281	PASS	A	T	56144	0.916037	43	40,10,28693,27315	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749389	28282	PASS	T	A	56146	0.911712	8	29,17,28640,27329	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749389	28881	PASS	G	A	10016	0.80601	0	0,0,4996,4937	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749389	28882	PASS	G	A	10016	0.839257	4	4,1,5013,4928	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749389	28883	PASS	G	C	10016	0.92522	3	2,0,5012,4986	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749389	28977	PASS	C	T	5083	0.931143	0	0,2,0,5071	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749389	28978	PASS	T	G	5083	0.976785	0	0,4,0,5077	LOW	SILENT	SYNONYMOUS_CODING	N	tcT/tcG	S235	N	0.001946	0.976785	2	2	T>G
ERR5749389	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	38600	0.005052	1675	33479,4880,5,199	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749389	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	66579	9.76E-4	0	33421,33039,46,43	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749389	29543	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	7560	0.00172	1	6709,825,13,2	.	.	.	.	.	.	.	0.001058	0.973475	3	1	G>A
ERR5749389	29679	PASS	C	T	13384	0.838763	3	0,2,6663,6671	.	.	.	.	.	.	.	0.000443	0.838763	2	1	C>T
ERR5749390	241	PASS	C	T	15624	0.855543	6	0,3,7776,7786	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749390	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	14212	0.001829	0	14186,5,26,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749390	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	14217	0.001407	0	14119,9,20,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749390	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	14217	0.004291	13	14119,9,60,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749390	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	14202	0.003098	2	12923,12,1124,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749390	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	14202	9.86E-4	0	14175,13,14,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749390	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	14200	6.34E-4	0	14173,13,9,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749390	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	40224	4.47E-4	31	25967,14239,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749390	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	40225	0.001417	5	25938,14218,41,16	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749390	913	PASS	C	T	25980	0.92602	0	0,11,0,25947	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749390	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	92453	9.41E-4	2147483647	46121,43685,82,2342	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749390	3037	PASS	C	T	25164	0.822961	50	1,20,12568,12385	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749390	3267	PASS	C	T	24741	0.97296	0	2,0,24723,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749390	4237	PASS	T	C	47103	0.917882	2	1,2,23582,23420	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaT/aaC	N506	nsp3	0.000302	0.918634	2	2	T>C
ERR5749390	4255	PASS	G	A	47150	0.825027	69	44,7,23434,23374	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccG/ccA	P512	nsp3	0.001102	0.871853	2	1	G>A
ERR5749390	4578	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTAACGATC	T	17786	5.62E-4	0	0,17776,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	aacgatctaaat/	NDLN621	nsp3	0.000519	0.082979	2	2	TTAACGATC>T
ERR5749390	5388	PASS	C	A	8992	0.964413	2147483647	0,0,8990,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749390	5575	PASS	C	T	8998	0.956546	66	2,0,3,8989	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y952	nsp3	0.01018	0.961493	1	1	C>T
ERR5749390	5986	PASS	C	T	16790	0.977129	0	1,0,16775,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749390	6954	PASS	T	C	28041	0.835063	0	0,5,3,27905	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749390	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	35347	9.34E-4	82	19699,15615,33,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749390	10323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	21962	0.001093	0	0,21899,0,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749390	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25835	0.0012	0	25757,11,35,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749390	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	25808	0.003681	0	25679,0,116,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749390	11287	PASS	GTCTGGTTTT	G	25821	0.997831	0	0,56,0,25765	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749390	11507	PASS	G	A	35681	0.912446	17	15,4,17828,17736	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Att	V179I	nsp6	0.007744	0.914418	2	2	G>A
ERR5749390	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	24447	9.0E-4	0	24405,0,22,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749390	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	45491	0.001517	0	22711,22654,38,38	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749390	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	18313	0.003932	2147483647	17869,162,5,266	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749390	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	35605	0.001489	1	17837,17737,28,25	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749390	14408	PASS	C	T	35605	0.847465	4	3,6,17759,17556	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749390	14676	PASS	C	T	16779	0.730198	0	8,0,16705,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749390	15279	PASS	C	T	28793	0.89883	0	3,0,28757,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749390	15420	PASS	T	G	28761	0.934773	0	0,37,0,28710	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcG	A660	RdRp	0.908883	0.934773	1	1	T>G
ERR5749390	16176	PASS	T	C	26886	0.983002	0	1,2,13046,13825	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749390	16508	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	28151	0.001101	0	28078,20,52,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGt/gTt	G91V	helicase	0.000561	0.074909	2	2	G>T
ERR5749390	17135	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19907	0.014216	0	19587,11,306,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P300L	helicase	0.010417	0.96005	2	2	C>T
ERR5749390	17502	PASS	C	T	19370	0.983738	0	2,0,19358,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F422	helicase	0.000611	0.9865	2	2	C>T
ERR5749390	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	30747	9.76E-4	0	30717,0,30,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749390	19011	PASS	C	T	31632	0.972718	0	2,0,31614,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D324	ExoN	0.000408	0.975746	4	2	C>T
ERR5749390	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	31609	3.8E-4	0	0,31597,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749390	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	37764	0.001774	0	37667,0,72,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749390	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	40057	4.49E-4	0	19988,20053,8,10	HIGH	NONE	FRAME_SHIFT	S	ctt/Tctt	L5S?	S	0.000394	0.091869	4	1	G>GT
ERR5749390	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	40016	0.001349	0	19615,19976,28,30	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749390	21764	PASS	ATACATG	A	16005	0.997501	0	39,0,15965,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749390	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	16005	5.62E-4	0	15996,0,9,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749390	21990	PASS	TTTA	T	16009	0.998064	0	0,31,2,15976	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749390	23063	PASS	A	T	14	0.714286	2147483647	0,0,0,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749390	23271	PASS	C	A	27989	0.922184	0	3,0,27957,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749390	23403	PASS	A	G	27988	0.97624	0	0,9,3,27956	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749390	23604	PASS	C	A	19806	0.944815	0	12,0,19782,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749390	23709	PASS	C	T	19784	0.945966	0	0,6,0,19753	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749390	24506	PASS	T	G	24480	0.975449	0	11,0,24465,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749390	24914	PASS	G	C	46993	0.96242	0	0,0,23424,23532	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749390	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	26520	0.001433	430	26424,19,20,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749390	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	60118	3.99E-4	0	5,60089,0,24	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749390	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	15501	0.001871	0	1,15468,0,29	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749390	27389	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22762	0.002109	0	85,22591,0,51	.	.	.	.	.	.	.	0.001157	0.899553	2	1	C>T
ERR5749390	27765	PASS	C	T	28189	0.970449	0	0,3,0,28168	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7b	Ctt/Ttt	L4F	orf7b	0.00109	0.970449	1	1	C>T
ERR5749390	27972	PASS	C	T	14360	0.906825	20	1,1,14257,60	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749390	28048	PASS	G	T	14323	0.924178	0	0,15,0,14298	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749390	28111	PASS	A	G	41532	0.980497	17	15,1,27170,14329	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749390	28239	PASS	GTTGTT	G	27128	0.981348	0	509,0,26622,0	HIGH	NONE	FRAME_SHIFT	ORF8	gtttta/	VL117	orf8	0.000417	0.984998	9	2	GTTGTT>G
ERR5749390	28249	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	ATC	26743	7.48E-4	0	26719,0,20,0	HIGH	NONE	FRAME_SHIFT	ORF8	ttc/CTttc	F120L?	orf8	0.000443	0.063605	3	2	A>ATC
ERR5749390	28250	PASS	T	TCTG	26743	0.99312	0	138,0,26559,0	MODERATE	NONE	CODON_INSERTION	ORF8	ttc/CTGttc	F120LF	orf8	0.000494	0.993968	5	3	T>TCTG
ERR5749390	28250	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TATG	26743	7.1E-4	0	138,0,19,0	MODERATE	NONE	CODON_INSERTION	ORF8	ttc/ATGttc	F120MF	orf8	0.000494	0.993968	5	3	T>TATG
ERR5749390	28253	PASS	CA	C	26743	0.995214	0	128,0,26615,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749390	28270	PASS	TA	T	52001	0.996365	281	160,17,26573,25239	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749390	28271	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AA	A	52001	0.001135	170	26682,25257,59,0	.	.	.	.	.	.	.	0.000482	0.924941	3	2	AA>A
ERR5749390	28280	PASS	G	C	52001	0.949866	16	13,3,26672,25231	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749390	28281	PASS	A	T	52001	0.937982	32	20,3,26669,25230	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749390	28282	PASS	T	A	52005	0.909701	3	22,15,26634,25232	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749390	28881	PASS	G	A	20184	0.771651	18	12,2,9965,9950	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749390	28882	PASS	G	A	20181	0.843516	4	4,1,10077,9925	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749390	28883	PASS	G	C	20181	0.943957	0	1,1,10087,10072	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749390	28977	PASS	C	T	10256	0.93945	0	0,3,0,10236	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749390	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	69164	0.001099	0	34703,34335,46,46	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749391	203	PASS	C	T	3363	0.942611	0	1,0,3358,1	.	.	.	.	.	.	.	0.001818	0.942611	1	1	C>T
ERR5749391	241	PASS	C	T	6698	0.867722	0	0,0,3333,3337	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749391	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	10189	0.004907	0	10119,22,50,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749391	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	10189	0.001472	0	10092,22,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749391	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	10189	0.002355	0	10092,22,24,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749391	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	10189	0.003435	0	10092,22,35,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749391	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10200	0.001863	7	9397,38,618,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749391	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	10200	0.003333	0	10127,38,34,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749391	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	10200	0.001176	0	10140,39,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749391	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	10201	0.002451	0	10122,40,25,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749391	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATGGTTG	T	10201	0.001078	0	10122,40,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	atggttgag/	MVE85	leader	0.000587	0.476744	4	1	TATGGTTG>T
ERR5749391	657	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10183	0.002062	0	5,10153,0,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A131V	leader	0.001202	0.365979	3	1	C>T
ERR5749391	673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTTA	27918	7.88E-4	96	17740,10156,0,22	MODERATE	NONE	CODON_INSERTION	ORF1ab	ggc/TTAggc	G137LG	leader	0.000454	0.602236	3	2	C>CTTA
ERR5749391	673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27918	0.001433	161	17729,10112,3,45	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y136	leader	0.000454	0.602236	3	2	C>T
ERR5749391	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27896	9.68E-4	1	17719,10121,16,11	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L140	leader	0.000316	0.135802	3	2	C>T
ERR5749391	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	27896	6.09E-4	8	17676,10131,14,3	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749391	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	27896	0.002545	5	17676,10131,50,21	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749391	913	PASS	C	T	17735	0.919312	0	0,18,0,17696	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749391	1862	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTTTATGCA	C	20511	6.83E-4	0	0,20496,0,14	HIGH	NONE	FRAME_SHIFT	ORF1ab	tatgcattt/	YAF354	nsp2	0.000585	0.936867	4	2	CTTTATGCA>C
ERR5749391	2110	PASS	C	T	19263	0.804444	0	0,11,0,19129	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N435	nsp2	0.024426	0.811371	1	1	C>T
ERR5749391	2713	PASS	A	G	118	0.059322	0	52,51,6,6	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaA/aaG	K636	nsp2	0.000941	0.059322	2	2	A>G
ERR5749391	3037	PASS	C	T	19596	0.838896	63	0,21,9788,9702	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749391	3267	PASS	C	T	17773	0.972149	0	2,0,17760,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749391	3832	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTT	C	13633	0.001174	0	13594,5,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L373	nsp3	0.000689	0.327273	4	2	CTT>C
ERR5749391	5144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25292	9.09E-4	2	12631,12449,14,17	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L809	nsp3	0.000909	0.822022	1	1	C>T
ERR5749391	5388	PASS	C	A	6882	0.960913	2147483647	0,0,6877,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749391	5986	PASS	C	T	14045	0.97686	2147483647	0,0,14031,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749391	6954	PASS	T	C	20369	0.839118	0	0,15,0,20253	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749391	7070	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	32594	0.003712	536	11909,20429,124,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggc/Agc	G1451S	nsp3	0.000698	0.101434	3	1	G>A
ERR5749391	7070	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	32594	0.003774	470	11909,20429,126,5	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggc/Tgc	G1451C	nsp3	0.000698	0.101434	3	1	G>T
ERR5749391	8964	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	18082	5.53E-4	0	18061,7,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K138	nsp4	0.000553	0.981649	4	2	CA>C
ERR5749391	9430	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6343	0.002207	0	2,6308,0,14	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I292	nsp4	0.001411	0.960894	1	1	C>T
ERR5749391	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	22224	0.00117	35	15850,6348,26,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749391	11073	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TC	24064	4.99E-4	0	24051,1,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/Cttt	F35L?	nsp6	0.000385	0.092251	6	2	T>TC
ERR5749391	11074	PASS	C	CT	24064	0.06757	0	22047,1,1626,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CT
ERR5749391	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	24064	0.010389	0	22047,1,250,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749391	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTTT	24064	0.003989	0	22047,1,96,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_INSERTION	ORF1ab	ttg/ttTTTg	L37FL	nsp6	0.000965	0.945355	5	2	C>CTTT
ERR5749391	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24064	0.002576	0	23957,1,67,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749391	11082	PASS	TG	T	23972	0.096529	0	21748,0,2314,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000427	0.179468	2	1	TG>T
ERR5749391	11083	PASS	G	T	23972	0.857334	0	10,0,21543,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749391	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GTT	23972	0.004839	0	23077,0,116,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/tTTat	Y38F?	nsp6	0.000477	0.901695	5	2	G>GTT
ERR5749391	11095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTT	C	23962	5.84E-4	0	23934,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L43	nsp6	0.000515	0.887707	7	2	CTT>C
ERR5749391	11110	PASS	T	C	23923	0.803913	0	2,0,23830,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcC	A46	nsp6	0.000477	0.803913	2	2	T>C
ERR5749391	11287	PASS	GTCTGGTTTT	G	24054	0.995843	0	0,100,0,23954	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749391	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	34789	0.001265	13	21492,13226,21,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749391	11750	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	42203	0.001185	0	21431,20662,33,29	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L260F	nsp6	0.001019	0.70989	2	1	C>T
ERR5749391	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	21684	0.001199	0	21629,0,28,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749391	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	15565	0.00167	0	15540,0,26,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749391	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	39143	0.001328	0	19541,19494,28,29	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749391	14120	PASS	C	T	31494	0.786944	12	0,4,15702,15378	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCa/cTa	P227L	RdRp	0.00121	0.786944	2	2	C>T
ERR5749391	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	11849	0.003545	2750	11535,133,8,165	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749391	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	23000	0.00113	0	11525,11463,14,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749391	14408	PASS	C	T	23000	0.847609	1	5,6,11478,11366	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749391	14676	PASS	C	T	13427	0.841662	0	4,0,13396,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749391	15279	PASS	C	T	21048	0.895049	0	2,0,21021,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749391	15981	PASS	C	T	10841	0.965686	2147483647	0,0,10833,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I847	RdRp	0.001324	0.965686	2	2	C>T
ERR5749391	16176	PASS	T	C	18954	0.983856	0	1,1,8082,10861	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749391	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	29349	9.54E-4	0	29321,0,28,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749391	18747	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	29346	3.75E-4	0	29332,6,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tataat/	YN237	ExoN	0.000375	0.982946	4	2	CTA>C
ERR5749391	19328	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	20823	6.72E-4	0	20809,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F431	ExoN	0.000459	0.937906	4	2	CT>C
ERR5749391	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21965	0.001867	0	21903,0,43,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749391	20420	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	27973	4.29E-4	0	40,27921,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F268	endoR	0.000383	0.069626	2	1	AT>A
ERR5749391	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26321	0.001216	0	26260,0,34,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749391	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30519	0.001212	5	14983,15223,19,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749391	21764	PASS	ATACATG	A	14463	0.996958	0	44,0,14419,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749391	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	14463	0.001106	0	14447,0,16,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749391	21990	PASS	TTTA	T	14469	0.998134	0	0,27,3,14439	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749391	22690	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	16570	0.001026	0	16228,9,19,0	LOW	SILENT	SYNONYMOUS_CODING	S	acT/acC	T376	S	0.000815	0.051311	2	1	T>C
ERR5749391	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	33310	8.41E-4	0	16649,16582,14,15	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749391	23031	PASS	T	C	16597	0.92095	0	0,1,31,16548	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tTt/tCt	F490S	S	0.001067	0.92095	2	1	T>C
ERR5749391	23063	PASS	A	T	16680	0.871763	0	0,3,0,16600	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749391	23271	PASS	C	A	21050	0.920523	0	3,0,21022,4	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749391	23403	PASS	A	G	21049	0.974773	0	0,0,4,21036	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749391	23604	PASS	C	A	16857	0.938601	0	16,0,16831,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749391	23709	PASS	C	T	16857	0.944118	0	0,5,9,16825	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749391	23817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	29623	9.11E-4	8	12744,16826,8,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTt/cCt	L752P	S	0.000646	0.066832	1	1	T>C
ERR5749391	24010	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATTTATTGAAGATCTAC	A	12829	6.24E-4	0	102,12726,0,8	HIGH	NONE	FRAME_SHIFT	S	attgaagatctacttttc/	IEDLLF818	S	0.000455	0.926398	4	2	ATTTATTGAAGATCTAC>A
ERR5749391	24506	PASS	T	G	20532	0.975356	0	15,0,20516,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749391	24914	PASS	G	C	44183	0.96304	4	1,4,22016,22141	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749391	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	10943	0.002924	612	10865,22,6,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749391	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	14423	0.00104	0	0,14408,0,15	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749391	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	14425	0.001664	0	0,14400,0,24	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749391	27404	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	22206	0.001441	0	0,22096,0,42	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	aTt/aCt	I4T	orf7a	0.001441	0.998768	2	2	T>C
ERR5749391	27972	PASS	C	T	11055	0.907191	0	0,0,10919,98	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749391	28048	PASS	G	T	10966	0.925041	0	0,11,0,10949	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749391	28095	PASS	A	T	10978	0.959829	194	6,3,0,10939	HIGH	NONSENSE	STOP_GAINED	ORF8	Aaa/Taa	K68*	orf8	0.002672	0.967672	2	2	A>T
ERR5749391	28111	PASS	A	G	34169	0.980831	2	8,2,23180,10970	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749391	28209	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	23195	0.003363	0	23103,0,87,0	HIGH	NONSENSE	STOP_GAINED	ORF8	Gaa/Taa	E106*	orf8	0.001409	0.963166	2	2	G>T
ERR5749391	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23180	0.002243	0	23058,3,56,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749391	28270	PASS	TA	T	45087	0.994987	627	234,3,22870,21991	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749391	28280	PASS	G	C	45009	0.941945	70	35,3,22910,21958	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749391	28281	PASS	A	T	45009	0.920438	51	37,7,22915,21953	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749391	28282	PASS	T	A	45010	0.913575	55	55,15,22856,21974	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749391	28407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TACCCAATA	T	23216	5.17E-4	0	18,23186,0,12	HIGH	NONE	FRAME_SHIFT	N	cccaataat/	PNN46	N	0.000382	0.179673	1	1	TACCCAATA>T
ERR5749391	28881	PASS	G	A	12562	0.791275	1	4,2,6226,6186	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749391	28882	PASS	G	A	12561	0.837593	1	5,3,6277,6157	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749391	28883	PASS	G	C	12561	0.947616	3	0,1,6289,6261	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749391	28977	PASS	C	T	6388	0.938478	0	0,1,0,6371	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749391	29095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30487	8.86E-4	0	30442,0,28,0	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F274	N	0.000792	0.961279	2	2	C>T
ERR5749391	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	60581	0.001122	0	30393,30075,45,43	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749391	29679	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	19264	8.31E-4	0	9635,9615,8,8	.	.	.	.	.	.	.	0.000443	0.838763	2	1	CT>C
ERR5749391	29743	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9660	0.007764	0	0,9562,0,84	.	.	.	.	.	.	.	0.001027	0.859785	2	1	C>T
ERR5749392	241	PASS	C	T	17419	0.846547	0	1,2,8655,8665	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749392	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	12942	0.004868	0	12874,7,63,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749392	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	12945	0.002163	16	12784,10,27,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749392	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	12945	0.001931	0	12784,10,25,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749392	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	12945	0.007261	11	12784,10,93,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749392	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12961	0.002623	9	11750,36,908,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749392	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	12961	0.002237	0	12894,38,29,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749392	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	12960	8.49E-4	0	12897,38,11,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttatg/gtg	VM84V	leader	0.000554	0.991848	4	1	GTTA>G
ERR5749392	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	12958	0.001775	0	12887,38,23,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749392	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	39867	8.28E-4	42	26870,12961,32,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749392	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	39869	3.26E-4	0	26784,12941,9,4	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749392	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	39869	0.00311	51	26784,12941,106,18	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749392	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26890	0.001004	0	0,26829,0,28	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749392	913	PASS	C	T	26890	0.90833	0	0,5,0,26846	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749392	1510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	25737	0.004701	0	0,25346,0,126	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G235	nsp2	0.002159	0.937304	1	1	T>C
ERR5749392	2702	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	46002	7.61E-4	2147483647	45676,37,61,148	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F633V	nsp2	0.000632	0.333333	1	1	T>G
ERR5749392	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	91139	0.001393	2147483647	45575,42525,78,2756	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749392	3037	PASS	C	T	30211	0.817815	69	0,23,15100,14921	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749392	3267	PASS	C	T	25653	0.970062	0	1,0,25642,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749392	3671	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	39185	9.19E-4	0	19534,19411,22,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E318K	nsp3	0.000351	0.0625	6	2	G>A
ERR5749392	5002	PASS	C	T	14320	0.974162	206	2,6,14303,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ctC/ctT	L761	nsp3	0.001115	0.976835	3	2	C>T
ERR5749392	5388	PASS	C	A	9033	0.959925	0	1,0,9026,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749392	5512	PASS	C	T	9026	0.95092	0	0,2,0,9012	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N931	nsp3	0.002299	0.987013	1	1	C>T
ERR5749392	5986	PASS	C	T	20150	0.97196	2147483647	0,0,20133,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749392	6954	PASS	T	C	28602	0.825886	0	0,9,0,28459	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749392	9130	PASS	G	T	22580	0.453277	0	1,11926,1,10642	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtG/gtT	V192	nsp4	0.001321	0.963415	2	1	G>T
ERR5749392	10138	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	32585	9.51E-4	6	24181,8363,20,11	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N28	3Cpro	0.000458	0.983567	3	3	C>T
ERR5749392	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	23112	0.002163	0	22512,6,50,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749392	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23112	0.001385	0	23040,6,37,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749392	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	23098	0.001385	0	23029,0,49,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749392	11287	PASS	GTCTGGTTTT	G	23094	0.995064	0	0,114,0,22980	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749392	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	48359	7.44E-4	0	28563,19721,24,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749392	12676	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24436	0.024595	0	0,23716,0,669	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V195	nsp8	0.000716	0.87302	3	2	C>T
ERR5749392	12754	PASS	C	T	43820	0.947969	17	5,0,19365,24441	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C23	nsp9	0.001216	0.947969	1	1	C>T
ERR5749392	12809	PASS	C	T	19227	0.901337	0	1,0,19204,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Ttt	L42F	nsp9	0.001562	1	1	1	C>T
ERR5749392	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	36745	0.001606	0	18344,18300,31,31	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749392	14120	PASS	C	T	36780	0.760712	21	0,7,18343,17875	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCa/cTa	P227L	RdRp	0.00121	0.786944	2	2	C>T
ERR5749392	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	19616	0.004384	2147483647	19146,171,8,285	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749392	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	38108	0.00244	0	19087,18960,48,45	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749392	14408	PASS	C	T	38108	0.835678	11	2,8,18989,18755	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749392	14676	PASS	C	T	15768	0.790969	0	6,0,15715,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749392	15279	PASS	C	T	28151	0.891833	0	2,0,28117,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749392	16176	PASS	T	C	26048	0.98092	0	0,0,13177,12855	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749392	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	31134	6.75E-4	0	31113,0,21,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749392	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	30647	3.92E-4	0	2,30634,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749392	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	43740	0.001738	0	43635,0,82,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749392	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	44169	7.24E-4	0	44076,0,33,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749392	21255	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	89776	5.35E-4	0	46582,43119,29,26	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcG/gcA	A199	MethTr	0.000341	0.917425	4	2	G>A
ERR5749392	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	39951	7.01E-4	0	19930,19998,13,15	HIGH	NONE	FRAME_SHIFT	S	ctt/Tctt	L5S?	S	0.000394	0.091869	4	1	G>GT
ERR5749392	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	39908	8.27E-4	3	19541,19921,18,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749392	21595	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20058	0.001296	0	4,20008,0,28	LOW	SILENT	SYNONYMOUS_CODING	S	gtC/gtT	V11	S	0.001296	0.918559	3	2	C>T
ERR5749392	21724	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	19113	0.021242	0	18652,13,443,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	ttG/ttT	L54F	S	0.000586	0.911899	2	2	G>T
ERR5749392	21762	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTATACA	C	19100	0.001623	0	19069,0,31,0	MODERATE	NONE	CODON_DELETION	S	atacat/	IH68	S	0.001297	0.875707	2	2	CTATACA>C
ERR5749392	21764	PASS	ATACATG	A	19100	0.997539	0	47,0,19053,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749392	21990	PASS	TTTA	T	19105	0.996912	0	0,59,4,19042	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749392	22225	PASS	G	T	25473	0.924979	0	0,2,0,25458	LOW	SILENT	SYNONYMOUS_CODING	S	tcG/tcT	S221	S	0.001195	0.94526	3	1	G>T
ERR5749392	22289	PASS	G	T	25490	0.909337	0	0,3,0,25444	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gct/Tct	A243S	S	0.000446	0.915917	3	2	G>T
ERR5749392	23063	PASS	A	T	20644	0.861752	0	0,3,4,20534	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749392	23271	PASS	C	A	27161	0.918044	0	4,0,27126,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749392	23403	PASS	A	G	27158	0.972089	0	0,5,0,27134	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749392	23604	PASS	C	A	22865	0.943494	0	10,0,22844,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749392	23709	PASS	C	T	22844	0.940116	0	0,11,13,22780	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749392	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	44974	3.34E-4	0	22095,22864,7,8	HIGH	NONE	FRAME_SHIFT	S	ttg/	L753	S	0.000334	0.080808	2	2	CT>C
ERR5749392	24010	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATTTATTGAAGATCTAC	A	22214	5.4E-4	0	162,22048,0,12	HIGH	NONE	FRAME_SHIFT	S	attgaagatctacttttc/	IEDLLF818	S	0.000455	0.926398	4	2	ATTTATTGAAGATCTAC>A
ERR5749392	24127	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	40148	3.24E-4	1	18050,22094,5,8	HIGH	NONE	FRAME_SHIFT	S	aac/	N856	S	0.000324	0.111888	4	1	TA>T
ERR5749392	24237	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18056	0.001329	0	18019,0,27,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gTt	A892V	S	0.001242	0.889739	1	1	C>T
ERR5749392	24506	PASS	T	G	21747	0.973698	0	6,0,21738,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749392	24914	PASS	G	C	46710	0.959002	0	0,0,23258,23424	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749392	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	32955	0.002306	84	24299,8562,85,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749392	25523	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	22984	0.001088	153	339,20342,0,2296	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	gGa/gTa	G44V	orf3a	0.000994	0.895931	1	1	G>T
ERR5749392	25531	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	23594	0.003348	2	8,20951,0,2623	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Att/Ttt	I47F	orf3a	0.000473	0.975891	5	2	A>T
ERR5749392	25553	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24602	0.006056	0	3,24005,0,173	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	gCt/gTt	A54V	orf3a	0.001165	0.868131	3	2	C>T
ERR5749392	25555	PASS	G	T	24602	0.88314	0	0,3,3,24447	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gtt/Ttt	V55F	orf3a	0.000552	0.900573	5	2	G>T
ERR5749392	25555	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	24602	0.025486	0	3,23965,0,627	HIGH	NONE	FRAME_SHIFT	ORF3a	cag/Tcag	Q57S?	orf3a	0.000552	0.900573	5	2	G>GT
ERR5749392	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	28269	0.001486	378	28150,25,27,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749392	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	28224	0.001063	0	28194,0,30,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749392	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	28435	0.001547	1660	27994,173,128,113	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749392	26060	PASS	C	T	72524	0.811607	0	12,0,71971,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aCt/aTt	T223I	orf3a	0.000459	0.822477	2	2	C>T
ERR5749392	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	72406	4.14E-4	0	2,72370,0,30	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749392	26748	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	17281	0.001505	1	46,16764,0,465	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Atc/Ctc	I76L	M	0.001056	0.926238	2	1	A>C
ERR5749392	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	G	17300	5.2E-4	0	2,17259,0,9	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/	ACLVGLMWLSYFIASF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT>G
ERR5749392	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	17300	0.001272	0	2,17259,0,22	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749392	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	17300	6.94E-4	0	1,17286,0,12	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749392	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	17299	0.003584	0	0,17226,0,62	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749392	27670	PASS	GTTCAAGAACTTTACTCTCCAATTT	G	25094	0.98932	501	39,230,62,24764	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF7a	caagaactttactctccaatttttctt/ctt	QELYSPIFL94L	orf7a	0.002392	0.990588	3	2	GTTCAAGAACTTTACTCTCCAATTT>G
ERR5749392	27972	PASS	C	T	17556	0.902597	32	3,2,17354,138	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749392	28001	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	34801	9.48E-4	0	17362,17378,18,19	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ccG/ccA	P36	orf8	0.00085	0.830607	2	1	G>A
ERR5749392	28048	PASS	G	T	17437	0.918793	0	0,23,0,17402	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749392	28095	PASS	A	T	17452	0.959603	170	5,4,0,17404	HIGH	NONSENSE	STOP_GAINED	ORF8	Aaa/Taa	K68*	orf8	0.002672	0.967672	2	2	A>T
ERR5749392	28111	PASS	A	G	42915	0.976978	4	9,3,25446,17440	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749392	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	25447	4.32E-4	0	25436,5,11,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749392	28270	PASS	TA	T	49299	0.994138	696	288,9,25075,23935	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749392	28271	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AA	A	49293	5.27E-4	74	25327,23944,26,0	.	.	.	.	.	.	.	0.000482	0.924941	3	2	AA>A
ERR5749392	28280	PASS	G	C	49194	0.937919	27	20,4,25151,23907	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749392	28281	PASS	A	T	49194	0.902082	36	34,9,25129,23912	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749392	28282	PASS	T	A	49199	0.922661	11	33,18,25127,23927	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749392	28881	PASS	G	A	22193	0.778714	19	10,1,11023,10864	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749392	28882	PASS	G	A	22190	0.826093	9	4,0,11141,10809	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749392	28883	PASS	G	C	22190	0.946327	0	1,0,11146,11015	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749392	28977	PASS	C	T	11312	0.930958	0	0,5,2,11283	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749392	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	49213	7.72E-4	151	37862,11263,7,34	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749392	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	75193	0.001037	0	37780,37268,52,50	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749392	29421	PASS	C	T	11722	0.052892	0	11062,0,647,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	cCg/cTg	P383L	N	0.002705	0.052892	2	2	C>T
ERR5749393	96	PASS	C	T	15210	0.986522	0	1,0,15206,0	.	.	.	.	.	.	.	0.986522	0.986522	1	1	C>T
ERR5749393	241	PASS	C	T	30194	0.864907	1	4,6,14989,15083	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749393	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	18744	0.003041	0	18668,15,57,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749393	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	18749	6.93E-4	0	18592,19,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749393	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	18749	0.00112	0	18592,19,21,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749393	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	18749	0.005014	0	18592,19,94,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749393	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	18734	0.001334	1	17516,26,920,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749393	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	18734	0.001815	0	18672,27,34,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749393	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	18734	6.41E-4	0	18689,28,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749393	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	18730	0.001228	14	18663,27,22,1	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749393	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATGGTTG	T	18730	5.87E-4	0	18663,27,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	atggttgag/	MVE85	leader	0.000587	0.476744	4	1	TATGGTTG>T
ERR5749393	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	50634	4.15E-4	19	31871,18740,19,2	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749393	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	50635	0.001718	18	31811,18716,66,21	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749393	913	PASS	C	T	31864	0.908863	0	0,14,0,31796	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749393	1510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	32788	0.00247	0	0,32416,0,101	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G235	nsp2	0.002159	0.937304	1	1	T>C
ERR5749393	1661	PASS	G	T	21579	0.98948	2147483647	0,0,21571,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gac/Tac	D286Y	nsp2	0.983409	0.98948	1	1	G>T
ERR5749393	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	121008	0.001405	2147483647	60412,56681,104,3517	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749393	3037	PASS	C	T	32426	0.812558	55	4,30,16198,15981	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749393	3267	PASS	C	T	29506	0.969193	0	3,0,29490,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749393	3671	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GA	39917	3.51E-4	0	19964,19947,7,7	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/aaAt	N319K?	nsp3	0.000351	0.0625	6	2	G>GA
ERR5749393	5388	PASS	C	A	10229	0.959722	0	1,0,10226,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749393	5986	PASS	C	T	20911	0.973076	0	4,0,20888,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749393	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19336	0.001138	0	17,19119,0,29	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749393	6954	PASS	T	C	36335	0.821907	0	0,6,2,36144	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749393	10077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	9399	0.002234	502	2,9354,18,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTc/tCc	F8S	3Cpro	0.001833	0.454545	1	1	T>C
ERR5749393	10138	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34910	7.73E-4	4	25499,9376,22,5	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N28	3Cpro	0.000458	0.983567	3	3	C>T
ERR5749393	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	25529	0.001998	0	24807,10,51,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749393	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	25510	0.001803	0	25425,0,74,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749393	11287	PASS	GTCTGGTTTT	G	25505	0.996432	24	1,91,0,25414	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749393	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	45483	0.001473	0	22709,22649,36,38	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749393	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	19650	0.003969	2147483647	19173,161,17,290	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749393	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	38199	0.00178	0	19138,19015,35,33	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749393	14408	PASS	C	T	38199	0.841279	5	5,9,19061,18812	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749393	14676	PASS	C	T	19328	0.804636	0	8,0,19270,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749393	15279	PASS	C	T	34409	0.885001	0	8,0,34342,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749393	16176	PASS	T	C	31330	0.978455	0	0,0,15097,16217	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749393	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	34984	5.43E-4	0	0,34965,0,19	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749393	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	45186	0.002147	0	45066,2,99,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749393	20233	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	41866	0.004084	0	41663,8,172,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ccc/Tcc	P205S	endoR	0.000964	0.980008	2	1	C>T
ERR5749393	21764	PASS	ATACATG	A	19599	0.997296	0	53,0,19546,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749393	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	19599	5.61E-4	0	19588,0,11,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749393	21990	PASS	TTTA	T	19608	0.998011	0	0,39,5,19564	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749393	22293	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TACATA	T	45528	3.08E-4	0	13156,32353,4,10	HIGH	NONE	FRAME_SHIFT	S	ttacataga/	LHR244	S	0.000308	0.160511	4	1	TACATA>T
ERR5749393	23063	PASS	A	T	16819	0.872882	0	0,4,1,16744	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749393	23271	PASS	C	A	32793	0.907846	0	0,0,32752,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749393	23403	PASS	A	G	32787	0.967152	0	0,4,0,32754	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749393	23426	PASS	G	T	32801	0.916192	0	0,11,0,32725	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gtt/Ttt	V622F	S	0.000428	0.916192	4	2	G>T
ERR5749393	23604	PASS	C	A	23381	0.937642	0	16,0,23354,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749393	23709	PASS	C	T	23355	0.935688	0	0,10,2,23310	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749393	24506	PASS	T	G	27952	0.974599	0	9,0,27939,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749393	24914	PASS	G	C	46733	0.960863	3	1,0,23252,23428	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749393	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	37103	0.001348	83	24647,12369,62,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749393	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	38742	5.42E-4	0	38721,0,21,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749393	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	39014	0.001077	1867	38401,242,182,132	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749393	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	77431	2.84E-4	0	2,77402,0,22	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749393	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	15907	0.001006	0	4,15886,0,16	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749393	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	15908	0.003395	0	2,15845,0,54	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749393	27972	PASS	C	T	17016	0.902033	33	3,2,16850,107	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749393	28048	PASS	G	T	16928	0.916647	0	0,28,0,16893	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749393	28095	PASS	A	T	16946	0.958574	163	5,6,0,16910	HIGH	NONSENSE	STOP_GAINED	ORF8	Aaa/Taa	K68*	orf8	0.002672	0.967672	2	2	A>T
ERR5749393	28111	PASS	A	G	43707	0.977532	1	5,2,26750,16936	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749393	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	26724	5.24E-4	0	26715,3,14,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749393	28270	PASS	TA	T	51502	0.994893	577	259,12,26380,24859	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749393	28271	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AA	A	51491	5.63E-4	82	26600,24872,29,0	.	.	.	.	.	.	.	0.000482	0.924941	3	2	AA>A
ERR5749393	28280	PASS	G	C	51391	0.935806	23	16,3,26429,24841	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749393	28281	PASS	A	T	51392	0.89154	58	33,4,26399,24850	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749393	28282	PASS	T	A	51400	0.924883	0	19,18,26397,24861	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749393	28406	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTACCCAATA	T	26807	4.48E-4	0	39,26753,0,12	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	N	ttacccaataat/tat	LPNN45Y	N	0.00043	0.921074	3	2	TTACCCAATA>T
ERR5749393	28881	PASS	G	A	23041	0.753613	19	10,1,11386,11318	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749393	28882	PASS	G	A	23040	0.820877	14	8,1,11527,11267	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749393	28883	PASS	G	C	23040	0.944488	0	1,0,11555,11466	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749393	28977	PASS	C	T	11781	0.925898	0	0,4,5,11747	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749393	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	43179	6.72E-4	100	31399,11712,6,27	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749393	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	62280	8.99E-4	0	31295,30884,34,33	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749393	29642	PASS	C	T	26834	0.923008	9	0,3,13696,13104	HIGH	NONSENSE	STOP_GAINED	ORF10	Caa/Taa	Q29*	orf10	0.001806	0.941176	2	2	C>T
ERR5749394	241	PASS	C	T	418	0.849282	0	0,0,208,206	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749394	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	898	0.010022	0	888,1,9,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749394	680	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	8682	0.001728	4	7765,827,16,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gat/Tat	D139Y	leader	0.000661	0.166667	3	2	G>T
ERR5749394	913	PASS	C	T	7777	0.905491	0	0,4,0,7758	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749394	1813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	9090	0.00275	0	0,9064,0,25	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K338	nsp2	0.001022	0.152738	4	2	TA>T
ERR5749394	2110	PASS	C	T	7991	0.776874	0	0,3,0,7925	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N435	nsp2	0.024426	0.811371	1	1	C>T
ERR5749394	2146	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8007	0.007119	0	0,7942,0,62	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V447	nsp2	0.007119	0.933672	1	1	C>T
ERR5749394	3037	PASS	C	T	5359	0.809666	12	0,4,2684,2634	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749394	3267	PASS	C	T	9070	0.971444	2147483647	0,0,9067,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749394	4206	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6457	0.004491	0	6420,0,34,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCg/gTg	A496V	nsp3	0.003069	0.879444	1	1	C>T
ERR5749394	4230	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12871	0.005128	0	6405,6378,39,38	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T504I	nsp3	0.005128	0.819055	1	1	C>T
ERR5749394	4582	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	7973	0.005644	0	0,7914,0,57	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaC/aaA	N621K	nsp3	0.005644	0.938733	2	2	C>A
ERR5749394	5002	PASS	C	T	5655	0.976835	94	2,3,5646,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ctC/ctT	L761	nsp3	0.001115	0.976835	3	2	C>T
ERR5749394	5388	PASS	C	A	1333	0.96174	2147483647	0,0,1333,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749394	5512	PASS	C	T	1332	0.942192	2147483647	0,0,0,1330	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N931	nsp3	0.002299	0.987013	1	1	C>T
ERR5749394	5944	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5435	0.00276	0	5409,2,16,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D1075	nsp3	0.002228	0.977177	1	1	C>T
ERR5749394	5986	PASS	C	T	5433	0.973127	2147483647	0,0,5427,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749394	6337	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	7354	0.004351	0	7321,1,32,0	HIGH	NONE	FRAME_SHIFT+STOP_GAINED	ORF1ab	gat/Tgat	D1208*?	nsp3	0.000579	0.91624	3	2	G>GT
ERR5749394	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5015	0.005184	0	0,4919,0,36	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749394	6954	PASS	T	C	8893	0.816597	0	0,2,0,8845	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749394	7600	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5980	0.002508	0	0,5958,0,15	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C1627	nsp3	0.001321	0.973632	1	1	C>T
ERR5749394	7735	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16231	0.002772	0	16165,0,50,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I1672	nsp3	0.000658	0.954659	3	2	C>T
ERR5749394	9198	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	11968	0.003426	0	0,11927,0,41	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F216	nsp4	0.000543	0.93476	4	2	CT>C
ERR5749394	10323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	11939	0.005696	0	0,11836,0,70	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749394	10369	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11957	0.00184	0	4,11927,0,22	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	cgC/cgT	R105	3Cpro	0.001225	0.120075	1	1	C>T
ERR5749394	11082	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	17934	0.004405	0	17859,0,79,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L37	nsp6	0.000427	0.179468	2	1	TG>T
ERR5749394	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	17934	0.004963	0	17748,0,101,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749394	11104	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	17929	0.005131	0	17777,0,98,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccT/ccC	P44	nsp6	0.000866	0.675414	2	1	T>C
ERR5749394	11287	PASS	GTCTGGTTTT	G	17929	0.999219	0	0,14,0,17915	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749394	12125	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	17071	0.011481	0	0,16816,0,202	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y12H	nsp8	0.000847	0.113436	1	1	T>C
ERR5749394	12439	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5222	0.004787	0	1,5181,0,35	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P116	nsp8	0.000666	0.637117	2	2	C>T
ERR5749394	12754	PASS	C	T	10749	0.908643	0	0,0,2438,8309	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C23	nsp9	0.001216	0.947969	1	1	C>T
ERR5749394	12809	PASS	C	T	2419	0.882596	2147483647	0,0,2416,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Ttt	L42F	nsp9	0.001562	1	1	1	C>T
ERR5749394	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	12394	0.002905	0	12357,1,36,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749394	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16229	0.001417	0	8106,8081,13,13	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749394	14098	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	7878	0.002285	0	7807,48,18,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggt/Agt	G220S	RdRp	0.000806	0.065317	4	2	G>A
ERR5749394	14120	PASS	C	T	15618	0.738763	3	2,4,7776,7554	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCa/cTa	P227L	RdRp	0.00121	0.786944	2	2	C>T
ERR5749394	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	2182	0.004583	1	1091,1075,6,4	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749394	14408	PASS	C	T	2182	0.856554	0	0,0,1087,1069	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749394	14599	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6519	0.003988	0	6487,0,28,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L387	RdRp	0.000639	0.922766	3	2	C>T
ERR5749394	14646	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	6519	0.00675	0	6472,0,45,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acG	T402	RdRp	0.00675	0.970154	2	1	T>G
ERR5749394	14676	PASS	C	T	6519	0.822519	0	2,0,6502,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749394	14766	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	12586	0.00286	0	6060,6451,19,21	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttT/ttC	F442	RdRp	0.00286	0.317972	2	2	T>C
ERR5749394	15279	PASS	C	T	5831	0.88664	0	1,0,5824,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749394	16176	PASS	T	C	8176	0.977862	0	0,0,973,7200	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749394	17058	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	9159	0.00262	0	0,9129,0,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atT	M274I	helicase	0.00262	0.976037	2	1	G>T
ERR5749394	17081	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	9161	0.002511	0	1,9122,0,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGa/gAa	G282E	helicase	0.001926	0.120301	3	2	G>A
ERR5749394	18576	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	10604	0.006413	0	0,10536,0,68	HIGH	NONE	FRAME_SHIFT	ORF1ab	agagtc/	RV180	ExoN	0.005404	0.876866	2	2	CAG>C
ERR5749394	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	25780	8.15E-4	0	25759,0,21,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749394	19263	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	G	26525	9.43E-4	127	8924,17563,27,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaC/aaG	N408K	ExoN	0.000943	0.943181	2	2	C>G
ERR5749394	19343	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	8956	0.002456	0	8904,0,22,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F436	ExoN	0.000519	0.192257	7	2	CT>C
ERR5749394	19343	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTTTTGTTAAT	C	8956	0.00335	0	8904,0,30,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tttgttaattta/	FVNL436	ExoN	0.000519	0.192257	7	2	CTTTTGTTAAT>C
ERR5749394	19524	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8958	0.005358	0	0,8904,0,49	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ctC/ctT	L495	ExoN	0.000745	0.953697	2	2	C>T
ERR5749394	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4460	0.004484	0	4437,0,21,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749394	20844	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTATAATATGAGAGT	C	25159	0.002027	133	13691,11417,51,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aatatgagagttata/	NMRVI64	MethTr	0.000293	0.905571	5	2	CTATAATATGAGAGT>C
ERR5749394	21255	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCA	G	22676	0.001367	87	11768,10877,31,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	tcatct/tct	SS201S	MethTr	0.000341	0.917425	4	2	GTCA>G
ERR5749394	21462	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	5618	0.004984	0	5581,0,28,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaT/aaC	N268	MethTr	0.00078	0.959051	2	2	T>C
ERR5749394	21764	PASS	ATACATG	A	7525	0.997608	0	18,0,7507,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749394	21990	PASS	TTTA	T	7525	0.998405	0	0,12,0,7513	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749394	22225	PASS	G	T	11482	0.927452	0	0,4,0,11473	LOW	SILENT	SYNONYMOUS_CODING	S	tcG/tcT	S221	S	0.001195	0.94526	3	1	G>T
ERR5749394	22289	PASS	G	T	11488	0.91304	2147483647	0,0,0,11480	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gct/Tct	A243S	S	0.000446	0.915917	3	2	G>T
ERR5749394	23063	PASS	A	T	7018	0.852095	0	0,1,0,6943	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749394	23063	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	7018	0.00456	0	0,1,0,39	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Cat	N501H	S	0.00456	0.907193	2	1	A>C
ERR5749394	23271	PASS	C	A	11907	0.916268	0	1,0,11893,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749394	23403	PASS	A	G	12074	0.967616	0	0,2,85,11981	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749394	23604	PASS	C	A	7042	0.945328	0	3,0,7031,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749394	23624	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	7038	0.003694	0	6989,0,33,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gct/Act	A688T	S	0.003694	0.958606	2	1	G>A
ERR5749394	23709	PASS	C	T	7027	0.924292	0	0,36,0,6981	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749394	24127	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TTTG	9193	0.001088	57	6744,2449,0,10	MODERATE	NONE	CODON_INSERTION	S	aac/TTGaac	N856LN	S	0.000324	0.111888	4	1	T>TTTG
ERR5749394	24445	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	9638	0.007263	0	9553,10,73,0	LOW	SILENT	SYNONYMOUS_CODING	S	acG/acT	T961	S	0.007263	0.983905	2	1	G>T
ERR5749394	24506	PASS	T	G	9626	0.97112	0	4,0,9618,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749394	24745	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	29567	0.001082	164	19938,9588,2,39	LOW	SILENT	SYNONYMOUS_CODING	S	gtC/gtA	V1061	S	0.00048	0.961619	3	2	C>A
ERR5749394	24899	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	39759	0.00244	100	19843,19701,60,153	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Caa/Aaa	Q1113K	S	0.000315	0.09021	5	3	C>A
ERR5749394	24914	PASS	G	C	39613	0.957009	3	1,0,19735,19852	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749394	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	23022	0.00126	30	18585,4399,35,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749394	25523	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	17106	9.94E-4	4	16,15510,0,1575	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	gGa/gTa	G44V	orf3a	0.000994	0.895931	1	1	G>T
ERR5749394	25531	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	17773	0.003095	0	0,15687,0,2077	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Att/Ttt	I47F	orf3a	0.000473	0.975891	5	2	A>T
ERR5749394	25553	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	18558	0.019776	0	0,18189,0,367	HIGH	NONE	FRAME_SHIFT	ORF3a	gtt/Tgtt	V55C?	orf3a	0.001165	0.868131	3	2	C>CT
ERR5749394	25553	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18558	0.011262	0	0,18005,0,229	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	gCt/gTt	A54V	orf3a	0.001165	0.868131	3	2	C>T
ERR5749394	25555	PASS	G	T	18558	0.873909	0	0,1,0,18473	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gtt/Ttt	V55F	orf3a	0.000552	0.900573	5	2	G>T
ERR5749394	25555	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	18558	0.02608	0	0,18074,0,484	HIGH	NONE	FRAME_SHIFT	ORF3a	cag/Tcag	Q57S?	orf3a	0.000552	0.900573	5	2	G>GT
ERR5749394	25587	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	18631	0.00322	0	0,18571,0,60	HIGH	NONE	FRAME_SHIFT	ORF3a	aag/	K67	orf3a	0.000598	0.813206	6	2	CA>C
ERR5749394	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	959	0.014599	225	927,16,0,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749394	26060	PASS	C	T	12021	0.822477	0	1,0,11935,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aCt/aTt	T223I	orf3a	0.000459	0.822477	2	2	C>T
ERR5749394	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	5893	0.002376	0	0,5879,0,14	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749394	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	5893	0.00526	0	0,5862,0,31	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749394	27384	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	12772	0.006185	0	0,12654,0,90	LOW	SILENT	SYNONYMOUS_CODING	ORF6	gaT/gaC	D61	orf6	0.00154	0.931035	3	3	T>C
ERR5749394	27506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	26750	0.001009	81	13920,12792,29,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	gGa/gCa	G38A	orf7a	0.000715	0.985435	4	2	G>C
ERR5749394	27513	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13958	0.002293	0	13908,4,33,0	LOW	SILENT	SYNONYMOUS_CODING	ORF7a	taC/taT	Y40	orf7a	0.001863	0.982462	2	2	C>T
ERR5749394	27527	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13957	0.002508	0	13907,4,38,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	cCa/cTa	P45L	orf7a	0.001708	0.973593	1	1	C>T
ERR5749394	27629	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	14061	0.002205	9	13868,111,71,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	gCc/gAc	A79D	orf7a	0.000786	0.088751	2	1	C>A
ERR5749394	27643	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	27718	0.00166	67	13900,13677,35,93	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Cct/Act	P84T	orf7a	0.00166	0.858006	2	1	C>A
ERR5749394	27670	PASS	GTTCAAGAACTTTACTCTCCAATTT	G	13817	0.987913	788	40,127,0,13650	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF7a	caagaactttactctccaatttttctt/ctt	QELYSPIFL94L	orf7a	0.002392	0.990588	3	2	GTTCAAGAACTTTACTCTCCAATTT>G
ERR5749394	27741	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13949	0.00129	0	0,13904,0,20	LOW	SILENT	SYNONYMOUS_CODING	ORF7a	ctC/ctT	L116	orf7a	0.000363	0.954278	3	2	C>T
ERR5749394	27972	PASS	C	T	2306	0.897225	0	0,0,2291,6	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749394	28027	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTA	G	2299	0.00261	0	0,2293,0,6	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF8	tggtat/tgt	WY45C	orf8	0.00261	0.890611	2	2	GGTA>G
ERR5749394	28048	PASS	G	T	2299	0.903871	0	0,3,0,2294	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749394	28095	PASS	A	T	2306	0.960104	59	2,1,0,2302	HIGH	NONSENSE	STOP_GAINED	ORF8	Aaa/Taa	K68*	orf8	0.002672	0.967672	2	2	A>T
ERR5749394	28111	PASS	A	G	20309	0.980354	11	2,2,18001,2302	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749394	28209	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	18002	0.002278	0	17947,0,54,0	HIGH	NONSENSE	STOP_GAINED	ORF8	Gaa/Taa	E106*	orf8	0.001409	0.963166	2	2	G>T
ERR5749394	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17986	0.007005	0	17805,3,137,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749394	28270	PASS	TA	T	34827	0.995837	384	150,3,17782,16900	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749394	28280	PASS	G	C	34755	0.935923	15	6,0,17809,16879	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749394	28281	PASS	A	T	34756	0.912706	26	27,8,17798,16880	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749394	28282	PASS	T	A	34756	0.905772	4	16,10,17745,16892	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749394	28310	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17984	0.011677	0	0,17742,0,229	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Ccc/Tcc	P13S	N	0.00095	0.92832	2	1	C>T
ERR5749394	28396	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	18010	0.002443	0	6,17936,0,57	LOW	SILENT	SYNONYMOUS_CODING	N	cgG/cgT	R41	N	0.000496	0.946059	5	2	G>T
ERR5749394	28516	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	14967	0.001737	0	14923,0,27,0	LOW	SILENT	SYNONYMOUS_CODING	N	gaT/gaC	D81	N	0.001273	0.990661	2	2	T>C
ERR5749394	28878	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTAGGGGAACTTCTCCTGC	G	2351	0.004254	30	1183,1159,0,10	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	N	aggggaacttctcctgctaga/aga	RGTSPAR203R	N	0.001	0.909986	3	2	GTAGGGGAACTTCTCCTGC>G
ERR5749394	28881	PASS	G	A	2341	0.761213	30	11,0,1155,1140	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749394	28882	PASS	G	A	2331	0.822823	0	0,0,1162,1129	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749394	28883	PASS	G	C	2331	0.934363	0	0,0,1162,1158	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749394	28903	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTGGCAATGGCGGTGATGCTGCTC	G	1184	0.009291	0	0,1173,0,11	HIGH	NONE	FRAME_SHIFT	N	gctggcaatggcggtgatgctgctctt/	AGNGGDAAL211	N	0.009291	0.889271	2	2	GGCTGGCAATGGCGGTGATGCTGCTC>G
ERR5749394	28957	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1185	0.01097	0	0,1169,0,14	LOW	SILENT	SYNONYMOUS_CODING	N	aaC/aaT	N228	N	0.01097	0.950683	1	1	C>T
ERR5749394	28977	PASS	C	T	1185	0.904641	2147483647	0,0,0,1183	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749394	29171	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	17787	0.002586	0	17741,0,46,0	HIGH	NONE	FRAME_SHIFT	N	cat/	H300	N	0.00121	0.854685	2	2	CA>C
ERR5749394	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	35311	0.001671	1	17737,17491,40,35	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749394	29421	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	3613	0.004428	0	3597,0,16,0	HIGH	NONE	FRAME_SHIFT	N	ccg/	P383	N	0.002705	0.052892	2	2	CG>C
ERR5749394	29747	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	2823	0.006376	0	0,2803,0,18	.	.	.	.	.	.	.	0.006376	0.951309	2	1	G>C
ERR5749394	29774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2825	0.005664	0	0,2806,0,16	.	.	.	.	.	.	.	0.002525	0.973955	1	1	C>T
ERR5749395	241	PASS	C	T	10512	0.854833	3	0,2,5214,5252	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749395	478	PASS	C	T	12271	0.109934	0	10812,0,1451,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I71	leader	0.000799	0.109934	2	2	C>T
ERR5749395	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	12261	0.001468	0	12245,0,18,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749395	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	12261	6.52E-4	0	12220,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749395	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	12261	0.002121	0	12220,0,26,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749395	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12251	0.001714	0	11253,2,913,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749395	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	12251	0.001224	0	12234,2,15,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749395	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	32206	0.002795	79	19848,12264,80,10	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749395	913	PASS	C	T	19920	0.914659	0	0,19,0,19876	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749395	1333	PASS	T	C	19666	0.979457	177	7,6,19632,3	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T176	nsp2	0.979457	0.979457	1	1	T>C
ERR5749395	2305	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTAAATAAATTTTTGGCTTTGTGTGCTGACTCTATCATTATTGGTGGAGCTAAACTTAAAGC	G	12112	8.26E-4	0	12102,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtaaataaatttttggctttgtgtgctgactctatcattattggtggagctaaacttaaagccttg/	VNKFLALCADSIIIGGAKLKAL502	nsp2	0.000443	0.070409	4	3	GCTTGTAAATAAATTTTTGGCTTTGTGTGCTGACTCTATCATTATTGGTGGAGCTAAACTTAAAGC>G
ERR5749395	3037	PASS	C	T	16717	0.820841	33	0,11,8351,8254	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749395	3267	PASS	C	T	19249	0.968258	0	1,0,19238,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749395	4255	PASS	G	A	32749	0.836056	32	28,7,16267,16229	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccG/ccA	P512	nsp3	0.001102	0.871853	2	1	G>A
ERR5749395	5388	PASS	C	A	5270	0.960342	2147483647	0,0,5265,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749395	5986	PASS	C	T	10316	0.974796	2147483647	0,0,10307,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749395	6936	PASS	C	T	31701	0.910034	4	3,7,15605,15927	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCt/tTt	S1406F	nsp3	0.000553	0.91447	2	2	C>T
ERR5749395	6954	PASS	T	C	16068	0.823313	0	0,6,1,15970	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749395	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	28363	0.003561	274	15037,13225,101,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749395	10692	PASS	T	C	30765	0.982968	2	1,3,15113,15635	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I213T	3Cpro	0.000956	0.982968	4	2	T>C
ERR5749395	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	18653	0.002198	0	18587,0,53,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749395	11287	PASS	GTCTGGTTTT	G	18654	0.997641	0	0,44,0,18610	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749395	11344	PASS	C	T	31834	0.964849	1	1,3,13165,18655	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I124	nsp6	0.001229	0.964849	1	1	C>T
ERR5749395	11507	PASS	G	A	26200	0.909847	9	8,2,13090,13001	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Att	V179I	nsp6	0.007744	0.914418	2	2	G>A
ERR5749395	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	33427	9.87E-4	6	20220,13151,18,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749395	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	18086	0.001106	0	18046,0,20,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749395	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26885	0.00119	0	13423,13391,18,18	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749395	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12196	0.003526	2609	11971,76,6,140	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749395	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	23864	8.38E-4	0	11959,11901,10,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749395	14408	PASS	C	T	23864	0.852204	12	0,4,11907,11805	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749395	14676	PASS	C	T	10725	0.825734	0	5,0,10692,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749395	15279	PASS	C	T	19582	0.901542	2147483647	0,0,19551,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749395	16176	PASS	T	C	19111	0.979279	3	0,2,9375,9718	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749395	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20702	0.002608	0	20636,3,57,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749395	20091	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	20669	6.29E-4	0	1,20656,0,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	caa/Acaa	Q159T?	endoR	0.000368	0.051583	1	1	C>CA
ERR5749395	21658	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12923	0.002554	76	0,12872,3,34	LOW	SILENT	SYNONYMOUS_CODING	S	ttC/ttT	F32	S	0.001649	0.937508	2	2	C>T
ERR5749395	21764	PASS	ATACATG	A	10882	0.993751	0	68,0,10813,1	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749395	21990	PASS	TTTA	T	10892	0.998715	0	0,14,11,10867	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749395	23063	PASS	A	T	12671	0.862047	0	0,1,1,12617	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749395	23271	PASS	C	A	20244	0.924274	0	1,0,20227,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749395	23403	PASS	A	G	20240	0.96754	0	0,5,0,20221	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749395	23604	PASS	C	A	13800	0.925145	0	13,0,13782,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749395	23709	PASS	C	T	13786	0.935224	0	0,3,1,13766	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749395	23817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	29121	8.24E-4	4	15291,13787,17,10	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTt/cCt	L752P	S	0.000646	0.066832	1	1	T>C
ERR5749395	24506	PASS	T	G	16778	0.97455	0	3,0,16771,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749395	24914	PASS	G	C	35493	0.961344	6	2,0,17682,17778	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749395	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	19752	5.57E-4	0	19741,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749395	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	44609	3.81E-4	0	1,44590,0,17	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749395	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	12215	0.001474	0	1,12192,0,18	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749395	27567	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTTTAGCACTCAAT	C	19916	0.026511	0	19384,2,528,0	HIGH	NONE	FRAME_SHIFT	ORF7a	tttagcactcaattt/	FSTQF59	orf7a	0.000449	0.998291	4	1	CTTTAGCACTCAAT>C
ERR5749395	27972	PASS	C	T	10262	0.902943	23	0,1,10176,48	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749395	28048	PASS	G	T	10214	0.930585	0	0,9,0,10200	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749395	28093	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10224	0.03482	0	3,9849,0,364	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tCt/tTt	S67F	orf8	0.001515	0.967675	1	1	C>T
ERR5749395	28111	PASS	A	G	27275	0.976389	0	2,1,17048,10217	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749395	28270	PASS	TA	T	33093	0.995226	344	155,8,16838,16097	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749395	28280	PASS	G	C	33026	0.93596	3	5,2,16867,16069	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749395	28281	PASS	A	T	33026	0.91976	13	15,5,16854,16073	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749395	28282	PASS	T	A	33026	0.910374	1	23,20,16817,16083	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749395	28881	PASS	G	A	20237	0.769037	9	4,0,10008,9975	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749395	28882	PASS	G	A	20236	0.831241	2	3,1,10106,9933	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749395	28883	PASS	G	C	20236	0.945296	3	0,1,10123,10093	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749395	28977	PASS	C	T	10291	0.928773	0	0,3,0,10271	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749395	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	36531	0.001013	108	26227,10235,8,32	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749395	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	52146	8.25E-4	0	26185,25890,30,28	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749396	241	PASS	C	T	264	0.890152	0	0,0,132,132	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749396	283	PASS	T	C	132	0.984848	2147483647	0,0,0,132	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccT/ccC	P6	leader	0.0025	0.984848	2	2	T>C
ERR5749396	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	400	0.0125	0	395,0,5,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749396	913	PASS	C	T	1896	0.929852	2147483647	0,0,0,1895	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749396	1599	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	8853	0.003502	10	6230,2570,18,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGt/gCt	G265A	nsp2	0.001427	0.96468	2	1	G>C
ERR5749396	1599	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	8853	0.001694	18	6230,2570,20,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGt/gTt	G265V	nsp2	0.001427	0.96468	2	1	G>T
ERR5749396	2698	PASS	T	C	4168	0.955854	2147483647	0,0,4164,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaT/aaC	N631	nsp2	0.001712	0.955854	2	2	T>C
ERR5749396	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	8309	0.001324	566	4139,3917,6,215	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749396	3037	PASS	C	T	2617	0.806267	3	0,1,1307,1291	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749396	3267	PASS	C	T	2126	0.973659	2147483647	0,0,2126,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749396	3602	PASS	C	T	2470	0.97247	2147483647	0,0,2468,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cac/Tac	H295Y	nsp3	0.004454	0.97247	1	1	C>T
ERR5749396	3743	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2469	0.00405	0	0,2458,0,10	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cat/Tat	H342Y	nsp3	0.00405	0.893235	1	1	C>T
ERR5749396	4317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	2750	0.005091	0	0,2726,0,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aGt/aTt	S533I	nsp3	0.001619	0.118421	2	1	G>T
ERR5749396	4964	PASS	A	G	2611	0.986978	2147483647	0,0,0,2611	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Act/Gct	T749A	nsp3	0.986978	0.986978	1	1	A>G
ERR5749396	5388	PASS	C	A	750	0.973333	2147483647	0,0,750,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749396	5986	PASS	C	T	3274	0.971289	0	1,0,3269,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749396	6954	PASS	T	C	5051	0.831123	0	0,1,0,5025	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749396	7488	PASS	C	T	2068	0.889265	2147483647	0,0,2061,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T1590I	nsp3	0.001403	0.889265	2	1	C>T
ERR5749396	8603	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	2693	0.005199	0	0,2677,0,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Ctc	F17L	nsp4	0.002607	0.974959	2	1	T>C
ERR5749396	9165	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5799	0.011209	0	0,5730,0,66	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCc/aTc	T204I	nsp4	0.00112	0.253438	1	1	C>T
ERR5749396	10533	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	3262	0.010116	0	3210,0,50,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tGt/tTt	C160F	3Cpro	0.000835	0.917216	4	2	G>T
ERR5749396	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	8156	0.00564	0	7934,1,46,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749396	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	8152	0.01055	0	8050,0,96,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749396	11235	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTAG	C	8149	0.006136	0	0,8099,0,50	MODERATE	NONE	CODON_DELETION	ORF1ab	agt/	S89	nsp6	0.000512	0.942208	2	2	CTAG>C
ERR5749396	11287	PASS	GTCTGGTTTT	G	8153	0.993009	0	0,57,0,8096	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749396	12162	PASS	A	G	2571	0.982497	0	1,0,2570,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cAg/cGg	Q24R	nsp8	0.000894	0.982497	1	1	A>G
ERR5749396	13356	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10918	0.003755	51	2743,8131,0,42	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T111I	nsp10	0.000806	0.091518	1	1	C>T
ERR5749396	14408	PASS	C	T	273	0.85348	0	0,0,136,135	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749396	14676	PASS	C	T	1296	0.780093	0	1,0,1291,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749396	15240	PASS	C	T	2212	0.931284	0	2,0,2208,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N600	RdRp	0.000934	0.931284	2	2	C>T
ERR5749396	15279	PASS	C	T	2212	0.903707	2147483647	0,0,2208,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749396	15720	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7427	0.004309	0	0,7385,0,35	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D760	RdRp	0.001002	0.917823	1	1	C>T
ERR5749396	16176	PASS	T	C	2105	0.978147	0	0,0,625,1479	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749396	17562	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	9959	0.003012	2	4976,4943,18,22	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	cgG/cgT	R442	helicase	0.000543	0.90562	3	2	G>T
ERR5749396	17615	PASS	A	G	4990	0.906012	2147483647	0,0,0,4978	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749396	18636	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	16825	0.001783	215	13587,3208,0,30	HIGH	NONE	FRAME_SHIFT	ORF1ab	ata/	I201	ExoN	0.00055	0.963467	3	2	GA>G
ERR5749396	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	13587	0.003386	0	13541,0,46,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749396	18744	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13585	0.003975	0	13514,0,58,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y235	ExoN	0.000912	0.953624	2	2	C>T
ERR5749396	19067	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	5094	0.004122	0	5063,0,26,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cAa/cGa	Q343R	ExoN	0.004122	0.076355	1	1	A>G
ERR5749396	19320	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	5593	0.007152	0	5551,0,42,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caC/caA	H427Q	ExoN	0.004154	0.957053	2	2	C>A
ERR5749396	19386	PASS	C	T	5583	0.906323	2147483647	0,0,5572,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D449	ExoN	0.906323	0.906323	1	1	C>T
ERR5749396	20719	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2327	0.003438	0	0,2299,0,8	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L21	MethTr	0.000341	0.209091	2	2	C>T
ERR5749396	21621	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCAG	C	2825	0.006372	0	0,2807,0,18	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	accaga/aca	TR20T	S	0.00148	0.944623	2	2	CCAG>C
ERR5749396	21724	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	5491	0.003824	0	5465,0,26,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	ttG/ttT	L54F	S	0.000586	0.911899	2	2	G>T
ERR5749396	21764	PASS	ATACATG	A	5490	0.998178	0	10,0,5480,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749396	21990	PASS	TTTA	T	5491	0.991805	0	0,45,0,5446	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749396	22630	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	10698	0.005328	0	10622,1,74,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aaG/aaT	K356N	S	0.001137	0.921237	2	2	G>T
ERR5749396	22792	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	10696	0.004675	0	0,10646,0,50	HIGH	NONE	FRAME_SHIFT	S	gct/	A411	S	0.000722	0.949572	3	3	CG>C
ERR5749396	22927	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	4131	0.009683	0	4091,0,40,0	HIGH	NONE	FRAME_SHIFT	S	ttt/	F456	S	0.000791	0.909717	4	3	GT>G
ERR5749396	23063	PASS	A	T	4120	0.871359	2147483647	0,0,0,4102	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749396	23271	PASS	C	A	1928	0.915975	2147483647	0,0,1924,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749396	23403	PASS	A	G	1927	0.97042	2147483647	0,0,0,1926	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749396	23604	PASS	C	A	4564	0.950044	0	3,0,4558,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749396	23709	PASS	C	T	4558	0.932865	0	0,2,0,4554	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749396	23813	PASS	A	G	5488	0.985605	0	0,0,923,4562	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Gat	N751D	S	0.985605	0.985605	1	1	A>G
ERR5749396	24320	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	3573	0.005877	0	0,3552,0,21	HIGH	NONE	FRAME_SHIFT	S	aaa/	K921	S	0.000763	0.138365	4	2	CA>C
ERR5749396	24506	PASS	T	G	4767	0.9721	2147483647	0,0,4767,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749396	24914	PASS	G	C	14214	0.962572	0	0,0,7079,7119	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749396	25429	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	14089	0.006743	0	13857,117,109,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gta/Tta	V13L	orf3a	0.00064	0.906678	5	2	G>T
ERR5749396	25587	PASS	C	T	13978	0.813206	0	0,6,0,13942	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	ctC/ctT	L65	orf3a	0.000598	0.813206	6	2	C>T
ERR5749396	25626	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14377	0.002365	0	397,13943,0,34	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	caC/caT	H78	orf3a	0.000403	0.915633	3	2	C>T
ERR5749396	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	432	0.041667	192	395,18,1,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749396	26065	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	7756	0.001934	0	7734,0,21,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gtt/Att	V225I	orf3a	0.001242	0.906322	2	1	G>A
ERR5749396	26493	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	2164	0.004621	0	0,2154,0,10	.	.	.	.	.	.	.	0.001082	0.069277	3	1	GT>G
ERR5749396	27383	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	8623	0.004291	0	0,8560,0,57	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF6	gAt/gTt	D61V	orf6	0.001454	0.928985	1	1	A>T
ERR5749396	27384	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TCTC	8623	0.005798	0	0,8573,0,50	MODERATE	NONE	CODON_INSERTION+SPLICE_SITE_REGION	ORF6	taa/CTCtaa	*62L*	orf6	0.00154	0.931035	3	3	T>TCTC
ERR5749396	27741	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	7761	0.007602	0	0,7702,0,59	HIGH	NONE	FRAME_SHIFT	ORF7a	aga/	R118	orf7a	0.000363	0.954278	3	2	CA>C
ERR5749396	27972	PASS	C	T	1102	0.898367	0	0,0,1095,6	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749396	28027	PASS	G	T	1097	0.890611	2147483647	0,0,0,1092	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tGg/tTg	W45L	orf8	0.00261	0.890611	2	2	G>T
ERR5749396	28048	PASS	G	T	1099	0.926297	0	0,1,0,1098	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749396	28111	PASS	A	G	9205	0.980663	0	1,0,8101,1099	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749396	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8098	0.002717	0	8050,1,23,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749396	28270	PASS	TA	T	15733	0.99536	184	74,2,7995,7665	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749396	28280	PASS	G	C	15702	0.940135	6	5,1,8017,7657	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749396	28281	PASS	A	T	15702	0.920138	5	6,2,8013,7658	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749396	28282	PASS	T	A	15702	0.914278	1	5,3,7996,7662	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749396	28512	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	12481	0.004807	0	12421,0,60,0	HIGH	NONE	FRAME_SHIFT	N	gat/	D81	N	0.000621	0.172671	3	2	CAG>C
ERR5749396	28603	PASS	C	T	24845	0.883357	9	1,6,12373,12370	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F110	N	0.000427	0.883357	2	2	C>T
ERR5749396	28674	PASS	C	T	12474	0.958634	0	0,2,0,12460	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gCa/gTa	A134V	N	0.001338	0.958634	1	1	C>T
ERR5749396	28881	PASS	G	A	678	0.744838	0	1,0,335,334	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749396	28882	PASS	G	A	678	0.814159	0	0,0,338,335	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749396	28883	PASS	G	C	678	0.936578	0	0,0,339,338	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749396	28977	PASS	C	T	343	0.941691	2147483647	0,0,0,343	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749396	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	18746	0.001067	0	9437,9282,12,12	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749396	29555	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	4181	0.001674	18	2053,2121,0,7	.	.	.	.	.	.	.	0.000611	0.957048	3	1	CA>C
ERR5749396	29642	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	4182	0.003348	71	2030,2129,23,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF10	Caa/Aaa	Q29K	orf10	0.001806	0.941176	2	2	C>A
ERR5749397	186	PASS	C	T	484	0.950413	0	1,0,483,0	.	.	.	.	.	.	.	0.002255	0.966959	1	1	C>T
ERR5749397	241	PASS	C	T	965	0.848705	0	0,1,480,480	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749397	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	3554	0.006472	0	3532,0,23,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749397	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	3554	0.009848	0	3515,0,35,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749397	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	3550	0.004225	0	3535,0,15,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749397	673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14640	0.003552	303	11074,3503,3,56	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y136	leader	0.000454	0.602236	3	2	C>T
ERR5749397	673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	14640	0.002937	264	11081,3516,0,43	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggc/	G137	leader	0.000454	0.602236	3	2	CG>C
ERR5749397	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	14640	0.001298	21	11062,3559,19,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749397	841	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22104	0.001493	0	11040,11005,21,20	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G12	nsp2	0.000771	0.932538	2	1	C>T
ERR5749397	843	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22103	0.001041	0	11047,11014,13,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P13L	nsp2	0.000301	0.050923	4	2	C>T
ERR5749397	843	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTG	C	22103	0.001357	0	11051,11022,15,15	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctgat/	PD13	nsp2	0.000301	0.050923	4	2	CTG>C
ERR5749397	913	PASS	C	T	11071	0.906874	0	0,4,0,11050	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749397	1059	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10418	0.001728	0	10393,0,20,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCc/aTc	T85I	nsp2	0.001728	0.920973	1	1	C>T
ERR5749397	1440	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	9900	0.004949	0	9826,0,54,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGc/gCc	G212A	nsp2	0.004949	0.899148	2	1	G>C
ERR5749397	1685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GC	G	10878	0.001379	0	10863,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gcc/	A294	nsp2	0.001379	0.231183	3	2	GC>G
ERR5749397	2084	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22534	0.002308	0	11235,11227,28,28	HIGH	NONSENSE	STOP_GAINED	ORF1ab	Cag/Tag	Q427*	nsp2	0.001943	0.253112	1	1	C>T
ERR5749397	2185	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	11297	0.001947	0	6,11265,0,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gaG/gaT	E460D	nsp2	0.000441	0.963529	4	3	G>T
ERR5749397	2305	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	6475	0.003861	0	6445,0,29,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaG/aaC	K500N	nsp2	0.000443	0.070409	4	3	G>C
ERR5749397	2453	PASS	C	T	6461	0.726977	0	0,8,0,6365	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L550F	nsp2	0.00429	0.842201	2	2	C>T
ERR5749397	3037	PASS	C	T	8096	0.824852	18	0,6,4039,3988	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749397	3267	PASS	C	T	13222	0.971714	0	1,0,13219,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749397	4456	PASS	C	T	11032	0.964648	0	2,0,11015,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A579	nsp3	0.002579	0.964648	1	1	C>T
ERR5749397	4551	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	11038	0.001721	0	5,11014,0,19	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T612	nsp3	0.001721	0.897919	3	2	CA>C
ERR5749397	4693	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	8275	0.001571	0	8262,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/	V659	nsp3	0.000654	0.078873	1	1	TG>T
ERR5749397	4764	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	8273	0.001209	0	8263,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F683	nsp3	0.000673	0.93404	4	2	AT>A
ERR5749397	4835	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	16501	0.001394	67	8229,8149,29,83	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggt/Tgt	G706C	nsp3	0.001394	0.052356	2	1	G>T
ERR5749397	5388	PASS	C	A	2213	0.962042	2147483647	0,0,2210,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749397	5784	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19319	0.001294	0	9510,9768,14,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T1022I	nsp3	0.001294	0.919357	2	1	C>T
ERR5749397	5986	PASS	C	T	6265	0.968555	0	1,0,6254,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749397	6286	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12739	0.00157	0	12704,0,21,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acC/acT	T1189	nsp3	0.000549	0.949782	2	2	C>T
ERR5749397	6310	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	12738	0.001492	0	12701,0,35,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	agC/agA	S1197R	nsp3	0.00099	0.94715	2	2	C>A
ERR5749397	6337	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	12731	0.001571	0	12690,0,39,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcG/tcT	S1206	nsp3	0.000579	0.91624	3	2	G>T
ERR5749397	6516	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	18459	0.001138	32	5718,12720,0,21	HIGH	NONE	FRAME_SHIFT	ORF1ab	att/	I1268	nsp3	0.000479	0.186047	4	2	TA>T
ERR5749397	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5714	0.0021	0	8,5639,0,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749397	6954	PASS	T	C	11256	0.820274	0	0,1,0,11202	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749397	6990	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	11288	9.74E-4	0	0,11277,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L1425	nsp3	0.000504	0.101156	4	2	CT>C
ERR5749397	8084	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	9106	0.002526	0	9077,0,25,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E1789K	nsp3	0.000543	0.923413	4	2	G>A
ERR5749397	8084	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	9105	0.001977	0	9088,0,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1790	nsp3	0.000543	0.923413	4	2	GA>G
ERR5749397	8139	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9093	0.00209	0	9046,11,24,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCc/tTc	S1807F	nsp3	0.001297	0.889336	1	1	C>T
ERR5749397	8653	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTC	G	4935	0.001418	0	4928,0,7,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tct/	S34	nsp4	0.001328	0.132353	2	2	GTC>G
ERR5749397	9060	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	13757	0.001381	0	13704,0,22,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tAt/tTt	Y169F	nsp4	0.000621	0.433333	5	2	A>T
ERR5749397	10369	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12491	0.002882	0	3,12440,0,38	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	cgC/cgT	R105	3Cpro	0.001225	0.120075	1	1	C>T
ERR5749397	10595	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	12006	0.001499	0	0,11964,0,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F181L	3Cpro	0.000964	0.076408	1	1	T>C
ERR5749397	10702	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	12538	0.002951	3	502,11999,0,37	HIGH	NONE	FRAME_SHIFT	ORF1ab	agg/	R217	3Cpro	0.000396	0.098214	2	2	CAG>C
ERR5749397	10728	PASS	C	A	12538	0.066358	7	459,11187,43,847	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aAa	T225K	3Cpro	0.066358	0.066358	1	1	C>A
ERR5749397	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	14693	0.00422	0	14243,0,62,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749397	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14693	0.002314	0	14637,0,37,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749397	11199	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	29275	0.001605	0	14609,14619,23,24	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T77	nsp6	0.000309	0.056758	3	2	CCA>C
ERR5749397	11287	PASS	GTCTGGTTTT	G	14689	0.998707	0	0,19,0,14670	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749397	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	18442	0.001681	10	12940,5457,19,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749397	11876	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	12971	0.001696	0	3,12938,0,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtc/Atc	V12I	nsp7	0.001696	0.924185	1	1	G>A
ERR5749397	11935	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATG	A	14683	0.001226	0	14663,2,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtc/	V33	nsp7	0.000833	0.976236	2	2	ATG>A
ERR5749397	12025	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14674	0.001295	0	14632,0,19,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S61	nsp7	0.001295	0.948026	1	1	C>T
ERR5749397	12513	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CGT	C	11342	7.94E-4	0	11333,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tgtgat/	CD142	nsp8	0.000794	0.984064	2	2	CGT>C
ERR5749397	12676	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	11331	0.001147	0	0,11318,0,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K196	nsp8	0.000716	0.87302	3	2	CAA>C
ERR5749397	13378	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9075	0.002094	0	9047,5,20,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acC/acT	T118	nsp10	0.002094	0.968482	1	1	C>T
ERR5749397	14028	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	8615	0.003018	0	8585,0,30,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atT	M196I	RdRp	0.002405	0.051178	1	1	G>T
ERR5749397	14120	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	17211	0.001743	0	8598,8586,15,15	HIGH	NONE	FRAME_SHIFT	ORF1ab	ccaggt/	PG227	RdRp	0.00121	0.786944	2	2	CAG>C
ERR5749397	14408	PASS	C	T	1798	0.83871	0	0,0,895,889	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749397	14599	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	7402	0.003513	0	7376,0,26,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctatta/	LL387	RdRp	0.000639	0.922766	3	2	CTA>C
ERR5749397	14676	PASS	C	T	7401	0.806378	0	3,0,7386,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749397	15279	PASS	C	T	8662	0.897252	2147483647	0,0,8651,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749397	16117	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	7350	0.002177	0	0,7311,0,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gat/Cat	D893H	RdRp	0.001841	0.244898	3	1	G>C
ERR5749397	16176	PASS	T	C	9787	0.976397	0	0,1,2435,7343	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749397	16946	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11280	0.001418	0	11226,17,20,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCa/gTa	A237V	helicase	0.001418	0.951893	1	1	C>T
ERR5749397	17562	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	19777	0.001264	0	9895,9841,13,13	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	cgG/cgA	R442	helicase	0.000543	0.90562	3	2	G>A
ERR5749397	18357	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	15494	0.001226	0	15463,0,20,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccT/ccC	P106	ExoN	0.001226	0.057597	1	1	T>C
ERR5749397	18636	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	36391	5.5E-4	45	20883,15488,20,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ata/	I201	ExoN	0.00055	0.963467	3	2	GA>G
ERR5749397	18658	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	20911	0.001482	0	20873,7,31,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tgt/	C207	ExoN	0.000507	0.115741	3	2	TG>T
ERR5749397	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	20903	0.001052	0	20881,0,22,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749397	18984	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	19068	0.001101	0	19042,0,21,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atC	M315I	ExoN	0.000419	0.950929	5	2	G>C
ERR5749397	19011	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19068	0.001521	0	19030,0,30,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D324	ExoN	0.000408	0.975746	4	2	C>T
ERR5749397	19023	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	19067	0.001259	0	19032,0,24,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtT/gtC	V328	ExoN	0.001259	0.951351	2	1	T>C
ERR5749397	19114	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	37976	0.001264	13	18883,18958,41,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Aaa/Gaa	K359E	ExoN	0.00119	0.098958	2	2	A>G
ERR5749397	19328	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTT	C	9402	0.001276	0	9384,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F431	ExoN	0.000459	0.937906	4	2	CTT>C
ERR5749397	19524	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	9401	7.45E-4	0	0,9394,0,7	HIGH	NONE	FRAME_SHIFT	ORF1ab	gat/	D496	ExoN	0.000745	0.953697	2	2	CG>C
ERR5749397	19763	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	17911	0.001061	1	8907,8919,42,38	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aAa	T48K	endoR	0.000987	0.809304	2	1	C>A
ERR5749397	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6880	0.00625	0	6832,0,44,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749397	20125	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGA	G	6879	0.003053	0	0,6858,0,21	HIGH	NONE	FRAME_SHIFT	ORF1ab	gaa/	E170	endoR	0.003053	0.058496	1	1	GGA>G
ERR5749397	20461	PASS	A	G	18671	0.939585	0	0,2,0,18642	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Aca/Gca	T281A	endoR	0.939585	0.939585	1	1	A>G
ERR5749397	20544	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	22293	0.001301	0	22234,8,49,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcA	S308	endoR	0.000834	0.975334	2	1	C>A
ERR5749397	20578	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	22285	0.002423	0	22199,0,56,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtg/Ctg	V320L	endoR	0.00085	0.958277	3	1	G>C
ERR5749397	20592	PASS	T	C	22283	0.971458	0	5,0,22261,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taT/taC	Y324	endoR	0.001063	0.971458	1	1	T>C
ERR5749397	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22278	0.002873	0	22175,0,65,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749397	20630	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	22278	9.88E-4	0	22247,0,29,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cAt/cCt	H337P	endoR	0.000988	0.122449	2	1	A>C
ERR5749397	20718	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	22235	0.002069	0	0,22085,0,63	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atC	M20I	MethTr	0.000898	0.920213	3	1	G>C
ERR5749397	20844	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	37702	0.001061	44	15401,22225,12,57	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccA	P62	MethTr	0.000293	0.905571	5	2	C>A
ERR5749397	20951	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	15412	5.84E-4	0	15404,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gat/	D99	MethTr	0.000431	0.138667	3	3	CAG>C
ERR5749397	21077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	15420	0.002789	0	8,15357,0,54	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aAa	T140K	MethTr	0.000492	0.955529	4	2	C>A
ERR5749397	21123	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	32193	6.52E-4	58	16754,15418,21,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F156	MethTr	0.000257	0.90982	5	2	GT>G
ERR5749397	21234	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	16771	6.56E-4	0	16761,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F193	MethTr	0.000472	0.857572	5	2	CT>C
ERR5749397	21305	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	16755	0.001552	0	0,16701,0,33	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cGc/cAc	R216H	MethTr	0.000727	0.703943	1	1	G>A
ERR5749397	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15352	0.001694	0	7534,7644,14,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749397	21595	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	7710	0.001816	0	0,7685,0,22	LOW	SILENT	SYNONYMOUS_CODING	S	gtC/gtA	V11	S	0.001296	0.918559	3	2	C>A
ERR5749397	21622	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7713	0.002463	0	0,7688,0,23	LOW	SILENT	SYNONYMOUS_CODING	S	acC/acT	T20	S	0.000846	0.946634	3	2	C>T
ERR5749397	21657	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TCA	T	7716	0.001037	0	0,7708,0,8	HIGH	NONE	FRAME_SHIFT	S	acacgt/	TR33	S	0.000702	0.06812	2	2	TCA>T
ERR5749397	21762	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8292	0.002291	0	8258,0,20,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gTt	A67V	S	0.001297	0.875707	2	2	C>T
ERR5749397	21764	PASS	ATACATG	A	8292	0.995417	0	38,0,8254,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749397	21987	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	8295	0.002532	0	3,8270,0,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gGt/gTt	G142V	S	0.000998	0.922156	5	2	G>T
ERR5749397	21990	PASS	TTTA	T	8295	0.998433	0	0,13,3,8279	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749397	22293	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	20001	6.5E-4	18	6145,13843,0,13	HIGH	NONE	FRAME_SHIFT	S	tta/	L244	S	0.000308	0.160511	4	1	TA>T
ERR5749397	22454	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	12196	0.001722	5	6097,6011,30,39	HIGH	NONSENSE	STOP_GAINED	S	Gaa/Taa	E298*	S	0.001722	0.11678	2	2	G>T
ERR5749397	22771	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AG	A	12404	0.00129	0	0,12388,0,16	HIGH	NONE	FRAME_SHIFT	S	ggt/	G404	S	0.000511	0.112051	3	3	AG>A
ERR5749397	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCAAA	G	12407	0.001612	0	0,12387,0,20	HIGH	NONE	FRAME_SHIFT	S	caaact/	QT414	S	0.001101	0.887758	3	2	GCAAA>G
ERR5749397	23063	PASS	A	T	9263	0.863435	0	0,1,0,9211	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749397	23271	PASS	C	A	16998	0.90093	0	1,0,16972,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749397	23403	PASS	A	G	16987	0.972096	0	0,3,0,16974	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749397	23426	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	16996	0.001824	0	0,16965,0,31	HIGH	NONE	FRAME_SHIFT	S	gtt/	V622	S	0.000428	0.916192	4	2	GT>G
ERR5749397	23575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8394	0.002383	0	8365,0,21,0	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C671	S	0.001569	0.894896	2	2	C>T
ERR5749397	23604	PASS	C	A	8393	0.944478	0	5,0,8385,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749397	23664	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16657	0.001321	0	8280,8333,11,12	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCa/gTa	A701V	S	0.000837	0.918	2	2	C>T
ERR5749397	23709	PASS	C	T	8390	0.933731	0	0,5,4,8371	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749397	23766	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8393	0.001668	0	0,8372,0,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCa/tTa	S735L	S	0.001668	0.163547	1	1	C>T
ERR5749397	24320	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	6964	0.004882	0	0,6930,0,34	HIGH	NONE	FRAME_SHIFT	S	aaa/	K921	S	0.000763	0.138365	4	2	CA>C
ERR5749397	24506	PASS	T	G	9982	0.973452	0	3,0,9977,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749397	24914	PASS	G	C	36155	0.957544	0	1,1,18013,18112	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749397	25350	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15119	0.001654	0	15092,1,25,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCa/cTa	P1263L	S	0.000626	0.97904	4	2	C>T
ERR5749397	25413	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15118	0.001521	0	15068,0,26,0	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	atC/atT	I7	orf3a	0.00145	0.968329	2	1	C>T
ERR5749397	25429	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTA	G	15117	0.001323	0	15097,0,20,0	HIGH	NONE	FRAME_SHIFT	ORF3a	gta/	V13	orf3a	0.00064	0.906678	5	2	GTA>G
ERR5749397	25563	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	15110	0.001456	0	0,15074,0,29	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	caG/caT	Q57H	orf3a	0.001456	0.886549	2	1	G>T
ERR5749397	25572	PASS	C	T	15110	0.871807	0	0,9,0,15077	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	tcC/tcT	S60	orf3a	0.000543	0.959687	4	2	C>T
ERR5749397	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	2217	0.007217	242	2178,22,2,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749397	25916	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	2183	0.00229	0	2,2176,0,5	HIGH	NONE	FRAME_SHIFT	ORF3a	aca/	T176	orf3a	0.001191	0.964713	2	2	CA>C
ERR5749397	26151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	15764	0.002284	0	1,15727,0,36	HIGH	NONE	FRAME_SHIFT	ORF3a	gga/	G254	orf3a	0.000501	0.913698	4	2	CG>C
ERR5749397	26526	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	7357	0.001903	0	0,7332,0,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Gca/Tca	A2S	M	0.001224	0.951192	3	1	G>T
ERR5749397	26718	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	15289	0.001439	4	7632,7616,24,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Gtg/Ttg	V66L	M	0.001439	0.075949	1	1	G>T
ERR5749397	27557	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13284	0.00128	0	13262,0,17,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	gCa/gTa	A55V	orf7a	0.000949	0.267468	2	2	C>T
ERR5749397	27654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	25384	9.06E-4	6	13231,12104,28,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	ttC/ttA	F87L	orf7a	0.000906	0.947433	2	2	C>A
ERR5749397	27741	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	13278	0.001356	0	0,13260,0,18	HIGH	NONE	FRAME_SHIFT	ORF7a	aga/	R118	orf7a	0.000363	0.954278	3	2	CA>C
ERR5749397	27925	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	4302	0.002789	0	4289,0,12,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aCa/aAa	T11K	orf8	0.002789	0.084533	2	1	C>A
ERR5749397	27972	PASS	C	T	4316	0.895737	0	0,0,4279,23	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749397	28048	PASS	G	T	4298	0.925314	0	0,2,0,4296	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749397	28111	PASS	A	G	21799	0.974494	0	3,0,17487,4302	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749397	28249	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	17481	5.72E-4	0	17471,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF8	ttc/	F120	orf8	0.000443	0.063605	3	2	AT>A
ERR5749397	28270	PASS	TA	T	33895	0.993834	363	155,6,17249,16437	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749397	28270	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAA	T	33895	0.001564	134	155,6,26,27	.	.	.	.	.	.	.	0.000322	1	2	1	TAA>T
ERR5749397	28280	PASS	G	C	33834	0.940681	8	9,3,17325,16452	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749397	28281	PASS	A	T	33834	0.912484	39	25,4,17300,16450	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749397	28282	PASS	T	A	33836	0.90516	9	18,9,17252,16451	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749397	28292	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	34816	6.89E-4	0	17345,17435,12,12	HIGH	NONE	FRAME_SHIFT	N	aat/	N8	N	0.000304	0.055324	4	2	CAA>C
ERR5749397	28407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TACCCAATA	T	17506	7.43E-4	0	9,17484,0,13	HIGH	NONE	FRAME_SHIFT	N	cccaataat/	PNN46	N	0.000382	0.179673	1	1	TACCCAATA>T
ERR5749397	28512	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	15001	0.0012	0	14983,0,18,0	HIGH	NONE	FRAME_SHIFT	N	gat/	D81	N	0.000621	0.172671	3	2	CAG>C
ERR5749397	28881	PASS	G	A	5409	0.718062	6	2,0,2644,2664	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749397	28882	PASS	G	A	5409	0.823442	1	4,2,2692,2663	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749397	28883	PASS	G	C	5409	0.943797	0	0,0,2704,2697	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749397	28977	PASS	C	T	2763	0.923996	2147483647	0,0,0,2756	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749397	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	47416	7.38E-4	0	23793,23507,24,23	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749397	29253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CGG	C	23879	5.44E-4	0	0,23866,0,13	HIGH	NONE	FRAME_SHIFT	N	gga/	G328	N	0.000361	0.053998	4	2	CGG>C
ERR5749397	29386	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	5037	0.004765	0	5013,0,24,0	HIGH	NONE	FRAME_SHIFT	N	aag/aaAg	K373K?	N	0.000887	0.899197	4	2	C>CA
ERR5749397	29386	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	5037	0.002581	0	5024,0,13,0	HIGH	NONE	FRAME_SHIFT	N	aag/	K373	N	0.000887	0.899197	4	2	CAA>C
ERR5749397	29793	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	4112	0.002675	0	0,4099,0,11	.	.	.	.	.	.	.	0.002675	0.580539	2	1	T>A
ERR5749398	189	PASS	G	A	3941	0.928698	0	1,0,3934,0	.	.	.	.	.	.	.	0.926346	0.937678	1	1	G>A
ERR5749398	241	PASS	C	T	7856	0.871181	0	0,1,3910,3923	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749398	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	7708	0.001816	0	7086,0,598,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749398	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	29416	3.74E-4	1	21682,7720,9,2	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749398	913	PASS	C	T	21686	0.918427	0	0,10,0,21650	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749398	2453	PASS	C	T	15590	0.769275	0	0,10,0,15421	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L550F	nsp2	0.00429	0.842201	2	2	C>T
ERR5749398	3037	PASS	C	T	20600	0.824175	45	0,15,10290,10144	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749398	3144	PASS	T	G	21	0.761905	12	0,1,16,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749398	3189	PASS	A	T	23768	0.132615	0	20272,1,3485,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cAa/cTa	Q157L	nsp3	0.001758	0.132615	2	1	A>T
ERR5749398	3267	PASS	C	T	23766	0.970504	0	4,0,23741,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749398	3852	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	17237	0.008354	0	17080,1,146,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gAa/gCa	E378A	nsp3	0.008354	0.97973	2	1	A>C
ERR5749398	4331	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	37469	9.87E-4	1	16750,20635,16,23	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L538	nsp3	0.000987	0.928955	1	1	C>T
ERR5749398	5388	PASS	C	A	6308	0.961319	2147483647	0,0,6305,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749398	5986	PASS	C	T	15240	0.973819	0	3,0,15227,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749398	6954	PASS	T	C	25212	0.818658	0	0,0,1,25069	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749398	10138	PASS	C	T	29099	0.980755	5	9,1,21015,8062	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N28	3Cpro	0.000458	0.983567	3	3	C>T
ERR5749398	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25879	0.001275	0	25807,1,36,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749398	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	25859	0.001663	0	25786,0,69,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749398	11287	PASS	GTCTGGTTTT	G	25861	0.99884	0	0,30,0,25831	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749398	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	37364	0.001204	0	18660,18611,26,26	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749398	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	4044	0.004204	586	3958,46,2,34	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749398	14408	PASS	C	T	7886	0.851002	12	0,4,3941,3887	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749398	14676	PASS	C	T	14890	0.695702	0	4,0,14808,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749398	15279	PASS	C	T	22824	0.887706	0	3,0,22791,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749398	15371	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	45536	0.007005	0	22563,22517,205,209	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aTg	T644M	RdRp	0.00056	0.786959	4	2	C>T
ERR5749398	16176	PASS	T	C	20877	0.981271	0	0,1,7849,13020	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749398	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	27228	4.77E-4	0	27215,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749398	19888	PASS	A	G	48842	0.083187	16	23599,20807,2253,2134	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Aga/Gga	R90G	endoR	0.000587	0.083187	2	2	A>G
ERR5749398	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25849	0.001354	0	25795,0,36,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749398	20578	PASS	G	T	34063	0.088072	0	30835,0,3219,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtg/Ttg	V320L	endoR	0.00085	0.958277	3	1	G>T
ERR5749398	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34060	9.1E-4	0	33979,0,32,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749398	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	26842	8.2E-4	0	0,26820,0,22	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TA>T
ERR5749398	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	37584	3.99E-4	2	18752,18818,6,9	HIGH	NONE	FRAME_SHIFT	S	ctt/Tctt	L5S?	S	0.000394	0.091869	4	1	G>GT
ERR5749398	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	37554	8.79E-4	2	18392,18714,19,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749398	21764	PASS	ATACATG	A	15666	0.997064	0	46,0,15620,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749398	21990	PASS	TTTA	T	15675	0.99681	0	0,50,8,15617	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749398	22600	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	31754	8.82E-4	2	19506,12200,16,13	LOW	SILENT	SYNONYMOUS_CODING	S	agA/agG	R346	S	0.000471	0.963998	3	3	A>G
ERR5749398	23063	PASS	A	T	16923	0.871477	0	0,2,0,16858	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749398	23271	PASS	C	A	26326	0.91799	0	2,0,26293,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749398	23403	PASS	A	G	26321	0.975533	0	0,3,0,26309	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749398	23604	PASS	C	A	18121	0.9388	0	13,0,18099,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749398	23709	PASS	C	T	18099	0.938173	0	0,2,0,18067	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749398	24506	PASS	T	G	20410	0.974228	0	7,0,20400,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749398	24914	PASS	G	C	40588	0.959101	0	0,0,20229,20338	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749398	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	14231	0.002249	580	14153,16,8,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749398	26060	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	48363	0.001013	0	48283,0,58,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aCt/aTt	T223I	orf3a	0.000459	0.822477	2	2	C>T
ERR5749398	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	14946	8.7E-4	0	4,14928,0,13	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749398	27526	PASS	C	A	24449	0.131335	2	21164,9,3267,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Cca/Aca	P45T	orf7a	0.131335	0.131335	1	1	C>A
ERR5749398	27972	PASS	C	T	11965	0.899707	20	1,1,11862,49	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749398	28048	PASS	G	T	11921	0.92702	0	0,12,0,11903	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749398	28111	PASS	A	G	36305	0.978157	0	3,1,24374,11922	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749398	28270	PASS	TA	T	47300	0.995645	477	208,9,24073,23021	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749398	28280	PASS	G	C	47219	0.940702	5	10,5,24122,23001	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749398	28281	PASS	A	T	47219	0.920922	26	25,7,24114,22998	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749398	28282	PASS	T	A	47225	0.913774	5	23,15,24047,23011	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749398	28877	PASS	A	T	15145	0.88894	9	8,16,7783,7281	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Agt/Tgt	S202C	N	0.000959	0.88894	1	1	A>T
ERR5749398	28878	PASS	G	C	15141	0.908196	0	1,0,7801,7289	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGt/aCt	S202T	N	0.001	0.909986	3	2	G>C
ERR5749398	28881	PASS	G	A	15141	0.710851	38	14,0,7723,7130	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749398	28882	PASS	G	A	15141	0.787531	21	11,1,7777,7123	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749398	28883	PASS	G	C	15141	0.943993	3	2,0,7796,7298	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749398	28977	PASS	C	T	8684	0.921925	0	0,1,0,8665	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749398	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	46471	9.04E-4	248	37736,8631,5,42	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749398	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	75028	0.001146	1	37673,37227,58,53	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749399	203	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12099	0.001818	0	12041,0,23,0	.	.	.	.	.	.	.	0.001818	0.942611	1	1	C>T
ERR5749399	241	PASS	C	T	24112	0.862392	1	3,5,12003,12021	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749399	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	10639	0.001222	0	10627,0,13,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749399	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	10640	7.52E-4	0	10621,2,8,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749399	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	10640	7.52E-4	0	10621,2,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749399	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	10631	0.002258	0	9878,4,702,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749399	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	10631	9.41E-4	0	10617,4,10,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749399	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	33416	4.19E-4	1	22750,10648,9,5	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749399	913	PASS	C	T	22752	0.914733	0	0,15,0,22712	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749399	3037	PASS	C	T	22013	0.831054	51	0,17,11004,10855	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749399	3267	PASS	C	T	21576	0.969689	0	2,0,21563,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749399	5388	PASS	C	A	6914	0.957767	2147483647	0,0,6909,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749399	5986	PASS	C	T	14037	0.976277	0	2,0,14025,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749399	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	14175	0.008113	0	1,14058,0,115	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/Tctt	L1328S?	nsp3	0.000731	0.14377	4	2	C>CT
ERR5749399	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14175	0.00134	0	1,14019,0,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749399	6706	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	14181	8.46E-4	0	1,14168,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1330	nsp3	0.000687	0.883999	2	2	CA>C
ERR5749399	6954	PASS	T	C	13978	0.805408	0	0,3,0,13878	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749399	7067	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	31992	9.06E-4	37	17942,14010,31,5	HIGH	NONSENSE	STOP_GAINED	ORF1ab	Gaa/Taa	E1450*	nsp3	0.000274	0.059217	5	3	G>T
ERR5749399	8603	PASS	T	C	13863	0.969631	275	8,1,0,13840	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Ctc	F17L	nsp4	0.002607	0.974959	2	1	T>C
ERR5749399	8772	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23339	0.001457	0	23260,3,42,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T73I	nsp4	0.001457	0.166667	1	1	C>T
ERR5749399	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	33478	0.001045	92	18165,15278,35,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749399	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	23533	0.001657	0	23461,0,62,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749399	11104	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	23529	0.00136	0	23412,0,35,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccT/ccC	P44	nsp6	0.000866	0.675414	2	1	T>C
ERR5749399	11287	PASS	GTCTGGTTTT	G	23534	0.997833	0	0,51,0,23483	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749399	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	35380	0.001131	10	19417,15896,18,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749399	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	33803	0.001242	0	16881,16843,21,21	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749399	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	8239	0.003884	2165	8036,71,2,122	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749399	14408	PASS	C	T	16023	0.841041	4	1,3,7996,7921	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749399	14676	PASS	C	T	13569	0.721424	0	5,0,13501,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749399	15279	PASS	C	T	23340	0.915424	0	5,0,23309,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749399	16176	PASS	T	C	22041	0.980582	4	3,1,9716,12311	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749399	16524	PASS	A	G	21010	0.925226	0	6,0,20975,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acA/acG	T96	helicase	0.00047	0.926983	2	2	A>G
ERR5749399	17615	PASS	A	G	19042	0.909306	0	0,1,2,18998	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749399	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	28491	8.07E-4	0	28468,0,23,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749399	18981	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27158	0.002393	0	27072,0,79,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H314	ExoN	0.001184	0.929465	1	1	C>T
ERR5749399	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	31417	0.00191	0	31333,0,61,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749399	20091	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	31370	4.14E-4	0	5,31352,0,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	caa/Acaa	Q159T?	endoR	0.000368	0.051583	1	1	C>CA
ERR5749399	21255	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	69764	6.88E-4	2	36030,33666,28,22	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcG/gcA	A199	MethTr	0.000341	0.917425	4	2	G>A
ERR5749399	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4832	0.025248	0	4,4672,0,132	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749399	21727	PASS	C	T	15422	0.858903	180	1,5,15399,0	LOW	SILENT	SYNONYMOUS_CODING	S	ttC/ttT	F55	S	0.000896	0.878141	2	2	C>T
ERR5749399	21762	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTATACA	C	15417	0.001297	0	15395,0,20,0	MODERATE	NONE	CODON_DELETION	S	atacat/	IH68	S	0.001297	0.875707	2	2	CTATACA>C
ERR5749399	21764	PASS	ATACATG	A	15417	0.996043	0	59,0,15356,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749399	21990	PASS	TTTA	T	15419	0.9976	0	0,37,2,15380	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749399	23063	PASS	A	T	16803	0.864905	0	0,1,0,16714	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749399	23271	PASS	C	A	25357	0.92649	0	4,0,25336,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749399	23403	PASS	A	G	25355	0.968369	0	0,4,0,25332	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749399	23604	PASS	C	A	18057	0.951265	0	10,0,18038,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749399	23709	PASS	C	T	18032	0.933174	0	0,3,2,17997	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749399	24320	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	14211	0.002744	0	0,14172,0,39	HIGH	NONE	FRAME_SHIFT	S	aaa/	K921	S	0.000763	0.138365	4	2	CA>C
ERR5749399	24506	PASS	T	G	18187	0.974872	0	4,0,18178,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749399	24914	PASS	G	C	43222	0.958077	0	0,0,21540,21655	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749399	25437	PASS	G	T	21855	0.963441	0	4,0,21824,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	ttG/ttT	L15F	orf3a	0.001128	0.971411	2	2	G>T
ERR5749399	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	18752	0.001493	400	18669,22,11,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749399	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	18858	0.001273	684	18503,143,127,57	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749399	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	14823	0.001147	0	2,14804,0,17	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749399	27382	PASS	G	C	22978	0.92619	0	0,4,18,22947	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF6	Gat/Cat	D61H	orf6	0.001236	0.927964	2	2	G>C
ERR5749399	27383	PASS	A	T	22978	0.912003	0	0,20,18,22933	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF6	gAt/gTt	D61V	orf6	0.001454	0.928985	1	1	A>T
ERR5749399	27384	PASS	T	C	22978	0.888894	0	0,5,18,22898	LOW	SILENT	SYNONYMOUS_CODING	ORF6	gaT/gaC	D61	orf6	0.00154	0.931035	3	3	T>C
ERR5749399	27972	PASS	C	T	12675	0.906193	18	1,1,12548,81	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749399	28048	PASS	G	T	12601	0.929053	0	0,14,0,12582	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749399	28111	PASS	A	G	37849	0.979233	5	7,1,25222,12609	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749399	28270	PASS	TA	T	48933	0.995075	608	247,7,24862,23830	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749399	28280	PASS	G	C	48834	0.937093	23	16,3,24926,23805	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749399	28281	PASS	A	T	48834	0.919257	14	30,14,24914,23803	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749399	28282	PASS	T	A	48838	0.915209	8	24,14,24879,23824	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749399	28881	PASS	G	A	14968	0.767972	9	4,0,7385,7362	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749399	28882	PASS	G	A	14968	0.827432	4	4,1,7468,7339	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749399	28883	PASS	G	C	14968	0.942277	0	1,1,7486,7462	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749399	28977	PASS	C	T	7620	0.930577	2147483647	0,0,0,7607	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749399	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	74024	0.001594	0	37145,36706,73,72	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749400	241	PASS	C	T	5840	0.871747	0	0,0,2901,2914	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749400	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	11663	8.57E-4	0	11624,4,10,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749400	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	11663	0.001886	0	11624,4,22,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749400	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	11672	0.002999	3	10714,22,890,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749400	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	11672	0.001199	0	11633,22,14,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749400	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATGGTTG	T	11668	7.71E-4	0	11634,22,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	atggttgag/	MVE85	leader	0.000587	0.476744	4	1	TATGGTTG>T
ERR5749400	657	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	11675	0.003426	0	0,11625,0,44	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A131V	leader	0.001202	0.365979	3	1	C>T
ERR5749400	673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29374	0.001226	99	17679,11608,4,35	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y136	leader	0.000454	0.602236	3	2	C>T
ERR5749400	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	29373	6.47E-4	17	17678,11674,6,13	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749400	913	PASS	C	T	17673	0.913314	0	0,10,0,17635	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749400	1225	PASS	C	T	16943	0.929115	0	0,2,0,16915	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ctC/ctT	L140	nsp2	0.928522	0.929115	1	1	C>T
ERR5749400	3037	PASS	C	T	21499	0.806503	91	0,30,10736,10598	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749400	3267	PASS	C	T	18453	0.971712	0	5,0,18435,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749400	4280	PASS	G	A	21206	0.896067	0	0,1,6,21118	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gta/Ata	V521I	nsp3	0.002822	0.896067	2	1	G>A
ERR5749400	5170	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	11575	8.64E-4	0	0,11565,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T819	nsp3	0.000565	0.894036	2	2	CCA>C
ERR5749400	5388	PASS	C	A	7072	0.964932	2147483647	0,0,7072,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749400	5822	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17909	0.004244	0	0,17786,0,92	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Ttt	L1035F	nsp3	0.002438	0.069663	1	1	C>T
ERR5749400	5986	PASS	C	T	14838	0.973244	0	2,0,14824,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749400	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	13672	7.31E-4	0	4,13555,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctt/TTctt	L1328F?	nsp3	0.000731	0.14377	4	2	C>CTT
ERR5749400	6954	PASS	T	C	19895	0.812918	0	0,7,3,19773	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749400	6990	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	19949	6.02E-4	0	0,19937,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L1425	nsp3	0.000504	0.101156	4	2	CT>C
ERR5749400	7423	PASS	C	T	14880	0.968145	0	3,0,14827,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1568	nsp3	0.000941	0.970543	2	2	C>T
ERR5749400	7564	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	14865	0.001009	0	0,14850,0,15	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/	Y1617	nsp3	0.000586	0.056194	4	2	CT>C
ERR5749400	7735	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21301	0.002629	0	21229,0,58,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I1672	nsp3	0.000658	0.954659	3	2	C>T
ERR5749400	8084	PASS	G	A	21213	0.918682	0	11,0,21178,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E1789K	nsp3	0.000543	0.923413	4	2	G>A
ERR5749400	8084	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GA	21213	0.018951	0	20811,0,402,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctc/Actc	L1791T?	nsp3	0.000543	0.923413	4	2	G>GA
ERR5749400	8964	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	19033	0.001208	0	19010,0,23,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K138	nsp4	0.000553	0.981649	4	2	CA>C
ERR5749400	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	24343	0.00267	85	17815,6463,65,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749400	11073	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TCTTTTTTTTGTATGAAAATGCCTTTTTAC	T	22938	5.23E-4	0	22923,1,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tttttgtatgaaaatgcctttttacctttt/	FLYENAFLPF36	nsp6	0.000385	0.092251	6	2	TCTTTTTTTTGTATGAAAATGCCTTTTTAC>T
ERR5749400	11287	PASS	GTCTGGTTTT	G	22924	0.99795	0	0,47,0,22877	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749400	12125	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	22154	0.001264	0	2,22056,0,35	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y12H	nsp8	0.000847	0.113436	1	1	T>C
ERR5749400	13059	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTG	C	31236	4.48E-4	0	16991,14231,8,6	HIGH	NONE	FRAME_SHIFT	ORF1ab	gta/	V13	nsp10	0.000448	0.855104	3	2	CTG>C
ERR5749400	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34866	0.001147	0	17414,17364,23,24	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749400	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	8747	0.002401	1744	8529,108,4,104	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749400	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	16977	8.25E-4	0	8518,8459,7,7	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749400	14408	PASS	C	T	16977	0.843965	3	2,4,8471,8362	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749400	14676	PASS	C	T	12196	0.767875	0	6,0,12151,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749400	15279	PASS	C	T	19300	0.884715	2147483647	0,0,19268,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749400	15983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	10781	8.35E-4	0	10773,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T850	RdRp	0.000701	0.338235	2	1	TA>T
ERR5749400	16176	PASS	T	C	20118	0.981758	0	1,1,9317,10787	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749400	16575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22053	0.002947	0	21963,0,70,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D113	helicase	0.001088	0.827968	1	1	C>T
ERR5749400	17615	PASS	A	G	18955	0.893485	0	0,0,4,18891	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749400	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20839	0.002687	0	20772,0,60,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749400	20178	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20844	0.007532	0	2,20638,0,179	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V186	endoR	0.000533	0.867727	2	2	C>T
ERR5749400	20987	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	43914	7.97E-4	0	21902,21836,19,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T110I	MethTr	0.000276	0.056129	4	2	C>T
ERR5749400	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	22026	0.001362	0	4,21989,0,30	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TA>T
ERR5749400	21123	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	58737	3.23E-4	33	36701,22017,4,15	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F156	MethTr	0.000257	0.90982	5	2	GT>G
ERR5749400	21234	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	36675	5.73E-4	0	36657,0,21,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/Tgtt	V194C?	MethTr	0.000472	0.857572	5	2	C>CT
ERR5749400	21575	PASS	C	T	26890	0.057419	5	12296,12543,852,918	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749400	21764	PASS	ATACATG	A	15396	0.996168	0	60,0,15336,1	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749400	21846	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30706	0.005048	0	15270,15192,98,100	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCt/aTt	T95I	S	0.001104	0.788523	1	1	C>T
ERR5749400	21990	PASS	TTTA	T	15399	0.997727	0	0,35,2,15362	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749400	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34906	9.17E-4	0	17718,17147,17,15	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749400	23063	PASS	A	T	17710	0.874421	0	0,3,0,17633	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749400	23271	PASS	C	A	21207	0.923987	0	1,0,21185,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749400	23403	PASS	A	G	21199	0.964951	0	0,5,1,21172	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749400	23604	PASS	C	A	18154	0.945026	0	16,0,18129,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749400	23709	PASS	C	T	18136	0.944861	0	0,3,3,18109	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749400	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	30873	4.53E-4	5	12702,18156,8,6	HIGH	NONE	FRAME_SHIFT	S	ttg/	L753	S	0.000334	0.080808	2	2	CT>C
ERR5749400	24506	PASS	T	G	18243	0.973305	0	10,0,18229,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749400	24899	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	46883	3.2E-4	0	23452,23418,7,8	HIGH	NONE	FRAME_SHIFT	S	atc/	I1114	S	0.000315	0.09021	5	3	CA>C
ERR5749400	24914	PASS	G	C	46734	0.958724	0	1,2,23279,23411	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749400	25496	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	44420	6.08E-4	16	21810,21877,383,323	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aTa/aGa	I35R	orf3a	0.000369	0.96555	3	2	T>G
ERR5749400	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	10969	0.002279	649	10902,18,1,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749400	26416	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	21239	0.001036	43	10506,10614,81,37	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	Gtt/Ttt	V58F	E	0.000457	0.913418	2	2	G>T
ERR5749400	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	16171	6.8E-4	0	2,16158,0,11	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749400	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	16173	0.001669	0	1,16143,0,27	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749400	27603	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22401	0.002411	0	22319,2,58,0	LOW	SILENT	SYNONYMOUS_CODING	ORF7a	ggC/ggT	G70	orf7a	0.002411	0.959582	1	1	C>T
ERR5749400	27972	PASS	C	T	12762	0.906911	18	1,1,12615,99	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749400	28048	PASS	G	T	12670	0.926677	0	0,18,0,12641	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749400	28111	PASS	A	G	35250	0.977305	0	6,3,22544,12676	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749400	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	22550	5.32E-4	0	22542,4,12,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749400	28270	PASS	TA	T	43708	0.99531	355	190,17,22291,21212	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749400	28280	PASS	G	C	43613	0.9333	8	12,5,22306,21188	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749400	28281	PASS	A	T	43613	0.920872	43	40,10,22292,21194	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749400	28282	PASS	T	A	43613	0.910004	7	26,15,22260,21211	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749400	28881	PASS	G	A	14064	0.75448	6	5,1,6938,6897	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749400	28882	PASS	G	A	14064	0.825299	0	1,0,7030,6881	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749400	28883	PASS	G	C	14064	0.939775	3	0,1,7041,7002	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749400	28977	PASS	C	T	7179	0.927149	0	0,1,2,7165	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749400	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	41283	0.001332	260	34064,7123,12,49	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749400	29095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34097	7.92E-4	0	34053,0,27,0	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F274	N	0.000792	0.961279	2	2	C>T
ERR5749400	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	67692	0.001123	1	33956,33577,47,43	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749401	241	PASS	C	T	147	0.843537	0	0,0,73,74	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749401	412	PASS	C	T	404	0.977723	2147483647	0,0,404,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G49	leader	0.968277	0.983986	1	1	C>T
ERR5749401	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	403	0.007444	0	400,0,3,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749401	635	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	404	0.019802	0	0,395,0,9	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgt/Tgt	R124C	leader	0.00148	0.880435	1	1	C>T
ERR5749401	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1199	0.023353	11	771,399,24,5	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L140	leader	0.000316	0.135802	3	2	C>T
ERR5749401	913	PASS	C	T	795	0.930818	2147483647	0,0,0,795	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749401	2494	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	2228	0.010323	0	0,2200,0,25	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaG/gaA	E563	nsp2	0.002624	0.951457	2	2	G>A
ERR5749401	3037	PASS	C	T	2125	0.816	9	0,3,1062,1050	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749401	3096	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1069	0.006548	0	0,1061,0,7	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCa/tTa	S126L	nsp3	0.001801	0.932094	1	1	C>T
ERR5749401	3177	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2044	0.008317	2	965,1058,8,12	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P153L	nsp3	0.000773	0.96008	3	2	C>T
ERR5749401	3267	PASS	C	T	975	0.970256	2147483647	0,0,974,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749401	3602	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1310	0.005344	0	1303,0,7,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cac/Tac	H295Y	nsp3	0.004454	0.97247	1	1	C>T
ERR5749401	5388	PASS	C	A	666	0.951952	2147483647	0,0,666,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749401	5986	PASS	C	T	2328	0.975945	2147483647	0,0,2328,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749401	6185	PASS	C	T	2328	0.943729	0	0,1,0,2327	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cac/Tac	H1156Y	nsp3	0.910265	0.954999	1	1	C>T
ERR5749401	6954	PASS	T	C	3209	0.830788	2147483647	0,0,0,3196	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749401	8950	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4153	0.008909	11	3762,353,38,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I132	nsp4	0.002808	0.982604	1	1	C>T
ERR5749401	9286	PASS	C	T	70	0.957143	2147483647	0,0,70,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N244	nsp4	0.949239	0.971567	1	1	C>T
ERR5749401	10369	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6098	0.011151	0	1,6021,0,71	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	cgC/cgT	R105	3Cpro	0.001225	0.120075	1	1	C>T
ERR5749401	10386	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	8070	0.001363	5	1972,6087,1,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	tca/	S113	3Cpro	0.000642	0.160456	4	2	CT>C
ERR5749401	11287	PASS	GTCTGGTTTT	G	6638	0.998795	0	0,8,0,6630	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749401	11824	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1578	0.007605	0	0,1565,0,12	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I284	nsp6	0.000465	0.922016	2	2	C>T
ERR5749401	12513	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2616	0.009939	0	2588,0,26,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aTg	T141M	nsp8	0.000794	0.984064	2	2	C>T
ERR5749401	13458	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1875	0.0112	0	1850,0,23,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCg/tTg	S6L	nsp11	0.001017	0.058608	4	2	C>T
ERR5749401	14408	PASS	C	T	148	0.918919	0	0,0,74,72	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749401	14676	PASS	C	T	543	0.826888	2147483647	0,0,541,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749401	15279	PASS	C	T	1254	0.89075	0	1,0,1251,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749401	16176	PASS	T	C	1211	0.983485	0	0,0,479,732	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749401	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	5074	0.001971	0	5064,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749401	17615	PASS	A	G	3474	0.904145	0	0,1,0,3466	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749401	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	1160	0.017241	0	1140,0,20,0	HIGH	NONE	FRAME_SHIFT+STOP_GAINED	ORF1ab	gat/Tgat	D124*?	endoR	0.000884	0.981982	5	2	C>CT
ERR5749401	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4315	0.016918	0	2082,2113,40,41	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749401	21764	PASS	ATACATG	A	3950	0.998734	0	5,0,3945,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749401	21990	PASS	TTTA	T	3950	1.0	2147483647	0,0,0,3950	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749401	22384	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	4428	0.009485	0	4382,0,43,0	LOW	SILENT	SYNONYMOUS_CODING	S	acT/acC	T274	S	0.001609	0.118834	1	1	T>C
ERR5749401	22432	PASS	C	T	4425	0.755028	0	1,0,4385,0	LOW	SILENT	SYNONYMOUS_CODING	S	gaC/gaT	D290	S	0.002959	0.755028	1	1	C>T
ERR5749401	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	9541	0.001782	0	0,9520,0,17	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749401	23063	PASS	A	T	3541	0.87094	0	0,1,0,3517	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749401	23271	PASS	C	A	879	0.929465	2147483647	0,0,878,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749401	23403	PASS	A	G	878	0.973804	2147483647	0,0,0,877	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749401	23604	PASS	C	A	3564	0.944444	0	2,0,3560,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749401	23689	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	3560	0.008146	0	0,3511,0,32	LOW	SILENT	SYNONYMOUS_CODING	S	aaT/aaC	N709	S	0.008146	0.197861	1	1	T>C
ERR5749401	23709	PASS	C	T	3561	0.9385	2147483647	0,0,0,3556	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749401	24506	PASS	T	G	3542	0.972614	0	1,0,3540,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749401	24914	PASS	G	C	12083	0.96433	0	0,0,6023,6056	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749401	25422	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGGAACTGTA	T	12374	0.004041	0	12324,0,50,0	MODERATE	NONE	CODON_DELETION	ORF3a	ggaactgta/	GTV11	orf3a	0.000545	0.213989	6	1	TGGAACTGTA>T
ERR5749401	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	342	0.035088	146	316,14,0,12	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749401	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	316	0.025316	0	308,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749401	26256	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9498	0.004527	33	1616,7829,0,44	LOW	SILENT	SYNONYMOUS_CODING	E	ttC/ttT	F4	E	0.000748	0.969561	2	2	C>T
ERR5749401	26958	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8573	0.008282	0	8496,0,73,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Cgt/Tgt	R146C	M	0.00096	0.122326	1	1	C>T
ERR5749401	27065	PASS	G	A	8554	0.897124	0	0,4,0,8512	LOW	SILENT	SYNONYMOUS_CODING	M	ttG/ttA	L181	M	0.001008	0.897124	3	2	G>A
ERR5749401	27476	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15474	0.003037	133	8032,7356,1,47	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	aCa/aTa	T28I	orf7a	0.000547	0.22827	4	2	C>T
ERR5749401	27557	PASS	CACTGACTTGCTTTAGCACTCAATTTGCTTTTGCTTGTCCTGACGGCGTAAAACACGTCTATCAGTTACGTGCCAGATCAGTTTCACCT	C	8072	0.267468	58	5870,44,2159,0	HIGH	NONE	FRAME_SHIFT	ORF7a	ctgacttgctttagcactcaatttgcttttgcttgtcctgacggcgtaaaacacgtctatcagttacgtgccagatcagtttcacctaaa/	LTCFSTQFAFACPDGVKHVYQLRARSVSPK56	orf7a	0.000949	0.267468	2	2	CACTGACTTGCTTTAGCACTCAATTTGCTTTTGCTTGTCCTGACGGCGTAAAACACGTCTATCAGTTACGTGCCAGATCAGTTTCACCT>C
ERR5749401	27577	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7954	0.001509	0	5782,0,12,0	HIGH	NONSENSE	STOP_GAINED	ORF7a	Caa/Taa	Q62*	orf7a	0.000614	0.952205	4	2	C>T
ERR5749401	27598	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	7954	0.004526	0	5758,0,36,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Gac/Cac	D69H	orf7a	0.000699	0.958994	6	2	G>C
ERR5749401	27972	PASS	C	T	1153	0.912402	0	0,0,1149,3	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749401	28048	PASS	G	T	1151	0.926151	2147483647	0,0,0,1151	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749401	28111	PASS	A	G	9265	0.981112	9	0,1,8109,1151	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749401	28198	PASS	G	T	8113	0.93381	0	2,0,8060,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tGt/tTt	C102F	orf8	0.000718	0.94386	4	2	G>T
ERR5749401	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8109	0.041559	0	7707,0,382,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749401	28270	PASS	TA	T	15708	0.993761	269	99,1,7979,7631	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749401	28271	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AA	A	15708	0.001592	71	8051,7632,25,0	.	.	.	.	.	.	.	0.000482	0.924941	3	2	AA>A
ERR5749401	28280	PASS	G	C	15677	0.937488	9	4,0,8027,7624	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749401	28281	PASS	A	T	15677	0.906551	18	14,3,8020,7619	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749401	28282	PASS	T	A	15677	0.911399	1	4,2,8007,7626	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749401	28321	PASS	G	T	8107	0.944369	0	0,3,0,8091	LOW	SILENT	SYNONYMOUS_CODING	N	acG/acT	T16	N	0.00045	0.947809	3	2	G>T
ERR5749401	28406	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTACCCAATA	T	8120	0.004187	0	7,8079,0,34	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	N	ttacccaataat/tat	LPNN45Y	N	0.00043	0.921074	3	2	TTACCCAATA>T
ERR5749401	28881	PASS	G	A	405	0.730864	0	0,0,198,198	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749401	28882	PASS	G	A	405	0.824691	0	0,0,201,197	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749401	28883	PASS	G	C	405	0.940741	0	0,0,202,202	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749401	28977	PASS	C	T	204	0.936275	2147483647	0,0,0,202	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749401	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	14471	0.001313	0	7265,7179,11,10	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749401	29284	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7284	0.007139	0	0,7210,0,54	LOW	SILENT	SYNONYMOUS_CODING	N	atC/atT	I337	N	0.000393	0.931014	3	2	C>T
ERR5749401	29492	PASS	T	C	2337	0.912281	0	1,0,2329,2	LOW	SILENT	SYNONYMOUS_CODING	N	Ttg/Ctg	L407	N	0.029032	0.925	1	1	T>C
ERR5749401	29642	PASS	C	T	2346	0.941176	0	0,0,2,2342	HIGH	NONSENSE	STOP_GAINED	ORF10	Caa/Taa	Q29*	orf10	0.001806	0.941176	2	2	C>T
ERR5749401	29779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	1700	0.028824	0	0,1651,0,49	.	.	.	.	.	.	.	0.001489	0.975228	1	1	G>T
ERR5749402	71	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	9098	0.002088	0	9073,0,23,0	.	.	.	.	.	.	.	0.002088	0.926791	2	1	C>A
ERR5749402	241	PASS	C	T	17533	0.839617	0	0,0,8731,8697	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749402	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	16583	5.43E-4	0	16565,1,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749402	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	16568	0.002958	0	15044,3,1486,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749402	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	16568	6.04E-4	0	16555,3,10,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749402	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	43523	4.14E-4	6	26890,16612,14,4	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749402	913	PASS	C	T	26895	0.913478	0	0,19,0,26836	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749402	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	98337	0.001241	2147483647	49071,46040,76,2895	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749402	3037	PASS	C	T	28194	0.851777	28	4,19,14089,13950	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749402	3267	PASS	C	T	25969	0.972775	0	2,0,25954,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749402	5388	PASS	C	A	9440	0.962182	2147483647	0,0,9435,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749402	5986	PASS	C	T	18156	0.974168	0	1,0,18143,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749402	6954	PASS	T	C	31746	0.813362	0	0,9,3,31561	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749402	8139	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	33149	0.001297	0	33052,17,47,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCc/tTc	S1807F	nsp3	0.001297	0.889336	1	1	C>T
ERR5749402	8760	PASS	C	T	31965	0.862068	0	2,0,31845,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A69V	nsp4	0.003379	0.892678	1	1	C>T
ERR5749402	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	40169	7.72E-4	81	21769,18369,31,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749402	10996	PASS	G	A	19800	0.966263	0	0,0,1,19776	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaG/aaA	K8	nsp6	0.963406	0.980023	1	1	G>A
ERR5749402	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25225	0.00111	0	25163,2,32,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749402	11287	PASS	GTCTGGTTTT	G	25208	0.998215	0	0,45,0,25163	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749402	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	16326	5.51E-4	0	16319,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749402	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	42422	0.001155	0	21180,21135,27,27	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749402	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	14972	0.004074	2147483647	14637,117,7,203	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749402	14408	PASS	C	T	29138	0.833997	7	4,9,14562,14359	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749402	14676	PASS	C	T	17170	0.689517	0	9,0,17051,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749402	15279	PASS	C	T	29631	0.886605	0	8,0,29570,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749402	15933	PASS	C	T	14166	0.981434	2147483647	0,0,14162,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y831	RdRp	0.980056	0.983528	1	1	C>T
ERR5749402	16176	PASS	T	C	28954	0.980659	0	0,0,14770,14166	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749402	17154	PASS	T	C	20326	0.984896	0	5,0,20311,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taT/taC	Y306	helicase	0.983096	0.984896	1	1	T>C
ERR5749402	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	32114	4.67E-4	0	1,32098,0,15	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749402	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	41277	0.002108	0	41160,0,89,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749402	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	40360	7.19E-4	0	40276,0,30,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749402	20987	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	55731	0.00253	1	27761,27662,82,86	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T110I	MethTr	0.000276	0.056129	4	2	C>T
ERR5749402	21764	PASS	ATACATG	A	17193	0.996161	0	66,0,17127,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749402	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	17193	5.23E-4	0	17184,0,9,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749402	21990	PASS	TTTA	T	17203	0.9975	0	0,43,10,17150	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749402	23063	PASS	A	T	18335	0.863212	0	0,4,0,18262	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749402	23271	PASS	C	A	28092	0.915243	0	5,0,28053,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749402	23403	PASS	A	G	28078	0.967092	0	0,4,0,28064	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749402	23604	PASS	C	A	21710	0.931322	0	14,0,21689,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749402	23709	PASS	C	T	21678	0.937264	0	0,7,2,21637	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749402	23817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	45853	7.2E-4	19	24101,21686,26,9	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTt/cCt	L752P	S	0.000646	0.066832	1	1	T>C
ERR5749402	24506	PASS	T	G	25136	0.973703	0	7,0,25125,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749402	24914	PASS	G	C	50802	0.959214	0	0,1,25293,25469	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749402	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	29667	0.001449	515	29549,24,24,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749402	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	29813	0.001073	1384	29313,178,183,103	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749402	27494	PASS	C	T	55352	0.961447	0	8,7,30122,25186	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	cCt/cTt	P34L	orf7a	0.000672	0.961447	2	2	C>T
ERR5749402	27972	PASS	C	T	15601	0.892379	40	2,2,15478,60	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749402	28048	PASS	G	T	15554	0.927607	0	0,20,0,15529	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749402	28111	PASS	A	G	42832	0.976186	11	7,10,27257,15550	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749402	28270	PASS	TA	T	52720	0.994442	674	293,12,26837,25590	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749402	28280	PASS	G	C	52608	0.939572	27	22,5,26929,25563	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749402	28281	PASS	A	T	52608	0.911934	42	35,8,26876,25574	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749402	28282	PASS	T	A	52613	0.91352	3	29,22,26850,25586	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749402	28856	PASS	A	C	11034	0.980152	0	3,0,11023,4	LOW	SILENT	SYNONYMOUS_CODING	N	Aga/Cga	R195	N	0.979416	0.983392	1	1	A>C
ERR5749402	28881	PASS	G	A	21657	0.760955	12	5,0,10696,10660	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749402	28882	PASS	G	A	21657	0.829247	11	9,2,10836,10615	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749402	28883	PASS	G	C	21657	0.94182	4	3,6,10858,10766	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749402	28977	PASS	C	T	11040	0.922645	0	0,8,0,11022	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749402	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	47757	0.00111	250	36672,10970,6,50	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749403	241	PASS	C	T	17261	0.845953	4	1,4,8572,8578	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749403	412	PASS	C	T	13984	0.976402	0	5,0,13974,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G49	leader	0.968277	0.983986	1	1	C>T
ERR5749403	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	13958	0.001433	0	13940,0,20,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749403	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	13957	0.001361	0	13907,0,19,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749403	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	13957	0.001648	0	13907,0,23,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749403	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	13940	0.00165	0	13087,0,761,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749403	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	13939	9.33E-4	0	13921,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749403	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	13940	9.33E-4	0	13918,1,13,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749403	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	45407	0.001145	14	31371,13974,43,9	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749403	745	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	31421	0.002578	0	31323,0,85,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N160	leader	0.001671	0.915927	1	1	C>T
ERR5749403	913	PASS	C	T	31399	0.908437	0	0,21,0,31332	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749403	2702	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	52766	8.91E-4	2147483647	52356,63,68,166	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F633V	nsp2	0.000632	0.333333	1	1	T>G
ERR5749403	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	104595	0.001491	2147483647	52272,48656,69,3362	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749403	3037	PASS	C	T	31974	0.808626	76	0,25,15996,15722	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749403	3096	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16100	0.001801	0	0,16052,0,31	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCa/tTa	S126L	nsp3	0.001801	0.932094	1	1	C>T
ERR5749403	3267	PASS	C	T	30149	0.970911	0	1,0,30139,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749403	5388	PASS	C	A	9967	0.95766	0	3,0,9953,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749403	5986	PASS	C	T	19988	0.975035	0	3,0,19975,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749403	6185	PASS	C	T	19992	0.945778	0	0,5,0,19973	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cac/Tac	H1156Y	nsp3	0.910265	0.954999	1	1	C>T
ERR5749403	6348	PASS	T	A	72	0.125	0	0,49,0,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cTg/cAg	L1210Q	nsp3	0.001003	0.125	2	1	T>A
ERR5749403	6954	PASS	T	C	31054	0.811812	0	0,9,6,30868	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749403	8964	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	24447	5.73E-4	48	24424,8,12,2	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K138	nsp4	0.000553	0.981649	4	2	CA>C
ERR5749403	9286	PASS	C	T	22909	0.954996	0	1,0,22891,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N244	nsp4	0.949239	0.971567	1	1	C>T
ERR5749403	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	46731	0.001348	184	23758,22910,63,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749403	10077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	10441	0.001916	574	9,10355,21,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTc/tCc	F8S	3Cpro	0.001833	0.454545	1	1	T>C
ERR5749403	10323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	27125	0.001032	0	0,27046,0,30	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749403	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	27716	0.00249	0	27598,0,97,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749403	11287	PASS	GTCTGGTTTT	G	27717	0.998052	0	0,54,0,27663	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749403	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	52708	8.16E-4	0	31798,20834,27,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749403	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	27643	0.001483	0	27563,0,42,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749403	12741	PASS	C	T	51093	0.962245	1	4,6,23432,27631	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T19I	nsp9	0.000486	0.962552	2	2	C>T
ERR5749403	13115	PASS	C	T	18483	0.907915	0	3,0,18454,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L31	nsp10	0.001806	0.922167	1	1	C>T
ERR5749403	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	45308	0.00128	0	22628,22554,32,33	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749403	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	20856	0.004028	2147483647	20322,172,10,346	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749403	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	40476	0.001087	0	20291,20169,23,21	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749403	14408	PASS	C	T	40476	0.838645	19	1,9,20210,19950	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749403	14676	PASS	C	T	19198	0.735389	0	10,0,19100,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749403	14724	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19178	0.001304	0	19099,16,36,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F428	RdRp	0.000952	0.789267	3	2	C>T
ERR5749403	15279	PASS	C	T	33262	0.907342	0	4,0,33222,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749403	16176	PASS	T	C	29311	0.97953	3	1,0,13626,15667	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749403	16647	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	32638	7.66E-4	0	2,32407,0,28	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acG/acA	T137	helicase	0.000746	0.885245	2	1	G>A
ERR5749403	17615	PASS	A	G	24460	0.897915	0	0,3,2,24389	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749403	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	32564	7.06E-4	0	32540,1,23,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749403	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	35183	3.69E-4	0	0,35170,0,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749403	19164	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	35195	0.034295	0	0,33851,0,1324	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D375	ExoN	0.000358	0.075732	4	2	C>T
ERR5749403	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	44984	0.002134	0	44857,1,103,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749403	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	45483	7.7E-4	0	45400,0,35,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749403	20987	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	63229	2.85E-4	0	31635,31578,9,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L111	MethTr	0.000276	0.056129	4	2	CT>C
ERR5749403	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	42096	0.001045	4	20546,20992,27,35	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749403	21764	PASS	ATACATG	A	20233	0.995502	23	88,1,20142,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749403	21990	PASS	TTTA	T	20239	0.997678	0	0,47,5,20187	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749403	22432	PASS	C	T	15609	0.741752	0	4,0,15464,1	LOW	SILENT	SYNONYMOUS_CODING	S	gaC/gaT	D290	S	0.002959	0.755028	1	1	C>T
ERR5749403	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	41077	0.001096	17	19459,21538,30,16	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749403	23063	PASS	A	T	19465	0.87028	0	0,3,0,19376	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749403	23271	PASS	C	A	32881	0.926523	0	2,0,32849,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749403	23403	PASS	A	G	32857	0.961956	0	0,3,0,32835	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749403	23604	PASS	C	A	24248	0.928118	0	14,0,24221,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749403	23709	PASS	C	T	24223	0.935144	0	0,8,5,24177	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749403	23817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	51098	6.46E-4	2	26815,24229,20,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTt/cCt	L752P	S	0.000646	0.066832	1	1	T>C
ERR5749403	24506	PASS	T	G	27080	0.975739	0	8,0,27071,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749403	24914	PASS	G	C	51945	0.958456	0	0,0,25880,26018	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749403	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	33613	0.001309	721	33492,27,17,29	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749403	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	33556	4.47E-4	0	33541,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749403	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	33773	9.18E-4	1495	33295,192,144,103	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749403	25854	PASS	C	T	33503	0.938603	0	0,5,0,33459	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	taC/taT	Y154	orf3a	0.000876	0.939185	1	1	C>T
ERR5749403	26767	PASS	T	C	18607	0.954318	0	0,8,12,18579	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	aTc/aCc	I82T	M	0.954318	0.968313	2	1	T>C
ERR5749403	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	18625	6.44E-4	0	2,18608,0,12	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749403	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	18625	0.00204	0	2,18574,0,38	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749403	27065	PASS	G	A	43710	0.740082	0	0,10,3,43162	LOW	SILENT	SYNONYMOUS_CODING	M	ttG/ttA	L181	M	0.001008	0.897124	3	2	G>A
ERR5749403	27741	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	31627	4.11E-4	0	10,31602,0,13	HIGH	NONE	FRAME_SHIFT	ORF7a	aga/	R118	orf7a	0.000363	0.954278	3	2	CA>C
ERR5749403	27972	PASS	C	T	19548	0.894158	22	0,1,19354,118	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749403	28001	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	38826	8.5E-4	0	19355,19379,22,22	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ccG/ccA	P36	orf8	0.00085	0.830607	2	1	G>A
ERR5749403	28048	PASS	G	T	19453	0.920372	0	0,21,0,19417	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749403	28111	PASS	A	G	48586	0.976475	6	9,2,29093,19464	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749403	28198	PASS	G	T	29112	0.931265	0	11,0,29025,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tGt/tTt	C102F	orf8	0.000718	0.94386	4	2	G>T
ERR5749403	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29091	8.25E-4	0	28958,3,27,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749403	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	29085	6.19E-4	0	29070,3,18,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749403	28270	PASS	TA	T	56189	0.992792	963	395,11,28584,27200	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749403	28271	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AA	A	56182	0.001709	275	28870,27217,96,0	.	.	.	.	.	.	.	0.000482	0.924941	3	2	AA>A
ERR5749403	28280	PASS	G	C	56069	0.933974	43	27,4,28737,27185	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749403	28281	PASS	A	T	56069	0.905902	38	43,13,28716,27171	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749403	28282	PASS	T	A	56073	0.91042	43	42,11,28660,27207	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749403	28321	PASS	G	T	29081	0.93721	0	0,29,6,29005	LOW	SILENT	SYNONYMOUS_CODING	N	acG/acT	T16	N	0.00045	0.947809	3	2	G>T
ERR5749403	28881	PASS	G	A	24682	0.719796	30	18,3,12099,12130	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749403	28882	PASS	G	A	24681	0.817836	11	7,1,12333,12091	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749403	28883	PASS	G	C	24681	0.94125	0	2,2,12358,12290	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749403	28977	PASS	C	T	12569	0.935635	0	0,1,0,12547	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749403	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	50783	7.29E-4	146	38172,12519,7,35	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749403	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	75764	0.001346	0	38068,37543,64,63	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749403	29642	PASS	C	T	28790	0.926641	1	2,3,14848,13890	HIGH	NONSENSE	STOP_GAINED	ORF10	Caa/Taa	Q29*	orf10	0.001806	0.941176	2	2	C>T
ERR5749404	174	PASS	G	T	13603	0.740792	0	129,0,13445,0	.	.	.	.	.	.	.	0.710959	0.747093	1	1	G>T
ERR5749404	210	PASS	G	T	13703	0.633949	20	309,8,13260,118	.	.	.	.	.	.	.	0.001452	1	2	1	G>T
ERR5749404	241	PASS	C	T	27092	0.869002	1	3,5,13477,13530	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749404	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	14577	0.001715	0	14550,1,25,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749404	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	14577	0.001303	0	14497,1,19,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749404	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	14577	0.00295	0	14497,1,43,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749404	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	14569	0.002196	0	13486,2,954,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749404	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	14569	0.001304	0	14547,3,19,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749404	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	14569	9.61E-4	0	14534,3,14,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttatg/gtg	VM84V	leader	0.000554	0.991848	4	1	GTTA>G
ERR5749404	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	14569	0.00103	0	14534,3,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749404	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	42218	3.32E-4	7	27614,14588,12,2	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749404	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	42218	0.001137	2	27585,14575,34,14	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749404	913	PASS	C	T	27619	0.928419	0	0,8,0,27577	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749404	2453	PASS	C	T	20594	0.717539	0	0,17,2,20254	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L550F	nsp2	0.00429	0.842201	2	2	C>T
ERR5749404	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	105322	0.001206	2147483647	52592,49361,86,3006	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749404	3037	PASS	C	T	25156	0.813086	52	1,21,12572,12402	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749404	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12704	0.001732	552	10,12658,22,7	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749404	3267	PASS	C	T	25168	0.970478	0	3,0,25148,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749404	5388	PASS	C	A	7319	0.958738	2147483647	0,0,7318,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749404	5986	PASS	C	T	15730	0.978067	0	1,0,15720,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749404	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15070	0.001261	0	3,14921,0,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749404	6954	PASS	T	C	31234	0.838189	0	0,1,2,31107	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749404	7764	PASS	C	T	26142	0.964731	0	6,0,26117,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCc/tTc	S1682F	nsp3	0.001052	0.964731	1	1	C>T
ERR5749404	9016	PASS	T	C	17794	0.950039	0	2,0,17774,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcC	A154	nsp4	0.001138	0.950039	2	1	T>C
ERR5749404	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	40006	0.0012	167	17843,22115,48,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749404	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	21878	0.001234	0	21818,0,51,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749404	11287	PASS	GTCTGGTTTT	G	21872	0.997805	53	2,45,0,21824	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749404	11417	PASS	G	T	15928	0.951155	0	7,0,15914,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Ttt	V149F	nsp6	0.00274	0.951155	2	2	G>T
ERR5749404	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	43979	7.5E-4	5	28002,15917,25,9	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749404	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	46524	9.89E-4	0	23233,23184,26,27	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749404	13665	PASS	C	T	21518	0.977554	101	7,3,21496,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H75	RdRp	0.002046	0.977554	1	1	C>T
ERR5749404	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	15664	0.003703	2147483647	15319,118,5,218	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749404	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	30504	0.001115	4	15293,15199,20,14	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749404	14408	PASS	C	T	30504	0.84284	9	2,7,15219,15044	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749404	14676	PASS	C	T	17090	0.835459	0	3,0,17036,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749404	15279	PASS	C	T	30402	0.886751	0	1,0,30348,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749404	16176	PASS	T	C	25755	0.981984	3	1,0,11499,14244	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749404	16293	PASS	C	T	11501	0.968351	2147483647	0,0,11489,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C19	helicase	0.001538	0.968351	1	1	C>T
ERR5749404	17781	PASS	T	C	16818	0.986978	0	2,0,16804,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taT/taC	Y515	helicase	0.00065	0.986978	2	2	T>C
ERR5749404	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	28025	6.07E-4	0	28008,0,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749404	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	37924	0.002347	0	37800,0,93,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749404	21764	PASS	ATACATG	A	15110	0.995831	0	63,0,15047,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749404	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	15109	6.62E-4	0	15099,0,10,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749404	21990	PASS	TTTA	T	15115	0.997618	0	0,36,4,15075	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749404	22690	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	19625	8.15E-4	0	19231,0,362,0	LOW	SILENT	SYNONYMOUS_CODING	S	acT/acG	T376	S	0.000815	0.051311	2	1	T>G
ERR5749404	23271	PASS	C	A	28657	0.918973	0	4,0,28617,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749404	23403	PASS	A	G	28648	0.969352	0	0,5,0,28620	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749404	23604	PASS	C	A	18733	0.944536	0	13,0,18714,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749404	23709	PASS	C	T	18726	0.950069	0	0,7,9,18692	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749404	24506	PASS	T	G	24349	0.975358	0	9,0,24336,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749404	24914	PASS	G	C	40039	0.958915	0	0,0,19939,20077	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749404	25135	PASS	G	T	11360	0.884331	0	18,0,11329,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aaG/aaT	K1191N	S	0.003281	0.884331	3	2	G>T
ERR5749404	25523	PASS	G	T	20227	0.895931	0	0,44,3,20160	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	gGa/gTa	G44V	orf3a	0.000994	0.895931	1	1	G>T
ERR5749404	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	33960	0.001296	560	33843,13,26,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749404	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	34113	0.001143	1314	33625,193,160,94	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749404	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	62234	3.21E-4	0	5,62203,0,20	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749404	26606	PASS	C	T	13174	0.951495	0	4,0,13162,0	LOW	SILENT	SYNONYMOUS_CODING	M	ttC/ttT	F28	M	0.001284	0.951495	1	1	C>T
ERR5749404	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	13151	0.002129	0	1,13117,0,28	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749404	27424	PASS	A	G	20687	0.950404	0	0,5,68,20591	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Aca/Gca	T11A	orf7a	0.950404	0.950404	1	1	A>G
ERR5749404	27972	PASS	C	T	13625	0.909725	0	0,0,13495,76	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749404	28048	PASS	G	T	13555	0.913833	0	0,16,0,13530	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749404	28087	PASS	C	T	13574	0.963754	144	4,1,0,13559	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	gCt/gTt	A65V	orf8	0.001718	0.963754	2	1	C>T
ERR5749404	28111	PASS	A	G	32961	0.977033	2	4,5,19377,13565	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749404	28270	PASS	TA	T	37372	0.994381	525	210,5,19087,18075	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749404	28280	PASS	G	C	37294	0.939937	18	12,2,19147,18062	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749404	28281	PASS	A	T	37294	0.890224	43	22,2,19129,18061	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749404	28282	PASS	T	A	37297	0.924283	7	14,7,19125,18075	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749404	28881	PASS	G	A	20120	0.777187	15	6,0,9949,9879	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749404	28882	PASS	G	A	20120	0.82828	11	7,1,10045,9865	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749404	28883	PASS	G	C	20119	0.942393	0	1,1,10062,10038	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749404	28977	PASS	C	T	10245	0.930795	0	0,1,0,10234	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749404	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	37083	7.28E-4	109	26806,10204,5,28	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749404	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	53323	0.001069	0	26751,26479,34,33	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749404	29745	PASS	G	T	10733	0.920898	0	0,21,0,10707	.	.	.	.	.	.	.	0.039548	0.920898	2	1	G>T
ERR5749404	29774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10737	0.003446	0	0,10691,0,38	.	.	.	.	.	.	.	0.002525	0.973955	1	1	C>T
ERR5749405	241	PASS	C	T	3578	0.863052	3	0,1,1781,1779	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749405	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	5032	0.002782	0	5018,0,14,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749405	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	5036	0.001986	0	5006,4,10,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749405	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	5036	0.00278	0	5006,4,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749405	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	5034	0.001589	0	5022,4,8,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749405	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	5033	0.002186	0	5018,4,11,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749405	657	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5045	0.002973	0	3,5025,0,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A131V	leader	0.001202	0.365979	3	1	C>T
ERR5749405	676	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17282	0.001273	72	12232,5017,4,20	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G137	leader	0.000799	0.919273	2	1	C>T
ERR5749405	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	17282	0.001852	19	12206,5039,29,3	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749405	913	PASS	C	T	12234	0.923083	0	0,4,0,12214	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749405	967	PASS	T	C	22218	0.978486	8	1,6,9976,12228	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caT/caC	H54	nsp2	0.973649	0.978486	1	1	T>C
ERR5749405	1813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	18095	0.00105	0	0,18058,0,24	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcA	A336	nsp2	0.001022	0.152738	4	2	T>A
ERR5749405	2166	PASS	A	G	11092	0.94762	0	0,1,0,11072	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K454R	nsp2	0.932132	0.94762	1	1	A>G
ERR5749405	3037	PASS	C	T	15295	0.801242	54	0,18,7640,7539	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749405	3267	PASS	C	T	14827	0.970864	2147483647	0,0,14822,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749405	3832	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	9319	0.00118	0	9306,2,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L373	nsp3	0.000689	0.327273	4	2	CT>C
ERR5749405	4255	PASS	G	A	27855	0.854532	47	23,2,13836,13844	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccG/ccA	P512	nsp3	0.001102	0.871853	2	1	G>A
ERR5749405	5388	PASS	C	A	4276	0.960711	0	1,0,4274,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749405	5986	PASS	C	T	12412	0.979133	0	1,0,12406,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749405	6954	PASS	T	C	18679	0.810054	0	0,4,0,18564	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749405	7067	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	24304	0.001111	155	5538,18730,31,4	HIGH	NONSENSE	STOP_GAINED	ORF1ab	Gaa/Taa	E1450*	nsp3	0.000274	0.059217	5	3	G>T
ERR5749405	7564	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	12810	9.37E-4	0	0,12794,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/	Y1617	nsp3	0.000586	0.056194	4	2	CT>C
ERR5749405	8480	PASS	C	T	10750	0.88186	0	0,4,7,10714	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cct/Tct	P1921S	nsp3	0.003497	0.88186	1	1	C>T
ERR5749405	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	15544	0.00148	20	12282,3239,23,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749405	10798	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1215	0.009053	0	1201,0,12,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D248	3Cpro	0.003021	0.97286	1	1	C>T
ERR5749405	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21778	0.00124	0	21722,0,32,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749405	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	21775	0.001653	0	21712,0,55,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749405	11095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	21771	0.003583	0	21693,0,78,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/ttTa	L43F?	nsp6	0.000515	0.887707	7	2	C>CT
ERR5749405	11287	PASS	GTCTGGTTTT	G	21773	0.997428	0	0,55,0,21717	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749405	11507	PASS	G	A	18606	0.910244	0	1,0,9317,9226	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Att	V179I	nsp6	0.007744	0.914418	2	2	G>A
ERR5749405	11824	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	19340	4.65E-4	0	0,19331,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K285	nsp6	0.000465	0.922016	2	2	CA>C
ERR5749405	13458	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CGTTTTT	C	13770	0.001017	0	13756,0,14,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	tcgttttta/tca	SFL6S	nsp11	0.001017	0.058608	4	2	CGTTTTT>C
ERR5749405	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27500	0.001564	0	13729,13693,26,26	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749405	14408	PASS	C	T	2640	0.829545	0	0,0,1315,1304	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749405	14676	PASS	C	T	8735	0.826674	0	2,0,8712,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749405	15279	PASS	C	T	13729	0.905893	0	1,0,13718,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749405	15960	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8553	0.005963	0	8489,0,61,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A840	RdRp	0.001581	0.81574	1	1	C>T
ERR5749405	16176	PASS	T	C	13346	0.982916	5	2,1,4789,8551	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749405	18647	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGAGCGCACCTGT	C	45828	3.05E-4	42	22804,23010,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gagcgcacctgttgt/	ERTCC204	ExoN	0.000283	0.970507	4	2	CTGAGCGCACCTGT>C
ERR5749405	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	22818	0.001578	0	22782,0,36,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749405	18747	PASS	C	G	22810	0.982946	0	3,0,22775,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtG	V236	ExoN	0.000375	0.982946	4	2	C>G
ERR5749405	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	20742	0.001398	0	0,20713,0,29	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749405	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14949	0.001338	0	14923,0,20,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749405	20445	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TA	30873	5.18E-4	0	38,30819,0,16	HIGH	NONE	FRAME_SHIFT	ORF1ab	aac/aaAc	N277K?	endoR	0.000518	0.059736	4	2	T>TA
ERR5749405	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	20404	9.31E-4	0	0,20385,0,19	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TA>T
ERR5749405	21732	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	13882	5.76E-4	0	13853,21,8,0	HIGH	NONE	FRAME_SHIFT	S	ttc/	F58	S	0.000576	0.076745	4	2	CT>C
ERR5749405	21764	PASS	ATACATG	A	13861	0.99798	0	28,0,13833,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749405	21990	PASS	TTTA	T	13867	0.997981	0	0,28,4,13835	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749405	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	17864	0.001232	0	0,17832,0,23	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749405	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	31665	8.21E-4	7	13771,17835,15,11	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749405	23063	PASS	A	T	13784	0.86731	0	0,1,0,13721	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749405	23271	PASS	C	A	15310	0.923318	0	1,0,15293,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749405	23403	PASS	A	G	15305	0.968964	0	0,5,0,15291	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749405	23604	PASS	C	A	14791	0.943682	0	13,0,14765,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749405	23709	PASS	C	T	14775	0.936108	0	0,3,0,14756	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749405	23758	PASS	C	T	14792	0.962885	0	0,1,0,14782	LOW	SILENT	SYNONYMOUS_CODING	S	acC/acT	T732	S	0.001489	0.964055	1	1	C>T
ERR5749405	23817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	24504	8.98E-4	0	9700,14777,9,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTt/cCt	L752P	S	0.000646	0.066832	1	1	T>C
ERR5749405	24010	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATTTATTGAAGATCTAC	A	9763	0.001127	0	65,9689,0,11	HIGH	NONE	FRAME_SHIFT	S	attgaagatctacttttc/	IEDLLF818	S	0.000455	0.926398	4	2	ATTTATTGAAGATCTAC>A
ERR5749405	24506	PASS	T	G	15896	0.97339	0	6,0,15887,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749405	24914	PASS	G	C	33665	0.96284	2	1,3,16758,16863	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749405	25626	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	28413	4.93E-4	4	7065,21334,5,9	HIGH	NONE	FRAME_SHIFT	ORF3a	ttt/	F79	orf3a	0.000403	0.915633	3	2	CT>C
ERR5749405	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	36643	3.27E-4	0	0,36631,0,12	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749405	26416	PASS	G	T	19741	0.911605	2	23,19,9708,9969	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	Gtt/Ttt	V58F	E	0.000457	0.913418	2	2	G>T
ERR5749405	26526	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	10113	0.001582	0	0,10079,0,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Gca/Tca	A2S	M	0.001224	0.951192	3	1	G>T
ERR5749405	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	12387	6.46E-4	0	3,12376,0,8	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749405	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	12389	0.001856	0	3,12359,0,23	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749405	26895	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27881	0.002295	0	27807,3,67,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Cat/Tat	H125Y	M	0.000874	0.97046	1	1	C>T
ERR5749405	27532	PASS	C	T	20054	0.979206	441	2,13,20024,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Cat/Tat	H47Y	orf7a	0.001165	0.982473	2	1	C>T
ERR5749405	27567	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTTTAGCACTCAATTTGCT	C	20042	4.49E-4	0	20026,3,9,0	MODERATE	NONE	CODON_DELETION	ORF7a	agcactcaatttgctttt/	STQFAF60	orf7a	0.000449	0.998291	4	1	CTTTAGCACTCAATTTGCT>C
ERR5749405	27881	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8344	0.001798	0	8325,0,15,0	LOW	SILENT	SYNONYMOUS_CODING	ORF7b	caC/caT	H42	orf7b	0.001798	0.979167	2	2	C>T
ERR5749405	27955	PASS	G	A	8335	0.879424	0	0,0,8310,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGt/aAt	S21N	orf8	0.001684	0.879424	3	2	G>A
ERR5749405	27972	PASS	C	T	8373	0.903022	0	0,0,8292,44	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749405	28048	PASS	G	T	8338	0.926361	0	0,15,0,8319	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749405	28111	PASS	A	G	30148	0.9798	6	7,0,21790,8341	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749405	28270	PASS	TA	T	42323	0.994849	497	215,9,21494,20611	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749405	28280	PASS	G	C	42230	0.939309	37	22,3,21535,20597	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749405	28281	PASS	A	T	42230	0.922614	9	22,12,21529,20597	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749405	28282	PASS	T	A	42235	0.912206	6	21,13,21501,20613	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749405	28406	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTACCCAATA	T	21826	5.96E-4	0	19,21794,0,13	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	N	ttacccaataat/tat	LPNN45Y	N	0.00043	0.921074	3	2	TTACCCAATA>T
ERR5749405	28881	PASS	G	A	9938	0.771081	0	2,1,4915,4879	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749405	28882	PASS	G	A	9938	0.828839	0	1,0,4968,4894	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749405	28883	PASS	G	C	9938	0.951801	0	0,0,4973,4964	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749405	28977	PASS	C	T	5066	0.933873	2147483647	0,0,0,5061	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749405	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	32703	9.17E-4	111	27608,5025,23,30	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcG	A254	N	0.000601	0.054952	4	2	T>G
ERR5749405	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	54891	0.001421	0	27558,27225,47,46	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749406	241	PASS	C	T	18974	0.865395	0	4,5,9379,9518	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749406	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	18061	0.002934	0	17999,9,53,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749406	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	18060	0.001495	0	17926,12,27,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749406	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	18060	0.004485	0	17926,12,81,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749406	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	18053	0.001717	0	16769,16,1043,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749406	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	18053	0.00216	0	17996,18,39,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749406	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	18052	5.54E-4	0	18014,20,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749406	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	18052	0.001496	14	17986,22,26,1	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749406	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	50634	3.95E-4	7	32536,18074,16,4	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749406	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	50635	3.16E-4	0	32448,18019,10,6	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749406	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	50635	0.002824	0	32448,18019,92,51	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749406	913	PASS	C	T	32541	0.914416	0	0,18,0,32474	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749406	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	118873	0.001262	2147483647	59331,55692,118,3424	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749406	3037	PASS	C	T	32358	0.834013	87	1,33,16166,15973	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749406	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	16307	0.001349	632	4,16275,22,4	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749406	3177	PASS	C	T	46413	0.892638	1	8,5,30092,16238	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P153L	nsp3	0.000773	0.96008	3	2	C>T
ERR5749406	3267	PASS	C	T	30129	0.972153	0	4,0,30107,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749406	5077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	19660	0.001526	0	19587,0,31,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtT/gtC	V786	nsp3	0.001393	0.168205	1	1	T>C
ERR5749406	5388	PASS	C	A	11863	0.957936	0	1,0,11860,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749406	5986	PASS	C	T	21915	0.976089	0	1,0,21900,2	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749406	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20821	0.001105	0	11,20580,0,32	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749406	6954	PASS	T	C	35523	0.813698	0	0,5,2,35301	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749406	7528	PASS	C	T	23497	0.898923	0	0,12,62,23381	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V1603	nsp3	0.002527	0.916131	1	1	C>T
ERR5749406	7674	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	33832	9.46E-4	0	33772,15,33,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCg/gTg	A1652V	nsp3	0.000682	0.109264	3	2	C>T
ERR5749406	8327	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21326	0.001407	0	21263,20,34,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Ttt	L1870F	nsp3	0.001407	0.90398	1	1	C>T
ERR5749406	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	49955	6.21E-4	90	25039,24885,31,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749406	9802	PASS	G	T	25070	0.951137	70	2,3,1,25055	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcG/gcT	A416	nsp4	0.948822	0.951137	1	1	G>T
ERR5749406	10323	PASS	A	G	27696	0.956528	0	0,2,1,27649	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749406	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28256	0.001133	0	28177,8,38,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749406	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	28236	0.001133	0	28165,0,59,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749406	11287	PASS	GTCTGGTTTT	G	28229	0.99667	0	0,92,0,28135	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749406	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	55404	7.76E-4	3	32752,22568,24,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749406	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	51067	0.001195	0	25490,25443,34,34	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749406	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	23285	0.004724	2147483647	22731,178,7,363	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749406	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	45271	0.00106	1	22694,22558,26,22	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749406	14408	PASS	C	T	45271	0.848336	8	3,8,22588,22342	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749406	14676	PASS	C	T	19988	0.792976	0	11,0,19923,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749406	14724	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19967	9.52E-4	0	19876,27,24,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F428	RdRp	0.000952	0.789267	3	2	C>T
ERR5749406	15279	PASS	C	T	35803	0.893221	0	3,0,35745,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749406	16176	PASS	T	C	34090	0.982869	0	0,1,16966,17108	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749406	16647	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	30985	8.07E-4	0	5,30786,0,26	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acG/acA	T137	helicase	0.000746	0.885245	2	1	G>A
ERR5749406	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	35709	6.72E-4	0	35685,0,24,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749406	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	36353	3.58E-4	0	1,36339,0,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749406	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	50537	0.002256	0	50390,1,118,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749406	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	38312	0.001122	0	38219,0,47,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749406	21304	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	50804	0.00185	0	9,50649,0,123	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgc/Agc	R216S	MethTr	0.000411	0.605296	3	2	C>A
ERR5749406	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	42488	6.83E-4	2	20833,21166,17,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749406	21764	PASS	ATACATG	A	21496	0.997255	0	57,0,21437,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749406	21990	PASS	TTTA	T	21502	0.997954	0	0,44,5,21453	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749406	22450	PASS	C	T	15441	0.795933	56	2,3,15194,89	LOW	SILENT	SYNONYMOUS_CODING	S	ctC/ctT	L296	S	0.00215	0.803846	1	1	C>T
ERR5749406	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	22713	0.001101	0	0,22683,0,26	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749406	23063	PASS	A	T	18726	0.87002	0	0,4,0,18642	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749406	23271	PASS	C	A	34091	0.920654	0	2,0,34058,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749406	23403	PASS	A	G	34076	0.96948	0	0,14,0,34033	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749406	23604	PASS	C	A	25021	0.941449	0	16,0,24984,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749406	23709	PASS	C	T	25014	0.936955	0	0,12,12,24949	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749406	23816	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	53740	4.65E-4	13	28701,25014,8,17	HIGH	NONE	FRAME_SHIFT	S	ttg/	L753	S	0.000334	0.080808	2	2	CT>C
ERR5749406	24506	PASS	T	G	29318	0.973156	0	11,0,29304,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749406	24914	PASS	G	C	51577	0.962464	3	0,2,25693,25851	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749406	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	38376	0.001485	734	38225,30,30,31	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749406	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	38311	6.53E-4	0	38286,0,25,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749406	25904	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	38332	7.57E-4	0	22,38264,0,33	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	tCa/tTa	S171L	orf3a	0.000757	0.83473	1	1	C>T
ERR5749406	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	82386	3.88E-4	0	4,82349,0,32	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749406	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	17299	6.36E-4	0	5,17278,0,11	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749406	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	17297	0.002081	0	3,17251,0,36	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749406	27972	PASS	C	T	18391	0.90441	20	1,1,18241,87	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749406	28048	PASS	G	T	18313	0.923442	0	0,27,2,18274	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749406	28111	PASS	A	G	43236	0.979623	0	6,4,24887,18322	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749406	28270	PASS	TA	T	48254	0.996145	496	195,4,24623,23445	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749406	28280	PASS	G	C	48176	0.933598	40	18,1,24669,23416	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749406	28281	PASS	A	T	48176	0.916535	28	24,6,24655,23421	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749406	28282	PASS	T	A	48180	0.907057	7	21,12,24600,23438	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749406	28881	PASS	G	A	21069	0.769709	9	4,0,10453,10347	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749406	28882	PASS	G	A	21069	0.827234	6	8,3,10548,10308	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749406	28883	PASS	G	C	21070	0.941101	9	0,3,10560,10480	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749406	28977	PASS	C	T	10728	0.930369	0	0,4,1,10708	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749406	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	42086	6.89E-4	96	31354,10666,9,28	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749406	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	62276	9.63E-4	0	31266,30895,41,39	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749407	241	PASS	C	T	16408	0.863481	0	0,1,8166,8178	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749407	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	13042	0.001994	0	13015,6,26,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749407	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	13061	0.001148	0	12961,25,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749407	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	13061	0.003675	0	12961,25,48,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749407	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	13055	0.002758	5	11982,30,902,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749407	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	13055	0.001838	0	13001,30,24,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749407	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATGGTTG	T	13055	0.001532	48	13004,28,17,3	HIGH	NONE	FRAME_SHIFT	ORF1ab	atggttgag/	MVE85	leader	0.000587	0.476744	4	1	TATGGTTG>T
ERR5749407	556	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13068	0.003214	0	31,12973,0,55	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y97	leader	0.001497	0.173414	1	1	C>T
ERR5749407	657	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13059	0.001532	0	3,13028,0,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A131V	leader	0.001202	0.365979	3	1	C>T
ERR5749407	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	39697	5.79E-4	25	26618,13056,22,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749407	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	39697	0.001411	2	26593,13037,40,16	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749407	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26629	0.001127	0	0,26569,0,30	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749407	913	PASS	C	T	26629	0.914905	0	0,14,0,26572	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749407	1573	PASS	A	G	65	0.215385	134	0,48,14,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acA/acG	T256	nsp2	0.001231	0.75	1	1	A>G
ERR5749407	1684	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26220	0.001373	0	26169,0,39,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I293	nsp2	0.000638	0.973136	2	2	C>T
ERR5749407	2232	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	20028	4.99E-4	16	19975,42,9,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	tgt/	C477	nsp2	0.000499	0.381237	2	2	CT>C
ERR5749407	2453	PASS	C	T	19951	0.736956	0	0,11,0,19667	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L550F	nsp2	0.00429	0.842201	2	2	C>T
ERR5749407	2509	PASS	C	T	19993	0.949382	290	9,7,0,19953	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P568	nsp2	0.001408	0.949382	1	1	C>T
ERR5749407	2702	PASS	T	G	107	0.205607	49	9,24,0,74	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F633V	nsp2	0.000632	0.333333	1	1	T>G
ERR5749407	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	24270	0.003008	0	9,22768,0,1468	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749407	3037	PASS	C	T	27151	0.820964	57	0,19,13561,13392	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749407	3267	PASS	C	T	24631	0.97016	0	4,0,24605,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749407	4002	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27004	0.001296	0	0,26914,0,44	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T428I	nsp3	0.001296	0.806154	2	1	C>T
ERR5749407	4136	PASS	G	T	51936	0.974623	1	4,3,24827,27051	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Ttt	V473F	nsp3	0.00075	0.974623	4	2	G>T
ERR5749407	5170	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	17179	6.4E-4	0	3,17167,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T819	nsp3	0.000565	0.894036	2	2	CCA>C
ERR5749407	5388	PASS	C	A	7217	0.957323	0	1,0,7211,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749407	5986	PASS	C	T	18003	0.975004	2147483647	0,0,17987,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749407	6813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	46232	0.001082	0	29025,17112,33,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T1365I	nsp3	0.001082	0.95799	2	1	C>T
ERR5749407	6954	PASS	T	C	29004	0.821094	29	1,15,1,28836	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749407	7070	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	51591	6.98E-4	72	22455,29084,40,9	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggc/Tgc	G1451C	nsp3	0.000698	0.101434	3	1	G>T
ERR5749407	7564	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	20480	5.86E-4	0	0,20467,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/	Y1617	nsp3	0.000586	0.056194	4	2	CT>C
ERR5749407	7764	PASS	C	T	27355	0.962895	0	4,0,27321,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCc/tTc	S1682F	nsp3	0.001052	0.964731	1	1	C>T
ERR5749407	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	35524	0.00107	80	21629,13857,38,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749407	10323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	25045	9.58E-4	0	0,24961,0,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749407	10702	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	45402	3.96E-4	0	19860,25524,8,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	agg/	R217	3Cpro	0.000396	0.098214	2	2	CAG>C
ERR5749407	10704	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	45402	7.71E-4	8	19834,25483,18,36	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aGg/aTg	R217M	3Cpro	0.000771	0.158537	2	1	G>T
ERR5749407	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	31152	0.001509	0	31063,0,67,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749407	11287	PASS	GTCTGGTTTT	G	31154	0.997272	0	0,85,0,31069	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749407	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	47922	7.09E-4	0	29300,18552,22,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749407	11824	PASS	C	T	29333	0.067705	0	0,27159,0,2150	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I284	nsp6	0.000465	0.922016	2	2	C>T
ERR5749407	12125	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	23654	0.001057	0	4,23544,0,32	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y12H	nsp8	0.000847	0.113436	1	1	T>C
ERR5749407	12269	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	31524	5.08E-4	0	31509,0,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aag/	K61	nsp8	0.000434	0.213333	2	1	GA>G
ERR5749407	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	26489	0.001095	0	26431,0,30,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749407	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	45739	0.001028	1	22836,22772,25,27	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749407	14216	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21124	0.006249	0	4,20973,0,135	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T259I	RdRp	0.006249	0.962929	1	1	C>T
ERR5749407	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	18741	0.004802	2147483647	18255,199,6,274	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749407	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	36332	0.001239	0	18214,18096,23,22	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749407	14408	PASS	C	T	36332	0.852912	14	1,7,18130,17932	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749407	14676	PASS	C	T	18737	0.832204	0	8,0,18692,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749407	14688	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	18737	5.34E-4	0	18727,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K417	RdRp	0.000534	0.979772	2	2	CA>C
ERR5749407	15026	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAT	C	25829	5.03E-4	0	25816,1,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tataca/	YT530	RdRp	0.000503	0.869455	2	2	CAT>C
ERR5749407	15279	PASS	C	T	30471	0.887861	0	5,0,30420,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749407	16176	PASS	T	C	27548	0.981559	0	1,1,12473,15057	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749407	16508	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	30333	0.003989	0	30161,20,152,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGt/gTt	G91V	helicase	0.000561	0.074909	2	2	G>T
ERR5749407	17865	PASS	T	C	36365	0.861515	0	8,9,18429,17779	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taT/taC	Y543	helicase	0.850012	0.861515	1	1	T>C
ERR5749407	19328	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	26146	4.59E-4	0	26125,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F431	ExoN	0.000459	0.937906	4	2	CT>C
ERR5749407	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	35629	0.002105	0	35519,0,78,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749407	20578	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	17931	0.001617	0	17882,0,46,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtg/Ttg	V320L	endoR	0.00085	0.958277	3	1	G>T
ERR5749407	20786	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	17955	0.001392	687	0,17902,24,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAt/aTt	N43I	MethTr	0.001392	1	1	1	A>T
ERR5749407	20925	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	29316	0.003036	0	29206,0,104,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L89F	MethTr	0.001064	0.136967	2	1	G>T
ERR5749407	20987	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	58441	3.59E-4	0	29250,29170,11,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L111	MethTr	0.000276	0.056129	4	2	CT>C
ERR5749407	21194	PASS	A	G	41759	0.967815	0	2,0,41720,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gAt/gGt	D179G	MethTr	0.967815	0.967815	1	1	A>G
ERR5749407	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	41738	8.39E-4	1	20477,20828,18,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749407	21764	PASS	ATACATG	A	17801	0.996629	0	59,0,17741,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749407	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	17801	6.18E-4	0	17790,0,11,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749407	21981	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTTTGGGTGTTTA	T	17812	0.001347	0	9,17779,0,24	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	ttgggtgtttattac/tac	LGVYY141Y	S	0.000895	0.991703	2	1	TTTTGGGTGTTTA>T
ERR5749407	21990	PASS	TTTA	T	17812	0.995845	0	0,74,9,17729	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749407	22290	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	30865	3.89E-4	0	2,30851,0,12	HIGH	NONE	FRAME_SHIFT	S	tta/	L244	S	0.000389	0.578006	2	2	CT>C
ERR5749407	22295	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	44430	7.88E-4	5	13552,30820,8,29	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Cat/Tat	H245Y	S	0.000662	0.930915	2	2	C>T
ERR5749407	22483	PASS	T	C	26528	0.921102	3	1,0,13030,13462	LOW	SILENT	SYNONYMOUS_CODING	S	acT/acC	T307	S	0.001987	0.921102	2	2	T>C
ERR5749407	22690	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	20366	9.82E-4	0	20027,6,23,0	LOW	SILENT	SYNONYMOUS_CODING	S	acT/acC	T376	S	0.000815	0.051311	2	1	T>C
ERR5749407	22716	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	40652	7.38E-4	9	20276,20245,53,70	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCt/aAt	T385N	S	0.000738	0.865911	1	1	C>A
ERR5749407	22717	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	40652	8.36E-4	2	20257,20268,18,23	LOW	SILENT	SYNONYMOUS_CODING	S	acT/acC	T385	S	0.000395	0.918478	3	2	T>C
ERR5749407	23063	PASS	A	T	20062	0.866614	0	0,4,0,19967	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749407	23271	PASS	C	A	28671	0.922326	0	4,0,28626,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749407	23403	PASS	A	G	28669	0.972688	0	0,3,0,28640	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749407	23604	PASS	C	A	21242	0.949769	0	15,0,21214,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749407	23709	PASS	C	T	21228	0.941775	0	0,9,1,21192	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749407	24506	PASS	T	G	28609	0.973715	0	8,0,28593,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749407	24914	PASS	G	C	51191	0.96052	3	0,2,25505,25647	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749407	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	23460	0.001705	837	23364,13,11,32	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749407	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	23501	5.11E-4	0	23489,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749407	25782	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23494	0.001149	0	23388,3,27,0	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	tgC/tgT	C130	orf3a	0.000916	0.955348	1	1	C>T
ERR5749407	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	23683	0.001267	950	23340,164,80,66	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749407	26060	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	58813	7.14E-4	0	58722,0,52,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aCt/aTt	T223I	orf3a	0.000459	0.822477	2	2	C>T
ERR5749407	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	58704	4.77E-4	0	1,58674,0,28	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749407	26526	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	17220	0.002671	0	1,17147,0,62	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Gca/Tca	A2S	M	0.001224	0.951192	3	1	G>T
ERR5749407	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	17653	0.002436	0	0,17606,0,43	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749407	27603	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	31979	0.036399	0	30678,3,1268,0	LOW	SILENT	SYNONYMOUS_CODING	ORF7a	ggC/ggT	G70	orf7a	0.002411	0.959582	1	1	C>T
ERR5749407	27972	PASS	C	T	15246	0.904959	35	2,2,15086,104	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749407	28048	PASS	G	T	15155	0.918179	0	0,22,0,15123	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749407	28111	PASS	A	G	45817	0.978458	3	5,4,30636,15154	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749407	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30634	0.002089	0	30484,16,67,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749407	28270	PASS	TA	T	59405	0.994765	747	311,10,30211,28883	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749407	28280	PASS	G	C	59279	0.937887	15	16,5,30276,28851	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749407	28281	PASS	A	T	59279	0.918504	63	43,7,30260,28857	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749407	28282	PASS	T	A	59284	0.910667	18	38,18,30225,28878	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749407	28881	PASS	G	A	18918	0.788667	6	5,1,9399,9304	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749407	28882	PASS	G	A	18917	0.832902	9	6,1,9468,9299	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749407	28883	PASS	G	C	18917	0.94497	9	0,3,9482,9411	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749407	28977	PASS	C	T	9625	0.908156	0	0,3,0,9597	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749407	29095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	40836	0.001004	0	40753,0,43,0	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F274	N	0.000792	0.961279	2	2	C>T
ERR5749407	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	81114	0.00127	0	40694,40247,66,63	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749407	29543	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	26040	0.002957	6	12694,13213,68,57	.	.	.	.	.	.	.	0.001058	0.973475	3	1	G>T
ERR5749407	29733	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12762	0.002429	0	0,12718,0,31	.	.	.	.	.	.	.	0.001821	0.915943	2	1	C>T
ERR5749407	29779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	12763	0.001489	0	0,12729,0,29	.	.	.	.	.	.	.	0.001489	0.975228	1	1	G>T
ERR5749408	241	PASS	C	T	24	0.791667	0	0,0,12,12	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749408	597	PASS	T	G	36	0.333333	0	0,23,0,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gTg/gGg	V111G	leader	0.000983	0.333333	2	2	T>G
ERR5749408	635	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	36	0.111111	0	0,30,0,6	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgt/Tgt	R124C	leader	0.00148	0.880435	1	1	C>T
ERR5749408	913	PASS	C	T	423	0.917258	0	0,0,1,421	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749408	1234	PASS	TG	T	238	0.159664	0	0,200,0,38	HIGH	NONE	FRAME_SHIFT	ORF1ab	gat/	D144	nsp2	0.159664	0.159664	1	1	TG>T
ERR5749408	1685	PASS	G	T	186	0.231183	0	143,0,43,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gcc/Tcc	A294S	nsp2	0.001379	0.231183	3	2	G>T
ERR5749408	2779	PASS	T	C	375	0.16	0	0,311,0,64	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	agT/agC	S20	nsp3	0.003967	0.16	2	2	T>C
ERR5749408	2805	PASS	A	T	375	0.173333	0	0,305,0,69	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gAa/gTa	E29V	nsp3	0.001648	0.173333	2	1	A>T
ERR5749408	3037	PASS	C	T	159	0.855346	0	0,0,80,79	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749408	3267	PASS	C	T	218	0.954128	2147483647	0,0,217,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749408	4701	PASS	C	T	290	0.086207	0	265,0,25,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCa/tTa	S661L	nsp3	0.086207	0.086207	1	1	C>T
ERR5749408	5388	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	5	1.0	2147483647	0,0,5,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749408	5986	PASS	C	T	117	0.974359	2147483647	0,0,117,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749408	6516	PASS	TAA	T	430	0.186047	176	156,194,0,80	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaaatt/	KI1267	nsp3	0.000479	0.186047	4	2	TAA>T
ERR5749408	6741	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	189	0.031746	0	0,183,0,6	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cGg/cTg	R1341L	nsp3	0.001093	0.204082	3	2	G>T
ERR5749408	6954	PASS	T	C	142	0.84507	2147483647	0,0,0,142	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749408	7355	PASS	CTTATG	C	289	0.134948	0	249,1,39,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cttatgtgg/	LMW1546	nsp3	0.134948	0.134948	1	1	CTTATG>C
ERR5749408	8796	PASS	G	T	60	0.25	0	22,21,8,9	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aGt/aTt	S81I	nsp4	0.000257	0.25	2	2	G>T
ERR5749408	9060	PASS	ATTG	A	510	0.433333	3	289,0,220,1	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	tgttat/tat	CY170Y	nsp4	0.000621	0.433333	5	2	ATTG>A
ERR5749408	9165	PASS	C	T	509	0.253438	0	0,374,0,135	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCc/aTc	T204I	nsp4	0.00112	0.253438	1	1	C>T
ERR5749408	11287	PASS	GTCTGGTTTT	G	1405	0.998577	0	0,2,0,1403	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749408	12257	PASS	C	T	151	0.231788	0	111,0,39,0	HIGH	NONSENSE	STOP_GAINED	ORF1ab	Caa/Taa	Q56*	nsp8	0.231788	0.231788	1	1	C>T
ERR5749408	12269	PASS	GA	G	150	0.213333	0	118,0,32,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aag/	K61	nsp8	0.000434	0.213333	2	1	GA>G
ERR5749408	12273	PASS	A	T	150	0.2	0	111,0,32,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aTg	K61M	nsp8	0.000778	0.2	3	2	A>T
ERR5749408	13004	PASS	G	C	41	0.292683	0	0,29,0,12	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gct/Cct	A107P	nsp9	0.292683	0.292683	1	1	G>C
ERR5749408	13134	PASS	CA	C	1320	0.107576	0	1178,0,142,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	atc/	I38	nsp10	0.000682	0.107576	2	2	CA>C
ERR5749408	13162	PASS	TAC	T	1320	0.198485	0	1058,0,262,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749408	13290	PASS	T	G	1320	0.107576	0	0,1176,0,143	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTt/tGt	F89C	nsp10	0.029154	0.107576	2	1	T>G
ERR5749408	14168	PASS	CTA	C	127	0.314961	0	0,87,0,40	HIGH	NONE	FRAME_SHIFT	ORF1ab	atatta/	IL244	RdRp	0.000479	0.314961	1	1	CTA>C
ERR5749408	14408	PASS	C	T	82	0.792683	0	0,0,41,41	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749408	14676	PASS	C	T	150	0.866667	2147483647	0,0,150,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749408	14766	PASS	T	A	217	0.317972	157	68,74,0,75	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttT/ttA	F442L	RdRp	0.00286	0.317972	2	2	T>A
ERR5749408	15279	PASS	C	T	165	0.848485	2147483647	0,0,164,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749408	15289	PASS	TG	T	165	0.157576	0	139,0,26,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gat/	D618	RdRp	0.000698	0.157576	2	1	TG>T
ERR5749408	16176	PASS	T	C	235	0.974468	2147483647	0,0,0,235	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749408	16439	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	316	0.028481	0	3,304,0,9	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTg/aAg	M68K	helicase	0.016667	0.054348	1	1	T>A
ERR5749408	16508	PASS	G	T	1375	0.074909	0	1267,0,108,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGt/gTt	G91V	helicase	0.000561	0.074909	2	2	G>T
ERR5749408	16794	PASS	T	C	1314	0.077626	166	387,821,0,105	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	cgT/cgC	R186	helicase	0.000354	0.077626	2	2	T>C
ERR5749408	16837	PASS	GAA	G	387	0.100775	0	348,0,39,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GAA>G
ERR5749408	17167	PASS	C	T	84	0.238095	0	63,0,21,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cat/Tat	H311Y	helicase	0.001728	0.238095	1	1	C>T
ERR5749408	18722	PASS	A	T	1613	0.409175	0	873,0,739,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cAt/cTt	H228L	ExoN	0.409175	0.409175	1	1	A>T
ERR5749408	19329	PASS	T	C	332	0.228916	0	256,0,76,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcC	A430	ExoN	0.001217	0.228916	1	1	T>C
ERR5749408	20853	PASS	G	C	580	0.198276	151	328,132,120,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atC	M65I	MethTr	0.000856	0.198276	2	1	G>C
ERR5749408	21094	PASS	AAAGAGGGTTTT	A	450	0.211111	0	0,355,0,95	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaagagggtttt/	KEGF146	MethTr	0.000554	0.211111	5	2	AAAGAGGGTTTT>A
ERR5749408	21569	PASS	G	GT	947	0.091869	283	475,382,0,87	HIGH	NONE	FRAME_SHIFT	S	ctt/Tctt	L5S?	S	0.000394	0.091869	4	1	G>GT
ERR5749408	21575	PASS	C	T	848	0.120283	184	359,362,12,113	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749408	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	847	0.015348	30	373,461,0,13	HIGH	NONE	FRAME_SHIFT	S	gtt/Tgtt	V6C?	S	0.000619	0.877942	3	2	C>CT
ERR5749408	21764	PASS	ATACATG	A	471	0.997877	0	1,0,470,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749408	21990	PASS	TTTA	T	483	0.975155	0	0,13,0,471	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749408	22014	PASS	G	C	1005	0.20398	0	780,0,224,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aGt/aCt	S151T	S	0.001357	0.20398	2	1	G>C
ERR5749408	22091	PASS	A	G	904	0.144911	0	764,0,140,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Atg/Gtg	M177V	S	0.144911	0.144911	1	1	A>G
ERR5749408	22293	PASS	TA	T	1408	0.160511	483	504,678,0,226	HIGH	NONE	FRAME_SHIFT	S	tta/	L244	S	0.000308	0.160511	4	1	TA>T
ERR5749408	22413	PASS	C	T	504	0.204365	0	383,0,117,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCc/aTc	T284I	S	0.204365	0.204365	1	1	C>T
ERR5749408	23063	PASS	A	T	544	0.854779	2147483647	0,0,0,540	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749408	23271	PASS	C	A	551	0.916515	2147483647	0,0,551,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749408	23403	PASS	A	G	552	0.976449	2147483647	0,0,0,552	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749408	23604	PASS	C	A	622	0.927653	0	2,0,620,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749408	23606	PASS	C	T	622	0.064309	0	575,0,46,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Cgg/Tgg	R682W	S	0.001401	0.064309	2	2	C>T
ERR5749408	23709	PASS	C	T	622	0.934084	2147483647	0,0,0,622	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749408	24320	PASS	CAA	C	318	0.138365	0	0,274,0,44	HIGH	NONE	FRAME_SHIFT	S	aaa/	K921	S	0.000763	0.138365	4	2	CAA>C
ERR5749408	24506	PASS	T	G	242	0.983471	2147483647	0,0,242,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749408	24704	PASS	C	T	265	0.173585	0	0,213,0,52	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Cat/Tat	H1048Y	S	0.00125	0.173585	1	1	C>T
ERR5749408	26768	PASS	C	T	418	0.055024	0	0,393,0,25	LOW	SILENT	SYNONYMOUS_CODING	M	atC/atT	I82	M	0.001479	0.055024	1	1	C>T
ERR5749408	26958	PASS	C	T	1823	0.122326	0	1591,0,232,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Cgt/Tgt	R146C	M	0.00096	0.122326	1	1	C>T
ERR5749408	27240	PASS	G	T	1243	0.117458	0	1082,0,161,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF6	gaG/gaT	E13D	orf6	0.000521	0.117458	2	2	G>T
ERR5749408	27340	PASS	A	G	2478	0.110573	0	1080,1080,158,158	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF6	Aat/Gat	N47D	orf6	0.000451	0.25	2	2	A>G
ERR5749408	27972	PASS	C	T	134	0.925373	2147483647	0,0,134,0	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749408	28048	PASS	G	T	135	0.911111	2147483647	0,0,0,135	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749408	28095	PASS	A	T	137	0.19708	0	0,110,0,27	HIGH	NONSENSE	STOP_GAINED	ORF8	Aaa/Taa	K68*	orf8	0.002672	0.967672	2	2	A>T
ERR5749408	28111	PASS	A	G	135	0.977778	2147483647	0,0,0,135	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749408	28253	PASS	C	T	3525	0.157447	0	2923,0,593,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749408	28270	PASS	TA	T	6212	0.999034	7	3,3,1521,4685	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749408	28280	PASS	G	C	6212	0.933838	3	1,1,1523,4677	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749408	28281	PASS	A	T	6212	0.927721	8	2,1,1521,4680	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749408	28282	PASS	T	A	6212	0.949936	0	0,3,1521,4682	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749408	28292	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	6586	0.001518	1	1532,5044,3,7	HIGH	NONE	FRAME_SHIFT	N	aat/	N8	N	0.000304	0.055324	4	2	CA>C
ERR5749408	28378	PASS	G	C	6597	0.060482	328	1325,4842,208,214	LOW	SILENT	SYNONYMOUS_CODING	N	gcG/gcC	A35	N	0.001609	0.060482	3	1	G>C
ERR5749408	28881	PASS	G	A	34	0.794118	0	0,0,18,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749408	28882	PASS	G	A	34	0.911765	0	0,0,18,15	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749408	28883	PASS	G	C	34	0.911765	0	0,0,18,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749408	28977	PASS	C	T	18	0.944444	2147483647	0,0,0,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749408	29348	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	1146	0.011344	88	231,902,13,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gca/Tca	A359S	N	0.000865	0.968413	2	1	G>T
ERR5749408	29520	PASS	C	T	463	0.073434	5	206,221,14,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCa/tTa	S416L	N	0.001999	0.073434	1	1	C>T
ERR5749409	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	8368	0.002749	0	8328,15,23,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749409	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	8368	0.001912	0	8219,15,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749409	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	8368	0.001076	0	8219,15,9,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749409	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGT	G	8368	0.005497	0	8219,15,46,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggtt/	GHVMV82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGT>G
ERR5749409	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	8368	0.00717	0	8219,15,60,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749409	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	8356	0.001556	2	7637,15,512,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749409	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	8356	0.001915	0	8325,15,16,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749409	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGT	G	8356	0.001197	17	8315,14,9,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGT>G
ERR5749409	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	8356	0.001436	0	8315,14,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749409	521	PASS	G	T	8357	0.731722	0	110,0,7964,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Ttt	V86F	leader	0.00063	0.731722	2	2	G>T
ERR5749409	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	23691	7.6E-4	22	15300,8369,17,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749409	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	23691	0.002448	35	15257,8361,50,8	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749409	2110	PASS	C	T	17659	0.811371	0	0,9,0,17542	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N435	nsp2	0.024426	0.811371	1	1	C>T
ERR5749409	4529	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTTTACTTTTACACCAGTAAAACAAC	T	13423	0.001117	0	6,13396,0,15	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttttacttttacaccagtaaaacaact/	FYFYTSKTT604	nsp3	0.000527	0.402778	3	1	TTTTACTTTTACACCAGTAAAACAAC>T
ERR5749409	7070	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	27748	0.004217	530	9506,18113,119,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggc/Agc	G1451S	nsp3	0.000698	0.101434	3	1	G>A
ERR5749409	8605	PASS	C	T	10300	0.9	99	3,3,0,10275	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F17	nsp4	0.9	0.9	1	1	C>T
ERR5749409	8796	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	15601	6.41E-4	0	7802,7789,5,5	HIGH	NONE	FRAME_SHIFT	ORF1ab	tat/	Y82	nsp4	0.000257	0.25	2	2	GT>G
ERR5749409	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	17725	0.001636	31	13625,4071,29,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749409	9891	PASS	C	T	5959	0.957208	0	1,0,5951,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A446V	nsp4	0.002963	0.958011	1	1	C>T
ERR5749409	10201	PASS	G	T	17307	0.126654	0	15062,4,2237,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atT	M49I	3Cpro	0.018462	0.126654	2	1	G>T
ERR5749409	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19496	0.00159	0	19436,0,38,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749409	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	19486	0.003541	0	19391,0,87,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749409	11199	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	38785	8.77E-4	0	19300,19318,18,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCc/gTc	A76V	nsp6	0.000309	0.056758	3	2	C>T
ERR5749409	11230	PASS	G	T	19470	0.937083	0	0,12,9,19439	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atT	M86I	nsp6	0.937083	0.937083	1	1	G>T
ERR5749409	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	29438	8.49E-4	16	17904,11493,23,5	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749409	11674	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17947	0.001059	0	17916,8,20,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y234	nsp6	0.00054	0.985782	3	2	C>T
ERR5749409	12125	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	17953	0.001337	0	5,17872,0,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y12H	nsp8	0.000847	0.113436	1	1	T>C
ERR5749409	12970	PASS	C	T	12091	0.85973	0	0,2,0,12059	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N95	nsp9	0.8352	0.861883	1	1	C>T
ERR5749409	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	14010	8.57E-4	0	13998,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749409	13468	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	15309	0.001894	0	15256,0,35,0	LOW	SILENT	SPLICE_SITE_REGION+SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N9	RdRp	0.000713	0.076498	2	2	C>T
ERR5749409	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30579	0.001831	0	15261,15220,31,32	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749409	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	2816	0.004972	836	2723,39,1,52	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749409	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	18623	0.001665	0	18588,0,31,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749409	17749	PASS	G	C	11860	0.987943	40	0,1,11847,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gct/Cct	A505P	helicase	0.001521	0.987943	4	2	G>C
ERR5749409	17964	PASS	G	T	11857	0.846335	0	0,26,0,11823	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	atG/atT	M576I	helicase	0.002203	0.846335	1	1	G>T
ERR5749409	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	25539	4.7E-4	0	25527,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749409	19426	PASS	A	G	17609	0.883469	0	0,3,163,17374	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ata/Gta	I463V	ExoN	0.883469	0.883469	1	1	A>G
ERR5749409	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18368	0.002831	0	18303,0,53,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749409	20091	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	18338	4.91E-4	0	0,18329,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	caa/Acaa	Q159T?	endoR	0.000368	0.051583	1	1	C>CA
ERR5749409	20578	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	28232	8.5E-4	0	28170,0,60,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtg/Ttg	V320L	endoR	0.00085	0.958277	3	1	G>T
ERR5749409	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28227	0.001134	0	28157,0,32,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749409	21069	PASS	A	G	20024	0.923692	0	0,3,0,19965	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaA/aaG	K137	MethTr	0.923692	0.923692	1	1	A>G
ERR5749409	21255	PASS	G	T	28433	0.901628	1412	67,64,28256,16	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcG/gcT	A199	MethTr	0.000341	0.917425	4	2	G>T
ERR5749409	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	27112	5.9E-4	3	13532,13565,6,10	HIGH	NONE	FRAME_SHIFT	S	ctt/Tctt	L5S?	S	0.000394	0.091869	4	1	G>GT
ERR5749409	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27079	0.00277	1	13235,13460,42,46	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749409	21981	PASS	TTTTG	T	12294	0.991703	0	0,91,9,12183	HIGH	NONE	FRAME_SHIFT	S	tttttg/	FL140	S	0.000895	0.991703	2	1	TTTTG>T
ERR5749409	21981	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTTTGGGTGTTTA	T	12294	8.95E-4	0	0,91,0,11	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	ttgggtgtttattac/tac	LGVYY141Y	S	0.000895	0.991703	2	1	TTTTGGGTGTTTA>T
ERR5749409	21990	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTTA	T	12294	7.32E-4	0	9,12276,0,9	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749409	21991	PASS	TTA	T	12294	0.991378	0	0,106,9,12179	HIGH	NONE	FRAME_SHIFT	S	tat/	Y144	S	0.00078	0.991378	2	1	TTA>T
ERR5749409	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29886	8.7E-4	0	14381,15445,14,14	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749409	22907	PASS	T	C	14414	0.976342	0	4,0,14398,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tat/Cat	Y449H	S	0.004549	0.976342	1	1	T>C
ERR5749409	23063	PASS	A	T	14391	0.853659	0	0,4,0,14332	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749409	23255	PASS	T	C	19494	0.921001	0	3,0,19457,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ttt/Ctt	F565L	S	0.001637	0.921001	2	1	T>C
ERR5749409	23525	PASS	C	T	14273	0.97751	0	4,0,14261,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Cat/Tat	H655Y	S	0.001101	0.97751	2	2	C>T
ERR5749409	23541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTT	A	14273	9.11E-4	0	14256,2,13,0	HIGH	NONE	FRAME_SHIFT	S	tatgagtgtgacatacccattggtgcaggtatatgcgctagttat/	YECDIPIGAGICASY660	S	0.000911	0.950734	4	2	ATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTT>A
ERR5749409	23817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	25420	9.44E-4	13	11139,14246,6,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTt/cCt	L752P	S	0.000646	0.066832	1	1	T>C
ERR5749409	24127	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAACGGCCTTACTG	T	22174	9.02E-4	60	11010,11148,20,0	HIGH	NONE	FRAME_SHIFT	S	aacggccttactgtt/	NGLTV856	S	0.000324	0.111888	4	1	TAACGGCCTTACTG>T
ERR5749409	25422	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGGAACTGTA	T	18650	6.43E-4	0	18634,0,12,0	MODERATE	NONE	CODON_DELETION	ORF3a	ggaactgta/	GTV11	orf3a	0.000545	0.213989	6	1	TGGAACTGTA>T
ERR5749409	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	8354	0.003352	301	8293,18,13,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749409	25904	PASS	C	T	8356	0.83473	30	1,6,0,8311	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	tCa/tTa	S171L	orf3a	0.000757	0.83473	1	1	C>T
ERR5749409	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	34234	7.89E-4	0	3,34204,0,27	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749409	26767	PASS	T	G	12718	0.968313	0	0,9,27,12668	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	aTc/aGc	I82S	M	0.954318	0.968313	2	1	T>G
ERR5749409	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	G	12705	7.08E-4	0	0,12696,0,9	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/	ACLVGLMWLSYFIASF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT>G
ERR5749409	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	12705	0.001417	0	0,12686,0,18	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749409	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	12706	0.003227	0	0,12660,0,41	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749409	27604	PASS	G	T	19611	0.967671	0	5,0,19539,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Gta/Tta	V71L	orf7a	0.001008	0.967671	3	2	G>T
ERR5749409	27741	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19632	0.00163	0	1,19553,0,35	LOW	SILENT	SYNONYMOUS_CODING	ORF7a	ctC/ctT	L116	orf7a	0.000363	0.954278	3	2	C>T
ERR5749409	28093	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	2631	0.026986	0	10,2543,0,72	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tCt/tTt	S67F	orf8	0.001515	0.967675	1	1	C>T
ERR5749409	28144	PASS	T	C	21034	0.980793	0	6,0,18395,2619	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tTa/tCa	L84S	orf8	0.000989	0.980793	1	1	T>C
ERR5749409	28167	PASS	G	A	18415	0.976595	77	1,2,18410,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	Gaa/Aaa	E92K	orf8	0.976595	0.976595	1	1	G>A
ERR5749409	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	18397	0.001033	0	18376,3,19,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749409	28270	PASS	TA	T	36530	0.986723	82	180,305,18198,17847	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749409	28271	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AA	A	36528	0.002847	39	18305,18122,72,32	.	.	.	.	.	.	.	0.000482	0.924941	3	2	AA>A
ERR5749409	28273	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AA	A	36597	0.00306	111	18353,18134,21,91	HIGH	NONE	FRAME_SHIFT+START_LOST	N	atg/	M1	N	0.000399	0.842333	4	1	AA>A
ERR5749409	28302	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	36685	0.001527	0	18250,18340,28,31	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	cGa/cAa	R10Q	N	0.001527	0.953728	4	2	G>A
ERR5749409	28337	PASS	G	T	18404	0.935503	0	0,9,0,18377	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Tat	D22Y	N	0.001279	0.935503	2	1	G>T
ERR5749409	28878	PASS	G	A	11217	0.658465	0	0,1,5360,5476	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGt/aAt	S202N	N	0.001	0.909986	3	2	G>A
ERR5749409	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	36691	8.45E-4	184	31012,5621,5,29	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749409	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	61645	7.3E-4	1	30951,30594,30,26	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749409	29739	PASS	C	T	8441	0.706433	0	0,6,0,8350	.	.	.	.	.	.	.	0.001961	0.706433	1	1	C>T
ERR5749409	29742	PASS	G	A	8441	0.847293	0	0,4,0,8404	.	.	.	.	.	.	.	0.847293	0.931288	2	1	G>A
ERR5749409	29747	PASS	G	T	8441	0.951309	0	0,8,0,8432	.	.	.	.	.	.	.	0.006376	0.951309	2	1	G>T
ERR5749410	193	PASS	C	T	9490	0.823815	2147483647	0,0,9447,0	.	.	.	.	.	.	.	0.823815	0.866477	1	1	C>T
ERR5749410	241	PASS	C	T	18905	0.874425	0	1,2,9402,9455	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749410	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	15728	0.001335	0	15702,6,21,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749410	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	15728	5.72E-4	0	15650,6,9,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749410	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	15728	0.003433	0	15650,6,54,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749410	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	15720	0.002099	0	14464,11,1116,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749410	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	15720	9.54E-4	0	15693,12,15,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749410	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	15717	6.36E-4	0	15690,12,10,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttatg/gtg	VM84V	leader	0.000554	0.991848	4	1	GTTA>G
ERR5749410	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	43765	9.37E-4	24	27959,15752,35,6	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749410	913	PASS	C	T	27996	0.925454	0	0,8,0,27951	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749410	1510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	30113	0.002159	0	0,29751,0,72	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G235	nsp2	0.002159	0.937304	1	1	T>C
ERR5749410	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	106938	0.001057	2147483647	53391,50126,88,3065	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749410	3037	PASS	C	T	26610	0.817024	50	4,28,13276,13101	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749410	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	13441	0.002455	917	7,13395,34,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749410	3267	PASS	C	T	27446	0.969358	0	2,0,27428,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749410	5388	PASS	C	A	9778	0.95858	2147483647	0,0,9773,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749410	5986	PASS	C	T	18125	0.974566	0	2,0,18103,2	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749410	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16757	0.001492	0	2,16574,0,32	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749410	6954	PASS	T	C	33505	0.820892	0	0,6,1,33352	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749410	7926	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAA	C	28227	5.31E-4	0	0,28209,0,15	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1737	nsp3	0.000531	0.97019	5	2	CAA>C
ERR5749410	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	41818	9.33E-4	110	21744,20035,39,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749410	9962	PASS	C	T	11692	0.114523	0	10298,1,1381,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cat/Tat	H470Y	nsp4	0.003186	0.114523	1	1	C>T
ERR5749410	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	27074	0.001995	0	26339,4,54,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749410	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	27060	0.001663	0	26969,0,75,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749410	11287	PASS	GTCTGGTTTT	G	27060	0.998004	0	0,54,0,27006	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749410	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	49282	8.32E-4	3	28418,20777,31,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749410	12269	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	32282	4.34E-4	0	32268,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aag/	K61	nsp8	0.000434	0.213333	2	1	GA>G
ERR5749410	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	24579	0.001017	0	24528,0,25,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749410	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	57278	8.73E-4	0	28607,28534,26,26	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749410	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	15617	0.003586	2147483647	15214,165,6,223	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749410	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	30326	0.001187	0	15197,15110,18,18	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749410	14408	PASS	C	T	30326	0.844589	1	4,5,15118,14969	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749410	14676	PASS	C	T	19336	0.741208	0	12,0,19238,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749410	15279	PASS	C	T	31714	0.904742	0	11,0,31670,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749410	15371	PASS	C	T	63149	0.772332	6	10,16,31436,31126	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aTg	T644M	RdRp	0.00056	0.786959	4	2	C>T
ERR5749410	16176	PASS	T	C	30551	0.980263	0	0,0,14446,16089	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749410	17615	PASS	A	G	20804	0.922467	0	0,0,4,20750	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K460R	helicase	0.001492	0.938608	2	1	A>G
ERR5749410	18647	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	68703	6.4E-4	5	31037,37599,24,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P203L	ExoN	0.000283	0.970507	4	2	C>T
ERR5749410	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	33699	4.45E-4	0	3,33681,0,15	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749410	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	40043	0.002123	0	39919,0,88,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749410	21305	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	42635	7.27E-4	0	1,42536,0,34	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cGc/cAc	R216H	MethTr	0.000727	0.703943	1	1	G>A
ERR5749410	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	46503	7.1E-4	2	22810,23189,18,23	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749410	21764	PASS	ATACATG	A	17812	0.996856	0	55,0,17756,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749410	21990	PASS	TTTA	T	17820	0.998036	0	0,35,6,17779	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749410	23063	PASS	A	T	42	0.857143	2147483647	0,0,0,42	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749410	23122	PASS	A	T	58	0.155172	91	0,41,10,1	LOW	SILENT	SYNONYMOUS_CODING	S	gcA/gcT	A520	S	0.002483	0.155172	2	1	A>T
ERR5749410	23271	PASS	C	A	29190	0.922679	2147483647	0,0,29155,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749410	23403	PASS	A	G	29184	0.973136	0	0,13,0,29149	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749410	23604	PASS	C	A	21132	0.965645	0	10,0,21109,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749410	23709	PASS	C	T	21111	0.939463	0	0,8,4,21069	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749410	24506	PASS	T	G	26930	0.975938	0	10,0,26913,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749410	24914	PASS	G	C	46838	0.957897	0	0,0,23331,23486	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749410	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	36052	8.6E-4	71	22673,13329,36,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749410	25626	PASS	C	T	55360	0.73815	0	10,6,32359,22834	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	caC/caT	H78	orf3a	0.000403	0.915633	3	2	C>T
ERR5749410	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	32550	0.001137	633	32436,17,14,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749410	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	32517	6.15E-4	0	32495,0,20,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749410	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	32705	0.001162	1131	32147,198,215,90	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749410	26193	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	67201	0.002649	0	0,66984,0,182	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	ccG/ccA	P267	orf3a	0.002649	0.051188	1	1	G>A
ERR5749410	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	16577	0.001568	0	39,16511,0,26	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749410	26895	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	47872	0.001358	0	47774,6,66,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Cat/Tat	H125Y	M	0.000874	0.97046	1	1	C>T
ERR5749410	27459	PASS	G	T	24745	0.90782	2147483647	782,10,449,23501	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	gaG/gaT	E22D	orf7a	0.002024	0.943812	1	1	G>T
ERR5749410	27534	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	1240	0.009677	273	1227,1,0,12	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	caT/caA	H47Q	orf7a	0.002615	0.933333	2	2	T>A
ERR5749410	27972	PASS	C	T	15476	0.894805	90	5,5,15343,75	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749410	28048	PASS	G	T	15419	0.92172	0	0,20,0,15393	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749410	28093	PASS	C	T	15437	0.967675	238	7,1,1,15408	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tCt/tTt	S67F	orf8	0.001515	0.967675	1	1	C>T
ERR5749410	28111	PASS	A	G	37311	0.977594	0	5,4,21871,15424	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749410	28270	PASS	TA	T	42444	0.994699	544	224,7,21561,20658	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749410	28280	PASS	G	C	42358	0.936092	21	13,2,21625,20639	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749410	28281	PASS	A	T	42358	0.915954	23	20,5,21616,20645	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749410	28282	PASS	T	A	42361	0.908996	2	16,12,21590,20653	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749410	28881	PASS	G	A	23164	0.76144	24	12,1,11416,11408	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749410	28882	PASS	G	A	23161	0.828462	6	8,3,11558,11365	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749410	28883	PASS	G	C	23162	0.941844	0	2,2,11581,11548	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749410	28977	PASS	C	T	11818	0.926637	0	0,3,0,11793	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749410	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	45552	7.02E-4	129	33702,11780,7,33	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749410	29095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	33721	0.002076	0	33626,0,72,0	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F274	N	0.000792	0.961279	2	2	C>T
ERR5749410	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	66963	0.001195	0	33634,33223,45,43	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749411	241	PASS	C	T	11537	0.861316	0	0,1,5733,5739	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749411	292	PASS	C	T	5794	0.940456	2147483647	0,0,0,5787	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N9	leader	0.939339	0.96124	1	1	C>T
ERR5749411	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	14538	0.005709	0	14455,8,83,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749411	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	14544	0.001788	0	14319,12,26,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749411	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	14544	0.002063	34	14319,12,28,2	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749411	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	14544	0.009007	0	14319,12,131,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749411	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTTGA	G	14544	0.001238	0	14319,12,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTTGA>G
ERR5749411	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	14543	0.002132	3	13179,23,977,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749411	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	14543	0.003851	10	14462,25,55,1	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749411	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	14542	0.001307	0	14466,27,19,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttatg/gtg	VM84V	leader	0.000554	0.991848	4	1	GTTA>G
ERR5749411	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	14542	0.001719	0	14466,27,25,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749411	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	14547	0.002062	11	14471,32,29,1	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749411	520	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTT	G	14586	8.91E-4	0	14501,72,13,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttgag/gag	VE86E	leader	0.000583	0.051154	1	1	GGTT>G
ERR5749411	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	34288	8.46E-4	29	19706,14547,25,4	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749411	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	34288	0.004375	40	19616,14502,110,40	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749411	913	PASS	C	T	19725	0.91199	0	0,18,0,19675	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749411	1059	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17768	0.00591	0	17648,0,112,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCc/aTc	T85I	nsp2	0.001728	0.920973	1	1	C>T
ERR5749411	3037	PASS	C	T	24562	0.828678	41	1,17,12247,12133	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749411	3267	PASS	C	T	19956	0.971237	0	1,0,19940,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749411	3817	PASS	C	T	36629	0.961943	1	5,2,21512,15097	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D366	nsp3	0.000777	0.972816	2	2	C>T
ERR5749411	5388	PASS	C	A	7550	0.958278	2147483647	0,0,7542,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749411	5392	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	7550	0.020265	0	7382,0,162,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N891	nsp3	0.012876	0.944629	2	2	C>T
ERR5749411	5849	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	20548	0.009198	0	0,20298,0,218	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cct/Tct	P1044S	nsp3	0.00146	0.830206	2	1	C>T
ERR5749411	5986	PASS	C	T	15280	0.973626	2147483647	0,0,15272,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749411	6954	PASS	T	C	23874	0.811887	0	0,5,3,23733	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749411	7058	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	23972	0.001543	0	10,23906,0,38	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggt/Agt	G1447S	nsp3	0.000616	0.910617	2	2	G>A
ERR5749411	7674	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24676	9.32E-4	0	24626,13,23,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCg/gTg	A1652V	nsp3	0.000682	0.109264	3	2	C>T
ERR5749411	8581	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	15189	0.005201	0	0,15083,0,83	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caG/caA	Q9	nsp4	0.005201	0.96131	2	2	G>A
ERR5749411	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	31590	0.001963	117	20123,11405,62,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749411	10323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	22149	0.001806	0	0,22048,0,42	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749411	10798	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12249	0.003021	0	12209,0,38,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D248	3Cpro	0.003021	0.97286	1	1	C>T
ERR5749411	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22684	0.001367	0	22611,9,33,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749411	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	22665	0.002383	0	22566,0,74,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749411	11287	PASS	GTCTGGTTTT	G	22667	0.996118	0	0,88,0,22579	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749411	11339	PASS	C	T	40855	0.968425	6	3,9,18166,22664	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L123	nsp6	0.002071	0.968425	1	1	C>T
ERR5749411	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	40781	9.81E-4	3	22556,18151,26,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749411	12459	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	48664	9.25E-4	14	23790,24819,30,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T123I	nsp8	0.000658	0.986093	1	1	C>T
ERR5749411	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	37004	0.001054	0	18490,18425,21,21	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749411	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	11423	0.004027	2836	11097,131,12,175	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749411	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	22122	0.003029	0	11069,11002,35,32	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749411	14408	PASS	C	T	22122	0.834689	11	2,8,11013,10875	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749411	14676	PASS	C	T	14193	0.681815	0	4,0,14097,1	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749411	15240	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23545	9.34E-4	0	23487,24,22,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N600	RdRp	0.000934	0.931284	2	2	C>T
ERR5749411	15279	PASS	C	T	23521	0.914034	0	4,0,23489,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749411	16176	PASS	T	C	25022	0.980777	0	1,0,13131,11883	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749411	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	29755	6.72E-4	0	29735,0,20,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749411	19029	PASS	C	T	24821	0.693244	0	4,0,24591,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H330	ExoN	0.003777	0.923016	1	1	C>T
ERR5749411	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	31324	0.003001	0	31202,0,99,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749411	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	32072	8.73E-4	0	32004,0,29,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749411	20719	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	32002	0.00275	0	1,31454,0,98	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L21	MethTr	0.000341	0.209091	2	2	C>T
ERR5749411	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34478	0.001537	2	16888,17182,30,36	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749411	21764	PASS	ATACATG	A	15820	0.99488	19	80,1,15738,1	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749411	21990	PASS	TTTA	T	15821	0.997535	44	2,39,2,15780	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749411	22290	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	23167	5.61E-4	0	3,23150,0,13	HIGH	NONE	FRAME_SHIFT	S	tta/	L244	S	0.000389	0.578006	2	2	CT>C
ERR5749411	23063	PASS	A	T	17144	0.862284	0	0,5,4,17052	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749411	23271	PASS	C	A	21374	0.923646	0	2,0,21346,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749411	23403	PASS	A	G	21365	0.967985	0	0,4,2,21341	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749411	23426	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTT	G	21385	6.55E-4	0	4,21365,0,14	HIGH	NONE	FRAME_SHIFT	S	gtt/	V622	S	0.000428	0.916192	4	2	GTT>G
ERR5749411	23604	PASS	C	A	19124	0.966168	0	6,0,19107,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749411	23709	PASS	C	T	19108	0.945101	0	0,1,2,19074	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749411	23817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	36630	8.19E-4	4	17476,19100,18,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTt/cCt	L752P	S	0.000646	0.066832	1	1	T>C
ERR5749411	24010	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATTTATTGAAGATCTAC	A	17628	5.67E-4	0	150,17466,0,10	HIGH	NONE	FRAME_SHIFT	S	attgaagatctacttttc/	IEDLLF818	S	0.000455	0.926398	4	2	ATTTATTGAAGATCTAC>A
ERR5749411	24127	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	32965	5.16E-4	8	15458,17501,11,6	HIGH	NONE	FRAME_SHIFT	S	aac/	N856	S	0.000324	0.111888	4	1	TA>T
ERR5749411	24506	PASS	T	G	21118	0.97495	0	10,0,21106,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749411	24914	PASS	G	C	45655	0.958055	0	0,0,22741,22874	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749411	25603	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	21477	0.024165	0	4,20911,0,544	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	Cta/Tta	L71	orf3a	0.001967	0.924436	1	1	C>T
ERR5749411	25626	PASS	C	T	40737	0.779488	7	4,1,19196,21450	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	caC/caT	H78	orf3a	0.000403	0.915633	3	2	C>T
ERR5749411	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	19318	0.002071	587	19212,19,16,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749411	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	19273	6.23E-4	0	19261,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749411	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	53906	8.53E-4	0	0,53853,0,46	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749411	26208	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	54024	0.001314	0	6,53902,0,73	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	agC/agT	S272	orf3a	0.000315	0.922222	2	2	C>T
ERR5749411	26270	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	67079	7.01E-4	2	13040,53973,11,38	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	aCa/aTa	T9I	E	0.000586	0.930791	3	2	C>T
ERR5749411	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	G	15593	0.001283	0	4,15553,0,20	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/	ACLVGLMWLSYFIASF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT>G
ERR5749411	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	15593	0.001283	0	4,15567,0,20	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749411	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	15594	0.004489	0	4,15513,0,70	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749411	26907	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	36732	8.17E-4	0	36688,3,32,0	LOW	SILENT	SYNONYMOUS_CODING	M	Ctg/Ttg	L129	M	0.000817	0.976032	1	1	C>T
ERR5749411	27509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	47956	0.012345	27	24347,22987,351,256	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	aCa/aTa	T39I	orf7a	0.000843	0.067888	1	1	C>T
ERR5749411	27972	PASS	C	T	12519	0.896637	63	1,3,12411,59	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749411	28048	PASS	G	T	12469	0.918759	0	0,17,1,12444	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749411	28111	PASS	A	G	34302	0.977727	3	6,1,21811,12474	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749411	28270	PASS	TA	T	42161	0.995019	439	203,11,21529,20422	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749411	28280	PASS	G	C	42085	0.937294	14	12,3,21581,20407	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749411	28281	PASS	A	T	42085	0.912273	34	32,8,21565,20408	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749411	28282	PASS	T	A	42085	0.908637	23	25,8,21505,20424	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749411	28406	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTACCCAATA	T	21841	6.41E-4	0	17,21804,0,14	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	N	ttacccaataat/tat	LPNN45Y	N	0.00043	0.921074	3	2	TTACCCAATA>T
ERR5749411	28881	PASS	G	A	15746	0.762606	39	14,0,7756,7735	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749411	28882	PASS	G	A	15743	0.825954	11	7,1,7853,7720	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749411	28883	PASS	G	C	15743	0.942514	3	0,1,7876,7844	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749411	28977	PASS	C	T	8025	0.927601	0	0,3,0,7997	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749411	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	66683	0.00123	0	33483,33076,53,52	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749411	29348	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	44069	0.001929	3	10449,33491,19,75	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gca/Aca	A359T	N	0.000865	0.968413	2	1	G>A
ERR5749412	241	PASS	C	T	16257	0.870394	0	0,1,8083,8140	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749412	337	PASS	C	T	8188	0.981925	273	9,3,0,8175	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	cgC/cgT	R24	leader	0.981925	0.981925	1	1	C>T
ERR5749412	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	15149	0.001518	0	15115,4,23,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749412	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	15147	0.002311	0	14027,6,1061,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749412	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	41967	5.72E-4	8	26781,15159,19,5	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749412	913	PASS	C	T	26795	0.925023	0	0,12,1,26749	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749412	1510	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	28385	0.002184	0	0,28059,0,72	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggT/ggC	G235	nsp2	0.002159	0.937304	1	1	T>C
ERR5749412	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	97526	9.43E-4	2147483647	48670,45926,84,2611	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749412	3037	PASS	C	T	29036	0.819259	64	2,28,14511,14276	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749412	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	14652	0.001638	672	7,14612,25,5	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749412	3177	PASS	C	T	40127	0.890797	2	2,2,25474,14594	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P153L	nsp3	0.000773	0.96008	3	2	C>T
ERR5749412	3267	PASS	C	T	25511	0.970954	0	1,0,25485,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749412	3575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	18523	5.94E-4	0	18512,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/ttTa	L287F?	nsp3	0.000594	0.059126	3	1	G>GT
ERR5749412	5388	PASS	C	A	8332	0.959674	2147483647	0,0,8330,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749412	5986	PASS	C	T	18935	0.976023	0	2,0,18923,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749412	6954	PASS	T	C	30238	0.818573	0	0,6,0,30091	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749412	7528	PASS	C	T	20389	0.916131	0	0,6,20,20338	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V1603	nsp3	0.002527	0.916131	1	1	C>T
ERR5749412	8151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	63580	5.5E-4	1343	31211,31775,536,18	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gTc/gGc	V1811G	nsp3	0.00055	0.34	2	1	T>G
ERR5749412	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	42104	0.001069	123	22297,19762,45,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749412	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22473	0.001424	0	22409,9,35,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749412	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	22460	0.00138	0	22390,3,55,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749412	11287	PASS	GTCTGGTTTT	G	22453	0.998797	0	0,27,0,22426	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749412	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	41531	0.001035	0	20747,20693,23,24	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749412	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	18232	0.004662	2147483647	17836,128,8,254	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749412	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	35542	7.6E-4	0	17810,17723,14,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749412	14408	PASS	C	T	35542	0.845929	1	3,4,17738,17565	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749412	14676	PASS	C	T	16843	0.760553	0	8,0,16777,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749412	15279	PASS	C	T	28776	0.88612	0	6,0,28740,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749412	16176	PASS	T	C	27697	0.981623	0	1,0,14317,13372	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749412	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	31949	5.95E-4	0	31930,0,19,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749412	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	43098	0.002019	0	42980,0,88,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749412	20091	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	43016	3.95E-4	0	0,42999,0,17	HIGH	NONE	FRAME_SHIFT	ORF1ab	caa/Acaa	Q159T?	endoR	0.000368	0.051583	1	1	C>CA
ERR5749412	21622	PASS	C	T	20429	0.94312	0	0,3,1,20400	LOW	SILENT	SYNONYMOUS_CODING	S	acC/acT	T20	S	0.000846	0.946634	3	2	C>T
ERR5749412	21764	PASS	ATACATG	A	18404	0.996957	0	56,0,18348,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749412	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	18402	6.52E-4	0	18390,0,12,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749412	21990	PASS	TTTA	T	18408	0.998533	0	0,27,3,18378	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749412	22450	PASS	C	T	12887	0.787615	0	3,0,12690,56	LOW	SILENT	SYNONYMOUS_CODING	S	ctC/ctT	L296	S	0.00215	0.803846	1	1	C>T
ERR5749412	23063	PASS	A	T	16498	0.87053	0	0,3,0,16436	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749412	23271	PASS	C	A	26697	0.923662	0	2,0,26665,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749412	23403	PASS	A	G	26691	0.969915	0	0,7,0,26665	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749412	23604	PASS	C	A	21762	0.939941	0	20,0,21727,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749412	23709	PASS	C	T	21737	0.945623	0	0,4,0,21710	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749412	24506	PASS	T	G	23727	0.975766	0	8,0,23718,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749412	24914	PASS	G	C	47291	0.961261	0	0,0,23554,23705	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749412	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	31392	0.001752	739	31273,33,25,32	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749412	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	15479	7.75E-4	0	0,15467,0,12	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749412	27972	PASS	C	T	15857	0.897711	38	2,2,15721,74	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749412	28001	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	31524	8.56E-4	1	15725,15739,17,15	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ccG/ccA	P36	orf8	0.00085	0.830607	2	1	G>A
ERR5749412	28048	PASS	G	T	15789	0.931851	0	0,17,2,15759	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749412	28111	PASS	A	G	36919	0.978737	10	1,5,21115,15789	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749412	28270	PASS	TA	T	41032	0.99554	484	189,4,20869,19980	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749412	28280	PASS	G	C	40962	0.940384	16	11,2,20925,19961	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749412	28281	PASS	A	T	40962	0.919486	8	16,8,20921,19967	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749412	28282	PASS	T	A	40963	0.91236	5	21,14,20879,19972	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749412	28881	PASS	G	A	19040	0.782248	6	5,1,9418,9363	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749412	28882	PASS	G	A	19040	0.836082	15	6,0,9517,9381	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749412	28883	PASS	G	C	19040	0.943015	0	1,0,9532,9485	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749412	28977	PASS	C	T	9659	0.933326	2147483647	0,0,0,9648	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749412	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	58893	9.68E-4	1	29541,29259,36,32	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749413	239	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTC	T	1630	0.003681	0	812,812,3,3	.	.	.	.	.	.	.	0.000495	0.25	4	1	TTC>T
ERR5749413	241	PASS	C	T	1630	0.83865	0	0,0,807,807	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749413	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	5168	0.003483	0	5116,35,18,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749413	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	5167	0.004645	0	5052,35,24,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749413	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	5167	0.003677	0	5052,35,19,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749413	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	5167	0.004451	0	5052,35,23,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749413	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTTGA	G	5167	0.00271	0	5052,35,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTTGA>G
ERR5749413	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	5206	0.001729	18	4708,77,302,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749413	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	5206	0.002689	0	5115,77,14,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749413	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	5205	0.001153	0	5116,77,6,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttatg/gtg	VM84V	leader	0.000554	0.991848	4	1	GTTA>G
ERR5749413	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	5205	0.001153	0	5116,77,6,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749413	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	5207	0.001344	0	5112,80,7,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TA>T
ERR5749413	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	5207	0.001728	0	5112,80,9,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749413	673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTTA	13653	0.002417	140	8509,5110,0,33	MODERATE	NONE	CODON_INSERTION	ORF1ab	ggc/TTAggc	G137LG	leader	0.000454	0.602236	3	2	C>CTTA
ERR5749413	673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	13653	5.86E-4	15	8501,5144,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggc/	G137	leader	0.000454	0.602236	3	2	CG>C
ERR5749413	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	13618	0.001616	0	8495,5096,13,9	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749413	751	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8515	0.001644	0	8496,0,14,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N162	leader	0.000662	0.943591	2	2	C>T
ERR5749413	913	PASS	C	T	8512	0.90484	0	0,10,0,8489	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749413	932	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAC	G	8515	8.22E-4	0	0,8508,0,7	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T44	nsp2	0.00048	0.184416	2	2	GAC>G
ERR5749413	3037	PASS	C	T	11104	0.809888	24	0,8,5550,5466	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749413	3267	PASS	C	T	11505	0.968362	0	1,0,11498,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749413	3802	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	12201	9.02E-4	34	6228,5962,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N363	nsp3	0.000554	0.064198	4	2	TA>T
ERR5749413	4999	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8519	0.003287	0	8485,3,28,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N760	nsp3	0.001692	0.947468	1	1	C>T
ERR5749413	5388	PASS	C	A	3016	0.940981	2147483647	0,0,3011,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749413	5392	PASS	C	T	3016	0.944629	0	1,0,3012,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N891	nsp3	0.012876	0.944629	2	2	C>T
ERR5749413	5986	PASS	C	T	8622	0.9746	2147483647	0,0,8615,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749413	6954	PASS	T	C	14207	0.821848	0	0,2,0,14133	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749413	7860	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	13094	6.11E-4	0	0,13086,0,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T1714	nsp3	0.000611	0.666818	2	2	CT>C
ERR5749413	7926	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	13121	0.001067	0	0,13107,0,14	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1737	nsp3	0.000531	0.97019	5	2	CA>C
ERR5749413	8084	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	12371	8.89E-4	0	12361,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1790	nsp3	0.000543	0.923413	4	2	GA>G
ERR5749413	9198	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	11393	0.001317	0	0,11378,0,15	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F216	nsp4	0.000543	0.93476	4	2	CT>C
ERR5749413	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	12043	0.001495	10	10209,1816,18,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749413	10138	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19829	0.001816	4	14787,5002,30,6	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N28	3Cpro	0.000458	0.983567	3	3	C>T
ERR5749413	10189	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14817	0.001215	0	14796,0,18,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acC/acT	T45	3Cpro	0.000675	0.074883	2	2	C>T
ERR5749413	10189	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	14817	6.75E-4	0	14807,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tct/	S46	3Cpro	0.000675	0.074883	2	2	CT>C
ERR5749413	10323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	14803	0.001959	0	0,14745,0,29	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749413	11073	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TC	19437	8.75E-4	0	19420,0,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/Cttt	F35L?	nsp6	0.000385	0.092251	6	2	T>TC
ERR5749413	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	19431	0.003705	0	19327,0,95,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749413	11138	PASS	G	A	19420	0.119876	0	16943,0,2418,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gca/Aca	A56T	nsp6	0.119876	0.119876	1	1	G>A
ERR5749413	11152	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19414	0.003039	0	19286,0,63,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V60	nsp6	0.000678	0.974465	2	2	C>T
ERR5749413	11287	PASS	GTCTGGTTTT	G	19429	0.996449	0	0,69,0,19360	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749413	11572	PASS	C	T	6539	0.918642	249	9,1,4,6488	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F200	nsp6	0.005575	0.918642	2	2	C>T
ERR5749413	12493	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	13392	0.00112	0	13377,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tataac/	YN135	nsp8	0.000671	0.855797	2	2	CTA>C
ERR5749413	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	13392	0.001568	0	13352,0,21,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749413	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	13207	0.002802	0	13172,0,37,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749413	13459	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTT	G	10810	0.001203	0	10794,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L8	nsp11	0.000691	0.060726	5	2	GTT>G
ERR5749413	14097	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	12094	0.001406	0	12055,22,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggt/	G220	RdRp	0.000613	0.981481	2	2	CG>C
ERR5749413	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	3607	0.002495	0	1804,1799,5,4	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749413	14408	PASS	C	T	3607	0.841142	0	1,1,1794,1771	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749413	14676	PASS	C	T	7322	0.803469	2147483647	0,0,7301,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749413	15279	PASS	C	T	10128	0.88359	2147483647	0,0,10117,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749413	16176	PASS	T	C	10853	0.980466	0	0,0,3755,7091	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749413	17442	PASS	T	C	12473	0.972741	115	0,3,12467,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccT/ccC	P402	helicase	0.000887	0.972741	2	2	T>C
ERR5749413	18357	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	11538	0.001993	0	11501,0,23,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccT/ccC	P106	ExoN	0.001226	0.057597	1	1	T>C
ERR5749413	18647	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGAGCGCACCTGTTGTCTATG	C	32805	3.66E-4	19	21257,11536,12,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gagcgcacctgttgtctatgtgat/gat	ERTCCLCD204D	ExoN	0.000283	0.970507	4	2	CTGAGCGCACCTGTTGTCTATG>C
ERR5749413	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	21269	0.001222	0	21243,0,26,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749413	18699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	21267	0.001034	0	21240,0,23,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcC	A220	ExoN	0.001034	0.98002	1	1	T>C
ERR5749413	19299	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	12255	0.001877	0	12231,0,23,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taT/taC	Y420	ExoN	0.001065	0.987656	2	2	T>C
ERR5749413	19524	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	12256	0.001224	0	0,12241,0,15	HIGH	NONE	FRAME_SHIFT	ORF1ab	gat/	D496	ExoN	0.000745	0.953697	2	2	CG>C
ERR5749413	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9079	0.003414	0	9039,0,32,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749413	20178	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9086	0.002201	0	3,9048,0,22	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V186	endoR	0.000533	0.867727	2	2	C>T
ERR5749413	21066	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	15809	7.59E-4	0	0,15797,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N138	MethTr	0.000447	0.081824	3	2	TA>T
ERR5749413	21516	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	10811	0.001017	0	10800,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	agagtt/	RV287	MethTr	0.000412	0.905456	2	2	CAG>C
ERR5749413	21764	PASS	ATACATG	A	10691	0.994201	0	62,0,10629,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749413	21990	PASS	TTTA	T	10695	0.99841	0	0,17,5,10673	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749413	22227	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	18615	6.98E-4	0	0,18602,0,13	HIGH	NONE	FRAME_SHIFT	S	tta/	L223	S	0.000419	0.824305	2	2	CT>C
ERR5749413	22290	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	18629	0.001449	0	1,18601,0,27	HIGH	NONE	FRAME_SHIFT	S	tta/	L244	S	0.000389	0.578006	2	2	CT>C
ERR5749413	22483	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TG	T	3020	0.001987	0	0,3014,0,6	HIGH	NONE	FRAME_SHIFT	S	gta/	V308	S	0.001987	0.921102	2	2	TG>T
ERR5749413	22630	PASS	G	A	15972	0.921237	0	9,0,15938,0	LOW	SILENT	SYNONYMOUS_CODING	S	aaG/aaA	K356	S	0.001137	0.921237	2	2	G>A
ERR5749413	23063	PASS	A	T	11704	0.864064	0	0,1,0,11650	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749413	23271	PASS	C	A	11715	0.922749	0	2,0,11684,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749413	23403	PASS	A	G	11712	0.968665	2147483647	0,0,0,11706	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749413	23604	PASS	C	A	11132	0.939184	0	6,0,11122,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749413	23690	PASS	A	G	11113	0.929812	0	0,9,4,11084	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aac/Gac	N710D	S	0.002413	0.929812	1	1	A>G
ERR5749413	23709	PASS	C	T	11124	0.927454	0	0,1,3,11096	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749413	23855	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6772	0.002067	0	6757,0,14,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Cgt/Tgt	R765C	S	0.000815	0.181818	2	2	C>T
ERR5749413	24506	PASS	T	G	14044	0.975078	0	6,0,14035,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749413	24646	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	14034	0.001283	0	5,13974,0,18	LOW	SILENT	SYNONYMOUS_CODING	S	aaA/aaG	K1028	S	0.001283	0.957967	1	1	A>G
ERR5749413	24745	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	31228	4.8E-4	52	17184,14029,0,15	HIGH	NONE	FRAME_SHIFT	S	ttc/	F1062	S	0.00048	0.961619	3	2	CT>C
ERR5749413	24899	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	34267	4.38E-4	0	17136,17116,8,7	HIGH	NONE	FRAME_SHIFT	S	atc/	I1114	S	0.000315	0.09021	5	3	CA>C
ERR5749413	24914	PASS	G	C	34165	0.959286	0	0,0,17028,17116	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749413	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	4274	0.004212	181	4220,29,8,11	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749413	26158	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	25246	7.92E-4	0	0,25223,0,20	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF3a	gttaat/gat	VN256D	orf3a	0.000297	0.905181	6	2	GTTA>G
ERR5749413	26208	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25284	9.1E-4	0	2,25238,0,24	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	agC/agT	S272	orf3a	0.000315	0.922222	2	2	C>T
ERR5749413	26748	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	10267	0.001266	0	35,9980,0,251	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Atc/Ctc	I76L	M	0.001056	0.926238	2	1	A>C
ERR5749413	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	10272	0.00146	0	14,10243,0,15	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749413	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	10275	0.002725	0	14,10227,0,28	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749413	26895	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28599	8.74E-4	0	28568,1,26,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Cat/Tat	H125Y	M	0.000874	0.97046	1	1	C>T
ERR5749413	26958	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	28597	0.001713	0	28544,0,49,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Cgt/Tgt	R146C	M	0.00096	0.122326	1	1	C>T
ERR5749413	27384	PASS	T	C	203	0.931035	0	0,0,1,202	LOW	SILENT	SYNONYMOUS_CODING	ORF6	gaT/gaC	D61	orf6	0.00154	0.931035	3	3	T>C
ERR5749413	27972	PASS	C	T	6652	0.911004	32	2,2,6572,62	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749413	28048	PASS	G	T	6599	0.924989	0	0,10,0,6585	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749413	28111	PASS	A	G	25827	0.979479	0	1,0,19215,6602	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749413	28147	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	19224	7.28E-4	0	19207,1,14,0	HIGH	NONE	FRAME_SHIFT	ORF8	ttt/	F86	orf8	0.000438	0.981624	4	2	CT>C
ERR5749413	28239	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTGTT	G	19224	0.001248	0	19196,4,24,0	HIGH	NONE	FRAME_SHIFT	ORF8	gtttta/	VL117	orf8	0.000417	0.984998	9	2	GTTGTT>G
ERR5749413	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19218	0.001509	0	19113,11,31,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749413	28270	PASS	TA	T	37191	0.994864	418	187,9,18951,18049	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749413	28280	PASS	G	C	37115	0.936549	9	6,1,19003,18037	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749413	28281	PASS	A	T	37115	0.915021	32	24,5,18984,18044	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749413	28282	PASS	T	A	37117	0.913032	7	18,10,18961,18050	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749413	28292	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	38202	0.001256	0	19024,19118,24,24	HIGH	NONE	FRAME_SHIFT	N	aat/	N8	N	0.000304	0.055324	4	2	CA>C
ERR5749413	28407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TACCCAATA	T	19232	4.68E-4	0	9,19214,0,9	HIGH	NONE	FRAME_SHIFT	N	cccaataat/	PNN46	N	0.000382	0.179673	1	1	TACCCAATA>T
ERR5749413	28603	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	41328	9.92E-4	0	20620,20467,23,24	LOW	SILENT	SYNONYMOUS_CODING	N	ttC/ttT	F110	N	0.000427	0.883357	2	2	C>T
ERR5749413	28881	PASS	G	A	8050	0.778261	24	9,0,3986,3951	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749413	28882	PASS	G	A	8044	0.821109	3	2,0,4025,3926	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749413	28883	PASS	G	C	8044	0.944555	0	0,0,4025,4006	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749413	28977	PASS	C	T	4108	0.917235	0	0,1,0,4054	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749413	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	28122	0.001245	230	23989,4073,4,33	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749413	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	47669	0.001322	0	23936,23644,34,34	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749413	29451	PASS	C	T	9434	0.757685	0	1,0,9329,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aCt/aTt	T393I	N	0.007675	0.757685	2	2	C>T
ERR5749413	29627	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16556	0.001148	55	7091,9438,18,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF10	Cgt/Tgt	R24C	orf10	0.001148	0.967915	1	1	C>T
ERR5749414	241	PASS	C	T	14659	0.87332	0	4,5,7298,7304	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749414	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	13325	0.001876	0	13296,6,25,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749414	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	13323	6.76E-4	0	13274,6,9,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749414	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	13323	0.002402	0	13274,6,32,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749414	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	13324	0.001651	38	13293,9,20,2	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749414	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	13326	6.0E-4	0	13302,13,8,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttatg/gtg	VM84V	leader	0.000554	0.991848	4	1	GTTA>G
ERR5749414	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	13327	9.0E-4	0	13298,15,12,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749414	635	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13332	0.004275	0	0,13262,0,66	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cgt/Tgt	R124C	leader	0.00148	0.880435	1	1	C>T
ERR5749414	673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	35872	0.01051	824	22462,12980,70,344	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y136	leader	0.000454	0.602236	3	2	C>T
ERR5749414	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	35867	9.48E-4	54	22498,13328,33,1	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749414	913	PASS	C	T	22522	0.920345	0	0,18,0,22472	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749414	1108	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16389	0.002075	0	16332,0,35,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I101	nsp2	0.002075	0.964297	1	1	C>T
ERR5749414	1820	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	21027	0.001189	0	0,20969,0,28	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggt/Agt	G339S	nsp2	0.001189	0.949024	2	2	G>A
ERR5749414	3037	PASS	C	T	21766	0.852384	30	0,10,10880,10758	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749414	3267	PASS	C	T	21130	0.971084	0	1,0,21114,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749414	3602	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13269	0.00716	0	13163,0,98,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cac/Tac	H295Y	nsp3	0.004454	0.97247	1	1	C>T
ERR5749414	4237	PASS	T	C	40702	0.916343	3	0,1,20369,20224	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaT/aaC	N506	nsp3	0.000302	0.918634	2	2	T>C
ERR5749414	4255	PASS	G	A	40763	0.83593	23	14,2,20308,20132	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccG/ccA	P512	nsp3	0.001102	0.871853	2	1	G>A
ERR5749414	5388	PASS	C	A	6572	0.958917	2147483647	0,0,6566,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749414	5575	PASS	C	T	6575	0.946616	100	3,1,0,6567	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y952	nsp3	0.01018	0.961493	1	1	C>T
ERR5749414	5986	PASS	C	T	13686	0.974646	0	3,0,13670,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749414	6954	PASS	T	C	22153	0.808198	0	0,2,0,22033	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749414	7067	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	41398	7.49E-4	88	19113,22229,30,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gaa/Aaa	E1450K	nsp3	0.000274	0.059217	5	3	G>A
ERR5749414	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	32335	8.66E-4	67	18218,14089,28,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749414	11287	PASS	GTCTGGTTTT	G	23083	0.997617	0	0,55,0,23028	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749414	11507	PASS	G	A	29281	0.886172	3	2,0,14682,14469	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Att	V179I	nsp6	0.007744	0.914418	2	2	G>A
ERR5749414	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	37915	8.44E-4	0	23141,14720,20,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749414	12125	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	20390	0.001128	0	4,20289,0,29	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y12H	nsp8	0.000847	0.113436	1	1	T>C
ERR5749414	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	22143	0.001806	0	22061,0,40,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749414	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	15138	8.59E-4	0	15126,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749414	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	36068	8.04E-4	2	18011,17972,15,18	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749414	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	18914	0.005076	2147483647	18433,155,8,310	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749414	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	36702	4.63E-4	0	18418,18296,9,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749414	14408	PASS	C	T	36702	0.835731	5	2,5,18328,18095	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749414	14676	PASS	C	T	14347	0.788736	0	9,0,14291,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749414	15279	PASS	C	T	22608	0.931706	0	5,0,22584,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749414	15420	PASS	T	G	22579	0.925905	0	0,48,0,22523	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcG	A660	RdRp	0.908883	0.934773	1	1	T>G
ERR5749414	16176	PASS	T	C	23504	0.979876	3	1,0,11360,12133	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749414	17502	PASS	C	T	18088	0.983249	0	3,0,18065,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F422	helicase	0.000611	0.9865	2	2	C>T
ERR5749414	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	27777	7.2E-4	0	27757,0,20,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749414	19011	PASS	C	T	23604	0.969243	2147483647	0,0,23588,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D324	ExoN	0.000408	0.975746	4	2	C>T
ERR5749414	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29352	0.001567	0	29287,0,47,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749414	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34739	0.001583	3	17030,17308,29,36	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749414	21764	PASS	ATACATG	A	14794	0.997364	0	33,0,14755,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749414	21990	PASS	TTTA	T	14802	0.998311	0	0,25,7,14770	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749414	23063	PASS	A	T	15977	0.86274	0	0,4,0,15907	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749414	23271	PASS	C	A	24477	0.926502	0	1,0,24453,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749414	23403	PASS	A	G	24465	0.96914	0	0,3,0,24451	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749414	23604	PASS	C	A	17925	0.943487	0	9,0,17905,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749414	23709	PASS	C	T	17906	0.937954	0	0,17,6,17861	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749414	23817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	34439	7.84E-4	0	16488,17910,14,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTt/cCt	L752P	S	0.000646	0.066832	1	1	T>C
ERR5749414	24506	PASS	T	G	20423	0.975175	0	8,0,20405,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749414	24914	PASS	G	C	44236	0.958156	0	0,1,22055,22145	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749414	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	14472	0.002004	322	14385,20,16,15	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749414	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	15002	8.67E-4	0	0,14988,0,13	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749414	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	15004	0.001533	0	0,14979,0,23	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749414	27240	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAT	G	22145	5.87E-4	0	22132,0,13,0	HIGH	NONE	FRAME_SHIFT	ORF6	atatta/	IL14	orf6	0.000521	0.117458	2	2	GAT>G
ERR5749414	27494	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	44664	0.008284	16	22330,21922,172,213	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	cCt/cTt	P34L	orf7a	0.000672	0.961447	2	2	C>T
ERR5749414	27765	PASS	C	T	22506	0.961966	0	0,6,0,22480	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7b	Ctt/Ttt	L4F	orf7b	0.00109	0.970449	1	1	C>T
ERR5749414	27972	PASS	C	T	11989	0.901326	20	1,1,11883,57	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749414	28048	PASS	G	T	11941	0.925132	0	0,19,0,11914	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749414	28111	PASS	A	G	34590	0.976843	7	2,4,22628,11946	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749414	28239	PASS	GTTGTT	G	22584	0.984148	0	358,0,22226,0	HIGH	NONE	FRAME_SHIFT	ORF8	gtttta/	VL117	orf8	0.000417	0.984998	9	2	GTTGTT>G
ERR5749414	28249	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	ATC	22308	0.001524	0	22273,0,34,0	HIGH	NONE	FRAME_SHIFT	ORF8	ttc/CTttc	F120L?	orf8	0.000443	0.063605	3	2	A>ATC
ERR5749414	28250	PASS	T	TCTG	22308	0.992424	0	142,0,22139,0	MODERATE	NONE	CODON_INSERTION	ORF8	ttc/CTGttc	F120LF	orf8	0.000494	0.993968	5	3	T>TCTG
ERR5749414	28250	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TATG	22308	7.17E-4	0	142,0,16,0	MODERATE	NONE	CODON_INSERTION	ORF8	ttc/ATGttc	F120MF	orf8	0.000494	0.993968	5	3	T>TATG
ERR5749414	28253	PASS	CA	C	22308	0.994128	0	131,0,22177,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749414	28270	PASS	TA	T	42961	0.996788	283	128,6,22177,20646	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749414	28271	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AA	A	42961	0.001234	148	22254,20654,53,0	.	.	.	.	.	.	.	0.000482	0.924941	3	2	AA>A
ERR5749414	28280	PASS	G	C	42962	0.94132	4	12,7,22254,20625	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749414	28281	PASS	A	T	42962	0.931102	26	26,7,22244,20630	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749414	28282	PASS	T	A	42965	0.904969	5	20,12,22205,20635	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749414	28292	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	44867	8.92E-4	0	22284,22539,20,20	HIGH	NONE	FRAME_SHIFT	N	aat/	N8	N	0.000304	0.055324	4	2	CA>C
ERR5749414	28881	PASS	G	A	18808	0.767971	15	6,0,9316,9225	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749414	28882	PASS	G	A	18807	0.8223	9	6,1,9398,9196	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749414	28883	PASS	G	C	18807	0.943744	6	0,2,9419,9370	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749414	28977	PASS	C	T	9586	0.930837	0	0,3,0,9563	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749414	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	64634	0.001191	0	32458,32060,48,46	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749414	29835	PASS	C	T	9668	0.125879	0	0,8413,0,1253	.	.	.	.	.	.	.	0.125879	0.969363	1	1	C>T
ERR5749415	241	PASS	C	T	514	0.881323	0	0,0,257,256	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749415	292	PASS	C	T	258	0.96124	2147483647	0,0,0,258	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N9	leader	0.939339	0.96124	1	1	C>T
ERR5749415	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	4781	0.001673	0	4774,0,8,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749415	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	4781	0.003137	0	4737,0,15,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749415	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	4781	0.006066	0	4737,0,29,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749415	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	4773	0.001676	0	4767,0,8,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttatg/gtg	VM84V	leader	0.000554	0.991848	4	1	GTTA>G
ERR5749415	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	4773	0.001676	0	4765,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TA>T
ERR5749415	657	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4790	0.007724	0	1,4742,0,46	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A131V	leader	0.001202	0.365979	3	1	C>T
ERR5749415	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	13120	0.001905	25	8301,4787,23,2	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749415	843	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16617	0.001384	0	8294,8286,14,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P13L	nsp2	0.000301	0.050923	4	2	C>T
ERR5749415	913	PASS	C	T	8325	0.921441	0	0,5,0,8309	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749415	1357	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	9907	0.001514	0	9841,0,63,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcG	A184	nsp2	0.000493	0.077966	3	2	T>G
ERR5749415	1968	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	9911	0.001009	0	9901,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ata/	I389	nsp2	0.001009	0.95	2	2	CA>C
ERR5749415	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	30840	0.001751	2609	15403,14371,24,977	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749415	3037	PASS	C	T	8428	0.80636	30	1,13,4211,4142	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749415	3267	PASS	C	T	7727	0.969717	2147483647	0,0,7725,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749415	3671	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GA	16590	7.23E-4	0	8303,8283,6,6	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/aaAt	N319K?	nsp3	0.000351	0.0625	6	2	G>GA
ERR5749415	3817	PASS	C	T	12136	0.947841	10	2,0,3808,8316	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D366	nsp3	0.000777	0.972816	2	2	C>T
ERR5749415	3832	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	3812	0.001836	0	3804,1,7,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L373	nsp3	0.000689	0.327273	4	2	CT>C
ERR5749415	5180	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GATCCTA	G	6091	0.001806	0	0,6080,0,11	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gatcctagt/ggt	DPS821G	nsp3	0.001806	0.911187	2	2	GATCCTA>G
ERR5749415	5388	PASS	C	A	2679	0.964912	2147483647	0,0,2678,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749415	5986	PASS	C	T	7904	0.971533	2147483647	0,0,7893,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749415	6954	PASS	T	C	11792	0.82327	0	0,3,0,11742	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749415	6990	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	11822	8.46E-4	0	0,11812,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/	L1425	nsp3	0.000504	0.101156	4	2	CT>C
ERR5749415	7945	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16877	0.001244	0	5,16844,0,22	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y1742	nsp3	0.001244	0.950558	2	2	C>T
ERR5749415	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14840	0.002561	0	14773,0,43,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749415	11075	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TC	14840	0.001011	0	14824,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/tCtt	F35S?	nsp6	0.000555	0.885796	4	2	T>TC
ERR5749415	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	14837	0.002831	0	14773,0,63,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749415	11095	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14837	0.00155	0	14777,0,25,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A41	nsp6	0.000515	0.887707	7	2	C>T
ERR5749415	11235	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14827	0.001416	0	0,14791,0,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A88V	nsp6	0.000512	0.942208	2	2	C>T
ERR5749415	11287	PASS	GTCTGGTTTT	G	14829	0.998382	0	0,24,0,14805	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749415	11339	PASS	C	T	20502	0.961613	0	0,2,5662,14829	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	Cta/Tta	L123	nsp6	0.002071	0.968425	1	1	C>T
ERR5749415	11517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TC	T	11279	8.87E-4	0	5644,5625,5,5	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtc/	V182	nsp6	0.000887	0.255556	2	2	TC>T
ERR5749415	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	15407	0.002791	4	9710,5642,26,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749415	14408	PASS	C	T	6262	0.840786	6	0,2,3133,3085	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749415	14676	PASS	C	T	5640	0.759397	0	4,0,5611,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749415	15279	PASS	C	T	8619	0.880961	2147483647	0,0,8612,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749415	16176	PASS	T	C	8291	0.982873	0	1,2,2756,5529	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749415	16508	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	11728	0.003496	0	11672,2,54,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gGt/gTt	G91V	helicase	0.000561	0.074909	2	2	G>T
ERR5749415	16792	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CGT	C	24173	6.62E-4	19	12444,11713,3,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	gta/	V187	helicase	0.000335	0.072562	5	2	CGT>C
ERR5749415	17124	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TC	T	19096	4.71E-4	14	6650,12437,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	ctc/	L297	helicase	0.000471	0.985672	2	2	TC>T
ERR5749415	18281	PASS	G	A	20225	0.930779	2	2,0,13116,7088	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aGa/aAa	R81K	ExoN	0.930779	0.930779	1	1	G>A
ERR5749415	18647	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGAGCGCACCTGTTGTCTATG	C	36973	6.22E-4	41	23826,13124,23,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gagcgcacctgttgtctatgtgat/gat	ERTCCLCD204D	ExoN	0.000283	0.970507	4	2	CTGAGCGCACCTGTTGTCTATG>C
ERR5749415	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	23848	5.87E-4	0	23834,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749415	18744	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23843	0.00151	0	23764,0,38,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y235	ExoN	0.000912	0.953624	2	2	C>T
ERR5749415	19029	PASS	C	T	13782	0.923016	0	32,0,13733,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H330	ExoN	0.003777	0.923016	1	1	C>T
ERR5749415	19113	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	27427	5.47E-4	45	13731,13697,0,15	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K359	ExoN	0.000461	0.125	4	3	CA>C
ERR5749415	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	13761	0.002689	0	0,13724,0,37	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749415	19328	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	11793	6.78E-4	0	11785,0,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F431	ExoN	0.000459	0.937906	4	2	CT>C
ERR5749415	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	9888	0.001517	0	9868,0,15,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749415	20245	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	18506	0.001135	0	18468,0,25,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Atg/Gtg	M209V	endoR	0.001027	0.060575	3	2	A>G
ERR5749415	20245	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	18506	0.001027	0	18487,0,19,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	atg/	M209	endoR	0.001027	0.060575	3	2	AT>A
ERR5749415	21077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	11142	8.08E-4	0	5,11128,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K141	MethTr	0.000492	0.955529	4	2	CA>C
ERR5749415	21764	PASS	ATACATG	A	9513	0.997898	0	20,0,9493,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749415	21990	PASS	TTTA	T	9515	0.997162	0	0,27,1,9487	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749415	21991	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTA	T	9518	9.46E-4	0	4,9504,0,9	HIGH	NONE	FRAME_SHIFT	S	tat/	Y144	S	0.00078	0.991378	2	1	TTA>T
ERR5749415	22600	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	19125	4.71E-4	15	12003,7113,9,0	HIGH	NONE	FRAME_SHIFT	S	ttt/	F347	S	0.000471	0.963998	3	3	AT>A
ERR5749415	22690	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	11980	0.001419	0	11767,8,20,0	LOW	SILENT	SYNONYMOUS_CODING	S	acT/acC	T376	S	0.000815	0.051311	2	1	T>C
ERR5749415	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22287	0.001301	5	10255,11990,17,13	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749415	23063	PASS	A	T	10267	0.864712	2147483647	0,0,0,10218	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749415	23271	PASS	C	A	8799	0.927719	0	1,0,8791,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749415	23403	PASS	A	G	8796	0.976239	0	0,3,0,8787	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749415	23575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10198	0.001569	0	10173,0,16,0	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C671	S	0.001569	0.894896	2	2	C>T
ERR5749415	23604	PASS	C	A	10195	0.964296	0	5,0,10185,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749415	23709	PASS	C	T	10178	0.9382	0	0,2,0,10160	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749415	23817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	14363	0.001601	33	4164,10171,0,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTt/cCt	L752P	S	0.000646	0.066832	1	1	T>C
ERR5749415	24506	PASS	T	G	10576	0.972485	0	2,0,10561,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749415	24914	PASS	G	C	35633	0.959784	0	1,2,17734,17848	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749415	25350	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16761	0.001372	0	16732,1,24,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCa/cTa	P1263L	S	0.000626	0.97904	4	2	C>T
ERR5749415	25555	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	16754	8.36E-4	0	0,16740,0,14	HIGH	NONE	FRAME_SHIFT	ORF3a	cag/Tcag	Q57S?	orf3a	0.000552	0.900573	5	2	G>GT
ERR5749415	25626	PASS	C	T	18991	0.895003	0	1,8,2222,16738	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	caC/caT	H78	orf3a	0.000403	0.915633	3	2	C>T
ERR5749415	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	2257	0.00576	234	2226,14,1,12	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749415	26208	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	20100	7.46E-4	0	1,20084,0,15	HIGH	NONE	FRAME_SHIFT	ORF3a	gtg/	V273	orf3a	0.000315	0.922222	2	2	CG>C
ERR5749415	26270	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26819	8.95E-4	5	6700,20070,4,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	E	aCa/aTa	T9I	E	0.000586	0.930791	3	2	C>T
ERR5749415	26681	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8671	0.001845	0	8617,37,16,0	LOW	SILENT	SYNONYMOUS_CODING	M	ttC/ttT	F53	M	0.001297	0.074505	1	1	C>T
ERR5749415	26730	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	17127	5.25E-4	0	8544,8592,4,5	HIGH	NONE	FRAME_SHIFT	M	tac/	Y71	M	0.000371	0.919543	3	2	GT>G
ERR5749415	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	8624	0.002551	0	0,8598,0,22	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749415	26958	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	19028	0.001734	0	18988,0,34,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Cgt/Tgt	R146C	M	0.00096	0.122326	1	1	C>T
ERR5749415	27402	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATTCTTTTCTTGGCACTGATAACACTCGCTACTTGTGAGCTTTATCACTACCAAGAGTGTGTTA	T	16324	5.51E-4	0	0,16315,0,9	HIGH	NONE	FRAME_SHIFT	ORF7a	attcttttcttggcactgataacactcgctacttgtgagctttatcactaccaagagtgtgttaga/	ILFLALITLATCELYHYQECVR4	orf7a	0.000551	0.905711	3	3	TATTCTTTTCTTGGCACTGATAACACTCGCTACTTGTGAGCTTTATCACTACCAAGAGTGTGTTA>T
ERR5749415	27741	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13906	0.001582	0	0,13864,0,23	LOW	SILENT	SYNONYMOUS_CODING	ORF7a	ctC/ctT	L116	orf7a	0.000363	0.954278	3	2	C>T
ERR5749415	27746	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	13906	7.91E-4	0	0,13895,0,11	HIGH	NONE	FRAME_SHIFT	ORF7a	aag/	K119	orf7a	0.000528	0.94095	3	2	GA>G
ERR5749415	27972	PASS	C	T	5215	0.911218	59	3,3,5181,18	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749415	28048	PASS	G	T	5195	0.920693	0	0,12,0,5181	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749415	28111	PASS	A	G	17918	0.980299	0	2,0,12715,5198	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749415	28239	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTGTTTTAGATTTCATCTAAACGAACAAACTAA	G	12714	0.001258	0	12701,0,16,0	HIGH	NONE	FRAME_SHIFT+STOP_LOST+SPLICE_SITE_REGION	ORF8	gttgttttagatttcatctaa/	VVLDFI*116	orf8	0.000417	0.984998	9	2	GTTGTTTTAGATTTCATCTAAACGAACAAACTAA>G
ERR5749415	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12704	0.002598	0	12620,0,34,0	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ttC/ttT	F120	orf8	0.000422	0.995511	4	3	C>T
ERR5749415	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	12702	9.45E-4	0	12692,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749415	28270	PASS	TA	T	24558	0.995073	246	116,7,12549,11888	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749415	28280	PASS	G	C	24512	0.943783	14	10,2,12586,11881	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749415	28281	PASS	A	T	24512	0.920774	8	9,3,12582,11880	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749415	28282	PASS	T	A	24512	0.910942	3	5,2,12561,11891	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749415	28292	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	25294	0.001977	0	12591,12653,25,25	HIGH	NONE	FRAME_SHIFT	N	aat/	N8	N	0.000304	0.055324	4	2	CA>C
ERR5749415	28881	PASS	G	A	4366	0.780119	0	0,0,2163,2157	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749415	28882	PASS	G	A	4366	0.833257	0	1,0,2180,2154	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749415	28883	PASS	G	C	4366	0.940907	0	0,0,2185,2179	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749415	28977	PASS	C	T	2216	0.930957	0	0,1,0,2208	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749415	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	25638	0.001599	341	23398,2175,7,39	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749415	29077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAATGT	C	23420	7.26E-4	0	23403,0,17,0	HIGH	NONE	FRAME_SHIFT	N	aatgtaaca/	NVT269	N	0.000408	0.88565	3	2	CAATGT>C
ERR5749415	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	46487	0.001398	0	23329,23049,43,42	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749416	241	PASS	C	T	22191	0.855572	0	2,2,11049,11066	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749416	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	17241	8.12E-4	0	17225,2,14,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749416	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	17241	0.001392	0	17202,2,24,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749416	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	17230	0.002438	0	16061,4,1098,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749416	913	PASS	C	T	30468	0.908264	0	0,21,0,30384	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749416	2453	PASS	C	T	22656	0.71875	0	0,23,2,22217	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctc/Ttc	L550F	nsp2	0.00429	0.842201	2	2	C>T
ERR5749416	2509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	22722	0.001408	0	13,22657,0,36	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P568	nsp2	0.001408	0.949382	1	1	C>T
ERR5749416	2702	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	58993	7.63E-4	2147483647	58552,44,65,208	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F633V	nsp2	0.000632	0.333333	1	1	T>G
ERR5749416	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	116838	0.002003	2147483647	58386,53670,116,4371	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749416	3037	PASS	C	T	29151	0.791671	110	0,36,14579,14249	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749416	3267	PASS	C	T	29561	0.969994	0	3,0,29545,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749416	3817	PASS	C	T	55336	0.968194	12	8,0,37412,17892	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D366	nsp3	0.000777	0.972816	2	2	C>T
ERR5749416	3877	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	37427	0.004168	0	31323,0,6097,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcG	A386	nsp3	0.000588	0.960227	2	1	T>G
ERR5749416	5388	PASS	C	A	8301	0.961571	2147483647	0,0,8294,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749416	5986	PASS	C	T	18775	0.975553	0	2,0,18754,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749416	6337	PASS	G	T	30826	0.91624	0	49,0,30744,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcG/tcT	S1206	nsp3	0.000579	0.91624	3	2	G>T
ERR5749416	6525	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	48000	8.13E-4	1	17128,30807,13,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T1269I	nsp3	0.000813	0.968636	1	1	C>T
ERR5749416	6678	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	34055	8.22E-4	964	17021,16560,21,413	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aGa	I1320R	nsp3	0.000822	0.071482	2	1	T>G
ERR5749416	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17087	0.001463	0	2,16846,0,34	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749416	6954	PASS	T	C	35698	0.81139	0	0,8,1,35503	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749416	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	42598	8.45E-4	111	20853,21709,36,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749416	11071	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	25438	0.00401	0	25325,11,102,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttc/ttTc	F34F?	nsp6	0.001292	0.087481	5	3	G>GT
ERR5749416	11073	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TC	T	25437	0.008767	0	25204,11,223,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttc/	F34	nsp6	0.000385	0.092251	6	2	TC>T
ERR5749416	11074	PASS	C	T	25437	0.945355	257	109,11,25066,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749416	11075	PASS	T	C	25437	0.885796	0	345,0,25038,7	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F35L	nsp6	0.000555	0.885796	4	2	T>C
ERR5749416	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	25428	9.05E-4	0	25380,2,38,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749416	11287	PASS	GTCTGGTTTT	G	25407	0.99752	0	0,63,0,25344	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749416	12269	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	34205	4.39E-4	0	34190,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aag/	K61	nsp8	0.000434	0.213333	2	1	GA>G
ERR5749416	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	23474	9.8E-4	0	23428,0,23,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749416	13459	PASS	G	A	28685	0.052466	0	27069,0,1598,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcG/tcA	S6	nsp11	0.000691	0.060726	5	2	G>A
ERR5749416	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	57290	9.43E-4	0	28630,28532,29,30	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749416	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	17282	0.005786	2147483647	16797,119,10,350	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749416	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	33455	6.28E-4	0	16783,16666,11,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749416	14408	PASS	C	T	33456	0.828073	19	1,9,16714,16441	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749416	14676	PASS	C	T	19593	0.81866	0	7,0,19534,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749416	15279	PASS	C	T	32474	0.934317	0	4,0,32440,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749416	15439	PASS	G	A	32449	0.920028	0	0,211,0,32145	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtc/Atc	V667I	RdRp	0.920028	0.920028	1	1	G>A
ERR5749416	16176	PASS	T	C	30231	0.97711	0	0,1,14418,15795	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749416	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	31252	4.48E-4	0	31238,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749416	19263	PASS	C	T	62954	0.943181	8	8,4,28091,34817	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N408	ExoN	0.000943	0.943181	2	2	C>T
ERR5749416	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	41157	0.002017	0	41053,0,87,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749416	21764	PASS	ATACATG	A	17908	0.996985	0	51,0,17854,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749416	21990	PASS	TTTA	T	17920	0.997545	0	0,44,11,17865	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749416	22014	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	30952	0.001357	0	30890,10,49,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aGt/aTt	S151I	S	0.001357	0.20398	2	1	G>T
ERR5749416	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	38383	8.08E-4	2	16039,22305,11,20	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749416	23063	PASS	A	T	16023	0.854522	0	0,5,0,15941	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749416	23271	PASS	C	A	30820	0.912622	0	2,0,30777,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749416	23403	PASS	A	G	30805	0.957182	0	0,8,2,30766	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749416	23442	PASS	A	G	30832	0.969026	0	0,4,2,30736	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D627G	S	0.002043	0.969026	2	1	A>G
ERR5749416	23442	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	30832	0.002043	0	0,4,0,89	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gTt	D627V	S	0.002043	0.969026	2	1	A>T
ERR5749416	23604	PASS	C	A	21346	0.94561	0	14,0,21310,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749416	23709	PASS	C	T	21306	0.917957	0	0,5,5,21234	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749416	24506	PASS	T	G	27151	0.974771	0	10,0,27138,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749416	24914	PASS	G	C	45256	0.95837	0	0,1,22552,22681	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749416	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	36041	0.001304	399	35923,11,33,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749416	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	36165	3.59E-4	0	36150,2,13,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749416	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	36443	0.001784	2489	35788,185,240,173	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749416	25916	PASS	C	T	36180	0.95293	525	16,8,1,36130	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aCa/aTa	T175I	orf3a	0.001191	0.964713	2	2	C>T
ERR5749416	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	16585	0.001025	0	0,16567,0,17	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749416	27777	PASS	G	T	33748	0.947849	0	0,28,1,33704	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7b	Gac/Tac	D8Y	orf7b	0.947849	0.947849	1	1	G>T
ERR5749416	27972	PASS	C	T	15862	0.898878	38	2,2,15727,79	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749416	28048	PASS	G	T	15791	0.904883	0	0,29,0,15751	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749416	28111	PASS	A	G	41781	0.976592	3	5,1,25959,15801	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749416	28270	PASS	TA	T	49918	0.995392	454	224,15,25646,24042	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749416	28280	PASS	G	C	49839	0.931901	16	18,6,25690,24015	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749416	28281	PASS	A	T	49839	0.904773	28	27,7,25685,24020	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749416	28282	PASS	T	A	49845	0.913552	20	28,10,25660,24046	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749416	28881	PASS	G	A	34404	0.765609	11	7,1,17143,16767	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749416	28882	PASS	G	A	34403	0.815568	11	7,1,17281,16693	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749416	28883	PASS	G	C	34403	0.938639	18	0,6,17288,17060	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749416	28977	PASS	C	T	17561	0.910882	0	0,5,0,17517	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749416	29035	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	47600	0.001071	181	30000,17488,4,53	LOW	SILENT	SYNONYMOUS_CODING	N	gcT/gcC	A254	N	0.000601	0.054952	4	2	T>C
ERR5749416	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	59570	0.00141	0	29909,29535,51,51	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749416	29688	PASS	G	T	24796	0.664502	7	247,277,12151,12099	.	.	.	.	.	.	.	0.002374	0.664502	2	1	G>T
ERR5749417	913	PASS	C	T	210	0.9	2147483647	0,0,0,210	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749417	1813	PASS	T	TA	694	0.152738	0	0,588,0,106	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggt/Aggt	G339R?	nsp2	0.001022	0.152738	4	2	T>TA
ERR5749417	2110	PASS	C	T	177	0.762712	2147483647	0,0,0,177	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N435	nsp2	0.024426	0.811371	1	1	C>T
ERR5749417	3037	PASS	C	T	243	0.8107	0	0,0,122,121	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749417	3267	PASS	C	T	448	0.977679	2147483647	0,0,448,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749417	5002	PASS	C	T	581	0.547332	0	250,0,331,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ctC/ctT	L761	nsp3	0.001115	0.976835	3	2	C>T
ERR5749417	5388	PASS	C	A	77	0.961039	2147483647	0,0,77,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749417	5512	PASS	C	T	77	0.987013	2147483647	0,0,0,77	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N931	nsp3	0.002299	0.987013	1	1	C>T
ERR5749417	5986	PASS	C	T	148	0.993243	2147483647	0,0,148,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749417	6741	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	678	0.022124	0	0,662,0,16	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cGg/cTg	R1341L	nsp3	0.001093	0.204082	3	2	G>T
ERR5749417	6954	PASS	T	C	299	0.772575	2147483647	0,0,0,297	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749417	9694	PASS	TTA	T	435	0.057471	79	219,191,0,25	HIGH	NONE	FRAME_SHIFT	ORF1ab	atc/	I382	nsp4	0.000506	0.057471	1	1	TTA>T
ERR5749417	10386	PASS	C	CT	1315	0.160456	576	539,565,211,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tca/tTca	S113F?	3Cpro	0.000642	0.160456	4	2	C>CT
ERR5749417	11287	PASS	GTCTGGTTTT	G	1663	1.0	2147483647	0,0,0,1663	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749417	11517	PASS	T	C	90	0.255556	0	33,33,12,12	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gTc/gCc	V182A	nsp6	0.000887	0.255556	2	2	T>C
ERR5749417	11549	PASS	T	C	45	0.355556	0	0,28,0,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tgt/Cgt	C193R	nsp6	0.355556	0.355556	1	1	T>C
ERR5749417	12754	PASS	C	T	165	0.945455	0	0,0,26,139	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C23	nsp9	0.001216	0.947969	1	1	C>T
ERR5749417	12809	PASS	C	T	25	1.0	2147483647	0,0,25,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Ttt	L42F	nsp9	0.001562	1	1	1	C>T
ERR5749417	13990	PASS	CA	C	80	0.5	0	40,0,40,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	caa/	Q184	RdRp	0.002087	0.5	2	2	CA>C
ERR5749417	14120	PASS	C	T	159	0.779874	0	0,0,77,77	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCa/cTa	P227L	RdRp	0.00121	0.786944	2	2	C>T
ERR5749417	14408	PASS	C	T	40	0.825	0	0,0,20,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749417	14676	PASS	C	T	177	0.740113	2147483647	0,0,177,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749417	15223	PASS	T	C	467	0.074946	131	175,256,36,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y595H	RdRp	0.074946	0.074946	1	1	T>C
ERR5749417	15279	PASS	C	T	212	0.915094	2147483647	0,0,211,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749417	16176	PASS	T	C	445	0.98427	0	0,0,20,425	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749417	16439	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	540	0.016667	0	0,531,0,9	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTg/aAg	M68K	helicase	0.016667	0.054348	1	1	T>A
ERR5749417	20630	PASS	A	T	539	0.122449	0	465,0,74,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cAt/cTt	H337L	endoR	0.000988	0.122449	2	1	A>T
ERR5749417	21764	PASS	ATACATG	A	281	0.985765	0	4,0,277,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749417	21990	PASS	TTTA	T	312	0.900641	0	0,44,0,281	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749417	22225	PASS	G	T	749	0.94526	2147483647	0,0,0,749	LOW	SILENT	SYNONYMOUS_CODING	S	tcG/tcT	S221	S	0.001195	0.94526	3	1	G>T
ERR5749417	22289	PASS	G	T	830	0.819277	0	0,79,0,750	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gct/Tct	A243S	S	0.000446	0.915917	3	2	G>T
ERR5749417	23063	PASS	A	T	431	0.907193	2147483647	0,0,0,430	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749417	23271	PASS	C	A	312	0.923077	2147483647	0,0,312,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749417	23403	PASS	A	G	312	0.958333	2147483647	0,0,0,312	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749417	23604	PASS	C	A	475	0.947368	2147483647	0,0,475,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749417	23709	PASS	C	T	474	0.951477	2147483647	0,0,0,474	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749417	23855	PASS	C	T	88	0.181818	0	72,0,16,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Cgt/Tgt	R765C	S	0.000815	0.181818	2	2	C>T
ERR5749417	24506	PASS	T	G	430	0.965116	0	1,0,429,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749417	24914	PASS	G	C	6651	0.960758	0	0,0,3315,3333	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749417	25117	PASS	C	T	208	0.0625	0	195,0,13,0	LOW	SILENT	SYNONYMOUS_CODING	S	cgC/cgT	R1185	S	0.0625	0.0625	1	1	C>T
ERR5749417	25531	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	T	3868	0.004137	0	1,3408,0,459	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Att/Ttt	I47F	orf3a	0.000473	0.975891	5	2	A>T
ERR5749417	25555	PASS	G	T	4013	0.900573	0	0,1,0,4002	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	Gtt/Ttt	V55F	orf3a	0.000552	0.900573	5	2	G>T
ERR5749417	26044	PASS	C	T	224	0.102679	0	194,0,30,0	HIGH	NONSENSE	STOP_GAINED	ORF3a	Caa/Taa	Q218*	orf3a	0.000469	0.102679	3	3	C>T
ERR5749417	26060	PASS	C	T	224	0.8125	2147483647	0,0,222,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aCt/aTt	T223I	orf3a	0.000459	0.822477	2	2	C>T
ERR5749417	27670	PASS	GTTCAAGAACTTTACTCTCCAATTT	G	1700	0.990588	20	1,15,0,1684	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF7a	caagaactttactctccaatttttctt/ctt	QELYSPIFL94L	orf7a	0.002392	0.990588	3	2	GTTCAAGAACTTTACTCTCCAATTT>G
ERR5749417	27798	PASS	G	A	1951	0.051256	0	1,1844,0,105	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7b	Gcc/Acc	A15T	orf7b	0.002041	0.051256	2	1	G>A
ERR5749417	27972	PASS	C	T	134	0.88806	2147483647	0,0,134,0	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749417	28048	PASS	G	T	134	0.932836	2147483647	0,0,0,134	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749417	28095	PASS	A	T	145	0.862069	0	0,11,0,134	HIGH	NONSENSE	STOP_GAINED	ORF8	Aaa/Taa	K68*	orf8	0.002672	0.967672	2	2	A>T
ERR5749417	28111	PASS	A	G	3440	0.982558	0	1,0,3305,134	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749417	28270	PASS	TA	T	6425	0.995486	89	31,0,3259,3137	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749417	28280	PASS	G	C	6412	0.932002	0	1,0,3263,3124	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749417	28281	PASS	A	T	6412	0.916719	4	1,3,3261,3130	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749417	28282	PASS	T	A	6412	0.910792	0	5,4,3261,3133	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749417	28407	PASS	TACCCAATA	T	3306	0.179673	0	0,2712,0,594	HIGH	NONE	FRAME_SHIFT	N	cccaataat/	PNN46	N	0.000382	0.179673	1	1	TACCCAATA>T
ERR5749417	28881	PASS	G	A	73	0.794521	0	0,0,38,32	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749417	28882	PASS	G	A	73	0.835616	0	0,0,39,32	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749417	28883	PASS	G	C	73	0.90411	0	0,0,39,34	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749417	28977	PASS	C	T	36	0.861111	2147483647	0,0,0,36	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749417	29245	PASS	C	T	2104	0.081274	0	0,1924,0,176	LOW	SILENT	SYNONYMOUS_CODING	N	gtC/gtT	V324	N	0.081274	0.081274	1	1	C>T
ERR5749418	71	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	854	0.016393	0	839,0,15,0	.	.	.	.	.	.	.	0.002088	0.926791	2	1	C>A
ERR5749418	241	PASS	C	T	145	0.882759	0	0,0,72,73	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749418	913	PASS	C	T	7729	0.920559	0	0,5,0,7712	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749418	1614	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	6289	0.011131	3	6067,149,73,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cTt/cGt	L270R	nsp2	0.011131	0.055046	2	2	T>G
ERR5749418	1636	PASS	G	T	6140	0.963192	2147483647	0,0,6139,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gaG/gaT	E277D	nsp2	0.00204	0.963192	2	2	G>T
ERR5749418	1684	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6140	0.008143	0	6088,0,50,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I293	nsp2	0.000638	0.973136	2	2	C>T
ERR5749418	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	24257	0.001113	1717	12119,11390,24,678	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749418	3037	PASS	C	T	3321	0.81361	6	0,2,1662,1638	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749418	3117	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1672	0.013158	0	0,1648,0,24	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T133I	nsp3	0.013158	0.950413	1	1	C>T
ERR5749418	3267	PASS	C	T	7882	0.971327	2147483647	0,0,7879,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749418	3335	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	15652	0.011245	2	7774,7702,92,84	HIGH	NONE	FRAME_SHIFT	ORF1ab	gaa/	E206	nsp3	0.001289	0.891976	4	3	GA>G
ERR5749418	5388	PASS	C	A	616	0.952922	2147483647	0,0,616,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749418	5986	PASS	C	T	4250	0.976235	2147483647	0,0,4248,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749418	6954	PASS	T	C	5051	0.827559	2147483647	0,0,0,5030	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749418	6982	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5063	0.012838	0	0,4989,0,69	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C1421	nsp3	0.001915	0.911934	1	1	C>T
ERR5749418	7967	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14122	0.008639	0	1,13995,0,126	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Cct/Tct	P1750S	nsp3	0.002388	0.949148	1	1	C>T
ERR5749418	8950	PASS	C	T	14141	0.982604	0	0,0,12970,1167	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I132	nsp4	0.002808	0.982604	1	1	C>T
ERR5749418	9165	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12968	0.017736	0	0,12720,0,239	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCc/aTc	T204I	nsp4	0.00112	0.253438	1	1	C>T
ERR5749418	9170	PASS	C	T	12968	0.841764	0	0,5,0,12943	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Ttt	L206F	nsp4	0.82019	0.841764	1	1	C>T
ERR5749418	9561	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3732	0.007503	0	3700,0,32,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tCa/tTa	S336L	nsp4	0.00171	0.161742	2	2	C>T
ERR5749418	10323	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	8176	0.00318	0	0,8138,0,26	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aAg/aGg	K90R	3Cpro	0.000946	0.965046	2	1	A>G
ERR5749418	10369	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	8184	0.006476	0	2,8126,0,55	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	cgC/cgT	R105	3Cpro	0.001225	0.120075	1	1	C>T
ERR5749418	10386	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	17137	6.42E-4	1	8950,8176,5,6	HIGH	NONE	FRAME_SHIFT	ORF1ab	tca/	S113	3Cpro	0.000642	0.160456	4	2	CT>C
ERR5749418	11075	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	13228	0.028576	0	12689,0,436,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F35L	nsp6	0.000555	0.885796	4	2	T>C
ERR5749418	11104	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	13215	0.010972	0	13022,0,186,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccT/ccG	P44	nsp6	0.000866	0.675414	2	1	T>G
ERR5749418	11287	PASS	GTCTGGTTTT	G	13222	0.999017	0	0,13,0,13209	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749418	11344	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	14662	0.009276	6	1423,13094,9,132	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I124	nsp6	0.001229	0.964849	1	1	C>T
ERR5749418	11507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	2841	0.007744	0	1421,1398,11,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtt/	V179	nsp6	0.007744	0.914418	2	2	GT>G
ERR5749418	11572	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	1435	0.005575	0	3,1417,0,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttC/ttA	F200L	nsp6	0.005575	0.918642	2	2	C>A
ERR5749418	12513	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	5551	0.005404	0	5518,0,31,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCg/aTg	T141M	nsp8	0.000794	0.984064	2	2	C>T
ERR5749418	12809	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	1045	0.02488	0	1016,0,29,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Ttt	L42F	nsp9	0.001562	1	1	1	C>T
ERR5749418	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	10075	0.007444	0	9986,1,79,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgT/tgC	C46	nsp10	0.000528	0.198485	2	2	T>C
ERR5749418	13995	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	4474	0.009835	0	4427,0,47,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcC	A185	RdRp	0.000877	0.050235	2	2	T>C
ERR5749418	14408	PASS	C	T	5622	0.851654	3	0,1,2804,2783	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749418	14676	PASS	C	T	5835	0.815596	0	5,0,5818,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749418	15279	PASS	C	T	2868	0.906206	2147483647	0,0,2863,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749418	16176	PASS	T	C	5743	0.981194	0	0,0,430,5313	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749418	16794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	15168	0.002835	209	5161,9959,45,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	cgT/cgC	R186	helicase	0.000354	0.077626	2	2	T>C
ERR5749418	17181	PASS	T	C	4178	0.988272	0	4,0,4173,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaT/gaC	D315	helicase	0.986595	0.991193	1	1	T>C
ERR5749418	17766	PASS	C	T	3347	0.121303	0	2918,0,429,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V510	helicase	0.000768	0.920632	2	2	C>T
ERR5749418	17999	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	5494	0.002912	35	2147,3330,0,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aAa	T588K	helicase	0.001094	0.974498	2	1	C>A
ERR5749418	18576	PASS	C	T	13262	0.876866	0	0,8,0,13223	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D179	ExoN	0.005404	0.876866	2	2	C>T
ERR5749418	18636	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	39397	0.005051	896	26131,13067,2,197	HIGH	NONE	FRAME_SHIFT	ORF1ab	ata/	I201	ExoN	0.00055	0.963467	3	2	GA>G
ERR5749418	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	26133	7.27E-4	0	26114,0,19,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749418	18747	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26127	0.006354	0	25920,0,193,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V236	ExoN	0.000375	0.982946	4	2	C>T
ERR5749418	19343	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	5924	0.009453	0	5868,0,56,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F436	ExoN	0.000519	0.192257	7	2	CT>C
ERR5749418	21234	PASS	C	T	7695	0.601689	0	7,0,7549,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A192	MethTr	0.000472	0.857572	5	2	C>T
ERR5749418	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6767	0.009458	0	3285,3349,34,35	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749418	21618	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3401	0.014702	0	0,3346,0,54	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T19I	S	0.001611	0.955482	3	2	C>T
ERR5749418	21658	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	3403	0.014399	18	0,3354,1,48	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	ttC/ttA	F32L	S	0.001649	0.937508	2	2	C>A
ERR5749418	21764	PASS	ATACATG	A	6693	0.997161	0	19,0,6674,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749418	21772	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6693	0.011355	0	6604,0,83,0	LOW	SILENT	SYNONYMOUS_CODING	S	gtC/gtT	V70	S	0.011355	0.869843	1	1	C>T
ERR5749418	21846	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13347	0.001274	0	6663,6648,11,12	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCt/aTt	T95I	S	0.001104	0.788523	1	1	C>T
ERR5749418	21990	PASS	TTTA	T	6697	0.998507	0	0,10,4,6683	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749418	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	10117	0.00257	0	0,10090,0,26	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749418	23043	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAT	C	5938	0.006905	0	0,5897,0,41	HIGH	NONE	FRAME_SHIFT	S	tat/	Y495	S	0.000881	0.056585	2	2	CAT>C
ERR5749418	23063	PASS	A	T	5942	0.876641	0	0,1,0,5920	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749418	23271	PASS	C	A	12174	0.926811	0	3,0,12161,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749418	23403	PASS	A	G	12172	0.97256	0	0,3,0,12163	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749418	23604	PASS	C	A	5369	0.941702	0	3,0,5364,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749418	23635	PASS	C	T	5363	0.958978	2147483647	0,0,5357,0	LOW	SILENT	SYNONYMOUS_CODING	S	tcC/tcT	S691	S	0.002385	0.958978	1	1	C>T
ERR5749418	23709	PASS	C	T	5364	0.947614	2147483647	0,0,0,5358	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749418	24382	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	5261	0.004942	0	0,5226,0,34	LOW	SILENT	SYNONYMOUS_CODING	S	tcC/tcA	S940	S	0.002118	0.920404	2	1	C>A
ERR5749418	24506	PASS	T	G	5926	0.977557	0	2,0,5924,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749418	24914	PASS	G	C	47608	0.962002	0	0,0,23729,23857	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749418	25673	PASS	T	C	436	0.057339	283	391,19,0,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749418	25844	PASS	C	T	392	0.938776	2147483647	0,0,0,392	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aCt/aTt	T151I	orf3a	0.001226	0.938776	1	1	C>T
ERR5749418	26645	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	6188	0.004848	0	6149,0,36,0	LOW	SILENT	SYNONYMOUS_CODING	M	aaC/aaT	N41	M	0.00097	0.828654	2	2	C>T
ERR5749418	26717	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	12279	0.003828	1	6115,6085,24,26	LOW	SILENT	SYNONYMOUS_CODING	M	ttT/ttC	F65	M	0.001602	0.063291	2	2	T>C
ERR5749418	26985	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16583	0.005246	0	16476,0,96,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	M	Cat/Tat	H155Y	M	0.001017	0.889358	1	1	C>T
ERR5749418	27493	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24714	0.001133	106	10575,14105,29,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Cct/Tct	P34S	orf7a	0.000794	0.971493	2	1	C>T
ERR5749418	27532	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10608	0.002451	0	10575,1,30,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7a	Cat/Tat	H47Y	orf7a	0.001165	0.982473	2	1	C>T
ERR5749418	27577	PASS	C	T	10605	0.863461	0	3,0,10580,0	HIGH	NONSENSE	STOP_GAINED	ORF7a	Caa/Taa	Q62*	orf7a	0.000614	0.952205	4	2	C>T
ERR5749418	27603	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	10605	0.002546	0	10566,0,31,0	LOW	SILENT	SYNONYMOUS_CODING	ORF7a	ggC/ggT	G70	orf7a	0.002411	0.959582	1	1	C>T
ERR5749418	27972	PASS	C	T	3014	0.900464	0	0,0,2995,15	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749418	28048	PASS	G	T	2999	0.917639	0	0,2,0,2996	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749418	28111	PASS	A	G	18473	0.980999	4	10,0,15455,3002	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749418	28270	PASS	TA	T	30073	0.995577	292	129,6,15287,14653	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749418	28280	PASS	G	C	30017	0.940667	10	10,3,15310,14639	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749418	28281	PASS	A	T	30017	0.913949	18	19,6,15297,14642	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749418	28282	PASS	T	A	30017	0.914215	2	9,6,15287,14651	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749418	28321	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	15459	0.004075	0	0,15379,0,76	LOW	SILENT	SYNONYMOUS_CODING	N	acG/acT	T16	N	0.00045	0.947809	3	2	G>T
ERR5749418	28651	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16467	0.002915	0	0,16409,0,52	LOW	SILENT	SYNONYMOUS_CODING	N	aaC/aaT	N126	N	0.000502	0.918117	3	2	C>T
ERR5749418	28657	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16474	0.003096	0	0,16408,0,57	LOW	SILENT	SYNONYMOUS_CODING	N	gaC/gaT	D128	N	0.00124	0.862766	1	1	C>T
ERR5749418	28813	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	1580	0.005063	0	1569,0,8,0	LOW	SILENT	SYNONYMOUS_CODING	N	agT/agC	S180	N	0.005063	0.979908	1	1	T>C
ERR5749418	28881	PASS	G	A	3115	0.745746	9	3,0,1528,1537	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749418	28882	PASS	G	A	3115	0.826645	0	1,0,1551,1532	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749418	28883	PASS	G	C	3115	0.940931	0	1,1,1547,1547	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749418	28883	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	3115	0.005136	0	1,1,10,9	HIGH	NONSENSE	STOP_GAINED	N	Gga/Tga	G204*	N	0.005136	0.991071	2	2	G>T
ERR5749418	28977	PASS	C	T	1578	0.925222	2147483647	0,0,0,1577	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749418	29091	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CT	23404	0.003034	0	23283,50,71,0	HIGH	NONE	FRAME_SHIFT	N	ttc/ttTc	F274F?	N	0.000452	0.073908	3	1	C>CT
ERR5749418	29109	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	23404	0.004059	0	23259,50,95,0	HIGH	NONE	FRAME_SHIFT	N	cca/	P279	N	0.004059	0.940585	2	2	CA>C
ERR5749418	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	46303	0.001533	1	23234,22971,46,42	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749418	29284	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	23401	0.007051	0	50,23126,0,186	LOW	SILENT	SYNONYMOUS_CODING	N	atC/atT	I337	N	0.000393	0.931014	3	2	C>T
ERR5749418	29386	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	4068	0.003933	0	4052,0,16,0	HIGH	NONE	FRAME_SHIFT	N	aag/aaAg	K373K?	N	0.000887	0.899197	4	2	C>CA
ERR5749418	29421	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	4067	0.002705	0	4049,0,13,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	cCg/cTg	P383L	N	0.002705	0.052892	2	2	C>T
ERR5749419	241	PASS	C	T	8277	0.871451	0	0,1,4118,4123	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749419	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	12755	0.002509	0	12715,0,32,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749419	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12745	0.001962	0	11797,0,899,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749419	657	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	12777	0.001565	0	4,12671,0,28	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A131D	leader	0.001202	0.365979	3	1	C>A
ERR5749419	657	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	12777	0.004774	0	4,12671,0,73	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gTt	A131V	leader	0.001202	0.365979	3	1	C>T
ERR5749419	892	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	27395	5.84E-4	0	0,27379,0,16	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K30	nsp2	0.000495	0.082222	2	2	TA>T
ERR5749419	913	PASS	C	T	27413	0.911319	0	0,19,0,27358	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749419	1027	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	20111	0.002138	308	20025,23,29,15	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccT/ccC	P74	nsp2	0.001454	0.276316	1	1	T>C
ERR5749419	2305	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTAAATAAATTTTTGGCTTTGTGTGCTGACTCTATCATTATTGGTGGAGCTAAACTTAAAGC	G	22571	4.43E-4	0	22561,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gtaaataaatttttggctttgtgtgctgactctatcattattggtggagctaaacttaaagccttg/	VNKFLALCADSIIIGGAKLKAL502	nsp2	0.000443	0.070409	4	3	GCTTGTAAATAAATTTTTGGCTTTGTGTGCTGACTCTATCATTATTGGTGGAGCTAAACTTAAAGC>G
ERR5749419	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	86569	0.001525	2147483647	43227,40499,59,2556	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749419	2775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	AG	43497	4.37E-4	0	0,43478,0,19	HIGH	NONE	FRAME_SHIFT	ORF1ab	agt/Gagt	S20E?	nsp3	0.000437	0.951613	3	2	A>AG
ERR5749419	3037	PASS	C	T	27046	0.82319	58	1,23,13512,13326	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749419	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	13655	0.001904	684	11,13608,26,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749419	3267	PASS	C	T	28575	0.973368	0	1,0,28567,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749419	3832	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	17182	0.001164	0	17157,5,20,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L373	nsp3	0.000689	0.327273	4	2	CT>C
ERR5749419	4237	PASS	T	C	50113	0.913037	0	1,1,25098,24904	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaT/aaC	N506	nsp3	0.000302	0.918634	2	2	T>C
ERR5749419	4255	PASS	G	A	50192	0.828499	37	24,4,24981,24883	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccG/ccA	P512	nsp3	0.001102	0.871853	2	1	G>A
ERR5749419	5388	PASS	C	A	8660	0.964088	2147483647	0,0,8656,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749419	5575	PASS	C	T	8663	0.952557	70	2,1,0,8655	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y952	nsp3	0.01018	0.961493	1	1	C>T
ERR5749419	5986	PASS	C	T	18313	0.97712	2147483647	0,0,18302,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749419	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18243	0.001206	0	0,18054,0,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749419	6741	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	18303	0.001093	0	6,18216,0,21	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cGg/cAg	R1341Q	nsp3	0.001093	0.204082	3	2	G>A
ERR5749419	6954	PASS	T	C	29537	0.822121	0	0,10,0,29378	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749419	7070	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	46810	0.003867	787	16991,29619,185,1	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggc/Agc	G1451S	nsp3	0.000698	0.101434	3	1	G>A
ERR5749419	7926	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	25765	8.54E-4	0	0,25734,0,22	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1737	nsp3	0.000531	0.97019	5	2	CA>C
ERR5749419	8084	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	31564	8.24E-4	0	31538,0,26,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1790	nsp3	0.000543	0.923413	4	2	GA>G
ERR5749419	8254	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AG	A	31579	4.12E-4	0	5,31561,0,13	HIGH	NONE	FRAME_SHIFT	ORF1ab	gaa/	E1846	nsp3	0.000412	0.959563	2	2	AG>A
ERR5749419	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	28431	0.001477	69	19268,9121,42,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749419	10595	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	28374	9.87E-4	0	0,28279,0,32	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F181L	3Cpro	0.000964	0.076408	1	1	T>C
ERR5749419	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	33895	0.001151	0	33816,0,61,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749419	11287	PASS	GTCTGGTTTT	G	33887	0.997492	0	0,84,0,33802	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749419	11335	PASS	G	T	49883	0.4187	60	9380,19111,6596,14784	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtG/gtT	V121	nsp6	0.4187	0.4187	1	1	G>T
ERR5749419	11507	PASS	G	A	31758	0.904276	0	1,0,15914,15751	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Att	V179I	nsp6	0.007744	0.914418	2	2	G>A
ERR5749419	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	48064	9.57E-4	6	32044,15952,28,20	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749419	12459	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	58112	0.002237	34	28247,29722,85,47	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T123I	nsp8	0.000658	0.986093	1	1	C>T
ERR5749419	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	28335	8.82E-4	0	28286,0,27,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749419	13384	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30275	8.26E-4	0	30220,0,31,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C120	nsp10	0.000578	0.056161	3	3	C>T
ERR5749419	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	60431	0.001076	0	30180,30104,34,34	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749419	13994	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	23445	4.27E-4	0	23435,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/	L186	RdRp	0.000427	0.114441	3	2	CT>C
ERR5749419	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	15349	0.004039	2147483647	14974,131,5,234	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749419	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	29835	5.7E-4	0	14961,14881,9,8	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749419	14408	PASS	C	T	29835	0.843942	15	0,5,14892,14723	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749419	14676	PASS	C	T	21146	0.756597	0	5,0,21079,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749419	14688	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	21143	5.68E-4	0	21131,0,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K417	RdRp	0.000534	0.979772	2	2	CA>C
ERR5749419	15279	PASS	C	T	29126	0.894218	0	2,0,29085,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749419	15420	PASS	T	G	29080	0.93033	0	0,47,0,29025	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcG	A660	RdRp	0.908883	0.934773	1	1	T>G
ERR5749419	16176	PASS	T	C	28667	0.981198	2	0,2,10370,18285	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749419	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GA	G	29209	0.001232	0	29164,0,36,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GA>G
ERR5749419	17502	PASS	C	T	24536	0.980926	0	2,0,24506,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F422	helicase	0.000611	0.9865	2	2	C>T
ERR5749419	18747	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	37140	3.77E-4	0	37126,0,14,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tataat/	YN237	ExoN	0.000375	0.982946	4	2	CTA>C
ERR5749419	19011	PASS	C	T	28188	0.973819	0	2,0,28177,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D324	ExoN	0.000408	0.975746	4	2	C>T
ERR5749419	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	28153	4.97E-4	0	0,28139,0,14	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749419	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24433	0.002906	0	24347,0,75,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749419	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25071	0.001077	0	25008,0,29,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749419	21516	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAG	C	24280	4.12E-4	0	24270,0,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	agagtt/	RV287	MethTr	0.000412	0.905456	2	2	CAG>C
ERR5749419	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	48324	0.001138	0	23686,24065,33,36	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749419	21614	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24280	0.001194	0	0,24239,0,31	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L18F	S	0.001194	0.949239	2	2	C>T
ERR5749419	21764	PASS	ATACATG	A	19519	0.994672	0	104,0,19415,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749419	21781	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	19519	5.12E-4	0	19509,0,10,0	HIGH	NONE	FRAME_SHIFT	S	aat/aaAt	N74K?	S	0.000512	0.104485	2	2	C>CA
ERR5749419	21990	PASS	TTTA	T	19528	0.9979	17	1,40,7,19480	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749419	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	26649	0.001351	0	0,26606,0,38	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749419	23063	PASS	A	T	22699	0.868188	0	0,6,0,22574	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749419	23271	PASS	C	A	31284	0.926768	0	1,0,31249,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749419	23403	PASS	A	G	31267	0.968465	0	0,7,0,31235	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749419	23604	PASS	C	A	23042	0.946142	0	18,0,23015,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749419	23709	PASS	C	T	23013	0.942293	0	0,7,1,22983	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749419	24506	PASS	T	G	29798	0.975133	0	10,0,29778,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749419	24914	PASS	G	C	61295	0.958463	0	0,0,30542,30714	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749419	25350	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	28846	7.63E-4	0	28819,5,22,0	HIGH	NONE	FRAME_SHIFT	S	cca/	P1263	S	0.000626	0.97904	4	2	CA>C
ERR5749419	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	12389	0.002906	640	12310,21,8,28	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749419	26571	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	19692	5.08E-4	0	19674,6,10,0	HIGH	NONE	FRAME_SHIFT	M	ctt/	L17	M	0.000508	0.905823	3	2	CT>C
ERR5749419	27765	PASS	C	T	34814	0.965589	0	0,4,0,34792	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7b	Ctt/Ttt	L4F	orf7b	0.00109	0.970449	1	1	C>T
ERR5749419	27972	PASS	C	T	15006	0.909703	41	1,2,14890,72	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749419	28048	PASS	G	T	14943	0.919963	0	0,19,0,14919	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749419	28111	PASS	A	G	48362	0.980398	1	7,2,33384,14944	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749419	28239	PASS	GTTGTT	G	33352	0.983959	0	529,0,32811,6	HIGH	NONE	FRAME_SHIFT	ORF8	gtttta/	VL117	orf8	0.000417	0.984998	9	2	GTTGTT>G
ERR5749419	28249	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	ATC	32935	0.001306	0	32873,6,43,0	HIGH	NONE	FRAME_SHIFT	ORF8	ttc/CTttc	F120L?	orf8	0.000443	0.063605	3	2	A>ATC
ERR5749419	28250	PASS	T	TCTG	32935	0.992409	0	205,0,32679,6	MODERATE	NONE	CODON_INSERTION	ORF8	ttc/CTGttc	F120LF	orf8	0.000494	0.993968	5	3	T>TCTG
ERR5749419	28250	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TATG	32935	5.77E-4	0	205,0,19,0	MODERATE	NONE	CODON_INSERTION	ORF8	ttc/ATGttc	F120MF	orf8	0.000494	0.993968	5	3	T>TATG
ERR5749419	28253	PASS	CA	C	32935	0.994626	0	176,0,32752,6	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749419	28254	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	ATC	32935	6.07E-4	0	32908,6,20,0	HIGH	NONE	FRAME_SHIFT+STOP_LOST+SPLICE_SITE_REGION	ORF8	taa/tCTaa	*122S?	orf8	0.000541	0.914398	3	2	A>ATC
ERR5749419	28270	PASS	TA	T	63676	0.997079	338	169,12,32755,30735	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749419	28271	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AA	A	63676	0.001351	226	32841,30746,85,1	.	.	.	.	.	.	.	0.000482	0.924941	3	2	AA>A
ERR5749419	28280	PASS	G	C	63677	0.943276	24	12,1,32852,30710	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749419	28281	PASS	A	T	63677	0.937419	32	31,8,32849,30719	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749419	28282	PASS	T	A	63684	0.907386	14	31,15,32781,30727	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749419	28881	PASS	G	A	21519	0.772108	18	7,0,10640,10604	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749419	28882	PASS	G	A	21518	0.833628	14	8,1,10754,10556	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749419	28883	PASS	G	C	21518	0.941909	3	2,0,10777,10724	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749419	28977	PASS	C	T	10969	0.932628	0	0,0,2,10948	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749419	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	70990	0.001127	0	35644,35210,53,55	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749419	29311	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	35771	3.35E-4	0	8,35751,0,12	HIGH	NONE	FRAME_SHIFT	N	aaa/	K347	N	0.000335	0.790798	3	2	CA>C
ERR5749419	29386	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CA	15814	0.001454	0	15789,2,23,0	HIGH	NONE	FRAME_SHIFT	N	aag/aaAg	K373K?	N	0.000887	0.899197	4	2	C>CA
ERR5749420	241	PASS	C	T	13081	0.849553	0	0,0,6513,6523	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749420	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	16078	0.004914	12	15997,11,78,1	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749420	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTT	G	16080	0.001368	0	15821,10,22,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgtt/	GHV82	leader	0.00045	0.081241	6	1	GGTCATGTT>G
ERR5749420	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTA	G	16080	0.002612	0	15821,10,42,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatg/gtg	GHVM82V	leader	0.00045	0.081241	6	1	GGTCATGTTA>G
ERR5749420	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	16080	0.010012	50	15821,10,157,4	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749420	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTTGA	G	16080	7.46E-4	0	15821,10,12,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTTGA>G
ERR5749420	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	16084	0.002611	7	14478,29,1192,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749420	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	16084	0.003109	38	16003,31,47,3	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749420	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	16083	0.001244	0	15995,34,20,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	gttatg/gtg	VM84V	leader	0.000554	0.991848	4	1	GTTA>G
ERR5749420	515	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTATGGTT	G	16083	0.001617	12	15995,34,25,1	HIGH	NONE	FRAME_SHIFT	ORF1ab	gttatggtt/	VMV84	leader	0.000554	0.991848	4	1	GTTATGGTT>G
ERR5749420	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	16082	0.001492	0	16009,35,24,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749420	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	42017	0.001047	55	25882,16080,41,3	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749420	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATT	A	42017	8.33E-4	20	25809,16045,29,6	HIGH	NONE	FRAME_SHIFT	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATT>A
ERR5749420	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	42017	0.002904	21	25809,16045,90,32	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749420	913	PASS	C	T	25921	0.921724	0	0,12,0,25871	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749420	1661	PASS	G	T	24350	0.983409	0	2,0,24339,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gac/Tac	D286Y	nsp2	0.983409	0.98948	1	1	G>T
ERR5749420	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	86545	0.001202	2147483647	43169,40760,90,2306	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749420	3037	PASS	C	T	27087	0.815299	50	1,20,13529,13333	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749420	3267	PASS	C	T	24600	0.969146	0	2,0,24579,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749420	4578	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TTAACGATC	T	17329	5.19E-4	0	0,17320,0,9	HIGH	NONE	FRAME_SHIFT	ORF1ab	aacgatctaaat/	NDLN621	nsp3	0.000519	0.082979	2	2	TTAACGATC>T
ERR5749420	5388	PASS	C	A	8893	0.95727	2147483647	0,0,8888,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749420	5986	PASS	C	T	17838	0.974773	2147483647	0,0,17823,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749420	6954	PASS	T	C	27108	0.823668	0	0,5,13,26935	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749420	7067	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAA	G	54787	2.74E-4	42	27597,27175,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	gaa/	E1450	nsp3	0.000274	0.059217	5	3	GAA>G
ERR5749420	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	35754	6.15E-4	50	20759,14973,22,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749420	10336	PASS	C	T	25174	0.949353	0	0,12,0,25118	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A94	3Cpro	0.002849	0.949353	2	2	C>T
ERR5749420	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	25191	0.001469	0	25093,0,70,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749420	11287	PASS	GTCTGGTTTT	G	25192	0.995792	23	1,105,0,25086	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749420	12797	PASS	G	T	18236	0.069588	0	16725,2,1504,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ggt/Tgt	G38C	nsp9	0.069588	0.069588	1	1	G>T
ERR5749420	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	17456	5.73E-4	0	17444,3,10,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749420	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	44241	0.001198	0	22087,22048,27,27	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749420	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	16403	0.00378	2147483647	16032,157,5,202	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749420	14407	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCTACAAG	C	31955	0.002472	0	15985,15906,40,39	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctacaagt/	PTS323	RdRp	0.000388	0.799973	2	2	CCTACAAG>C
ERR5749420	14408	PASS	C	T	31955	0.832295	0	3,3,15924,15727	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749420	14676	PASS	C	T	17825	0.863562	0	10,0,17782,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749420	15279	PASS	C	T	26133	0.886886	0	3,0,26082,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749420	16176	PASS	T	C	26784	0.981519	0	0,0,13565,13205	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749420	18248	PASS	C	T	16609	0.606358	0	0,6084,0,10520	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P70L	ExoN	0.606358	0.606358	1	1	C>T
ERR5749420	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	32108	7.47E-4	0	32084,0,24,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749420	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	29919	5.01E-4	0	0,29904,0,15	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749420	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	38486	0.001793	0	38392,0,73,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749420	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	29379	9.87E-4	0	29313,0,29,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749420	21569	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	38045	3.94E-4	0	18982,19053,7,8	HIGH	NONE	FRAME_SHIFT	S	ctt/Tctt	L5S?	S	0.000394	0.091869	4	1	G>GT
ERR5749420	21764	PASS	ATACATG	A	17630	0.996937	0	53,0,17576,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749420	21990	PASS	TTTA	T	17643	0.998073	0	0,34,10,17599	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749420	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	24911	9.23E-4	7	6663,18195,10,15	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749420	23063	PASS	A	T	6646	0.85149	0	0,4,2,6599	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749420	23271	PASS	C	A	28195	0.915801	0	4,0,28155,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749420	23403	PASS	A	G	28198	0.969005	0	0,4,0,28179	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749420	23604	PASS	C	A	21172	0.942849	0	16,0,21143,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749420	23709	PASS	C	T	21157	0.941343	0	0,4,7,21110	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749420	23817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	40711	7.61E-4	16	19497,21163,22,10	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTt/cCt	L752P	S	0.000646	0.066832	1	1	T>C
ERR5749420	24127	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	36832	4.34E-4	22	17318,19516,2,14	HIGH	NONE	FRAME_SHIFT	S	aac/	N856	S	0.000324	0.111888	4	1	TA>T
ERR5749420	24506	PASS	T	G	23129	0.972934	0	8,0,23108,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749420	24914	PASS	G	C	48298	0.9618	0	0,0,24074,24189	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749420	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	19501	0.001744	496	19373,32,12,22	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749420	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	19450	5.66E-4	0	19436,3,11,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749420	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	19591	0.001582	999	19252,119,117,73	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749420	26157	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTA	T	59642	5.03E-4	0	5,59606,0,30	HIGH	NONE	FRAME_SHIFT	ORF3a	gttaat/	VN256	orf3a	0.000249	0.122153	5	2	TGTTA>T
ERR5749420	26158	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTTA	G	59643	3.86E-4	0	5,59612,0,23	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF3a	gttaat/gat	VN256D	orf3a	0.000297	0.905181	6	2	GTTA>G
ERR5749420	26774	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT	G	17342	0.001153	0	1,17302,0,20	HIGH	NONE	FRAME_SHIFT	M	gcttgtcttgtaggcttgatgtggctcagctacttcattgcttctttcagactgttt/	ACLVGLMWLSYFIASFRLF85	M	0.000483	0.943732	7	2	GGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTT>G
ERR5749420	26775	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT	G	17342	0.001672	0	1,17312,0,29	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	M	tgtcttgtaggcttgatgtggctcagctacttcattgcttctttc/ttc	CLVGLMWLSYFIASF86F	M	0.000483	0.053997	3	1	GCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTT>G
ERR5749420	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	17346	0.007322	0	1,17204,0,127	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749420	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT	G	17346	6.34E-4	0	1,17204,0,11	HIGH	NONE	FRAME_SHIFT	M	cttgtaggcttgatgtggctcagctacttcattgcttctttc/	LVGLMWLSYFIASF87	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTT>G
ERR5749420	27684	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTCTCCAATTTT	C	25111	4.78E-4	0	36,25069,0,12	HIGH	NONE	FRAME_SHIFT	ORF7a	ccaatttttctt/	PIFL99	orf7a	0.000478	0.90411	2	2	CTCTCCAATTTT>C
ERR5749420	27972	PASS	C	T	15189	0.907565	68	3,4,15021,122	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749420	28048	PASS	G	T	15068	0.923679	0	0,14,0,15044	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749420	28095	PASS	A	T	15090	0.964082	302	9,2,0,15025	HIGH	NONSENSE	STOP_GAINED	ORF8	Aaa/Taa	K68*	orf8	0.002672	0.967672	2	2	A>T
ERR5749420	28111	PASS	A	G	39071	0.978654	5	4,0,23979,15073	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749420	28270	PASS	TA	T	46473	0.991651	1030	396,7,23463,22622	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749420	28280	PASS	G	C	46194	0.940187	7	10,4,23505,22611	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749420	28281	PASS	A	T	46194	0.916483	32	35,11,23480,22604	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749420	28282	PASS	T	A	46195	0.907046	20	22,7,23415,22619	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749420	28302	PASS	G	C	47264	0.953728	2	2,1,23356,23856	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	cGa/cCa	R10P	N	0.001527	0.953728	4	2	G>C
ERR5749420	28881	PASS	G	A	20368	0.766938	9	4,0,10067,10015	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749420	28882	PASS	G	A	20367	0.828448	5	6,2,10170,9995	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749420	28883	PASS	G	C	20368	0.943784	0	1,1,10186,10146	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749420	28977	PASS	C	T	10370	0.932787	0	0,3,0,10346	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749420	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	78252	0.001035	0	39282,38828,51,48	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749421	241	PASS	C	T	19371	0.851789	1	2,4,9627,9632	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749421	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	16344	0.003488	0	16285,3,57,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749421	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	16348	0.00208	0	16288,7,34,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749421	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	16336	0.001898	0	15086,7,1111,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749421	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	16336	0.001408	0	16306,7,23,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749421	673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	46299	0.001015	43	29912,16317,20,34	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y136	leader	0.000454	0.602236	3	2	C>T
ERR5749421	673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CG	C	46299	4.54E-4	46	29932,16346,4,17	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggc/	G137	leader	0.000454	0.602236	3	2	CG>C
ERR5749421	683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	46299	3.46E-4	11	29920,16361,14,2	HIGH	NONE	FRAME_SHIFT	ORF1ab	cta/	L140	leader	0.000316	0.135802	3	2	CTA>C
ERR5749421	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	46299	8.42E-4	11	29893,16354,31,8	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749421	913	PASS	C	T	29929	0.933643	0	0,16,0,29882	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749421	2702	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	56989	6.32E-4	3190	56528,115,67,150	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F633V	nsp2	0.000632	0.333333	1	1	T>G
ERR5749421	2713	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	112925	0.001585	2147483647	56362,52504,82,3661	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aaA/aaC	K636N	nsp2	0.000941	0.059322	2	2	A>C
ERR5749421	3037	PASS	C	T	28077	0.812195	70	1,27,14038,13809	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749421	3144	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	14174	0.001552	646	5,14139,23,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	tTg/tGg	L142W	nsp3	0.001349	0.761905	2	1	T>G
ERR5749421	3267	PASS	C	T	30140	0.969841	0	1,0,30119,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749421	3802	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TA	T	49812	7.43E-4	3	31444,18322,21,16	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/	N363	nsp3	0.000554	0.064198	4	2	TA>T
ERR5749421	4237	PASS	T	C	51442	0.909335	0	4,4,25750,25529	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaT/aaC	N506	nsp3	0.000302	0.918634	2	2	T>C
ERR5749421	4255	PASS	G	A	51520	0.806153	58	30,3,25644,25386	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccG/ccA	P512	nsp3	0.001102	0.871853	2	1	G>A
ERR5749421	5170	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	24175	6.62E-4	0	0,24159,0,16	HIGH	NONE	FRAME_SHIFT	ORF1ab	aca/	T819	nsp3	0.000565	0.894036	2	2	CCA>C
ERR5749421	5388	PASS	C	A	8964	0.955935	2147483647	0,0,8961,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749421	5497	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	8961	0.001116	0	0,8949,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	aga/	R928	nsp3	0.000964	0.897745	3	2	CA>C
ERR5749421	5575	PASS	C	T	9011	0.938409	664	27,0,18,8959	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y952	nsp3	0.01018	0.961493	1	1	C>T
ERR5749421	5986	PASS	C	T	17980	0.971691	2147483647	0,0,17962,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749421	6954	PASS	T	C	36704	0.817922	0	0,16,0,36490	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749421	8123	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	37586	0.001144	0	37472,3,57,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Ttt	L1802F	nsp3	0.001144	0.778589	1	1	C>T
ERR5749421	9541	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTGTTTAACACCAGTTTACTCATTCTTACCTGG	C	37954	0.001212	120	20581,17327,46,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	acaccagtttactcattcttacctggtgtttat/	TPVYSFLPGVY332	nsp4	0.000346	0.955771	2	2	CTGTTTAACACCAGTTTACTCATTCTTACCTGG>C
ERR5749421	9661	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	40865	9.54E-4	0	20551,20219,22,21	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F369	nsp4	0.000584	0.920378	2	2	C>T
ERR5749421	10507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30057	0.001331	0	29933,0,58,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaC/aaT	N151	3Cpro	0.00123	0.842913	2	2	C>T
ERR5749421	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	34520	0.001767	0	33666,9,61,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttg/ttTTg	L37F?	nsp6	0.000965	0.945355	5	2	C>CTT
ERR5749421	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34520	0.001477	0	34397,9,57,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749421	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	34496	9.86E-4	0	34407,0,66,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749421	11287	PASS	GTCTGGTTTT	G	34497	0.997362	0	0,90,0,34406	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749421	11507	PASS	G	A	36619	0.898987	4	4,1,18321,18178	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Att	V179I	nsp6	0.007744	0.914418	2	2	G>A
ERR5749421	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	51788	9.46E-4	9	33314,18394,40,13	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749421	12459	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	63220	6.96E-4	1	26458,36700,17,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T123I	nsp8	0.000658	0.986093	1	1	C>T
ERR5749421	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	26479	0.001322	0	26421,0,35,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749421	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	17836	0.00129	0	17814,0,23,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749421	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	68649	0.001194	0	34283,34186,45,46	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749421	14168	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	25163	6.76E-4	0	6,25140,0,17	HIGH	NONE	FRAME_SHIFT	ORF1ab	atatta/	IL244	RdRp	0.000479	0.314961	1	1	CTA>C
ERR5749421	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	20450	0.00533	2147483647	19856,194,14,371	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749421	14408	PASS	C	T	39551	0.833633	14	3,11,19758,19523	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749421	14676	PASS	C	T	23265	0.778208	0	16,0,23187,2	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749421	15279	PASS	C	T	35183	0.893102	0	4,0,35130,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749421	15420	PASS	T	G	35138	0.918407	0	0,80,0,35037	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcG	A660	RdRp	0.908883	0.934773	1	1	T>G
ERR5749421	16176	PASS	T	C	33256	0.980154	7	2,0,13784,19443	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749421	16837	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GAA	G	26725	7.86E-4	0	26669,0,21,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K202	helicase	0.000535	0.100775	3	2	GAA>G
ERR5749421	17502	PASS	C	T	20516	0.980698	0	5,0,20497,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F422	helicase	0.000611	0.9865	2	2	C>T
ERR5749421	18687	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	32683	6.43E-4	0	32662,0,21,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tcc/	S218	ExoN	0.000374	0.981963	3	2	CT>C
ERR5749421	19011	PASS	C	T	36641	0.969106	0	4,0,36616,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D324	ExoN	0.000408	0.975746	4	2	C>T
ERR5749421	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	34042	0.002115	0	33939,0,72,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749421	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	36281	9.1E-4	0	36199,0,34,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749421	20844	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	68573	3.65E-4	0	32266,36282,11,14	HIGH	NONE	FRAME_SHIFT	ORF1ab	tataat/	YN63	MethTr	0.000293	0.905571	5	2	CTA>C
ERR5749421	21077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	32283	8.05E-4	0	11,32225,0,27	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCa/aTa	T140I	MethTr	0.000492	0.955529	4	2	C>T
ERR5749421	21077	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	32283	8.36E-4	0	11,32238,0,27	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K141	MethTr	0.000492	0.955529	4	2	CA>C
ERR5749421	21255	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	81603	6.0E-4	1	42088,39431,31,26	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcG/gcA	A199	MethTr	0.000341	0.917425	4	2	G>A
ERR5749421	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	54726	0.001042	2	26802,27292,30,35	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749421	21622	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	27519	8.72E-4	0	0,27489,0,25	LOW	SILENT	SYNONYMOUS_CODING	S	acC/acT	T20	S	0.000846	0.946634	3	2	C>T
ERR5749421	21764	PASS	ATACATG	A	17422	0.996384	18	61,1,17356,3	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749421	21817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	17410	6.89E-4	0	17399,0,12,0	HIGH	NONE	FRAME_SHIFT	S	ttt/	F86	S	0.000689	0.961354	3	2	AT>A
ERR5749421	21990	PASS	TTTA	T	17422	0.997704	0	0,40,3,17379	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749421	23063	PASS	A	T	20044	0.862952	0	0,3,0,19943	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749421	23271	PASS	C	A	31931	0.920704	0	1,0,31890,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749421	23403	PASS	A	G	31926	0.974441	0	0,5,2,31883	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749421	23604	PASS	C	A	22038	0.938198	0	18,0,22014,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749421	23709	PASS	C	T	22026	0.932398	0	0,8,2,21972	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749421	24010	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATTTATTGAAGATCTAC	A	26346	6.07E-4	0	316,26024,0,16	HIGH	NONE	FRAME_SHIFT	S	attgaagatctacttttc/	IEDLLF818	S	0.000455	0.926398	4	2	ATTTATTGAAGATCTAC>A
ERR5749421	24506	PASS	T	G	31942	0.976082	0	8,0,31929,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749421	24914	PASS	G	C	52210	0.956273	0	0,0,26011,26153	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749421	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	25962	0.001156	460	25843,25,13,19	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749421	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	26165	0.001376	1111	25599,213,212,96	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749421	26256	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	80216	7.48E-4	10	21410,58672,11,54	LOW	SILENT	SYNONYMOUS_CODING	E	ttC/ttT	F4	E	0.000748	0.969561	2	2	C>T
ERR5749421	26730	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	35582	6.46E-4	0	17748,17842,12,11	HIGH	NONE	FRAME_SHIFT	M	tac/	Y71	M	0.000371	0.919543	3	2	GT>G
ERR5749421	26779	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT	G	17903	7.26E-4	0	0,17883,0,13	HIGH	NONE	FRAME_SHIFT	M	gtaggcttgatgtggctcagctacttcattgcttctttc/	VGLMWLSYFIASF88	M	0.000581	0.064189	3	1	GTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCT>G
ERR5749421	26936	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	58885	0.001308	0	58787,0,79,0	LOW	SILENT	SYNONYMOUS_CODING	M	ctC/ctT	L138	M	0.001308	0.968147	2	1	C>T
ERR5749421	27741	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	38548	3.63E-4	0	4,38528,0,14	HIGH	NONE	FRAME_SHIFT	ORF7a	aga/	R118	orf7a	0.000363	0.954278	3	2	CA>C
ERR5749421	27765	PASS	C	T	38552	0.965475	0	0,4,1,38518	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7b	Ctt/Ttt	L4F	orf7b	0.00109	0.970449	1	1	C>T
ERR5749421	27972	PASS	C	T	15730	0.898474	51	3,3,15549,110	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749421	28048	PASS	G	T	15629	0.912662	0	0,25,0,15589	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749421	28111	PASS	A	G	48190	0.97819	0	6,3,32525,15634	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749421	28239	PASS	GTTGTT	G	32440	0.98172	0	596,0,31847,0	HIGH	NONE	FRAME_SHIFT	ORF8	gtttta/	VL117	orf8	0.000417	0.984998	9	2	GTTGTT>G
ERR5749421	28249	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	ATC	32029	0.001467	0	31971,0,47,0	HIGH	NONE	FRAME_SHIFT	ORF8	ttc/CTttc	F120L?	orf8	0.000443	0.063605	3	2	A>ATC
ERR5749421	28250	PASS	T	TCTG	32029	0.990852	0	241,0,31736,0	MODERATE	NONE	CODON_INSERTION	ORF8	ttc/CTGttc	F120LF	orf8	0.000494	0.993968	5	3	T>TCTG
ERR5749421	28250	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TATG	32029	0.00103	0	241,0,33,0	MODERATE	NONE	CODON_INSERTION	ORF8	ttc/ATGttc	F120MF	orf8	0.000494	0.993968	5	3	T>TATG
ERR5749421	28253	PASS	CA	C	32029	0.993381	0	212,0,31817,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749421	28253	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	CTT	32029	9.37E-4	0	31999,0,30,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/TTatc	I121L?	orf8	0.000422	0.995511	4	3	C>CTT
ERR5749421	28254	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	ATC	32029	7.18E-4	0	31997,0,23,0	HIGH	NONE	FRAME_SHIFT+STOP_LOST+SPLICE_SITE_REGION	ORF8	taa/tCTaa	*122S?	orf8	0.000541	0.914398	3	2	A>ATC
ERR5749421	28270	PASS	TA	T	61775	0.995451	455	238,19,31778,29716	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749421	28270	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAA	T	61775	3.72E-4	57	238,19,12,11	.	.	.	.	.	.	.	0.000322	1	2	1	TAA>T
ERR5749421	28271	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AA	A	61775	0.001554	254	31931,29744,95,1	.	.	.	.	.	.	.	0.000482	0.924941	3	2	AA>A
ERR5749421	28280	PASS	G	C	61777	0.943102	16	24,9,31916,29704	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749421	28281	PASS	A	T	61777	0.929035	31	34,10,31917,29700	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749421	28282	PASS	T	A	61782	0.903402	11	47,28,31841,29708	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749421	28881	PASS	G	A	24314	0.761249	12	5,0,12073,11914	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749421	28882	PASS	G	A	24312	0.815729	36	13,0,12177,11850	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749421	28883	PASS	G	C	24312	0.941305	3	0,1,12203,12082	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749421	28977	PASS	C	T	12392	0.918899	0	0,3,0,12359	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749421	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	76418	0.001008	2	38402,37887,53,47	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749422	241	PASS	C	T	14762	0.860453	2	1,3,7331,7372	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749422	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	12689	0.001103	0	12680,1,14,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749422	509	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GGTCATGTTATGGTT	G	12689	0.002049	0	12655,1,26,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	ggtcatgttatggttgag/	GHVMVE82	leader	0.00045	0.081241	6	1	GGTCATGTTATGGTT>G
ERR5749422	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	12682	0.002523	0	11720,1,906,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	caT/caG	H83Q	leader	0.000596	0.061404	2	2	T>G
ERR5749422	514	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TGTTATG	T	12682	7.1E-4	0	12672,1,9,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atggtt/	MV85	leader	0.000596	0.061404	2	2	TGTTATG>T
ERR5749422	517	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TATG	T	12681	8.67E-4	0	12664,1,11,0	MODERATE	NONE	CODON_DELETION	ORF1ab	atg/	M85	leader	0.000587	0.476744	4	1	TATG>T
ERR5749422	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	33124	5.13E-4	0	20404,12702,10,7	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749422	913	PASS	C	T	20405	0.91458	0	0,7,0,20367	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749422	1573	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	G	3261	0.0046	405	0,3242,15,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acA/acG	T256	nsp2	0.001231	0.75	1	1	A>G
ERR5749422	1594	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	3261	0.007973	0	16,3213,0,31	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S263	nsp2	0.0019	0.963177	1	1	C>T
ERR5749422	1636	PASS	G	T	17668	0.957211	2147483647	0,0,17664,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gaG/gaT	E277D	nsp2	0.00204	0.963192	2	2	G>T
ERR5749422	1684	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	17663	0.002038	0	17616,0,36,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I293	nsp2	0.000638	0.973136	2	2	C>T
ERR5749422	3037	PASS	C	T	22151	0.821588	36	2,18,11062,10931	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749422	3267	PASS	C	T	19306	0.969388	2147483647	0,0,19294,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749422	3671	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GA	27788	7.2E-4	0	13886,13883,10,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	aat/aaAt	N319K?	nsp3	0.000351	0.0625	6	2	G>GA
ERR5749422	5388	PASS	C	A	7308	0.961823	2147483647	0,0,7305,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749422	5986	PASS	C	T	14181	0.972428	0	2,0,14170,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749422	6696	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13618	0.001689	0	4,13428,0,33	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P1326L	nsp3	0.000731	0.14377	4	2	C>T
ERR5749422	6954	PASS	T	C	22850	0.81558	0	0,3,2,22719	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749422	8950	PASS	C	T	42126	0.973033	5	5,3,17374,24724	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	atC/atT	I132	nsp4	0.002808	0.982604	1	1	C>T
ERR5749422	9170	PASS	C	T	17369	0.824054	0	0,19,0,17314	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ctt/Ttt	L206F	nsp4	0.82019	0.841764	1	1	C>T
ERR5749422	11074	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	18406	0.001413	0	18333,11,32,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F34	nsp6	0.000965	0.945355	5	2	C>T
ERR5749422	11083	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	T	18392	0.001196	0	18349,0,39,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	ttG/ttT	L37F	nsp6	0.000477	0.901695	5	2	G>T
ERR5749422	11287	PASS	GTCTGGTTTT	G	18393	0.99826	0	0,32,1,18360	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749422	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	31319	0.00166	0	15632,15592,29,28	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749422	14401	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	13521	0.003476	2147483647	13259,83,4,168	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttc/Gtc	F321V	RdRp	0.001926	0.204134	1	1	T>G
ERR5749422	14408	PASS	C	T	26411	0.843323	3	0,1,13190,13049	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749422	14676	PASS	C	T	12668	0.793417	0	3,0,12636,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749422	15279	PASS	C	T	22032	0.876498	2147483647	0,0,21997,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749422	16176	PASS	T	C	21849	0.982059	3	2,0,11191,10644	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749422	17181	PASS	T	C	15308	0.988633	0	11,0,15296,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaT/gaC	D315	helicase	0.986595	0.991193	1	1	T>C
ERR5749422	18576	PASS	C	T	27994	0.867936	0	0,4,0,27906	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D179	ExoN	0.005404	0.876866	2	2	C>T
ERR5749422	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	23201	5.17E-4	0	0,23189,0,12	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749422	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	32239	0.002202	0	32149,0,71,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749422	20628	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	32757	9.16E-4	0	32672,3,32,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggT	G336	endoR	0.000719	0.968531	2	1	C>T
ERR5749422	21234	PASS	C	T	32053	0.624247	0	21,0,31559,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcC/gcT	A192	MethTr	0.000472	0.857572	5	2	C>T
ERR5749422	21575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	30267	8.92E-4	1	14825,15110,14,17	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Ctt/Ttt	L5F	S	0.000619	0.877942	3	2	C>T
ERR5749422	21762	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTATACA	C	13745	0.00211	0	13716,0,29,0	MODERATE	NONE	CODON_DELETION	S	atacat/	IH68	S	0.001297	0.875707	2	2	CTATACA>C
ERR5749422	21764	PASS	ATACATG	A	13745	0.997163	0	39,0,13706,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749422	21990	PASS	TTTA	T	13748	0.997018	0	0,41,2,13705	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749422	23063	PASS	A	T	13837	0.872227	0	0,1,0,13768	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749422	23271	PASS	C	A	22325	0.919821	0	2,0,22298,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749422	23403	PASS	A	G	22328	0.968604	0	0,3,0,22305	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749422	23604	PASS	C	A	17039	0.946945	0	11,0,17014,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749422	23635	PASS	C	T	17016	0.945874	0	3,0,16987,0	LOW	SILENT	SYNONYMOUS_CODING	S	tcC/tcT	S691	S	0.002385	0.958978	1	1	C>T
ERR5749422	23709	PASS	C	T	17018	0.94212	0	0,3,0,16995	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749422	24506	PASS	T	G	18368	0.969893	0	4,0,18363,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749422	24914	PASS	G	C	38448	0.957943	0	0,0,19166,19255	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749422	25317	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	A	26483	0.001699	65	17990,8436,53,2	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	tCc/tAc	S1252Y	S	0.000828	0.956514	4	2	C>A
ERR5749422	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	21891	0.001233	303	21797,33,15,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749422	25699	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GC	21844	5.04E-4	0	21833,0,11,0	HIGH	NONE	FRAME_SHIFT	ORF3a	cct/ccCt	P104P?	orf3a	0.000359	0.059829	2	2	G>GC
ERR5749422	25794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	G	22031	0.00118	1246	21679,141,100,86	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	cgT/cgG	R134	orf3a	0.000918	0.095652	1	1	T>G
ERR5749422	25844	PASS	C	T	21809	0.91178	0	0,8,3,21765	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	aCt/aTt	T151I	orf3a	0.001226	0.938776	1	1	C>T
ERR5749422	26151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	52874	9.08E-4	0	3,52792,0,56	LOW	SILENT	SYNONYMOUS_CODING	ORF3a	tcC/tcT	S253	orf3a	0.000501	0.913698	4	2	C>T
ERR5749422	27577	PASS	C	T	21083	0.807001	0	6,0,20995,0	HIGH	NONSENSE	STOP_GAINED	ORF7a	Caa/Taa	Q62*	orf7a	0.000614	0.952205	4	2	C>T
ERR5749422	27972	PASS	C	T	12478	0.904392	71	4,4,12370,69	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749422	28001	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	24789	9.68E-4	0	12363,12375,13,13	LOW	SILENT	SYNONYMOUS_CODING	ORF8	ccG/ccA	P36	orf8	0.00085	0.830607	2	1	G>A
ERR5749422	28048	PASS	G	T	12410	0.920306	0	0,9,0,12395	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749422	28111	PASS	A	G	30693	0.978497	0	4,3,18260,12414	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749422	28270	PASS	TA	T	35409	0.995001	430	180,6,18013,17219	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749422	28271	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AA	A	35404	6.5E-4	65	18158,17226,23,0	.	.	.	.	.	.	.	0.000482	0.924941	3	2	AA>A
ERR5749422	28280	PASS	G	C	35333	0.939518	29	11,0,18049,17208	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749422	28281	PASS	A	T	35333	0.911358	7	17,9,18044,17205	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749422	28282	PASS	T	A	35333	0.912461	13	21,9,18002,17215	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749422	28881	PASS	G	A	17270	0.653966	11	9,2,8545,8184	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749422	28881	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	17270	0.002258	40	9,2,122,403	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aCg	R203T	N	0.000709	0.947368	4	2	G>C
ERR5749422	28882	PASS	G	A	17270	0.745223	18	7,0,8654,8213	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749422	28883	PASS	G	C	17270	0.945223	2	3,1,8664,8583	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749422	28977	PASS	C	T	8840	0.927602	0	0,1,1,8822	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749422	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	53296	0.001276	0	26762,26424,42,41	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A
ERR5749423	241	PASS	C	T	2497	0.865439	0	0,0,1242,1236	.	.	.	.	.	.	.	0.75	0.9375	1	1	C>T
ERR5749423	507	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	ATGGTCATGTTATGGT	A	6323	0.001582	0	6315,0,10,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	ORF1ab	ggtcatgttatggttgag/gag	GHVMVE82E	leader	0.000686	0.081932	3	1	ATGGTCATGTTATGGT>A
ERR5749423	676	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	G	22620	0.00137	177	16276,6296,0,32	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ggC/ggG	G137	leader	0.000799	0.919273	2	1	C>G
ERR5749423	685	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AAAGTCATTT	A	22620	7.07E-4	0	16272,6332,12,4	MODERATE	NONE	CODON_DELETION	ORF1ab	aagtcattt/	KSF141	leader	0.000303	0.999303	4	1	AAAGTCATTT>A
ERR5749423	906	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	16275	0.001413	0	0,16230,0,25	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T34I	nsp2	0.000551	0.081967	3	2	C>T
ERR5749423	913	PASS	C	T	16276	0.908638	0	0,11,0,16238	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tcC/tcT	S36	nsp2	0.859102	0.942623	1	1	C>T
ERR5749423	3037	PASS	C	T	13031	0.817666	27	0,9,6498,6429	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F106	nsp3	0.768421	0.921053	1	1	C>T
ERR5749423	3267	PASS	C	T	15746	0.967801	2147483647	0,0,15740,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aCt/aTt	T183I	nsp3	0.954128	1	1	1	C>T
ERR5749423	3575	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	GT	10365	8.68E-4	0	10356,0,9,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	tta/ttTa	L287F?	nsp3	0.000594	0.059126	3	1	G>GT
ERR5749423	4237	PASS	T	C	29519	0.91392	6	0,2,14765,14645	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	aaT/aaC	N506	nsp3	0.000302	0.918634	2	2	T>C
ERR5749423	4255	PASS	G	A	29560	0.839547	47	23,2,14705,14646	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccG/ccA	P512	nsp3	0.001102	0.871853	2	1	G>A
ERR5749423	5388	PASS	C	A	3230	0.956966	2147483647	0,0,3229,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	gCt/gAt	A890D	nsp3	0.446301	1	2	1	C>A
ERR5749423	5575	PASS	C	T	3235	0.952705	154	5,0,0,3229	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	taC/taT	Y952	nsp3	0.01018	0.961493	1	1	C>T
ERR5749423	5986	PASS	C	T	10450	0.978086	2147483647	0,0,10442,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F1089	nsp3	0.925373	1	1	1	C>T
ERR5749423	6272	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	A	16504	0.002242	0	16445,5,52,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Aat	Y1185N	nsp3	0.001735	0.156069	2	1	T>A
ERR5749423	6706	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	10442	0.001341	0	0,10428,0,14	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K1330	nsp3	0.000687	0.883999	2	2	CA>C
ERR5749423	6954	PASS	T	C	15153	0.821092	0	0,4,0,15067	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	aTa/aCa	I1412T	nsp3	0.001872	0.892308	2	2	T>C
ERR5749423	10642	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	C	15026	0.001597	0	0,14979,0,26	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acG/acC	T196	3Cpro	0.001264	0.951979	3	1	G>C
ERR5749423	11287	PASS	GTCTGGTTTT	G	18647	0.999088	0	0,15,0,18630	MODERATE	NONE	CODON_DELETION	ORF1ab	tctggtttt/	SGF106	nsp6	0.168258	1	1	1	GTCTGGTTTT>G
ERR5749423	11507	PASS	G	A	16317	0.905804	4	4,1,8160,8101	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Gtt/Att	V179I	nsp6	0.007744	0.914418	2	2	G>A
ERR5749423	11654	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	25455	0.001179	25	17202,8205,30,3	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Ttt/Ctt	F228L	nsp6	0.000709	0.129921	1	1	T>C
ERR5749423	12125	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	19568	0.00138	0	2,19493,0,32	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y12H	nsp8	0.000847	0.113436	1	1	T>C
ERR5749423	12503	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	16410	0.001219	0	16384,0,21,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	Tat/Cat	Y138H	nsp8	0.000882	0.108696	1	1	T>C
ERR5749423	13162	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	TAC	T	14284	0.00105	0	14269,0,15,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	act/	T49	nsp10	0.000528	0.198485	2	2	TAC>T
ERR5749423	13506	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	25357	0.001538	0	12659,12631,20,21	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	tgC/tgT	C22	RdRp	0.000536	0.074627	4	2	C>T
ERR5749423	14168	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTA	C	11755	8.51E-4	0	0,11742,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	atatta/	IL244	RdRp	0.000479	0.314961	1	1	CTA>C
ERR5749423	14408	PASS	C	T	2541	0.844549	0	0,0,1269,1257	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF1ab	cCt/cTt	P323L	RdRp	0.771429	0.931818	1	1	C>T
ERR5749423	14676	PASS	C	T	10248	0.830894	0	12,0,10220,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ccC/ccT	P412	RdRp	0.6	0.893939	1	1	C>T
ERR5749423	14688	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CA	C	10248	0.001561	0	10232,0,16,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	aaa/	K417	RdRp	0.000534	0.979772	2	2	CA>C
ERR5749423	15279	PASS	C	T	12445	0.860747	0	1,0,12419,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	caC/caT	H613	RdRp	0.822779	0.970449	1	1	C>T
ERR5749423	15420	PASS	T	G	12430	0.927434	0	0,22,0,12402	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gcT/gcG	A660	RdRp	0.908883	0.934773	1	1	T>G
ERR5749423	16176	PASS	T	C	13038	0.978448	0	0,1,3889,9142	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	acT/acC	T912	RdRp	0.956044	1	1	1	T>C
ERR5749423	16794	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	35296	7.93E-4	0	16451,18801,14,17	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	cgT/cgC	R186	helicase	0.000354	0.077626	2	2	T>C
ERR5749423	17502	PASS	C	T	14236	0.979559	2147483647	0,0,14221,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	ttC/ttT	F422	helicase	0.000611	0.9865	2	2	C>T
ERR5749423	17747	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CTG	C	9536	8.39E-4	0	9527,1,8,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	cctgct/	PA504	helicase	0.000839	0.968462	2	2	CTG>C
ERR5749423	19011	PASS	C	T	21592	0.971888	0	3,0,21581,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gaC/gaT	D324	ExoN	0.000408	0.975746	4	2	C>T
ERR5749423	19151	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CCA	C	21560	4.64E-4	0	0,21550,0,10	HIGH	NONE	FRAME_SHIFT	ORF1ab	cat/	H373	ExoN	0.00034	0.247423	2	2	CCA>C
ERR5749423	19983	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	13447	0.001785	0	13418,0,26,0	LOW	SILENT	SYNONYMOUS_CODING	ORF1ab	gtC/gtT	V121	endoR	0.000884	0.981982	5	2	C>T
ERR5749423	20320	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CAT	C	22898	7.42E-4	0	22881,0,17,0	HIGH	NONE	FRAME_SHIFT	ORF1ab	atc/	I235	endoR	0.000651	0.916979	2	2	CAT>C
ERR5749423	20420	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AT	A	22877	4.81E-4	0	22,22844,0,11	HIGH	NONE	FRAME_SHIFT	ORF1ab	ttt/	F268	endoR	0.000383	0.069626	2	1	AT>A
ERR5749423	21764	PASS	ATACATG	A	12152	0.996626	0	41,0,12111,0	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	atacatgtc/atc	IHV68I	S	0.001908	1	3	1	ATACATG>A
ERR5749423	21990	PASS	TTTA	T	12157	0.997532	0	0,30,4,12123	MODERATE	NONE	CODON_CHANGE_PLUS_CODON_DELETION	S	tattac/tac	YY144Y	S	0.000732	1	1	1	TTTA>T
ERR5749423	22690	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	13604	0.002058	0	13336,0,32,0	LOW	SILENT	SYNONYMOUS_CODING	S	acT/acC	T376	S	0.000815	0.051311	2	1	T>C
ERR5749423	22801	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	13647	0.001539	0	0,13623,0,22	LOW	SILENT	SYNONYMOUS_CODING	S	ggG/ggA	G413	S	0.001101	0.887758	3	2	G>A
ERR5749423	22858	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	C	T	26364	9.1E-4	10	12699,13627,8,18	LOW	SILENT	SYNONYMOUS_CODING	S	tgC/tgT	C432	S	0.000792	0.973187	2	2	C>T
ERR5749423	23063	PASS	A	T	12689	0.867917	2147483647	0,0,0,12628	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Aat/Tat	N501Y	S	0.00456	0.907193	2	1	A>T
ERR5749423	23271	PASS	C	A	18876	0.918521	0	1,0,18853,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gCt/gAt	A570D	S	0.89579	1	1	1	C>A
ERR5749423	23403	PASS	A	G	18868	0.966398	0	0,2,0,18850	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	gAt/gGt	D614G	S	0.945235	0.982749	1	1	A>G
ERR5749423	23604	PASS	C	A	12808	0.936914	0	11,0,12788,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cCt/cAt	P681H	S	0.003105	0.969595	3	1	C>A
ERR5749423	23683	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	CT	C	12784	7.04E-4	0	0,12775,0,9	HIGH	NONE	FRAME_SHIFT	S	tct/	S708	S	0.000704	0.467521	2	2	CT>C
ERR5749423	23709	PASS	C	T	12793	0.937544	0	0,13,0,12763	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	aCa/aTa	T716I	S	0.907839	1	1	1	C>T
ERR5749423	23817	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	20022	0.001349	10	7196,12789,15,14	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	cTt/cCt	L752P	S	0.000646	0.066832	1	1	T>C
ERR5749423	24506	PASS	T	G	13388	0.974604	0	3,0,13380,0	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Tca/Gca	S982A	S	0.953488	0.985629	1	1	T>G
ERR5749423	24902	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	C	41345	9.92E-4	937	20661,20272,13,375	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Atc/Ctc	I1114L	S	0.000992	0.759959	2	1	A>C
ERR5749423	24914	PASS	G	C	41219	0.962881	0	0,0,20552,20648	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	S	Gac/Cac	D1118H	S	0.815458	1	2	1	G>C
ERR5749423	25019	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GATAA	G	27078	4.8E-4	13	6341,20724,0,13	HIGH	NONE	FRAME_SHIFT	S	aaatat/	KY1154	S	0.00048	0.981297	3	2	GATAA>G
ERR5749423	25673	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	C	3862	0.004402	173	3821,19,8,10	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF3a	cTt/cCt	L94P	orf3a	0.000936	0.4	1	1	T>C
ERR5749423	26730	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	GT	G	21902	4.57E-4	0	10941,10971,5,5	HIGH	NONE	FRAME_SHIFT	M	tac/	Y71	M	0.000371	0.919543	3	2	GT>G
ERR5749423	27765	PASS	C	T	15261	0.964878	2147483647	0,0,0,15242	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF7b	Ctt/Ttt	L4F	orf7b	0.00109	0.970449	1	1	C>T
ERR5749423	27972	PASS	C	T	6521	0.907836	20	1,1,6476,27	HIGH	NONSENSE	STOP_GAINED	ORF8	Caa/Taa	Q27*	orf8	0.868182	0.966102	1	1	C>T
ERR5749423	28048	PASS	G	T	6502	0.931713	0	0,9,0,6491	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	aGa/aTa	R52I	orf8	0.846154	1	1	1	G>T
ERR5749423	28111	PASS	A	G	26563	0.980311	11	11,0,20038,6508	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	ORF8	tAc/tGc	Y73C	orf8	0.6	0.985169	1	1	A>G
ERR5749423	28239	PASS	GTTGTT	G	20012	0.984509	0	312,0,19702,0	HIGH	NONE	FRAME_SHIFT	ORF8	gtttta/	VL117	orf8	0.000417	0.984998	9	2	GTTGTT>G
ERR5749423	28249	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	ATC	19778	0.001163	0	19751,0,23,0	HIGH	NONE	FRAME_SHIFT	ORF8	ttc/CTttc	F120L?	orf8	0.000443	0.063605	3	2	A>ATC
ERR5749423	28250	PASS	T	TCTG	19778	0.99095	0	151,0,19599,0	MODERATE	NONE	CODON_INSERTION	ORF8	ttc/CTGttc	F120LF	orf8	0.000494	0.993968	5	3	T>TCTG
ERR5749423	28250	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	T	TATG	19778	7.08E-4	0	151,0,14,0	MODERATE	NONE	CODON_INSERTION	ORF8	ttc/ATGttc	F120MF	orf8	0.000494	0.993968	5	3	T>TATG
ERR5749423	28253	PASS	CA	C	19778	0.992466	0	149,0,19629,0	HIGH	NONE	FRAME_SHIFT	ORF8	atc/	I121	orf8	0.000422	0.995511	4	3	CA>C
ERR5749423	28254	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	A	ATC	19778	7.08E-4	0	19760,0,14,0	HIGH	NONE	FRAME_SHIFT+STOP_LOST+SPLICE_SITE_REGION	ORF8	taa/tCTaa	*122S?	orf8	0.000541	0.914398	3	2	A>ATC
ERR5749423	28270	PASS	TA	T	38122	0.996406	211	122,13,19655,18330	.	.	.	.	.	.	.	0.000322	1	2	1	TA>T
ERR5749423	28271	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	AA	A	38122	0.001338	126	19727,18343,50,1	.	.	.	.	.	.	.	0.000482	0.924941	3	2	AA>A
ERR5749423	28280	PASS	G	C	38121	0.945148	13	8,1,19723,18326	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gat/Cat	D3H	N	0.001608	1	2	2	G>C
ERR5749423	28281	PASS	A	T	38121	0.927284	32	20,3,19709,18325	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gAt/gTt	D3V	N	0.811871	1	1	1	A>T
ERR5749423	28282	PASS	T	A	38130	0.91508	4	31,22,19682,18323	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	gaT/gaA	D3E	N	0.001009	0.957283	3	2	T>A
ERR5749423	28881	PASS	G	A	6892	0.774666	6	3,0,3418,3395	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	aGg/aAg	R203K	N	0.000709	0.947368	4	2	G>A
ERR5749423	28882	PASS	G	A	6892	0.822693	3	2,0,3445,3392	LOW	SILENT	SYNONYMOUS_CODING	N	agG/agA	R203	N	0.716981	0.911765	1	1	G>A
ERR5749423	28883	PASS	G	C	6892	0.94646	3	0,1,3454,3435	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	Gga/Cga	G204R	N	0.005136	0.991071	2	2	G>C
ERR5749423	28977	PASS	C	T	3500	0.932	0	0,1,0,3493	MODERATE	MISSENSE	NON_SYNONYMOUS_CODING	N	tCt/tTt	S235F	N	0.001219	1	3	2	C>T
ERR5749423	29179	min_af_0.05Xmin_dp_1Xmin_dp_alt_10	G	A	57448	0.001097	1	28858,28491,43,38	LOW	SILENT	SYNONYMOUS_CODING	N	ccG/ccA	P302	N	0.000713	0.913732	2	1	G>A