TBProfiler report ================= The following report has been generated by TBProfiler. Summary ------- ID: tbprofiler Date: Tue Oct 3 15:46:34 2023 Strain: lineage4.4.1.1.1 Drug-resistance: MDR-TB Median Depth: 140 Lineage report -------------- Lineage Estimated Fraction Spoligotype Rd lineage4 1.000 LAM;T;S;X;H None lineage4.4 0.994 S;T None lineage4.4.1 1.000 S;T None lineage4.4.1.1 0.998 S;Orphans None lineage4.4.1.1.1 1.000 S;Orphans None Resistance report ----------------- Drug Genotypic Resistance Mutations Rifampicin R rpoB p.Ser450Leu (0.99) Isoniazid R katG p.Ser315Thr (1.00) Ethambutol R embB p.Met306Val (1.00) Pyrazinamide R pncA p.Tyr34Asp (1.00) Streptomycin R rpsL p.Lys43Arg (0.99) Fluoroquinolones Moxifloxacin Ofloxacin Levofloxacin Ciprofloxacin Aminoglycosides R rrs n.1402C>A (0.13) Amikacin R rrs n.1402C>A (0.13) Capreomycin R rrs n.1402C>A (0.13) Kanamycin R rrs n.1402C>A (0.13) Cycloserine Ethionamide Clofazimine Para-aminosalicylic_acid Delamanid Bedaquiline Linezolid Resistance variants report ----------------- Genome Position Locus Tag Gene Variant Type Change Estimated Fraction Drug Annotation 761155 Rv0667 rpoB missense_variant p.Ser450Leu 0.991 rifampicin type=who_confidence|drug=rifampicin|who_confidence=Assoc w R 781687 Rv0682 rpsL missense_variant p.Lys43Arg 0.987 streptomycin type=who_confidence|drug=streptomycin|who_confidence=Assoc w R 1473247 EBG00000313325 rrs non_coding_transcript_exon_variant n.1402C>A 0.128 kanamycin,capreomycin,aminoglycosides,amikacin type=who_confidence|drug=kanamycin|who_confidence=;type=who_confidence|drug=capreomycin|who_confidence=;type=who_confidence|drug=aminoglycosides|who_confidence=;type=who_confidence|drug=amikacin|who_confidence= 2155168 Rv1908c katG missense_variant p.Ser315Thr 1.000 isoniazid type=who_confidence|drug=isoniazid|who_confidence=Assoc w R 2289142 Rv2043c pncA missense_variant p.Tyr34Asp 1.000 pyrazinamide type=who_confidence|drug=pyrazinamide|who_confidence=Assoc w R 4247429 Rv3795 embB missense_variant p.Met306Val 1.000 ethambutol type=who_confidence|drug=ethambutol|who_confidence=Assoc w R Other variants report --------------------- Genome Position Locus Tag Gene Variant Type Change Estimated Fraction Annotation 7362 Rv0006 gyrA missense_variant p.Glu21Gln 1.000 type=who_confidence|drug=moxifloxacin|who_confidence=Not assoc w R;type=who_confidence|drug=levofloxacin|who_confidence=Not assoc w R 7585 Rv0006 gyrA missense_variant p.Ser95Thr 1.000 type=who_confidence|drug=levofloxacin|who_confidence=Not assoc w R;type=who_confidence|drug=moxifloxacin|who_confidence=Not assoc w R 9304 Rv0006 gyrA missense_variant p.Gly668Asp 0.985 type=who_confidence|drug=moxifloxacin|who_confidence=Not assoc w R;type=who_confidence|drug=levofloxacin|who_confidence=Not assoc w R 766487 Rv0668 rpoC missense_variant p.Pro1040Ser 1.000 775639 Rv0676c mmpL5 missense_variant p.Ile948Val 1.000 type=who_confidence|drug=bedaquiline|who_confidence=Not assoc w R;type=who_confidence|drug=clofazimine|who_confidence=Not assoc w R 781395 Rv0682 rpsL upstream_gene_variant c.-165T>C 1.000 type=who_confidence|drug=streptomycin|who_confidence=Not assoc w R 1471659 EBG00000313325 rrs upstream_gene_variant n.-187C>T 1.000 1472106 EBG00000313325 rrs non_coding_transcript_exon_variant n.261G>A 0.154 1472123 EBG00000313325 rrs non_coding_transcript_exon_variant n.278A>T 0.125 1472137 EBG00000313325 rrs non_coding_transcript_exon_variant n.292G>A 0.100 1472150 EBG00000313325 rrs non_coding_transcript_exon_variant n.305T>A 0.316 type=who_confidence|drug=kanamycin|who_confidence=Uncertain significance;type=who_confidence|drug=amikacin|who_confidence=Uncertain significance;type=who_confidence|drug=capreomycin|who_confidence=Uncertain significance 1472151 EBG00000313325 rrs non_coding_transcript_exon_variant n.306C>T 0.158 type=who_confidence|drug=streptomycin|who_confidence=Uncertain significance;type=who_confidence|drug=capreomycin|who_confidence=Uncertain significance;type=who_confidence|drug=amikacin|who_confidence=Uncertain significance;type=who_confidence|drug=kanamycin|who_confidence=Uncertain significance 1472172 EBG00000313325 rrs non_coding_transcript_exon_variant n.327T>C 0.375 type=who_confidence|drug=kanamycin|who_confidence=Uncertain significance;type=who_confidence|drug=capreomycin|who_confidence=Uncertain significance;type=who_confidence|drug=amikacin|who_confidence=Uncertain significance 1472210 EBG00000313325 rrs non_coding_transcript_exon_variant n.365A>C 0.129 1472234 EBG00000313325 rrs non_coding_transcript_exon_variant n.389T>C 0.107 1472240 EBG00000313325 rrs non_coding_transcript_exon_variant n.395G>A 0.286 1472251 EBG00000313325 rrs non_coding_transcript_exon_variant n.406G>A 0.233 type=who_confidence|drug=amikacin|who_confidence=Uncertain significance 1472256 EBG00000313325 rrs non_coding_transcript_exon_variant n.411T>A 0.167 1472259 EBG00000313325 rrs non_coding_transcript_exon_variant n.414C>A 0.139 1472530 EBG00000313325 rrs non_coding_transcript_exon_variant n.685G>A 0.111 1472571 EBG00000313325 rrs non_coding_transcript_exon_variant n.726G>C 0.111 1472581 EBG00000313325 rrs non_coding_transcript_exon_variant n.736A>C 0.111 1472598 EBG00000313325 rrs non_coding_transcript_exon_variant n.753A>C 0.120 1473226 EBG00000313325 rrs non_coding_transcript_exon_variant n.1381C>T 0.103 1474000 EBG00000313339 rrl non_coding_transcript_exon_variant n.343C>G 0.167 1474065 EBG00000313339 rrl non_coding_transcript_exon_variant n.408C>T 0.143 type=who_confidence|drug=linezolid|who_confidence=Uncertain significance 1474294 EBG00000313339 rrl non_coding_transcript_exon_variant n.637C>T 0.118 type=who_confidence|drug=linezolid|who_confidence=Uncertain significance 1474537 EBG00000313339 rrl non_coding_transcript_exon_variant n.880G>A 0.143 1474612 EBG00000313339 rrl non_coding_transcript_exon_variant n.955T>C 0.118 1474702 EBG00000313339 rrl non_coding_transcript_exon_variant n.1045G>T 0.111 1475196 EBG00000313339 rrl non_coding_transcript_exon_variant n.1539T>A 0.154 1475775 EBG00000313339 rrl non_coding_transcript_exon_variant n.2118G>T 0.100 1475881 EBG00000313339 rrl non_coding_transcript_exon_variant n.2224T>C 0.150 1475896 EBG00000313339 rrl non_coding_transcript_exon_variant n.2239A>G 0.158 1475897 EBG00000313339 rrl non_coding_transcript_exon_variant n.2240T>C 0.158 1475898 EBG00000313339 rrl non_coding_transcript_exon_variant n.2241A>G 0.158 1475899 EBG00000313339 rrl non_coding_transcript_exon_variant n.2242G>A 0.158 1475926 EBG00000313339 rrl non_coding_transcript_exon_variant n.2269A>T 0.111 1476115 EBG00000313339 rrl non_coding_transcript_exon_variant n.2458T>C 0.130 1476131 EBG00000313339 rrl non_coding_transcript_exon_variant n.2474C>T 0.120 1476160 EBG00000313339 rrl non_coding_transcript_exon_variant n.2503T>C 0.120 1476165 EBG00000313339 rrl non_coding_transcript_exon_variant n.2508T>A 0.120 1476224 EBG00000313339 rrl non_coding_transcript_exon_variant n.2567A>G 0.111 1476245 EBG00000313339 rrl non_coding_transcript_exon_variant n.2588C>T 0.133 1476281 EBG00000313339 rrl non_coding_transcript_exon_variant n.2624T>C 0.125 1476297 EBG00000313339 rrl non_coding_transcript_exon_variant n.2640C>G 0.133 1476298 EBG00000313339 rrl non_coding_transcript_exon_variant n.2641C>G 0.133 1476309 EBG00000313339 rrl non_coding_transcript_exon_variant n.2652G>C 0.154 1476311 EBG00000313339 rrl non_coding_transcript_exon_variant n.2654G>C 0.143 1476337 EBG00000313339 rrl non_coding_transcript_exon_variant n.2680C>T 0.154 1476359 EBG00000313339 rrl non_coding_transcript_exon_variant n.2702C>G 0.188 1476372 EBG00000313339 rrl non_coding_transcript_exon_variant n.2715T>C 0.105 1476381 EBG00000313339 rrl non_coding_transcript_exon_variant n.2724G>C 0.222 1476382 EBG00000313339 rrl non_coding_transcript_exon_variant n.2725A>C 0.133 1476383 EBG00000313339 rrl non_coding_transcript_exon_variant n.2726T>C 0.133 1476384 EBG00000313339 rrl non_coding_transcript_exon_variant n.2727G>A 0.118 1476408 EBG00000313339 rrl non_coding_transcript_exon_variant n.2751G>A 0.167 1476411 EBG00000313339 rrl non_coding_transcript_exon_variant n.2754G>A 0.214 1476425 EBG00000313339 rrl non_coding_transcript_exon_variant n.2768G>A 0.222 1476428 EBG00000313339 rrl non_coding_transcript_exon_variant n.2771C>T 0.211 1476466 EBG00000313339 rrl non_coding_transcript_exon_variant n.2809C>T 0.154 type=who_confidence|drug=linezolid|who_confidence=Uncertain significance 1476481 EBG00000313339 rrl non_coding_transcript_exon_variant n.2824T>C 0.143 1476506 EBG00000313339 rrl non_coding_transcript_exon_variant n.2849T>C 0.133 1476512 EBG00000313339 rrl non_coding_transcript_exon_variant n.2855C>T 0.133 1476522 EBG00000313339 rrl non_coding_transcript_exon_variant n.2865G>A 0.154 1476596 EBG00000313339 rrl non_coding_transcript_exon_variant n.2939C>T 0.111 type=who_confidence|drug=linezolid|who_confidence=Uncertain significance 1917972 Rv1694 tlyA synonymous_variant c.33A>G 1.000 2102990 Rv1854c ndh missense_variant p.Val18Ala 1.000 type=who_confidence|drug=isoniazid|who_confidence=Not assoc w R;type=who_confidence|drug=ethionamide|who_confidence=Uncertain significance 2169840 Rv1918c PPE35 missense_variant p.Gly258Asp 1.000 2223293 Rv1979c Rv1979c upstream_gene_variant c.-129A>G 1.000 type=who_confidence|drug=bedaquiline|who_confidence=Not assoc w R;type=who_confidence|drug=clofazimine|who_confidence=Not assoc w R 2986827 Rv2671 ribD upstream_gene_variant c.-12G>A 1.000 3064993 Rv2752c Rv2752c stop_gained p.Trp400* 1.000 type=who_confidence|drug=rifampicin|who_confidence=Uncertain significance;type=who_confidence|drug=isoniazid|who_confidence=Uncertain significance 3086788 Rv2780 ald upstream_gene_variant c.-32T>C 1.000 3339287 Rv2983 fbiD missense_variant p.Arg57Leu 1.000 type=who_confidence|drug=delamanid|who_confidence=Uncertain significance 3448608 Rv3083 Rv3083 synonymous_variant c.105G>A 1.000 3473996 Rv3106 fprA upstream_gene_variant c.-11_-10insA 1.000 3612665 Rv3236c Rv3236c missense_variant p.Val151Ala 0.989 type=who_confidence|drug=pyrazinamide|who_confidence=Not assoc w R 4242643 Rv3794 embA upstream_gene_variant c.-590C>T 0.994 4269671 Rv3806c ubiA missense_variant p.Val55Leu 1.000 4338595 Rv3862c whiB6 upstream_gene_variant c.-75delG 1.000 type=who_confidence|drug=streptomycin|who_confidence=Not assoc w R;type=who_confidence|drug=capreomycin|who_confidence=Uncertain significance;type=who_confidence|drug=streptomycin|who_confidence=Uncertain significance;type=who_confidence|drug=capreomycin|who_confidence=Not assoc w R;type=who_confidence|drug=amikacin|who_confidence=Not assoc w R;type=who_confidence|drug=amikacin|who_confidence=Uncertain significance Coverage report --------------------- Gene Locus_Tag Cutoff Fraction gyrB Rv0005 0 0.000 gyrA Rv0006 0 0.000 fgd1 Rv0407 0 0.000 mshA Rv0486 0 0.000 ccsA Rv0529 0 0.000 rpoB Rv0667 0 0.000 rpoC Rv0668 0 0.000 mmpL5 Rv0676c 0 0.000 mmpS5 Rv0677c 0 0.000 mmpR5 Rv0678 0 0.000 rpsL Rv0682 0 0.000 rplC Rv0701 0 0.000 fbiC Rv1173 0 0.000 Rv1258c Rv1258c 0 0.000 embR Rv1267c 0 0.000 atpE Rv1305 0 0.000 rrs EBG00000313325 0 0.000 rrl EBG00000313339 0 0.000 fabG1 Rv1483 0 0.000 inhA Rv1484 0 0.000 rpsA Rv1630 0 0.000 tlyA Rv1694 0 0.000 ndh Rv1854c 0 0.000 katG Rv1908c 0 0.000 PPE35 Rv1918c 0 0.000 Rv1979c Rv1979c 0 0.000 pncA Rv2043c 0 0.000 kasA Rv2245 0 0.000 eis Rv2416c 0 0.000 ahpC Rv2428 0 0.000 folC Rv2447c 0 0.000 pepQ Rv2535c 0 0.000 ribD Rv2671 0 0.000 Rv2752c Rv2752c 0 0.000 thyX Rv2754c 0 0.000 thyA Rv2764c 0 0.000 ald Rv2780 0 0.000 fbiD Rv2983 0 0.000 Rv3083 Rv3083 0 0.000 fprA Rv3106 0 0.000 whiB7 Rv3197A 0 0.000 Rv3236c Rv3236c 0 0.000 fbiA Rv3261 0 0.000 fbiB Rv3262 0 0.000 alr Rv3423c 0 0.000 rpoA Rv3457c 0 0.000 ddn Rv3547 0 0.000 clpC1 Rv3596c 0 0.000 panD Rv3601c 0 0.000 embC Rv3793 0 0.000 embA Rv3794 0 0.000 embB Rv3795 0 0.000 aftB Rv3805c 0 0.000 ubiA Rv3806c 0 0.000 ethA Rv3854c 0 0.000 ethR Rv3855 0 0.000 whiB6 Rv3862c 0 0.000 gid Rv3919c 0 0.000 Missing positions report --------------------- Gene Locus_Tag Position Variants Drugs rrs EBG00000313325 1473003 n.1158G>T aminoglycosides,amikacin Analysis pipeline specifications -------------------------------- Pipeline version: 4.4.1 Database version: tbdb_c2fb9a2_jodyphelan _Tue Oct 4 11:40:15 2022 +0100 Analysis Program Mapping N/A Variant calling freebayes Citation -------- Coll, F. et al. Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences. Genome Medicine 7, 51. 2015 Phelan, JE. et al. Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs. Genome Medicine 11, 41. 2019