Input data and parameters
QualiMap command line
| qualimap bamqc -bam /data/dnb03/galaxy_db/files/6/1/1/dataset_611a91b1-feaa-4544-8298-cb245b41107a.dat -c -nw 400 -hm 3 -sd |
Alignment
| Command line: | bwa mem -t 8 -v 1 -R @RG\tID:Cutadapt_on_data_17_and_data_16__Read_\tSM:Cutadapt_on_data_17_and_data_16__Read_\tPL:ILLUMINA\tLB:Cutadapt_on_data_17_and_data_16__Read_\tPU:run /data/db/data_managers/hg19/bwa_mem_index/hg19/hg19.fa /data/dnb03/galaxy_db/files/c/b/8/dataset_cb82dd39-d2d5-4e78-91a5-40344e162887.dat /data/dnb03/galaxy_db/files/0/1/3/dataset_013c90b9-b7ae-4e94-83ff-d1df5ab99eec.dat |
| Draw chromosome limits: | yes |
| Analyze overlapping paired-end reads: | yes |
| Program: | bwa (0.7.17-r1188) |
| Analysis date: | Sat May 22 06:53:55 CEST 2021 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | yes (only flagged) |
| Number of windows: | 400 |
| BAM file: | /data/dnb03/galaxy_db/files/6/1/1/dataset_611a91b1-feaa-4544-8298-cb245b41107a.dat |
Summary
Warnings
| No flagged duplicates are detected | Make sure duplicate alignments are flagged in the BAM file or apply a different skip duplicates mode. |
Globals
| Reference size | 3,137,161,264 |
| Number of reads | 99,107,016 |
| Mapped reads | 98,952,668 / 99.84% |
| Unmapped reads | 154,348 / 0.16% |
| Mapped paired reads | 98,952,668 / 99.84% |
| Mapped reads, first in pair | 49,486,597 / 49.93% |
| Mapped reads, second in pair | 49,466,071 / 49.91% |
| Mapped reads, both in pair | 98,919,718 / 99.81% |
| Mapped reads, singletons | 32,950 / 0.03% |
| Secondary alignments | 0 |
| Supplementary alignments | 272,261 / 0.27% |
| Read min/max/mean length | 20 / 101 / 99.68 |
| Overlapping read pairs | 11,975,659 / 24.17% |
| Duplicated reads (flagged) | 0 / 0% |
| Duplicated reads (estimated) | 51,015,054 / 51.47% |
| Duplication rate | 42.19% |
| Clipped reads | 1,617,706 / 1.63% |
ACGT Content
| Number/percentage of A's | 2,275,796,792 / 23.13% |
| Number/percentage of C's | 2,656,648,262 / 27% |
| Number/percentage of T's | 2,315,990,262 / 23.54% |
| Number/percentage of G's | 2,589,146,315 / 26.32% |
| Number/percentage of N's | 281,839 / 0% |
| GC Percentage | 53.32% |
Coverage
| Mean | 3.1362 |
| Standard Deviation | 38.4225 |
| Mean (paired-end reads overlap ignored) | 3.02 |
Mapping Quality
| Mean Mapping Quality | 46.45 |
Insert size
| Mean | 69,763.73 |
| Standard Deviation | 2,601,598.08 |
| P25/Median/P75 | 200 / 240 / 291 |
Mismatches and indels
| General error rate | 0.23% |
| Mismatches | 21,893,817 |
| Insertions | 321,311 |
| Mapped reads with at least one insertion | 0.32% |
| Deletions | 425,342 |
| Mapped reads with at least one deletion | 0.42% |
| Homopolymer indels | 44.67% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| chr10 | 135534747 | 330544506 | 2.4388 | 20.0285 |
| chr11 | 135006516 | 525361676 | 3.8914 | 26.0195 |
| chr11_gl000202_random | 40103 | 9898 | 0.2468 | 0.6323 |
| chr12 | 133851895 | 498427651 | 3.7237 | 24.5986 |
| chr13 | 115169878 | 119315015 | 1.036 | 10.4177 |
| chr14 | 107349540 | 214607568 | 1.9991 | 17.1052 |
| chr15 | 102531392 | 425589219 | 4.1508 | 31.0769 |
| chr16 | 90354753 | 453000285 | 5.0136 | 31.8702 |
| chr17_ctg5_hap1 | 1680828 | 6413717 | 3.8158 | 20.0842 |
| chr17 | 81195210 | 626713744 | 7.7186 | 41.2618 |
| chr17_gl000203_random | 37498 | 2221 | 0.0592 | 0.2939 |
| chr17_gl000204_random | 81310 | 41422 | 0.5094 | 4.1395 |
| chr17_gl000205_random | 174588 | 1247662 | 7.1463 | 65.9795 |
| chr17_gl000206_random | 41001 | 6464 | 0.1577 | 0.6413 |
| chr18 | 78077248 | 142466363 | 1.8247 | 26.0244 |
| chr18_gl000207_random | 4262 | 1731 | 0.4061 | 0.771 |
| chr19 | 59128983 | 600431589 | 10.1546 | 41.8714 |
| chr19_gl000208_random | 92689 | 32946 | 0.3554 | 1.2035 |
| chr19_gl000209_random | 159169 | 527975 | 3.3171 | 15.8036 |
| chr1 | 249250621 | 1007668648 | 4.0428 | 32.6468 |
| chr1_gl000191_random | 106433 | 251759 | 2.3654 | 10.3655 |
| chr1_gl000192_random | 547496 | 1650120 | 3.0139 | 13.0907 |
| chr20 | 63025520 | 260795614 | 4.1379 | 27.4052 |
| chr21 | 48129895 | 107603784 | 2.2357 | 25.3936 |
| chr21_gl000210_random | 27682 | 4237 | 0.1531 | 0.5628 |
| chr22 | 51304566 | 288966756 | 5.6324 | 40.2895 |
| chr2 | 243199373 | 575460185 | 2.3662 | 19.557 |
| chr3 | 198022430 | 486836894 | 2.4585 | 27.1872 |
| chr4_ctg9_hap1 | 590426 | 762819 | 1.292 | 9.7332 |
| chr4 | 191154276 | 329351696 | 1.723 | 23.8763 |
| chr4_gl000193_random | 189789 | 329413 | 1.7357 | 24.6393 |
| chr4_gl000194_random | 191469 | 1956149 | 10.2165 | 101.0639 |
| chr5 | 180915260 | 421830686 | 2.3316 | 44.027 |
| chr6_apd_hap1 | 4622290 | 5087441 | 1.1006 | 8.7961 |
| chr6_cox_hap2 | 4795371 | 12421935 | 2.5904 | 11.7973 |
| chr6_dbb_hap3 | 4610396 | 11318239 | 2.4549 | 11.4316 |
| chr6 | 171115067 | 351912375 | 2.0566 | 17.164 |
| chr6_mann_hap4 | 4683263 | 7585636 | 1.6197 | 8.1504 |
| chr6_mcf_hap5 | 4833398 | 10495435 | 2.1714 | 9.1862 |
| chr6_qbl_hap6 | 4611984 | 11235013 | 2.436 | 12.1452 |
| chr6_ssto_hap7 | 4928567 | 9662588 | 1.9605 | 9.8019 |
| chr7 | 159138663 | 627945406 | 3.9459 | 68.077 |
| chr7_gl000195_random | 182896 | 1208529 | 6.6077 | 63.4327 |
| chr8 | 146364022 | 644850911 | 4.4058 | 110.0847 |
| chr8_gl000196_random | 38914 | 27586 | 0.7089 | 3.4923 |
| chr8_gl000197_random | 37175 | 74852 | 2.0135 | 10.0683 |
| chr9 | 141213431 | 415073094 | 2.9393 | 25.0253 |
| chr9_gl000198_random | 90085 | 97625 | 1.0837 | 10.0178 |
| chr9_gl000199_random | 169874 | 417257 | 2.4563 | 9.8343 |
| chr9_gl000200_random | 187035 | 100748 | 0.5387 | 4.4213 |
| chr9_gl000201_random | 36148 | 213936 | 5.9183 | 15.345 |
| chrM | 16571 | 311979 | 18.8268 | 6.1986 |
| chrUn_gl000211 | 166566 | 1453892 | 8.7286 | 26.1268 |
| chrUn_gl000212 | 186858 | 3207955 | 17.1679 | 75.2574 |
| chrUn_gl000213 | 164239 | 1183416 | 7.2055 | 64.0585 |
| chrUn_gl000214 | 137718 | 2478821 | 17.9993 | 54.8258 |
| chrUn_gl000215 | 172545 | 560086 | 3.246 | 18.7048 |
| chrUn_gl000216 | 172294 | 248332 | 1.4413 | 10.0519 |
| chrUn_gl000217 | 172149 | 201852 | 1.1725 | 10.3003 |
| chrUn_gl000218 | 161147 | 1509788 | 9.369 | 60.5554 |
| chrUn_gl000219 | 179198 | 764791 | 4.2679 | 48.8744 |
| chrUn_gl000220 | 161802 | 9112788 | 56.3206 | 418.3962 |
| chrUn_gl000221 | 155397 | 1940520 | 12.4875 | 50.7498 |
| chrUn_gl000222 | 186861 | 1279498 | 6.8473 | 50.7531 |
| chrUn_gl000223 | 180455 | 516760 | 2.8637 | 10.4381 |
| chrUn_gl000224 | 179693 | 277900 | 1.5465 | 6.0644 |
| chrUn_gl000225 | 211173 | 1012262 | 4.7935 | 44.8094 |
| chrUn_gl000226 | 15008 | 265133 | 17.6661 | 12.9931 |
| chrUn_gl000227 | 128374 | 1015536 | 7.9108 | 52.3683 |
| chrUn_gl000228 | 129120 | 1079007 | 8.3566 | 33.5392 |
| chrUn_gl000229 | 19913 | 419633 | 21.0733 | 55.4873 |
| chrUn_gl000230 | 43691 | 92671 | 2.1211 | 8.1358 |
| chrUn_gl000231 | 27386 | 219942 | 8.0312 | 31.9889 |
| chrUn_gl000232 | 40652 | 78656 | 1.9349 | 15.4069 |
| chrUn_gl000233 | 45941 | 4079 | 0.0888 | 0.3478 |
| chrUn_gl000234 | 40531 | 112369 | 2.7724 | 24.7765 |
| chrUn_gl000235 | 34474 | 67867 | 1.9686 | 16.2492 |
| chrUn_gl000236 | 41934 | 125026 | 2.9815 | 11.3154 |
| chrUn_gl000237 | 45867 | 201834 | 4.4004 | 29.577 |
| chrUn_gl000238 | 39939 | 412019 | 10.3162 | 35.1686 |
| chrUn_gl000239 | 33824 | 58507 | 1.7297 | 7.4156 |
| chrUn_gl000240 | 41933 | 39347 | 0.9383 | 5.4653 |
| chrUn_gl000241 | 42152 | 210759 | 5 | 22.7907 |
| chrUn_gl000242 | 43523 | 362404 | 8.3267 | 26.0023 |
| chrUn_gl000243 | 43341 | 72901 | 1.682 | 10.0999 |
| chrUn_gl000244 | 39929 | 242064 | 6.0624 | 40.2114 |
| chrUn_gl000245 | 36651 | 5797 | 0.1582 | 0.4386 |
| chrUn_gl000246 | 38154 | 22629 | 0.5931 | 3.8279 |
| chrUn_gl000247 | 36422 | 9703 | 0.2664 | 1.6561 |
| chrUn_gl000248 | 39786 | 1688 | 0.0424 | 0.2171 |
| chrUn_gl000249 | 38502 | 55603 | 1.4442 | 5.7867 |
| chrX | 155270560 | 201519142 | 1.2979 | 11.4061 |
| chrY | 59373566 | 68206736 | 1.1488 | 21.4194 |
