Input data and parameters
QualiMap command line
| qualimap bamqc -bam ../qualimap2/test-data/test.bam -nw 400 -hm 3 |
Alignment
| Command line: | bwa mem -K 100000000 -p -v 3 -t 16 -Y /cromwell_root/broad-references/hg19/v0/Homo_sapiens_assembly19.fasta |
| Draw chromosome limits: | no |
| Analyze overlapping paired-end reads: | no |
| Program: | bwamem (0.7.15-r1140) |
| Analysis date: | Thu Jul 26 16:33:35 EDT 2018 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | ../qualimap2/test-data/test.bam |
Summary
Globals
| Reference size | 3,101,976,562 |
| Number of reads | 61,169 |
| Mapped reads | 60,246 / 98.49% |
| Unmapped reads | 923 / 1.51% |
| Mapped paired reads | 60,246 / 98.49% |
| Mapped reads, first in pair | 30,268 / 49.48% |
| Mapped reads, second in pair | 29,978 / 49.01% |
| Mapped reads, both in pair | 59,810 / 97.78% |
| Mapped reads, singletons | 436 / 0.71% |
| Secondary alignments | 0 |
| Supplementary alignments | 1,169 / 1.91% |
| Read min/max/mean length | 250 / 250 / 250 |
| Duplicated reads (flagged) | 48 / 0.08% |
| Clipped reads | 33,606 / 54.94% |
ACGT Content
| Number/percentage of A's | 3,912,917 / 29.53% |
| Number/percentage of C's | 2,699,395 / 20.37% |
| Number/percentage of T's | 3,942,019 / 29.75% |
| Number/percentage of G's | 2,694,640 / 20.34% |
| Number/percentage of N's | 14,397 / 0.11% |
| GC Percentage | 40.71% |
Coverage
| Mean | 0.0043 |
| Standard Deviation | 0.0869 |
Mapping Quality
| Mean Mapping Quality | 49.97 |
Insert size
| Mean | 75,226.79 |
| Standard Deviation | 2,849,315.96 |
| P25/Median/P75 | 339 / 427 / 535 |
Mismatches and indels
| General error rate | 1.49% |
| Mismatches | 190,508 |
| Insertions | 2,279 |
| Mapped reads with at least one insertion | 3.3% |
| Deletions | 2,316 |
| Mapped reads with at least one deletion | 3.41% |
| Homopolymer indels | 50.79% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| 1 | 249250621 | 1063202 | 0.0043 | 0.1147 |
| 2 | 243199373 | 1091086 | 0.0045 | 0.082 |
| 3 | 198022430 | 906302 | 0.0046 | 0.0765 |
| 4 | 191154276 | 899976 | 0.0047 | 0.088 |
| 5 | 180915260 | 759318 | 0.0042 | 0.0739 |
| 6 | 171115067 | 734471 | 0.0043 | 0.0752 |
| 7 | 159138663 | 654165 | 0.0041 | 0.0773 |
| 8 | 146364022 | 676934 | 0.0046 | 0.1184 |
| 9 | 141213431 | 525097 | 0.0037 | 0.0766 |
| 10 | 135534747 | 724777 | 0.0053 | 0.1311 |
| 11 | 135006516 | 589118 | 0.0044 | 0.082 |
| 12 | 133851895 | 581268 | 0.0043 | 0.0745 |
| 13 | 115169878 | 424915 | 0.0037 | 0.0689 |
| 14 | 107349540 | 385363 | 0.0036 | 0.068 |
| 15 | 102531392 | 361006 | 0.0035 | 0.0671 |
| 16 | 90354753 | 405846 | 0.0045 | 0.0833 |
| 17 | 81195210 | 351366 | 0.0043 | 0.0765 |
| 18 | 78077248 | 355035 | 0.0045 | 0.0817 |
| 19 | 59128983 | 263166 | 0.0045 | 0.0888 |
| 20 | 63025520 | 262814 | 0.0042 | 0.0805 |
| 21 | 48129895 | 179259 | 0.0037 | 0.0748 |
| 22 | 51304566 | 150578 | 0.0029 | 0.0612 |
| X | 155270560 | 669025 | 0.0043 | 0.0753 |
| Y | 59373566 | 28998 | 0.0005 | 0.049 |
| MT | 16569 | 56251 | 3.395 | 2.0903 |
| GL000207.1 | 4262 | 0 | 0 | 0 |
| GL000226.1 | 15008 | 21953 | 1.4628 | 1.7817 |
| GL000229.1 | 19913 | 0 | 0 | 0 |
| GL000231.1 | 27386 | 1169 | 0.0427 | 0.2278 |
| GL000210.1 | 27682 | 0 | 0 | 0 |
| GL000239.1 | 33824 | 0 | 0 | 0 |
| GL000235.1 | 34474 | 0 | 0 | 0 |
| GL000201.1 | 36148 | 0 | 0 | 0 |
| GL000247.1 | 36422 | 0 | 0 | 0 |
| GL000245.1 | 36651 | 481 | 0.0131 | 0.1138 |
| GL000197.1 | 37175 | 0 | 0 | 0 |
| GL000203.1 | 37498 | 459 | 0.0122 | 0.1178 |
| GL000246.1 | 38154 | 0 | 0 | 0 |
| GL000249.1 | 38502 | 483 | 0.0125 | 0.1113 |
| GL000196.1 | 38914 | 0 | 0 | 0 |
| GL000248.1 | 39786 | 456 | 0.0115 | 0.1064 |
| GL000244.1 | 39929 | 0 | 0 | 0 |
| GL000238.1 | 39939 | 410 | 0.0103 | 0.1008 |
| GL000202.1 | 40103 | 423 | 0.0105 | 0.1417 |
| GL000234.1 | 40531 | 733 | 0.0181 | 0.1675 |
| GL000232.1 | 40652 | 543 | 0.0134 | 0.1194 |
| GL000206.1 | 41001 | 0 | 0 | 0 |
| GL000240.1 | 41933 | 475 | 0.0113 | 0.1056 |
| GL000236.1 | 41934 | 924 | 0.022 | 0.1466 |
| GL000241.1 | 42152 | 930 | 0.0221 | 0.1716 |
| GL000243.1 | 43341 | 110 | 0.0025 | 0.0503 |
| GL000242.1 | 43523 | 444 | 0.0102 | 0.1005 |
| GL000230.1 | 43691 | 939 | 0.0215 | 0.1544 |
| GL000237.1 | 45867 | 852 | 0.0186 | 0.135 |
| GL000233.1 | 45941 | 0 | 0 | 0 |
| GL000204.1 | 81310 | 1345 | 0.0165 | 0.1549 |
| GL000198.1 | 90085 | 1750 | 0.0194 | 0.1441 |
| GL000208.1 | 92689 | 3998 | 0.0431 | 0.2697 |
| GL000191.1 | 106433 | 0 | 0 | 0 |
| GL000227.1 | 128374 | 476 | 0.0037 | 0.0608 |
| GL000228.1 | 129120 | 4339 | 0.0336 | 0.3105 |
| GL000214.1 | 137718 | 2220 | 0.0161 | 0.1342 |
| GL000221.1 | 155397 | 2809 | 0.0181 | 0.174 |
| GL000209.1 | 159169 | 463 | 0.0029 | 0.0574 |
| GL000218.1 | 161147 | 1369 | 0.0085 | 0.1116 |
| GL000220.1 | 161802 | 40235 | 0.2487 | 0.6522 |
| GL000213.1 | 164239 | 490 | 0.003 | 0.0545 |
| GL000211.1 | 166566 | 384 | 0.0023 | 0.0679 |
| GL000199.1 | 169874 | 21154 | 0.1245 | 0.5192 |
| GL000217.1 | 172149 | 2403 | 0.014 | 0.1307 |
| GL000216.1 | 172294 | 13420 | 0.0779 | 0.4454 |
| GL000215.1 | 172545 | 960 | 0.0056 | 0.0995 |
| GL000205.1 | 174588 | 1778 | 0.0102 | 0.1251 |
| GL000219.1 | 179198 | 1205 | 0.0067 | 0.092 |
| GL000224.1 | 179693 | 2523 | 0.014 | 0.1396 |
| GL000223.1 | 180455 | 622 | 0.0034 | 0.0586 |
| GL000195.1 | 182896 | 2173 | 0.0119 | 0.1236 |
| GL000212.1 | 186858 | 1274 | 0.0068 | 0.1243 |
| GL000222.1 | 186861 | 437 | 0.0023 | 0.0482 |
| GL000200.1 | 187035 | 370 | 0.002 | 0.0629 |
| GL000193.1 | 189789 | 3642 | 0.0192 | 0.1547 |
| GL000194.1 | 191469 | 1260 | 0.0066 | 0.0909 |
| GL000225.1 | 211173 | 10094 | 0.0478 | 0.2717 |
| GL000192.1 | 547496 | 3452 | 0.0063 | 0.0849 |
| NC_007605 | 171823 | 12864 | 0.0749 | 0.298 |
