Input data and parameters
QualiMap command line
| qualimap bamqc -bam output/mappings/longReadMapping/ont-Crg-CapTrap_HpreCap_0+_Brain01Rep2.bam -nw 400 -hm 3 |
Alignment
| Command line: | minimap2 --MD -x splice -t 12 --secondary=no -L -a genomes/hg38.sorted.fa fastqs/ont-Crg-CapTrap_HpreCap_0+_Brain01Rep2.fastq.gz |
| Draw chromosome limits: | no |
| Analyze overlapping paired-end reads: | no |
| Program: | minimap2 (2.22-r1101) |
| Analysis date: | Tue Nov 15 23:47:28 CET 2022 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | output/mappings/longReadMapping/ont-Crg-CapTrap_HpreCap_0+_Brain01Rep2.bam |
Summary
Globals
| Reference size | 3,110,632,377 |
| Number of reads | 9,796,279 |
| Mapped reads | 9,796,279 / 100% |
| Unmapped reads | 0 / 0% |
| Mapped paired reads | 0 / 0% |
| Secondary alignments | 0 |
| Read min/max/mean length | 91 / 91,349 / 1,148.54 |
| Duplicated reads (estimated) | 8,920,590 / 91.06% |
| Duplication rate | 37.13% |
| Clipped reads | 9,792,518 / 99.96% |
ACGT Content
| Number/percentage of A's | 1,603,208,412 / 24.98% |
| Number/percentage of C's | 1,593,065,262 / 24.82% |
| Number/percentage of T's | 1,606,130,438 / 25.03% |
| Number/percentage of G's | 1,615,534,041 / 25.17% |
| Number/percentage of N's | 0 / 0% |
| GC Percentage | 49.99% |
Coverage
| Mean | 29.2624 |
| Standard Deviation | 199.728 |
Mapping Quality
| Mean Mapping Quality | 7.38 |
Mismatches and indels
| General error rate | 0.4% |
| Mismatches | 258,101,886 |
| Insertions | 49,820,726 |
| Mapped reads with at least one insertion | 92.87% |
| Deletions | 86,730,715 |
| Mapped reads with at least one deletion | 97.39% |
| Homopolymer indels | 34.39% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| chr1 | 248956422 | 8493092280 | 34.1148 | 152.9409 |
| chr10 | 133797422 | 2682682962 | 20.0503 | 103.1409 |
| chr11 | 135086622 | 4448829856 | 32.9332 | 253.6569 |
| chr12 | 133275309 | 4921490403 | 36.9272 | 172.5679 |
| chr13 | 114364328 | 1376263409 | 12.034 | 93.7321 |
| chr14 | 107043718 | 3953875255 | 36.937 | 352.3573 |
| chr15 | 101991189 | 2577598242 | 25.2728 | 198.1301 |
| chr16 | 90338345 | 2757529653 | 30.5245 | 281.3801 |
| chr17 | 83257441 | 3443929887 | 41.3648 | 248.2661 |
| chr18 | 80373285 | 2625832059 | 32.6705 | 224.0826 |
| chr19 | 58617616 | 5213096537 | 88.934 | 378.9987 |
| chr2 | 242193529 | 7911262220 | 32.665 | 272.6226 |
| chr20 | 64444167 | 2183092691 | 33.8757 | 156.8601 |
| chr21 | 46709983 | 2454401129 | 52.5455 | 317.6616 |
| chr22 | 50818468 | 1559363844 | 30.685 | 159.7424 |
| chr3 | 198295559 | 6295747899 | 31.7493 | 159.6607 |
| chr4 | 190214555 | 3621113837 | 19.037 | 128.588 |
| chr5 | 181538259 | 5663882477 | 31.1994 | 156.4507 |
| chr6 | 170805979 | 4176429143 | 24.4513 | 177.7356 |
| chr7 | 159345973 | 4524634628 | 28.395 | 193.0975 |
| chr8 | 145138636 | 4055573949 | 27.9428 | 111.9301 |
| chr9 | 138394717 | 2597638440 | 18.7698 | 179.5261 |
| chrIS | 10567884 | 0 | 0 | 0 |
| chrM | 16569 | 27299049 | 1,647.5979 | 1,396.7512 |
| chrX | 156040895 | 2941179498 | 18.8488 | 157.1186 |
| chrY | 57227415 | 153312014 | 2.679 | 11.6217 |
| ERCC-00002 | 1061 | 32697695 | 30,817.8087 | 3,369.1793 |
| ERCC-00003 | 1023 | 6051 | 5.915 | 0.9502 |
| ERCC-00004 | 523 | 99737 | 190.7017 | 27.2645 |
| ERCC-00009 | 984 | 1080272 | 1,097.8374 | 111.9998 |
| ERCC-00012 | 994 | 0 | 0 | 0 |
| ERCC-00013 | 808 | 806 | 0.9975 | 0.086 |
| ERCC-00014 | 1957 | 0 | 0 | 0 |
| ERCC-00016 | 844 | 0 | 0 | 0 |
| ERCC-00017 | 1136 | 0 | 0 | 0 |
| ERCC-00019 | 644 | 44857 | 69.6537 | 8.8379 |
| ERCC-00022 | 751 | 124348 | 165.5766 | 19.9477 |
| ERCC-00024 | 536 | 523 | 0.9757 | 0.1852 |
| ERCC-00025 | 1994 | 3331 | 1.6705 | 0.9763 |
| ERCC-00028 | 1130 | 0 | 0 | 0 |
| ERCC-00031 | 1138 | 1124 | 0.9877 | 0.2382 |
| ERCC-00033 | 2022 | 0 | 0 | 0 |
| ERCC-00034 | 1019 | 13722 | 13.4661 | 1.7803 |
| ERCC-00035 | 1130 | 27573 | 24.4009 | 2.2291 |
| ERCC-00039 | 740 | 2187 | 2.9554 | 0.4349 |
| ERCC-00040 | 744 | 0 | 0 | 0 |
| ERCC-00041 | 1122 | 0 | 0 | 0 |
| ERCC-00042 | 1023 | 9138 | 8.9326 | 1.2764 |
| ERCC-00043 | 1023 | 97233 | 95.0469 | 8.9372 |
| ERCC-00044 | 1156 | 16746 | 14.4862 | 1.7098 |
| ERCC-00046 | 522 | 766897 | 1,469.1513 | 194.4395 |
| ERCC-00048 | 992 | 0 | 0 | 0 |
| ERCC-00051 | 274 | 0 | 0 | 0 |
| ERCC-00053 | 1023 | 0 | 0 | 0 |
| ERCC-00054 | 274 | 3420 | 12.4818 | 2.233 |
| ERCC-00057 | 1021 | 0 | 0 | 0 |
| ERCC-00058 | 1136 | 0 | 0 | 0 |
| ERCC-00059 | 525 | 32835 | 62.5429 | 8.4296 |
| ERCC-00060 | 523 | 2899 | 5.543 | 0.9922 |
| ERCC-00061 | 1136 | 0 | 0 | 0 |
| ERCC-00062 | 1023 | 39430 | 38.5435 | 3.8213 |
| ERCC-00067 | 644 | 3152 | 4.8944 | 0.6816 |
| ERCC-00069 | 1137 | 1126 | 0.9903 | 0.1317 |
| ERCC-00071 | 642 | 79492 | 123.8193 | 13.2761 |
| ERCC-00073 | 603 | 592 | 0.9818 | 0.2007 |
| ERCC-00074 | 522 | 559627 | 1,072.0824 | 140.6394 |
| ERCC-00075 | 1023 | 0 | 0 | 0 |
| ERCC-00076 | 642 | 278761 | 434.2072 | 51.3548 |
| ERCC-00077 | 273 | 0 | 0 | 0 |
| ERCC-00078 | 993 | 28850 | 29.0534 | 4.24 |
| ERCC-00079 | 644 | 92489 | 143.6165 | 17.5906 |
| ERCC-00081 | 534 | 521 | 0.9757 | 0.1949 |
| ERCC-00083 | 1022 | 0 | 0 | 0 |
| ERCC-00084 | 994 | 11831 | 11.9024 | 3.2405 |
| ERCC-00085 | 844 | 4150 | 4.9171 | 0.6652 |
| ERCC-00086 | 1020 | 0 | 0 | 0 |
| ERCC-00092 | 1124 | 257684 | 229.2562 | 25.8082 |
| ERCC-00095 | 521 | 505 | 0.9693 | 0.3564 |
| ERCC-00096 | 1107 | 21064863 | 19,028.7832 | 1,919.4419 |
| ERCC-00097 | 523 | 1539 | 2.9426 | 0.464 |
| ERCC-00098 | 1143 | 0 | 0 | 0 |
| ERCC-00099 | 1350 | 10081 | 7.4674 | 1.1036 |
| ERCC-00104 | 2022 | 0 | 0 | 0 |
| ERCC-00108 | 1022 | 507239 | 496.32 | 52.7695 |
| ERCC-00109 | 536 | 1578 | 2.944 | 0.3757 |
| ERCC-00111 | 994 | 351668 | 353.7907 | 34.2337 |
| ERCC-00112 | 1136 | 73705 | 64.8812 | 6.0851 |
| ERCC-00113 | 840 | 4150362 | 4,940.9071 | 507.8658 |
| ERCC-00116 | 1991 | 5313 | 2.6685 | 0.9268 |
| ERCC-00117 | 1136 | 0 | 0 | 0 |
| ERCC-00120 | 536 | 1579 | 2.9459 | 0.423 |
| ERCC-00123 | 1022 | 0 | 0 | 0 |
| ERCC-00126 | 1118 | 2212 | 1.9785 | 0.3755 |
| ERCC-00130 | 1059 | 9838244 | 9,290.1265 | 937.623 |
| ERCC-00131 | 771 | 123225 | 159.8249 | 17.9383 |
| ERCC-00134 | 274 | 0 | 0 | 0 |
| ERCC-00136 | 1033 | 826348 | 799.9497 | 72.424 |
| ERCC-00137 | 537 | 0 | 0 | 0 |
| ERCC-00138 | 1024 | 0 | 0 | 0 |
| ERCC-00142 | 493 | 0 | 0 | 0 |
| ERCC-00143 | 784 | 1549 | 1.9758 | 0.3007 |
| ERCC-00144 | 538 | 35410 | 65.8178 | 9.4602 |
| ERCC-00145 | 1042 | 280140 | 268.8484 | 30.3512 |
| ERCC-00147 | 1023 | 0 | 0 | 0 |
| ERCC-00148 | 494 | 8752 | 17.7166 | 2.4332 |
| ERCC-00150 | 743 | 1462 | 1.9677 | 0.3316 |
| ERCC-00154 | 537 | 4226 | 7.8696 | 0.9206 |
| ERCC-00156 | 494 | 484 | 0.9798 | 0.2256 |
| ERCC-00157 | 1019 | 6044 | 5.9313 | 0.6669 |
| ERCC-00158 | 1027 | 0 | 0 | 0 |
| ERCC-00160 | 743 | 10739 | 14.4536 | 1.9579 |
| ERCC-00162 | 523 | 0 | 0 | 0 |
| ERCC-00163 | 543 | 26588 | 48.965 | 6.5534 |
| ERCC-00164 | 1022 | 0 | 0 | 0 |
| ERCC-00165 | 872 | 85225 | 97.7351 | 10.5788 |
| ERCC-00168 | 1024 | 0 | 0 | 0 |
| ERCC-00170 | 1023 | 13132 | 12.8368 | 1.3697 |
| ERCC-00171 | 505 | 4461209 | 8,834.0772 | 1,337.2638 |
| GL000008.2 | 209709 | 123 | 0.0006 | 0.0239 |
| GL000009.2 | 201709 | 2238 | 0.0111 | 0.0251 |
| GL000194.1 | 191469 | 8014699 | 41.859 | 41.6481 |
| GL000195.1 | 182896 | 977142 | 5.3426 | 5.5462 |
| GL000205.2 | 185591 | 467533 | 2.5192 | 4.1016 |
| GL000208.1 | 92689 | 0 | 0 | 0 |
| GL000213.1 | 164239 | 0 | 0 | 0 |
| GL000214.1 | 137718 | 0 | 0 | 0 |
| GL000216.2 | 176608 | 0 | 0 | 0 |
| GL000218.1 | 161147 | 3586892 | 22.2585 | 22.2359 |
| GL000219.1 | 179198 | 4461101 | 24.8948 | 28.9076 |
| GL000220.1 | 161802 | 732623 | 4.5279 | 11.1342 |
| GL000221.1 | 155397 | 175028 | 1.1263 | 1.1272 |
| GL000224.1 | 179693 | 428879 | 2.3867 | 3.9946 |
| GL000225.1 | 211173 | 0 | 0 | 0 |
| GL000226.1 | 15008 | 0 | 0 | 0 |
| KI270302.1 | 2274 | 0 | 0 | 0 |
| KI270303.1 | 1942 | 0 | 0 | 0 |
| KI270304.1 | 2165 | 0 | 0 | 0 |
| KI270305.1 | 1472 | 0 | 0 | 0 |
| KI270310.1 | 1201 | 0 | 0 | 0 |
| KI270311.1 | 12399 | 0 | 0 | 0 |
| KI270312.1 | 998 | 0 | 0 | 0 |
| KI270315.1 | 2276 | 0 | 0 | 0 |
| KI270316.1 | 1444 | 0 | 0 | 0 |
| KI270317.1 | 37690 | 0 | 0 | 0 |
| KI270320.1 | 4416 | 0 | 0 | 0 |
| KI270322.1 | 21476 | 0 | 0 | 0 |
| KI270329.1 | 1040 | 0 | 0 | 0 |
| KI270330.1 | 1652 | 0 | 0 | 0 |
| KI270333.1 | 2699 | 0 | 0 | 0 |
| KI270334.1 | 1368 | 0 | 0 | 0 |
| KI270335.1 | 1048 | 0 | 0 | 0 |
| KI270336.1 | 1026 | 0 | 0 | 0 |
| KI270337.1 | 1121 | 0 | 0 | 0 |
| KI270338.1 | 1428 | 0 | 0 | 0 |
| KI270340.1 | 1428 | 0 | 0 | 0 |
| KI270362.1 | 3530 | 0 | 0 | 0 |
| KI270363.1 | 1803 | 0 | 0 | 0 |
| KI270364.1 | 2855 | 0 | 0 | 0 |
| KI270366.1 | 8320 | 0 | 0 | 0 |
| KI270371.1 | 2805 | 0 | 0 | 0 |
| KI270372.1 | 1650 | 0 | 0 | 0 |
| KI270373.1 | 1451 | 0 | 0 | 0 |
| KI270374.1 | 2656 | 0 | 0 | 0 |
| KI270375.1 | 2378 | 0 | 0 | 0 |
| KI270376.1 | 1136 | 0 | 0 | 0 |
| KI270378.1 | 1048 | 0 | 0 | 0 |
| KI270379.1 | 1045 | 0 | 0 | 0 |
| KI270381.1 | 1930 | 0 | 0 | 0 |
| KI270382.1 | 4215 | 0 | 0 | 0 |
| KI270383.1 | 1750 | 0 | 0 | 0 |
| KI270384.1 | 1658 | 0 | 0 | 0 |
| KI270385.1 | 990 | 0 | 0 | 0 |
| KI270386.1 | 1788 | 0 | 0 | 0 |
| KI270387.1 | 1537 | 0 | 0 | 0 |
| KI270388.1 | 1216 | 0 | 0 | 0 |
| KI270389.1 | 1298 | 0 | 0 | 0 |
| KI270390.1 | 2387 | 0 | 0 | 0 |
| KI270391.1 | 1484 | 0 | 0 | 0 |
| KI270392.1 | 971 | 0 | 0 | 0 |
| KI270393.1 | 1308 | 0 | 0 | 0 |
| KI270394.1 | 970 | 0 | 0 | 0 |
| KI270395.1 | 1143 | 0 | 0 | 0 |
| KI270396.1 | 1880 | 0 | 0 | 0 |
| KI270411.1 | 2646 | 0 | 0 | 0 |
| KI270412.1 | 1179 | 0 | 0 | 0 |
| KI270414.1 | 2489 | 0 | 0 | 0 |
| KI270417.1 | 2043 | 0 | 0 | 0 |
| KI270418.1 | 2145 | 0 | 0 | 0 |
| KI270419.1 | 1029 | 0 | 0 | 0 |
| KI270420.1 | 2321 | 0 | 0 | 0 |
| KI270422.1 | 1445 | 0 | 0 | 0 |
| KI270423.1 | 981 | 0 | 0 | 0 |
| KI270424.1 | 2140 | 0 | 0 | 0 |
| KI270425.1 | 1884 | 0 | 0 | 0 |
| KI270429.1 | 1361 | 0 | 0 | 0 |
| KI270435.1 | 92983 | 0 | 0 | 0 |
| KI270438.1 | 112505 | 0 | 0 | 0 |
| KI270442.1 | 392061 | 0 | 0 | 0 |
| KI270448.1 | 7992 | 0 | 0 | 0 |
| KI270465.1 | 1774 | 0 | 0 | 0 |
| KI270466.1 | 1233 | 0 | 0 | 0 |
| KI270467.1 | 3920 | 0 | 0 | 0 |
| KI270468.1 | 4055 | 0 | 0 | 0 |
| KI270507.1 | 5353 | 0 | 0 | 0 |
| KI270508.1 | 1951 | 0 | 0 | 0 |
| KI270509.1 | 2318 | 0 | 0 | 0 |
| KI270510.1 | 2415 | 0 | 0 | 0 |
| KI270511.1 | 8127 | 0 | 0 | 0 |
| KI270512.1 | 22689 | 0 | 0 | 0 |
| KI270515.1 | 6361 | 0 | 0 | 0 |
| KI270516.1 | 1300 | 0 | 0 | 0 |
| KI270517.1 | 3253 | 0 | 0 | 0 |
| KI270518.1 | 2186 | 0 | 0 | 0 |
| KI270519.1 | 138126 | 0 | 0 | 0 |
| KI270521.1 | 7642 | 0 | 0 | 0 |
| KI270522.1 | 5674 | 0 | 0 | 0 |
| KI270528.1 | 2983 | 0 | 0 | 0 |
| KI270529.1 | 1899 | 0 | 0 | 0 |
| KI270530.1 | 2168 | 0 | 0 | 0 |
| KI270538.1 | 91309 | 0 | 0 | 0 |
| KI270539.1 | 993 | 0 | 0 | 0 |
| KI270544.1 | 1202 | 0 | 0 | 0 |
| KI270548.1 | 1599 | 0 | 0 | 0 |
| KI270579.1 | 31033 | 0 | 0 | 0 |
| KI270580.1 | 1553 | 0 | 0 | 0 |
| KI270581.1 | 7046 | 0 | 0 | 0 |
| KI270582.1 | 6504 | 0 | 0 | 0 |
| KI270583.1 | 1400 | 0 | 0 | 0 |
| KI270584.1 | 4513 | 0 | 0 | 0 |
| KI270587.1 | 2969 | 0 | 0 | 0 |
| KI270588.1 | 6158 | 0 | 0 | 0 |
| KI270589.1 | 44474 | 0 | 0 | 0 |
| KI270590.1 | 4685 | 0 | 0 | 0 |
| KI270591.1 | 5796 | 0 | 0 | 0 |
| KI270593.1 | 3041 | 0 | 0 | 0 |
| KI270706.1 | 175055 | 88892 | 0.5078 | 0.5215 |
| KI270707.1 | 32032 | 0 | 0 | 0 |
| KI270708.1 | 127682 | 0 | 0 | 0 |
| KI270709.1 | 66860 | 0 | 0 | 0 |
| KI270710.1 | 40176 | 0 | 0 | 0 |
| KI270711.1 | 42210 | 1789 | 0.0424 | 0.3006 |
| KI270712.1 | 176043 | 60803 | 0.3454 | 0.5935 |
| KI270713.1 | 40745 | 25262 | 0.62 | 3.3434 |
| KI270714.1 | 41717 | 37216 | 0.8921 | 1.0195 |
| KI270715.1 | 161471 | 0 | 0 | 0 |
| KI270716.1 | 153799 | 0 | 0 | 0 |
| KI270717.1 | 40062 | 13481 | 0.3365 | 0.3726 |
| KI270718.1 | 38054 | 350 | 0.0092 | 0.1561 |
| KI270719.1 | 176845 | 964 | 0.0055 | 0.0704 |
| KI270720.1 | 39050 | 1346 | 0.0345 | 0.0717 |
| KI270721.1 | 100316 | 79769 | 0.7952 | 0.8581 |
| KI270722.1 | 194050 | 0 | 0 | 0 |
| KI270723.1 | 38115 | 0 | 0 | 0 |
| KI270724.1 | 39555 | 0 | 0 | 0 |
| KI270725.1 | 172810 | 0 | 0 | 0 |
| KI270726.1 | 43739 | 0 | 0 | 0 |
| KI270727.1 | 448248 | 39861 | 0.0889 | 0.1049 |
| KI270728.1 | 1872759 | 24489 | 0.0131 | 0.1106 |
| KI270729.1 | 280839 | 0 | 0 | 0 |
| KI270730.1 | 112551 | 0 | 0 | 0 |
| KI270731.1 | 150754 | 2571 | 0.0171 | 0.1409 |
| KI270732.1 | 41543 | 0 | 0 | 0 |
| KI270733.1 | 179772 | 1059302 | 5.8925 | 13.793 |
| KI270734.1 | 165050 | 5360774 | 32.4797 | 81.704 |
| KI270735.1 | 42811 | 0 | 0 | 0 |
| KI270736.1 | 181920 | 0 | 0 | 0 |
| KI270737.1 | 103838 | 0 | 0 | 0 |
| KI270738.1 | 99375 | 0 | 0 | 0 |
| KI270739.1 | 73985 | 0 | 0 | 0 |
| KI270740.1 | 37240 | 0 | 0 | 0 |
| KI270741.1 | 157432 | 242372 | 1.5395 | 1.793 |
| KI270742.1 | 186739 | 2470669 | 13.2306 | 13.1905 |
| KI270743.1 | 210658 | 2764292 | 13.1222 | 13.0986 |
| KI270744.1 | 168472 | 1438 | 0.0085 | 0.1098 |
| KI270745.1 | 41891 | 17693 | 0.4224 | 0.4976 |
| KI270746.1 | 66486 | 0 | 0 | 0 |
| KI270747.1 | 198735 | 0 | 0 | 0 |
| KI270748.1 | 93321 | 353 | 0.0038 | 0.0601 |
| KI270749.1 | 158759 | 0 | 0 | 0 |
| KI270750.1 | 148850 | 0 | 0 | 0 |
| KI270751.1 | 150742 | 0 | 0 | 0 |
| KI270752.1 | 27745 | 313 | 0.0113 | 0.1455 |
| KI270753.1 | 62944 | 0 | 0 | 0 |
| KI270754.1 | 40191 | 0 | 0 | 0 |
| KI270755.1 | 36723 | 0 | 0 | 0 |
| KI270756.1 | 79590 | 0 | 0 | 0 |
| KI270757.1 | 71251 | 0 | 0 | 0 |
| SIRVome_isoforms | 231019 | 255988723 | 1,108.0851 | 1,303.5996 |
