Input data and parameters
QualiMap command line
| qualimap bamqc -bam output/mappings/longReadMapping/ont-Crg-CapTrap_HpreCap_0+_Brain02Rep1.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+_Brain02Rep1.fastq.gz |
| Draw chromosome limits: | no |
| Analyze overlapping paired-end reads: | no |
| Program: | minimap2 (2.22-r1101) |
| Analysis date: | Wed Nov 16 00:33:26 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+_Brain02Rep1.bam |
Summary
Globals
| Reference size | 3,110,632,377 |
| Number of reads | 13,840,799 |
| Mapped reads | 13,840,799 / 100% |
| Unmapped reads | 0 / 0% |
| Mapped paired reads | 0 / 0% |
| Secondary alignments | 0 |
| Read min/max/mean length | 87 / 29,220 / 1,017.43 |
| Duplicated reads (estimated) | 12,493,488 / 90.27% |
| Duplication rate | 37.39% |
| Clipped reads | 13,836,372 / 99.97% |
ACGT Content
| Number/percentage of A's | 2,199,388,184 / 24.62% |
| Number/percentage of C's | 2,232,293,711 / 24.99% |
| Number/percentage of T's | 2,252,122,778 / 25.21% |
| Number/percentage of G's | 2,248,647,013 / 25.17% |
| Number/percentage of N's | 0 / 0% |
| GC Percentage | 50.16% |
Coverage
| Mean | 38.8882 |
| Standard Deviation | 291.7917 |
Mapping Quality
| Mean Mapping Quality | 7.83 |
Mismatches and indels
| General error rate | 0.39% |
| Mismatches | 332,372,259 |
| Insertions | 67,544,964 |
| Mapped reads with at least one insertion | 91.67% |
| Deletions | 109,767,844 |
| Mapped reads with at least one deletion | 96.32% |
| Homopolymer indels | 34.19% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| chr1 | 248956422 | 10782538008 | 43.3109 | 168.8513 |
| chr10 | 133797422 | 4245076575 | 31.7276 | 118.9754 |
| chr11 | 135086622 | 6411656345 | 47.4633 | 325.7741 |
| chr12 | 133275309 | 5928284869 | 44.4815 | 250.785 |
| chr13 | 114364328 | 2390506138 | 20.9026 | 161.5427 |
| chr14 | 107043718 | 5221688375 | 48.7809 | 235.3568 |
| chr15 | 101991189 | 4089022224 | 40.0919 | 332.7066 |
| chr16 | 90338345 | 3759692636 | 41.6179 | 513.1946 |
| chr17 | 83257441 | 6044185955 | 72.5963 | 410.2301 |
| chr18 | 80373285 | 1510094087 | 18.7885 | 115.8031 |
| chr19 | 58617616 | 7123534308 | 121.5255 | 710.5979 |
| chr2 | 242193529 | 9953254284 | 41.0963 | 365.6344 |
| chr20 | 64444167 | 3054213883 | 47.3932 | 207.0304 |
| chr21 | 46709983 | 1670089562 | 35.7544 | 142.4248 |
| chr22 | 50818468 | 3674771137 | 72.3117 | 254.5186 |
| chr3 | 198295559 | 7665276171 | 38.6558 | 252.0561 |
| chr4 | 190214555 | 3940066847 | 20.7138 | 124.054 |
| chr5 | 181538259 | 6936002969 | 38.2068 | 244.8579 |
| chr6 | 170805979 | 7703494114 | 45.1008 | 404.8773 |
| chr7 | 159345973 | 5324761112 | 33.4164 | 155.6248 |
| chr8 | 145138636 | 4730797696 | 32.595 | 200.6257 |
| chr9 | 138394717 | 4548778100 | 32.8681 | 492.952 |
| chrIS | 10567884 | 0 | 0 | 0 |
| chrM | 16569 | 10318083 | 622.7342 | 566.9127 |
| chrX | 156040895 | 3339831738 | 21.4036 | 152.2524 |
| chrY | 57227415 | 286404196 | 5.0047 | 29.3696 |
| ERCC-00002 | 1061 | 52697648 | 49,667.9057 | 5,747.5435 |
| ERCC-00003 | 1023 | 10414 | 10.1799 | 3.0946 |
| ERCC-00004 | 523 | 161621 | 309.0268 | 43.7128 |
| ERCC-00009 | 984 | 1284691 | 1,305.5803 | 136.6436 |
| ERCC-00012 | 994 | 0 | 0 | 0 |
| ERCC-00013 | 808 | 1930 | 2.3886 | 0.7748 |
| ERCC-00014 | 1957 | 387 | 0.1978 | 0.3983 |
| ERCC-00016 | 844 | 0 | 0 | 0 |
| ERCC-00017 | 1136 | 0 | 0 | 0 |
| ERCC-00019 | 644 | 69327 | 107.6506 | 12.4278 |
| ERCC-00022 | 751 | 253156 | 337.0919 | 40.8284 |
| ERCC-00024 | 536 | 0 | 0 | 0 |
| ERCC-00025 | 1994 | 9150 | 4.5888 | 1.1246 |
| ERCC-00028 | 1130 | 4151 | 3.6735 | 0.6073 |
| ERCC-00031 | 1138 | 1807 | 1.5879 | 0.5183 |
| ERCC-00033 | 2022 | 0 | 0 | 0 |
| ERCC-00034 | 1019 | 22038 | 21.6271 | 2.3796 |
| ERCC-00035 | 1130 | 79862 | 70.6743 | 6.9172 |
| ERCC-00039 | 740 | 2926 | 3.9541 | 0.3966 |
| ERCC-00040 | 744 | 0 | 0 | 0 |
| ERCC-00041 | 1122 | 0 | 0 | 0 |
| ERCC-00042 | 1023 | 12625 | 12.3412 | 1.4108 |
| ERCC-00043 | 1023 | 90395 | 88.3627 | 7.27 |
| ERCC-00044 | 1156 | 33946 | 29.3651 | 2.2474 |
| ERCC-00046 | 522 | 833949 | 1,597.6034 | 210.2655 |
| ERCC-00048 | 992 | 0 | 0 | 0 |
| ERCC-00051 | 274 | 0 | 0 | 0 |
| ERCC-00053 | 1023 | 3256 | 3.1828 | 0.5854 |
| ERCC-00054 | 274 | 5189 | 18.938 | 3.7245 |
| ERCC-00057 | 1021 | 0 | 0 | 0 |
| ERCC-00058 | 1136 | 1104 | 0.9718 | 0.1752 |
| ERCC-00059 | 525 | 62164 | 118.4076 | 16.0932 |
| ERCC-00060 | 523 | 7113 | 13.6004 | 2.0381 |
| ERCC-00061 | 1136 | 0 | 0 | 0 |
| ERCC-00062 | 1023 | 14765 | 14.433 | 1.6232 |
| ERCC-00067 | 644 | 8186 | 12.7112 | 2.113 |
| ERCC-00069 | 1137 | 2250 | 1.9789 | 0.2471 |
| ERCC-00071 | 642 | 144479 | 225.0452 | 24.366 |
| ERCC-00073 | 603 | 2213 | 3.67 | 0.6962 |
| ERCC-00074 | 522 | 921937 | 1,766.1628 | 227.371 |
| ERCC-00075 | 1023 | 0 | 0 | 0 |
| ERCC-00076 | 642 | 492591 | 767.2757 | 90.1509 |
| ERCC-00077 | 273 | 0 | 0 | 0 |
| ERCC-00078 | 993 | 38542 | 38.8137 | 4.8664 |
| ERCC-00079 | 644 | 194076 | 301.3602 | 35.921 |
| ERCC-00081 | 534 | 0 | 0 | 0 |
| ERCC-00083 | 1022 | 0 | 0 | 0 |
| ERCC-00084 | 994 | 15122 | 15.2133 | 2.3647 |
| ERCC-00085 | 844 | 11151 | 13.2121 | 1.7017 |
| ERCC-00086 | 1020 | 0 | 0 | 0 |
| ERCC-00092 | 1124 | 382118 | 339.9626 | 43.2972 |
| ERCC-00095 | 521 | 1349 | 2.5893 | 0.5809 |
| ERCC-00096 | 1107 | 31629436 | 28,572.2096 | 2,961.917 |
| ERCC-00097 | 523 | 0 | 0 | 0 |
| ERCC-00098 | 1143 | 0 | 0 | 0 |
| ERCC-00099 | 1350 | 3034 | 2.2474 | 0.5994 |
| ERCC-00104 | 2022 | 0 | 0 | 0 |
| ERCC-00108 | 1022 | 739013 | 723.1047 | 82.64 |
| ERCC-00109 | 536 | 718 | 1.3396 | 0.5243 |
| ERCC-00111 | 994 | 516479 | 519.5966 | 49.4721 |
| ERCC-00112 | 1136 | 128941 | 113.5044 | 10.7397 |
| ERCC-00113 | 840 | 6723809 | 8,004.5345 | 798.0806 |
| ERCC-00116 | 1991 | 17785 | 8.9327 | 3.0826 |
| ERCC-00117 | 1136 | 0 | 0 | 0 |
| ERCC-00120 | 536 | 1036 | 1.9328 | 0.5535 |
| ERCC-00123 | 1022 | 0 | 0 | 0 |
| ERCC-00126 | 1118 | 5515 | 4.9329 | 0.5635 |
| ERCC-00130 | 1059 | 14728750 | 13,908.1681 | 1,422.2498 |
| ERCC-00131 | 771 | 166978 | 216.5733 | 26.0267 |
| ERCC-00134 | 274 | 0 | 0 | 0 |
| ERCC-00136 | 1033 | 1212545 | 1,173.8093 | 103.6911 |
| ERCC-00137 | 537 | 526 | 0.9795 | 0.1901 |
| ERCC-00138 | 1024 | 0 | 0 | 0 |
| ERCC-00142 | 493 | 0 | 0 | 0 |
| ERCC-00143 | 784 | 6934 | 8.8444 | 1.1143 |
| ERCC-00144 | 538 | 75693 | 140.6933 | 19.0802 |
| ERCC-00145 | 1042 | 474784 | 455.6468 | 49.1259 |
| ERCC-00147 | 1023 | 0 | 0 | 0 |
| ERCC-00148 | 494 | 17094 | 34.6032 | 4.2427 |
| ERCC-00150 | 743 | 2252 | 3.031 | 0.5871 |
| ERCC-00154 | 537 | 5255 | 9.7858 | 1.6102 |
| ERCC-00156 | 494 | 1943 | 3.9332 | 0.5983 |
| ERCC-00157 | 1019 | 1489 | 1.4612 | 0.5204 |
| ERCC-00158 | 1027 | 0 | 0 | 0 |
| ERCC-00160 | 743 | 31402 | 42.2638 | 5.1705 |
| ERCC-00162 | 523 | 0 | 0 | 0 |
| ERCC-00163 | 543 | 45829 | 84.3996 | 11.2049 |
| ERCC-00164 | 1022 | 0 | 0 | 0 |
| ERCC-00165 | 872 | 125958 | 144.4472 | 15.3677 |
| ERCC-00168 | 1024 | 0 | 0 | 0 |
| ERCC-00170 | 1023 | 17107 | 16.7224 | 2.6472 |
| ERCC-00171 | 505 | 8259413 | 16,355.2733 | 2,423.4479 |
| GL000008.2 | 209709 | 965596 | 4.6045 | 4.5626 |
| GL000009.2 | 201709 | 1068738 | 5.2984 | 5.2331 |
| GL000194.1 | 191469 | 9755581 | 50.9512 | 50.4796 |
| GL000195.1 | 182896 | 1132953 | 6.1945 | 7.8957 |
| GL000205.2 | 185591 | 2971738 | 16.0123 | 30.7573 |
| GL000208.1 | 92689 | 0 | 0 | 0 |
| GL000213.1 | 164239 | 156266 | 0.9515 | 1.0074 |
| GL000214.1 | 137718 | 1579190 | 11.4668 | 11.275 |
| GL000216.2 | 176608 | 76820 | 0.435 | 0.5512 |
| GL000218.1 | 161147 | 11097849 | 68.8679 | 68.8576 |
| GL000219.1 | 179198 | 2169629 | 12.1074 | 14.0338 |
| GL000220.1 | 161802 | 747515 | 4.6199 | 5.5825 |
| GL000221.1 | 155397 | 1557548 | 10.023 | 9.9741 |
| GL000224.1 | 179693 | 626547 | 3.4868 | 6.5505 |
| GL000225.1 | 211173 | 754819 | 3.5744 | 3.5208 |
| 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 | 234581 | 0.5983 | 0.6277 |
| KI270448.1 | 7992 | 0 | 0 | 0 |
| KI270465.1 | 1774 | 0 | 0 | 0 |
| KI270466.1 | 1233 | 759 | 0.6156 | 0.658 |
| KI270467.1 | 3920 | 12640 | 3.2245 | 3.0193 |
| 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 | 420180 | 2.4003 | 2.3447 |
| KI270707.1 | 32032 | 0 | 0 | 0 |
| KI270708.1 | 127682 | 61946 | 0.4852 | 0.4854 |
| KI270709.1 | 66860 | 0 | 0 | 0 |
| KI270710.1 | 40176 | 1760 | 0.0438 | 0.1382 |
| KI270711.1 | 42210 | 26724 | 0.6331 | 1.2428 |
| KI270712.1 | 176043 | 18476 | 0.105 | 0.286 |
| KI270713.1 | 40745 | 340645 | 8.3604 | 7.7925 |
| KI270714.1 | 41717 | 37095 | 0.8892 | 0.8936 |
| KI270715.1 | 161471 | 0 | 0 | 0 |
| KI270716.1 | 153799 | 0 | 0 | 0 |
| KI270717.1 | 40062 | 86351 | 2.1554 | 2.1862 |
| KI270718.1 | 38054 | 19785 | 0.5199 | 0.6129 |
| KI270719.1 | 176845 | 1448158 | 8.1889 | 8.0978 |
| KI270720.1 | 39050 | 8498 | 0.2176 | 0.2412 |
| KI270721.1 | 100316 | 140522 | 1.4008 | 2.2646 |
| KI270722.1 | 194050 | 93233 | 0.4805 | 1.2415 |
| KI270723.1 | 38115 | 6010 | 0.1577 | 0.4741 |
| KI270724.1 | 39555 | 5976 | 0.1511 | 0.2304 |
| KI270725.1 | 172810 | 11611 | 0.0672 | 0.1154 |
| KI270726.1 | 43739 | 99106 | 2.2658 | 2.741 |
| KI270727.1 | 448248 | 7804805 | 17.4118 | 17.35 |
| KI270728.1 | 1872759 | 5054703 | 2.6991 | 4.0216 |
| KI270729.1 | 280839 | 0 | 0 | 0 |
| KI270730.1 | 112551 | 0 | 0 | 0 |
| KI270731.1 | 150754 | 90011 | 0.5971 | 1.1218 |
| KI270732.1 | 41543 | 486 | 0.0117 | 0.1068 |
| KI270733.1 | 179772 | 492979 | 2.7422 | 7.4134 |
| KI270734.1 | 165050 | 2714873 | 16.4488 | 40.7772 |
| KI270735.1 | 42811 | 17516 | 0.4091 | 0.4565 |
| 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 | 5257778 | 33.3971 | 33.1757 |
| KI270742.1 | 186739 | 5601902 | 29.9986 | 29.7598 |
| KI270743.1 | 210658 | 2217657 | 10.5273 | 10.4586 |
| KI270744.1 | 168472 | 917297 | 5.4448 | 5.428 |
| KI270745.1 | 41891 | 2942 | 0.0702 | 0.4373 |
| KI270746.1 | 66486 | 17066 | 0.2567 | 0.3011 |
| KI270747.1 | 198735 | 2408 | 0.0121 | 0.1295 |
| KI270748.1 | 93321 | 11103 | 0.119 | 0.3235 |
| KI270749.1 | 158759 | 3019 | 0.019 | 0.1918 |
| KI270750.1 | 148850 | 955711 | 6.4206 | 6.5082 |
| KI270751.1 | 150742 | 936537 | 6.2128 | 6.1855 |
| KI270752.1 | 27745 | 0 | 0 | 0 |
| KI270753.1 | 62944 | 263179 | 4.1812 | 4.2603 |
| KI270754.1 | 40191 | 10142 | 0.2523 | 0.4988 |
| KI270755.1 | 36723 | 27843 | 0.7582 | 2.8612 |
| KI270756.1 | 79590 | 0 | 0 | 0 |
| KI270757.1 | 71251 | 0 | 0 | 0 |
| SIRVome_isoforms | 231019 | 429480138 | 1,859.0685 | 2,196.3759 |
