Input data and parameters
QualiMap command line
| qualimap bamqc -bam output/mappings/longReadMapping/ont-Crg-CapTrap_HpreCap_0+_Brain03Rep1.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+_Brain03Rep1.fastq.gz |
| Draw chromosome limits: | no |
| Analyze overlapping paired-end reads: | no |
| Program: | minimap2 (2.22-r1101) |
| Analysis date: | Wed Nov 16 02:21:53 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+_Brain03Rep1.bam |
Summary
Globals
| Reference size | 3,110,632,377 |
| Number of reads | 13,689,397 |
| Mapped reads | 13,689,397 / 100% |
| Unmapped reads | 0 / 0% |
| Mapped paired reads | 0 / 0% |
| Secondary alignments | 0 |
| Read min/max/mean length | 108 / 25,134 / 1,177.33 |
| Duplicated reads (estimated) | 12,812,543 / 93.59% |
| Duplication rate | 38.57% |
| Clipped reads | 13,688,707 / 99.99% |
ACGT Content
| Number/percentage of A's | 2,366,790,066 / 24.22% |
| Number/percentage of C's | 2,487,738,229 / 25.45% |
| Number/percentage of T's | 2,419,609,986 / 24.76% |
| Number/percentage of G's | 2,499,514,264 / 25.57% |
| Number/percentage of N's | 0 / 0% |
| GC Percentage | 51.03% |
Coverage
| Mean | 42.6321 |
| Standard Deviation | 290.5596 |
Mapping Quality
| Mean Mapping Quality | 8.44 |
Mismatches and indels
| General error rate | 0.38% |
| Mismatches | 359,893,611 |
| Insertions | 73,162,488 |
| Mapped reads with at least one insertion | 94.27% |
| Deletions | 118,448,553 |
| Mapped reads with at least one deletion | 97.94% |
| Homopolymer indels | 34.05% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| chr1 | 248956422 | 12758481893 | 51.2479 | 224.8843 |
| chr10 | 133797422 | 4016740047 | 30.0211 | 139.2845 |
| chr11 | 135086622 | 6293851574 | 46.5912 | 323.2723 |
| chr12 | 133275309 | 8209686486 | 61.5995 | 313.9946 |
| chr13 | 114364328 | 1752004634 | 15.3195 | 92.8341 |
| chr14 | 107043718 | 5554744251 | 51.8923 | 520.3201 |
| chr15 | 101991189 | 3791568469 | 37.1755 | 250.9291 |
| chr16 | 90338345 | 4836418660 | 53.5367 | 512.5155 |
| chr17 | 83257441 | 5250750845 | 63.0664 | 346.505 |
| chr18 | 80373285 | 2828819779 | 35.196 | 194.3356 |
| chr19 | 58617616 | 9355904204 | 159.6091 | 649.0186 |
| chr2 | 242193529 | 10727462434 | 44.2929 | 331.5084 |
| chr20 | 64444167 | 3560804317 | 55.2541 | 181.4886 |
| chr21 | 46709983 | 2783209852 | 59.5849 | 346.0983 |
| chr22 | 50818468 | 2606025901 | 51.2811 | 268.3909 |
| chr3 | 198295559 | 9230443463 | 46.5489 | 218.8561 |
| chr4 | 190214555 | 4508698306 | 23.7032 | 165.7182 |
| chr5 | 181538259 | 7473638819 | 41.1684 | 198.8718 |
| chr6 | 170805979 | 5405966508 | 31.6497 | 221.4313 |
| chr7 | 159345973 | 6737146471 | 42.28 | 292.284 |
| chr8 | 145138636 | 5451344065 | 37.5596 | 137.4974 |
| chr9 | 138394717 | 3997493319 | 28.8847 | 286.5046 |
| chrIS | 10567884 | 0 | 0 | 0 |
| chrM | 16569 | 29929191 | 1,806.3366 | 1,562.4135 |
| chrX | 156040895 | 3905816658 | 25.0307 | 201.6584 |
| chrY | 57227415 | 198902691 | 3.4757 | 14.7159 |
| ERCC-00002 | 1061 | 107360386 | 101,187.9227 | 10,637.3842 |
| ERCC-00003 | 1023 | 135051 | 132.0147 | 14.4977 |
| ERCC-00004 | 523 | 761639 | 1,456.2887 | 209.2804 |
| ERCC-00009 | 984 | 3057674 | 3,107.3923 | 317.0898 |
| ERCC-00012 | 994 | 0 | 0 | 0 |
| ERCC-00013 | 808 | 2389 | 2.9567 | 0.3915 |
| ERCC-00014 | 1957 | 0 | 0 | 0 |
| ERCC-00016 | 844 | 0 | 0 | 0 |
| ERCC-00017 | 1136 | 0 | 0 | 0 |
| ERCC-00019 | 644 | 88929 | 138.0885 | 16.8 |
| ERCC-00022 | 751 | 442109 | 588.6937 | 66.3196 |
| ERCC-00024 | 536 | 0 | 0 | 0 |
| ERCC-00025 | 1994 | 15615 | 7.831 | 1.0186 |
| ERCC-00028 | 1130 | 3352 | 2.9664 | 0.3703 |
| ERCC-00031 | 1138 | 3373 | 2.964 | 0.3332 |
| ERCC-00033 | 2022 | 0 | 0 | 0 |
| ERCC-00034 | 1019 | 53841 | 52.8371 | 5.7046 |
| ERCC-00035 | 1130 | 179510 | 158.8584 | 13.86 |
| ERCC-00039 | 740 | 8761 | 11.8392 | 1.117 |
| ERCC-00040 | 744 | 2186 | 2.9382 | 0.4488 |
| ERCC-00041 | 1122 | 0 | 0 | 0 |
| ERCC-00042 | 1023 | 60901 | 59.5318 | 5.8081 |
| ERCC-00043 | 1023 | 257890 | 252.0919 | 21.1093 |
| ERCC-00044 | 1156 | 152952 | 132.3114 | 10.1281 |
| ERCC-00046 | 522 | 3099053 | 5,936.8831 | 805.075 |
| ERCC-00048 | 992 | 0 | 0 | 0 |
| ERCC-00051 | 274 | 781 | 2.8504 | 0.6136 |
| ERCC-00053 | 1023 | 9114 | 8.9091 | 0.8678 |
| ERCC-00054 | 274 | 5760 | 21.0219 | 3.9206 |
| ERCC-00057 | 1021 | 0 | 0 | 0 |
| ERCC-00058 | 1136 | 3379 | 2.9745 | 0.3265 |
| ERCC-00059 | 525 | 74016 | 140.9829 | 18.4228 |
| ERCC-00060 | 523 | 79876 | 152.7266 | 22.4124 |
| ERCC-00061 | 1136 | 0 | 0 | 0 |
| ERCC-00062 | 1023 | 87103 | 85.1447 | 8.069 |
| ERCC-00067 | 644 | 12583 | 19.5388 | 2.5528 |
| ERCC-00069 | 1137 | 3326 | 2.9252 | 0.3835 |
| ERCC-00071 | 642 | 261443 | 407.2321 | 45.87 |
| ERCC-00073 | 603 | 2354 | 3.9038 | 0.6158 |
| ERCC-00074 | 522 | 6559213 | 12,565.5421 | 1,645.9648 |
| ERCC-00075 | 1023 | 0 | 0 | 0 |
| ERCC-00076 | 642 | 763726 | 1,189.6044 | 140.2561 |
| ERCC-00077 | 273 | 0 | 0 | 0 |
| ERCC-00078 | 993 | 113997 | 114.8006 | 11.3667 |
| ERCC-00079 | 644 | 236022 | 366.4938 | 44.5659 |
| ERCC-00081 | 534 | 509 | 0.9532 | 0.2447 |
| ERCC-00083 | 1022 | 0 | 0 | 0 |
| ERCC-00084 | 994 | 31414 | 31.6036 | 4.9066 |
| ERCC-00085 | 844 | 9986 | 11.8318 | 1.3121 |
| ERCC-00086 | 1020 | 1014 | 0.9941 | 0.1358 |
| ERCC-00092 | 1124 | 923063 | 821.2304 | 82.2345 |
| ERCC-00095 | 521 | 21703 | 41.6564 | 5.5124 |
| ERCC-00096 | 1107 | 79852501 | 72,134.1472 | 6,892.1372 |
| ERCC-00097 | 523 | 1535 | 2.935 | 0.4774 |
| ERCC-00098 | 1143 | 0 | 0 | 0 |
| ERCC-00099 | 1350 | 23266 | 17.2341 | 1.8169 |
| ERCC-00104 | 2022 | 0 | 0 | 0 |
| ERCC-00108 | 1022 | 2071843 | 2,027.2436 | 208.0484 |
| ERCC-00109 | 536 | 525 | 0.9795 | 0.1806 |
| ERCC-00111 | 994 | 1630517 | 1,640.3592 | 155.4657 |
| ERCC-00112 | 1136 | 287612 | 253.1796 | 23.3418 |
| ERCC-00113 | 840 | 15057938 | 17,926.1167 | 1,785.2586 |
| ERCC-00116 | 1991 | 98321 | 49.3827 | 4.334 |
| ERCC-00117 | 1136 | 0 | 0 | 0 |
| ERCC-00120 | 536 | 5183 | 9.6698 | 1.6328 |
| ERCC-00123 | 1022 | 0 | 0 | 0 |
| ERCC-00126 | 1118 | 18850 | 16.8605 | 1.3139 |
| ERCC-00130 | 1059 | 40496139 | 38,239.9802 | 3,734.9369 |
| ERCC-00131 | 771 | 342459 | 444.1751 | 49.5096 |
| ERCC-00134 | 274 | 0 | 0 | 0 |
| ERCC-00136 | 1033 | 3359981 | 3,252.6438 | 284.1095 |
| ERCC-00137 | 537 | 2081 | 3.8752 | 0.6801 |
| ERCC-00138 | 1024 | 1008 | 0.9844 | 0.1774 |
| ERCC-00142 | 493 | 1468 | 2.9777 | 0.3157 |
| ERCC-00143 | 784 | 8926 | 11.3852 | 1.4593 |
| ERCC-00144 | 538 | 105732 | 196.5279 | 27.7452 |
| ERCC-00145 | 1042 | 1010205 | 969.4866 | 104.5292 |
| ERCC-00147 | 1023 | 1016 | 0.9932 | 0.1425 |
| ERCC-00148 | 494 | 23701 | 47.9777 | 7.0274 |
| ERCC-00150 | 743 | 11710 | 15.7604 | 1.6528 |
| ERCC-00154 | 537 | 17518 | 32.622 | 4.1723 |
| ERCC-00156 | 494 | 1460 | 2.9555 | 0.3836 |
| ERCC-00157 | 1019 | 19711 | 19.3435 | 2.0276 |
| ERCC-00158 | 1027 | 2041 | 1.9873 | 0.1801 |
| ERCC-00160 | 743 | 66686 | 89.7524 | 10.1269 |
| ERCC-00162 | 523 | 6544 | 12.5124 | 2.0458 |
| ERCC-00163 | 543 | 52074 | 95.9006 | 11.9967 |
| ERCC-00164 | 1022 | 0 | 0 | 0 |
| ERCC-00165 | 872 | 292600 | 335.5505 | 35.1258 |
| ERCC-00168 | 1024 | 0 | 0 | 0 |
| ERCC-00170 | 1023 | 68227 | 66.6931 | 7.1507 |
| ERCC-00171 | 505 | 10756952 | 21,300.895 | 3,127.1431 |
| GL000008.2 | 209709 | 0 | 0 | 0 |
| GL000009.2 | 201709 | 0 | 0 | 0 |
| GL000194.1 | 191469 | 10025088 | 52.3588 | 52.2647 |
| GL000195.1 | 182896 | 675304 | 3.6923 | 3.7578 |
| GL000205.2 | 185591 | 275753 | 1.4858 | 2.3624 |
| GL000208.1 | 92689 | 0 | 0 | 0 |
| GL000213.1 | 164239 | 0 | 0 | 0 |
| GL000214.1 | 137718 | 11423 | 0.0829 | 0.1846 |
| GL000216.2 | 176608 | 0 | 0 | 0 |
| GL000218.1 | 161147 | 2549775 | 15.8227 | 15.7554 |
| GL000219.1 | 179198 | 4313847 | 24.0731 | 30.1978 |
| GL000220.1 | 161802 | 283275 | 1.7508 | 3.271 |
| GL000221.1 | 155397 | 26704 | 0.1718 | 0.2259 |
| GL000224.1 | 179693 | 264207 | 1.4703 | 2.808 |
| 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 | 9297 | 0.0826 | 0.1112 |
| KI270442.1 | 392061 | 63644 | 0.1623 | 0.1863 |
| 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 | 889 | 0.0051 | 0.0709 |
| 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 | 7830 | 0.1855 | 0.3552 |
| KI270712.1 | 176043 | 77970 | 0.4429 | 0.6805 |
| KI270713.1 | 40745 | 34690 | 0.8514 | 3.6521 |
| KI270714.1 | 41717 | 5780 | 0.1386 | 0.1687 |
| KI270715.1 | 161471 | 0 | 0 | 0 |
| KI270716.1 | 153799 | 0 | 0 | 0 |
| KI270717.1 | 40062 | 445 | 0.0111 | 0.1045 |
| KI270718.1 | 38054 | 3456 | 0.0908 | 0.1696 |
| KI270719.1 | 176845 | 249 | 0.0014 | 0.037 |
| KI270720.1 | 39050 | 0 | 0 | 0 |
| KI270721.1 | 100316 | 58593 | 0.5841 | 0.7552 |
| KI270722.1 | 194050 | 0 | 0 | 0 |
| KI270723.1 | 38115 | 0 | 0 | 0 |
| KI270724.1 | 39555 | 0 | 0 | 0 |
| KI270725.1 | 172810 | 21751 | 0.1259 | 0.1311 |
| KI270726.1 | 43739 | 0 | 0 | 0 |
| KI270727.1 | 448248 | 54753 | 0.1221 | 0.1819 |
| KI270728.1 | 1872759 | 147983 | 0.079 | 0.224 |
| KI270729.1 | 280839 | 0 | 0 | 0 |
| KI270730.1 | 112551 | 0 | 0 | 0 |
| KI270731.1 | 150754 | 1601 | 0.0106 | 0.1442 |
| KI270732.1 | 41543 | 0 | 0 | 0 |
| KI270733.1 | 179772 | 592475 | 3.2957 | 7.3881 |
| KI270734.1 | 165050 | 13116033 | 79.467 | 193.8137 |
| 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 | 113051 | 0.7181 | 1.0745 |
| KI270742.1 | 186739 | 4276521 | 22.9011 | 22.8374 |
| KI270743.1 | 210658 | 3040243 | 14.4321 | 14.3962 |
| KI270744.1 | 168472 | 6954 | 0.0413 | 0.0669 |
| KI270745.1 | 41891 | 413 | 0.0099 | 0.1194 |
| KI270746.1 | 66486 | 0 | 0 | 0 |
| KI270747.1 | 198735 | 0 | 0 | 0 |
| KI270748.1 | 93321 | 0 | 0 | 0 |
| KI270749.1 | 158759 | 0 | 0 | 0 |
| KI270750.1 | 148850 | 0 | 0 | 0 |
| KI270751.1 | 150742 | 8323 | 0.0552 | 0.0884 |
| KI270752.1 | 27745 | 0 | 0 | 0 |
| 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 | 1026235767 | 4,442.2137 | 5,067.97 |
