Input data and parameters
QualiMap command line
| qualimap bamqc -bam output/mappings/longReadMapping/ont-Crg-CapTrap_HpreCap_0+_Heart02Rep1.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+_Heart02Rep1.fastq.gz |
| Draw chromosome limits: | no |
| Analyze overlapping paired-end reads: | no |
| Program: | minimap2 (2.22-r1101) |
| Analysis date: | Wed Nov 16 00:29:53 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+_Heart02Rep1.bam |
Summary
Globals
| Reference size | 3,110,632,377 |
| Number of reads | 15,302,379 |
| Mapped reads | 15,302,379 / 100% |
| Unmapped reads | 0 / 0% |
| Mapped paired reads | 0 / 0% |
| Secondary alignments | 0 |
| Read min/max/mean length | 114 / 23,417 / 973.38 |
| Duplicated reads (estimated) | 14,687,573 / 95.98% |
| Duplication rate | 39.68% |
| Clipped reads | 15,302,126 / 100% |
ACGT Content
| Number/percentage of A's | 2,701,671,862 / 24.15% |
| Number/percentage of C's | 2,842,950,269 / 25.42% |
| Number/percentage of T's | 2,816,087,895 / 25.18% |
| Number/percentage of G's | 2,825,084,857 / 25.26% |
| Number/percentage of N's | 0 / 0% |
| GC Percentage | 50.67% |
Coverage
| Mean | 47.6602 |
| Standard Deviation | 987.5917 |
Mapping Quality
| Mean Mapping Quality | 7.81 |
Mismatches and indels
| General error rate | 0.32% |
| Mismatches | 344,673,283 |
| Insertions | 69,820,104 |
| Mapped reads with at least one insertion | 91.48% |
| Deletions | 113,336,823 |
| Mapped reads with at least one deletion | 96.64% |
| Homopolymer indels | 35.02% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| chr1 | 248956422 | 13870733654 | 55.7155 | 321.0673 |
| chr10 | 133797422 | 4609986457 | 34.455 | 134.687 |
| chr11 | 135086622 | 7984497464 | 59.1065 | 623.4144 |
| chr12 | 133275309 | 23406122286 | 175.6223 | 4,360.9381 |
| chr13 | 114364328 | 2119883828 | 18.5362 | 345.8892 |
| chr14 | 107043718 | 3751972553 | 35.0508 | 177.0446 |
| chr15 | 101991189 | 6091930788 | 59.73 | 513.6043 |
| chr16 | 90338345 | 3319757968 | 36.748 | 299.1319 |
| chr17 | 83257441 | 4322501034 | 51.9173 | 1,380.2571 |
| chr18 | 80373285 | 1987630053 | 24.73 | 423.9212 |
| chr19 | 58617616 | 8075076976 | 137.7585 | 783.3446 |
| chr2 | 242193529 | 9309095860 | 38.4366 | 291.3226 |
| chr20 | 64444167 | 2235099176 | 34.6827 | 170.2009 |
| chr21 | 46709983 | 2292856495 | 49.0871 | 313.9726 |
| chr22 | 50818468 | 3951471020 | 77.7566 | 832.5931 |
| chr3 | 198295559 | 7415593948 | 37.3967 | 426.7223 |
| chr4 | 190214555 | 6904952894 | 36.3009 | 155.2915 |
| chr5 | 181538259 | 7942528227 | 43.7513 | 254.2539 |
| chr6 | 170805979 | 6963263190 | 40.7671 | 223.4518 |
| chr7 | 159345973 | 6616861102 | 41.5251 | 279.5458 |
| chr8 | 145138636 | 6305387717 | 43.4439 | 194.5745 |
| chr9 | 138394717 | 3625021348 | 26.1934 | 265.0813 |
| chrIS | 10567884 | 0 | 0 | 0 |
| chrM | 16569 | 37273087 | 2,249.5677 | 1,969.7048 |
| chrX | 156040895 | 4211640617 | 26.9906 | 222.9511 |
| chrY | 57227415 | 432575129 | 7.5589 | 51.7631 |
| ERCC-00002 | 1061 | 26253178 | 24,743.8058 | 2,630.1989 |
| ERCC-00003 | 1023 | 119380 | 116.696 | 16.9192 |
| ERCC-00004 | 523 | 1268427 | 2,425.2906 | 349.9756 |
| ERCC-00009 | 984 | 707487 | 718.9909 | 73.529 |
| ERCC-00012 | 994 | 0 | 0 | 0 |
| ERCC-00013 | 808 | 795 | 0.9839 | 0.1436 |
| ERCC-00014 | 1957 | 387 | 0.1978 | 0.396 |
| ERCC-00016 | 844 | 0 | 0 | 0 |
| ERCC-00017 | 1136 | 0 | 0 | 0 |
| ERCC-00019 | 644 | 22550 | 35.0155 | 4.3404 |
| ERCC-00022 | 751 | 135337 | 180.2091 | 20.4535 |
| ERCC-00024 | 536 | 0 | 0 | 0 |
| ERCC-00025 | 1994 | 9906 | 4.9679 | 0.8305 |
| ERCC-00028 | 1130 | 2237 | 1.9796 | 0.274 |
| ERCC-00031 | 1138 | 1102 | 0.9684 | 0.2352 |
| ERCC-00033 | 2022 | 0 | 0 | 0 |
| ERCC-00034 | 1019 | 14424 | 14.1551 | 1.6164 |
| ERCC-00035 | 1130 | 43349 | 38.3619 | 3.5588 |
| ERCC-00039 | 740 | 3668 | 4.9568 | 0.392 |
| ERCC-00040 | 744 | 2201 | 2.9583 | 0.375 |
| ERCC-00041 | 1122 | 0 | 0 | 0 |
| ERCC-00042 | 1023 | 55790 | 54.5357 | 8.0972 |
| ERCC-00043 | 1023 | 72473 | 70.8436 | 5.4911 |
| ERCC-00044 | 1156 | 34446 | 29.7976 | 2.2399 |
| ERCC-00046 | 522 | 3442386 | 6,594.6092 | 906.2823 |
| ERCC-00048 | 992 | 0 | 0 | 0 |
| ERCC-00051 | 274 | 266 | 0.9708 | 0.1684 |
| ERCC-00053 | 1023 | 12933 | 12.6422 | 1.5174 |
| ERCC-00054 | 274 | 3923 | 14.3175 | 2.9072 |
| ERCC-00057 | 1021 | 0 | 0 | 0 |
| ERCC-00058 | 1136 | 1349 | 1.1875 | 0.484 |
| ERCC-00059 | 525 | 17301 | 32.9543 | 4.5343 |
| ERCC-00060 | 523 | 53628 | 102.5392 | 14.7282 |
| ERCC-00061 | 1136 | 0 | 0 | 0 |
| ERCC-00062 | 1023 | 47152 | 46.0919 | 4.7543 |
| ERCC-00067 | 644 | 2711 | 4.2096 | 0.8193 |
| ERCC-00069 | 1137 | 1129 | 0.993 | 0.0979 |
| ERCC-00071 | 642 | 62173 | 96.8427 | 10.4865 |
| ERCC-00073 | 603 | 0 | 0 | 0 |
| ERCC-00074 | 522 | 8020567 | 15,365.0709 | 2,034.4293 |
| ERCC-00075 | 1023 | 0 | 0 | 0 |
| ERCC-00076 | 642 | 203926 | 317.6417 | 37.4144 |
| ERCC-00077 | 273 | 263 | 0.9634 | 0.243 |
| ERCC-00078 | 993 | 18839 | 18.9718 | 1.9737 |
| ERCC-00079 | 644 | 67648 | 105.0435 | 13.5125 |
| ERCC-00081 | 534 | 0 | 0 | 0 |
| ERCC-00083 | 1022 | 0 | 0 | 0 |
| ERCC-00084 | 994 | 2245 | 2.2586 | 0.4638 |
| ERCC-00085 | 844 | 0 | 0 | 0 |
| ERCC-00086 | 1020 | 0 | 0 | 0 |
| ERCC-00092 | 1124 | 221921 | 197.4386 | 20.0751 |
| ERCC-00095 | 521 | 37713 | 72.3858 | 9.4087 |
| ERCC-00096 | 1107 | 18981668 | 17,146.9449 | 1,637.1 |
| ERCC-00097 | 523 | 0 | 0 | 0 |
| ERCC-00098 | 1143 | 0 | 0 | 0 |
| ERCC-00099 | 1350 | 10681 | 7.9119 | 0.8384 |
| ERCC-00104 | 2022 | 0 | 0 | 0 |
| ERCC-00108 | 1022 | 468939 | 458.8444 | 47.4326 |
| ERCC-00109 | 536 | 0 | 0 | 0 |
| ERCC-00111 | 994 | 395957 | 398.3471 | 39.09 |
| ERCC-00112 | 1136 | 62120 | 54.6831 | 4.9653 |
| ERCC-00113 | 840 | 3297642 | 3,925.7643 | 395.8977 |
| ERCC-00116 | 1991 | 17408 | 8.7433 | 1.1215 |
| ERCC-00117 | 1136 | 0 | 0 | 0 |
| ERCC-00120 | 536 | 2093 | 3.9049 | 0.6266 |
| ERCC-00123 | 1022 | 0 | 0 | 0 |
| ERCC-00126 | 1118 | 4298 | 3.8444 | 0.4713 |
| ERCC-00130 | 1059 | 9870602 | 9,320.6818 | 905.3402 |
| ERCC-00131 | 771 | 91219 | 118.3126 | 13.4377 |
| ERCC-00134 | 274 | 0 | 0 | 0 |
| ERCC-00136 | 1033 | 909037 | 879.9971 | 78.3011 |
| ERCC-00137 | 537 | 0 | 0 | 0 |
| ERCC-00138 | 1024 | 0 | 0 | 0 |
| ERCC-00142 | 493 | 484 | 0.9817 | 0.1339 |
| ERCC-00143 | 784 | 3850 | 4.9107 | 0.6721 |
| ERCC-00144 | 538 | 28891 | 53.7007 | 7.2995 |
| ERCC-00145 | 1042 | 241034 | 231.3186 | 24.7078 |
| ERCC-00147 | 1023 | 0 | 0 | 0 |
| ERCC-00148 | 494 | 7712 | 15.6113 | 2.1656 |
| ERCC-00150 | 743 | 2936 | 3.9515 | 0.4646 |
| ERCC-00154 | 537 | 1364 | 2.54 | 0.6474 |
| ERCC-00156 | 494 | 0 | 0 | 0 |
| ERCC-00157 | 1019 | 6492 | 6.371 | 0.8903 |
| ERCC-00158 | 1027 | 0 | 0 | 0 |
| ERCC-00160 | 743 | 12398 | 16.6864 | 2.0154 |
| ERCC-00162 | 523 | 10051 | 19.218 | 2.6288 |
| ERCC-00163 | 543 | 17936 | 33.0313 | 4.2535 |
| ERCC-00164 | 1022 | 0 | 0 | 0 |
| ERCC-00165 | 872 | 63281 | 72.57 | 8.1484 |
| ERCC-00168 | 1024 | 0 | 0 | 0 |
| ERCC-00170 | 1023 | 15092 | 14.7527 | 1.586 |
| ERCC-00171 | 505 | 3433540 | 6,799.0891 | 1,005.4152 |
| GL000008.2 | 209709 | 428792 | 2.0447 | 2.0284 |
| GL000009.2 | 201709 | 84293 | 0.4179 | 0.4604 |
| GL000194.1 | 191469 | 18604791 | 97.1687 | 97.1245 |
| GL000195.1 | 182896 | 2847121 | 15.5669 | 16.8225 |
| GL000205.2 | 185591 | 2481493 | 13.3708 | 17.8092 |
| GL000208.1 | 92689 | 0 | 0 | 0 |
| GL000213.1 | 164239 | 0 | 0 | 0 |
| GL000214.1 | 137718 | 265686 | 1.9292 | 1.9043 |
| GL000216.2 | 176608 | 0 | 0 | 0 |
| GL000218.1 | 161147 | 10804592 | 67.048 | 67.2842 |
| GL000219.1 | 179198 | 846358 | 4.723 | 4.9345 |
| GL000220.1 | 161802 | 276217 | 1.7071 | 9.8117 |
| GL000221.1 | 155397 | 482104 | 3.1024 | 3.0894 |
| GL000224.1 | 179693 | 180347 | 1.0036 | 1.0877 |
| 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 | 825 | 0.0021 | 0.0349 |
| 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 | 208213 | 1.1894 | 1.184 |
| KI270707.1 | 32032 | 0 | 0 | 0 |
| KI270708.1 | 127682 | 0 | 0 | 0 |
| KI270709.1 | 66860 | 211 | 0.0032 | 0.0561 |
| KI270710.1 | 40176 | 0 | 0 | 0 |
| KI270711.1 | 42210 | 8305 | 0.1968 | 0.3539 |
| KI270712.1 | 176043 | 1911 | 0.0109 | 0.1031 |
| KI270713.1 | 40745 | 22159 | 0.5438 | 0.5747 |
| KI270714.1 | 41717 | 16793 | 0.4025 | 0.5531 |
| KI270715.1 | 161471 | 0 | 0 | 0 |
| KI270716.1 | 153799 | 0 | 0 | 0 |
| KI270717.1 | 40062 | 0 | 0 | 0 |
| KI270718.1 | 38054 | 94 | 0.0025 | 0.0496 |
| KI270719.1 | 176845 | 140 | 0.0008 | 0.028 |
| KI270720.1 | 39050 | 0 | 0 | 0 |
| KI270721.1 | 100316 | 138122 | 1.3769 | 5.6021 |
| 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 | 27891 | 0.0622 | 0.1015 |
| KI270728.1 | 1872759 | 1094603 | 0.5845 | 2.1005 |
| KI270729.1 | 280839 | 0 | 0 | 0 |
| KI270730.1 | 112551 | 0 | 0 | 0 |
| KI270731.1 | 150754 | 750 | 0.005 | 0.0979 |
| KI270732.1 | 41543 | 0 | 0 | 0 |
| KI270733.1 | 179772 | 307558 | 1.7108 | 8.9075 |
| KI270734.1 | 165050 | 6871931 | 41.6354 | 104.768 |
| 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 | 247190 | 1.5701 | 1.6238 |
| KI270742.1 | 186739 | 15674395 | 83.9374 | 83.7427 |
| KI270743.1 | 210658 | 553143 | 2.6258 | 2.6195 |
| KI270744.1 | 168472 | 103604 | 0.615 | 0.8448 |
| KI270745.1 | 41891 | 1174 | 0.028 | 0.1634 |
| 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 | 154838 | 1.0272 | 1.0233 |
| 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 | 327960202 | 1,419.6244 | 1,534.3732 |
