Input data and parameters
QualiMap command line
| qualimap bamqc -bam output/mappings/longReadMapping/ont-Cshl-CapTrap_HpreCap_0+_Brain01Rep1.bam -nw 400 -hm 3 |
Alignment
| Command line: | minimap2 --MD -x splice -t 12 --secondary=no -L -a genomes/hg38.sorted.fa fastqs/ont-Cshl-CapTrap_HpreCap_0+_Brain01Rep1.fastq.gz |
| Draw chromosome limits: | no |
| Analyze overlapping paired-end reads: | no |
| Program: | minimap2 (2.22-r1101) |
| Analysis date: | Mon Nov 21 23:35:02 CET 2022 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | output/mappings/longReadMapping/ont-Cshl-CapTrap_HpreCap_0+_Brain01Rep1.bam |
Summary
Globals
| Reference size | 3,110,632,377 |
| Number of reads | 8,204,419 |
| Mapped reads | 8,204,419 / 100% |
| Unmapped reads | 0 / 0% |
| Mapped paired reads | 0 / 0% |
| Secondary alignments | 0 |
| Read min/max/mean length | 112 / 247,506 / 871.61 |
| Duplicated reads (estimated) | 7,601,927 / 92.66% |
| Duplication rate | 36.12% |
| Clipped reads | 8,204,208 / 100% |
ACGT Content
| Number/percentage of A's | 1,357,282,507 / 24.87% |
| Number/percentage of C's | 1,351,343,481 / 24.76% |
| Number/percentage of T's | 1,379,727,139 / 25.28% |
| Number/percentage of G's | 1,368,408,569 / 25.08% |
| Number/percentage of N's | 0 / 0% |
| GC Percentage | 49.84% |
Coverage
| Mean | 24.2646 |
| Standard Deviation | 177.7908 |
Mapping Quality
| Mean Mapping Quality | 2.32 |
Mismatches and indels
| General error rate | 0.33% |
| Mismatches | 183,987,299 |
| Insertions | 35,427,308 |
| Mapped reads with at least one insertion | 89.69% |
| Deletions | 61,700,788 |
| Mapped reads with at least one deletion | 96.21% |
| Homopolymer indels | 34.32% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| chr1 | 248956422 | 7451584049 | 29.9313 | 135.605 |
| chr10 | 133797422 | 2214233273 | 16.5491 | 82.5508 |
| chr11 | 135086622 | 3366213299 | 24.9189 | 189.0253 |
| chr12 | 133275309 | 4073940234 | 30.5679 | 186.6503 |
| chr13 | 114364328 | 1103800636 | 9.6516 | 73.2066 |
| chr14 | 107043718 | 3025115094 | 28.2606 | 208.3886 |
| chr15 | 101991189 | 2071531031 | 20.3109 | 189.5093 |
| chr16 | 90338345 | 2325869772 | 25.7462 | 304.4534 |
| chr17 | 83257441 | 3050536901 | 36.6398 | 220.495 |
| chr18 | 80373285 | 1761698149 | 21.919 | 127.1876 |
| chr19 | 58617616 | 4817699636 | 82.1886 | 364.4428 |
| chr2 | 242193529 | 6822583849 | 28.17 | 298.5029 |
| chr20 | 64444167 | 2143841378 | 33.2666 | 147.3407 |
| chr21 | 46709983 | 1713513227 | 36.6841 | 196.5463 |
| chr22 | 50818468 | 1431309522 | 28.1651 | 158.6427 |
| chr3 | 198295559 | 5332254849 | 26.8904 | 140.6736 |
| chr4 | 190214555 | 3097786316 | 16.2857 | 146.6298 |
| chr5 | 181538259 | 4633095794 | 25.5213 | 145.3776 |
| chr6 | 170805979 | 3153851711 | 18.4645 | 146.7912 |
| chr7 | 159345973 | 4026341954 | 25.2679 | 184.503 |
| chr8 | 145138636 | 3569445592 | 24.5934 | 108.9624 |
| chr9 | 138394717 | 2056517387 | 14.8598 | 141.1371 |
| chrIS | 10567884 | 0 | 0 | 0 |
| chrM | 16569 | 12706780 | 766.9008 | 723.0195 |
| chrX | 156040895 | 2068030563 | 13.2531 | 104.731 |
| chrY | 57227415 | 132193056 | 2.31 | 10.1693 |
| ERCC-00002 | 1061 | 0 | 0 | 0 |
| ERCC-00003 | 1023 | 0 | 0 | 0 |
| ERCC-00004 | 523 | 0 | 0 | 0 |
| ERCC-00009 | 984 | 0 | 0 | 0 |
| ERCC-00012 | 994 | 0 | 0 | 0 |
| ERCC-00013 | 808 | 0 | 0 | 0 |
| ERCC-00014 | 1957 | 0 | 0 | 0 |
| ERCC-00016 | 844 | 0 | 0 | 0 |
| ERCC-00017 | 1136 | 0 | 0 | 0 |
| ERCC-00019 | 644 | 0 | 0 | 0 |
| ERCC-00022 | 751 | 0 | 0 | 0 |
| ERCC-00024 | 536 | 0 | 0 | 0 |
| ERCC-00025 | 1994 | 0 | 0 | 0 |
| ERCC-00028 | 1130 | 0 | 0 | 0 |
| ERCC-00031 | 1138 | 0 | 0 | 0 |
| ERCC-00033 | 2022 | 0 | 0 | 0 |
| ERCC-00034 | 1019 | 0 | 0 | 0 |
| ERCC-00035 | 1130 | 0 | 0 | 0 |
| ERCC-00039 | 740 | 0 | 0 | 0 |
| ERCC-00040 | 744 | 0 | 0 | 0 |
| ERCC-00041 | 1122 | 0 | 0 | 0 |
| ERCC-00042 | 1023 | 0 | 0 | 0 |
| ERCC-00043 | 1023 | 0 | 0 | 0 |
| ERCC-00044 | 1156 | 0 | 0 | 0 |
| ERCC-00046 | 522 | 0 | 0 | 0 |
| ERCC-00048 | 992 | 0 | 0 | 0 |
| ERCC-00051 | 274 | 0 | 0 | 0 |
| ERCC-00053 | 1023 | 0 | 0 | 0 |
| ERCC-00054 | 274 | 0 | 0 | 0 |
| ERCC-00057 | 1021 | 0 | 0 | 0 |
| ERCC-00058 | 1136 | 0 | 0 | 0 |
| ERCC-00059 | 525 | 0 | 0 | 0 |
| ERCC-00060 | 523 | 0 | 0 | 0 |
| ERCC-00061 | 1136 | 0 | 0 | 0 |
| ERCC-00062 | 1023 | 0 | 0 | 0 |
| ERCC-00067 | 644 | 0 | 0 | 0 |
| ERCC-00069 | 1137 | 0 | 0 | 0 |
| ERCC-00071 | 642 | 0 | 0 | 0 |
| ERCC-00073 | 603 | 0 | 0 | 0 |
| ERCC-00074 | 522 | 0 | 0 | 0 |
| ERCC-00075 | 1023 | 0 | 0 | 0 |
| ERCC-00076 | 642 | 0 | 0 | 0 |
| ERCC-00077 | 273 | 0 | 0 | 0 |
| ERCC-00078 | 993 | 0 | 0 | 0 |
| ERCC-00079 | 644 | 0 | 0 | 0 |
| ERCC-00081 | 534 | 0 | 0 | 0 |
| ERCC-00083 | 1022 | 0 | 0 | 0 |
| ERCC-00084 | 994 | 0 | 0 | 0 |
| ERCC-00085 | 844 | 0 | 0 | 0 |
| ERCC-00086 | 1020 | 0 | 0 | 0 |
| ERCC-00092 | 1124 | 0 | 0 | 0 |
| ERCC-00095 | 521 | 0 | 0 | 0 |
| ERCC-00096 | 1107 | 0 | 0 | 0 |
| ERCC-00097 | 523 | 0 | 0 | 0 |
| ERCC-00098 | 1143 | 0 | 0 | 0 |
| ERCC-00099 | 1350 | 0 | 0 | 0 |
| ERCC-00104 | 2022 | 0 | 0 | 0 |
| ERCC-00108 | 1022 | 0 | 0 | 0 |
| ERCC-00109 | 536 | 0 | 0 | 0 |
| ERCC-00111 | 994 | 0 | 0 | 0 |
| ERCC-00112 | 1136 | 0 | 0 | 0 |
| ERCC-00113 | 840 | 0 | 0 | 0 |
| ERCC-00116 | 1991 | 0 | 0 | 0 |
| ERCC-00117 | 1136 | 0 | 0 | 0 |
| ERCC-00120 | 536 | 0 | 0 | 0 |
| ERCC-00123 | 1022 | 0 | 0 | 0 |
| ERCC-00126 | 1118 | 0 | 0 | 0 |
| ERCC-00130 | 1059 | 0 | 0 | 0 |
| ERCC-00131 | 771 | 0 | 0 | 0 |
| ERCC-00134 | 274 | 0 | 0 | 0 |
| ERCC-00136 | 1033 | 0 | 0 | 0 |
| ERCC-00137 | 537 | 0 | 0 | 0 |
| ERCC-00138 | 1024 | 0 | 0 | 0 |
| ERCC-00142 | 493 | 0 | 0 | 0 |
| ERCC-00143 | 784 | 0 | 0 | 0 |
| ERCC-00144 | 538 | 0 | 0 | 0 |
| ERCC-00145 | 1042 | 0 | 0 | 0 |
| ERCC-00147 | 1023 | 0 | 0 | 0 |
| ERCC-00148 | 494 | 0 | 0 | 0 |
| ERCC-00150 | 743 | 0 | 0 | 0 |
| ERCC-00154 | 537 | 0 | 0 | 0 |
| ERCC-00156 | 494 | 0 | 0 | 0 |
| ERCC-00157 | 1019 | 0 | 0 | 0 |
| ERCC-00158 | 1027 | 0 | 0 | 0 |
| ERCC-00160 | 743 | 0 | 0 | 0 |
| ERCC-00162 | 523 | 0 | 0 | 0 |
| ERCC-00163 | 543 | 0 | 0 | 0 |
| ERCC-00164 | 1022 | 0 | 0 | 0 |
| ERCC-00165 | 872 | 0 | 0 | 0 |
| ERCC-00168 | 1024 | 0 | 0 | 0 |
| ERCC-00170 | 1023 | 0 | 0 | 0 |
| ERCC-00171 | 505 | 0 | 0 | 0 |
| GL000008.2 | 209709 | 116550 | 0.5558 | 0.5554 |
| GL000009.2 | 201709 | 16657 | 0.0826 | 0.0931 |
| GL000194.1 | 191469 | 5478770 | 28.6144 | 28.5063 |
| GL000195.1 | 182896 | 1262754 | 6.9042 | 6.826 |
| GL000205.2 | 185591 | 234493 | 1.2635 | 1.8231 |
| GL000208.1 | 92689 | 0 | 0 | 0 |
| GL000213.1 | 164239 | 0 | 0 | 0 |
| GL000214.1 | 137718 | 2278 | 0.0165 | 0.0484 |
| GL000216.2 | 176608 | 0 | 0 | 0 |
| GL000218.1 | 161147 | 1516661 | 9.4117 | 9.3952 |
| GL000219.1 | 179198 | 3035870 | 16.9414 | 19.3395 |
| GL000220.1 | 161802 | 93454 | 0.5776 | 2.4364 |
| GL000221.1 | 155397 | 97638 | 0.6283 | 0.6326 |
| GL000224.1 | 179693 | 217696 | 1.2115 | 2.1149 |
| 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 | 31766 | 0.081 | 0.0905 |
| KI270448.1 | 7992 | 0 | 0 | 0 |
| KI270465.1 | 1774 | 0 | 0 | 0 |
| KI270466.1 | 1233 | 1090 | 0.884 | 0.7695 |
| KI270467.1 | 3920 | 5271 | 1.3446 | 1.152 |
| 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 | 0 | 0 | 0 |
| KI270707.1 | 32032 | 0 | 0 | 0 |
| KI270708.1 | 127682 | 0 | 0 | 0 |
| KI270709.1 | 66860 | 309 | 0.0046 | 0.0678 |
| KI270710.1 | 40176 | 0 | 0 | 0 |
| KI270711.1 | 42210 | 1961 | 0.0465 | 0.2087 |
| KI270712.1 | 176043 | 42741 | 0.2428 | 0.5107 |
| KI270713.1 | 40745 | 20663 | 0.5071 | 1.3027 |
| KI270714.1 | 41717 | 5790 | 0.1388 | 0.1627 |
| KI270715.1 | 161471 | 0 | 0 | 0 |
| KI270716.1 | 153799 | 0 | 0 | 0 |
| KI270717.1 | 40062 | 12827 | 0.3202 | 0.3343 |
| KI270718.1 | 38054 | 11315 | 0.2973 | 0.3359 |
| KI270719.1 | 176845 | 1072 | 0.0061 | 0.0764 |
| KI270720.1 | 39050 | 0 | 0 | 0 |
| KI270721.1 | 100316 | 75495 | 0.7526 | 0.8347 |
| 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 | 61721 | 0.1377 | 0.1802 |
| KI270728.1 | 1872759 | 127847 | 0.0683 | 0.0863 |
| KI270729.1 | 280839 | 0 | 0 | 0 |
| KI270730.1 | 112551 | 0 | 0 | 0 |
| KI270731.1 | 150754 | 1497 | 0.0099 | 0.1299 |
| KI270732.1 | 41543 | 0 | 0 | 0 |
| KI270733.1 | 179772 | 411049 | 2.2865 | 5.0451 |
| KI270734.1 | 165050 | 3080826 | 18.666 | 48.9815 |
| KI270735.1 | 42811 | 0 | 0 | 0 |
| KI270736.1 | 181920 | 106105 | 0.5833 | 0.5828 |
| KI270737.1 | 103838 | 0 | 0 | 0 |
| KI270738.1 | 99375 | 553 | 0.0056 | 0.0741 |
| KI270739.1 | 73985 | 0 | 0 | 0 |
| KI270740.1 | 37240 | 0 | 0 | 0 |
| KI270741.1 | 157432 | 230168 | 1.462 | 1.505 |
| KI270742.1 | 186739 | 2895715 | 15.5068 | 15.4468 |
| KI270743.1 | 210658 | 3317273 | 15.7472 | 15.7143 |
| KI270744.1 | 168472 | 29920 | 0.1776 | 0.19 |
| KI270745.1 | 41891 | 0 | 0 | 0 |
| KI270746.1 | 66486 | 0 | 0 | 0 |
| KI270747.1 | 198735 | 38017 | 0.1913 | 0.1962 |
| KI270748.1 | 93321 | 969 | 0.0104 | 0.1428 |
| KI270749.1 | 158759 | 0 | 0 | 0 |
| KI270750.1 | 148850 | 0 | 0 | 0 |
| KI270751.1 | 150742 | 3661 | 0.0243 | 0.1056 |
| 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 | 0 | 0 | 0 |
