Input data and parameters
QualiMap command line
| qualimap bamqc -bam output/mappings/longReadMapping/ont-Crg-Telop_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-Telop_HpreCap_0+_Brain01Rep2.fastq.gz |
| Draw chromosome limits: | no |
| Analyze overlapping paired-end reads: | no |
| Program: | minimap2 (2.22-r1101) |
| Analysis date: | Wed Nov 16 00:49:01 CET 2022 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | output/mappings/longReadMapping/ont-Crg-Telop_HpreCap_0+_Brain01Rep2.bam |
Summary
Globals
| Reference size | 3,110,632,377 |
| Number of reads | 7,816,321 |
| Mapped reads | 7,816,321 / 100% |
| Unmapped reads | 0 / 0% |
| Mapped paired reads | 0 / 0% |
| Secondary alignments | 0 |
| Read min/max/mean length | 102 / 77,030 / 1,665.62 |
| Duplicated reads (estimated) | 7,353,796 / 94.08% |
| Duplication rate | 43.8% |
| Clipped reads | 7,816,173 / 100% |
ACGT Content
| Number/percentage of A's | 2,110,865,778 / 24.76% |
| Number/percentage of C's | 2,138,192,987 / 25.09% |
| Number/percentage of T's | 2,115,887,176 / 24.82% |
| Number/percentage of G's | 2,158,661,367 / 25.33% |
| Number/percentage of N's | 0 / 0% |
| GC Percentage | 50.41% |
Coverage
| Mean | 45.079 |
| Standard Deviation | 237.1288 |
Mapping Quality
| Mean Mapping Quality | 7.13 |
Mismatches and indels
| General error rate | 1.51% |
| Mismatches | 1,457,091,611 |
| Insertions | 117,984,261 |
| Mapped reads with at least one insertion | 98.65% |
| Deletions | 182,155,389 |
| Mapped reads with at least one deletion | 99.44% |
| Homopolymer indels | 37.22% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| chr1 | 248956422 | 10554356596 | 42.3944 | 154.0472 |
| chr10 | 133797422 | 4481996094 | 33.4984 | 164.9807 |
| chr11 | 135086622 | 5950190667 | 44.0472 | 457.0897 |
| chr12 | 133275309 | 4303139447 | 32.2876 | 250.8278 |
| chr13 | 114364328 | 1981943607 | 17.3301 | 107.2645 |
| chr14 | 107043718 | 4594432637 | 42.9211 | 133.9589 |
| chr15 | 101991189 | 4028718074 | 39.5006 | 189.3715 |
| chr16 | 90338345 | 5252148097 | 58.1386 | 369.9805 |
| chr17 | 83257441 | 7274895578 | 87.3783 | 354.2365 |
| chr18 | 80373285 | 7751702356 | 96.4463 | 435.0425 |
| chr19 | 58617616 | 5134878727 | 87.5996 | 278.3966 |
| chr2 | 242193529 | 9875236388 | 40.7742 | 111.0075 |
| chr20 | 64444167 | 11519283757 | 178.7483 | 646.5398 |
| chr21 | 46709983 | 2113441202 | 45.246 | 80.652 |
| chr22 | 50818468 | 3509706979 | 69.0636 | 145.2556 |
| chr3 | 198295559 | 5949437076 | 30.0029 | 73.1195 |
| chr4 | 190214555 | 12118332364 | 63.7088 | 170.9254 |
| chr5 | 181538259 | 6037731366 | 33.2587 | 111.7237 |
| chr6 | 170805979 | 4913960289 | 28.7693 | 413.2472 |
| chr7 | 159345973 | 6376836584 | 40.0188 | 101.6237 |
| chr8 | 145138636 | 8350271032 | 57.5331 | 182.9003 |
| chr9 | 138394717 | 3474840785 | 25.1082 | 108.0545 |
| chrIS | 10567884 | 0 | 0 | 0 |
| chrM | 16569 | 15555281 | 938.8183 | 1,068.8208 |
| chrX | 156040895 | 4489569205 | 28.7717 | 146.4579 |
| chrY | 57227415 | 4497019 | 0.0786 | 4.0034 |
| ERCC-00002 | 1061 | 3254182 | 3,067.0895 | 220.5525 |
| ERCC-00003 | 1023 | 173848 | 169.9394 | 14.2075 |
| ERCC-00004 | 523 | 1242124 | 2,374.9981 | 206.7744 |
| ERCC-00009 | 984 | 464248 | 471.7967 | 35.1831 |
| 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 | 7600 | 11.8012 | 1.4512 |
| ERCC-00022 | 751 | 30739 | 40.9308 | 4.6404 |
| ERCC-00024 | 536 | 0 | 0 | 0 |
| ERCC-00025 | 1994 | 9942 | 4.986 | 0.3831 |
| ERCC-00028 | 1130 | 2250 | 1.9912 | 0.2306 |
| ERCC-00031 | 1138 | 0 | 0 | 0 |
| ERCC-00033 | 2022 | 0 | 0 | 0 |
| ERCC-00034 | 1019 | 15158 | 14.8754 | 1.1555 |
| ERCC-00035 | 1130 | 7533 | 6.6664 | 0.842 |
| ERCC-00039 | 740 | 0 | 0 | 0 |
| ERCC-00040 | 744 | 0 | 0 | 0 |
| ERCC-00041 | 1122 | 0 | 0 | 0 |
| ERCC-00042 | 1023 | 222961 | 217.9482 | 14.1528 |
| ERCC-00043 | 1023 | 54807 | 53.5748 | 3.6472 |
| ERCC-00044 | 1156 | 14923 | 12.9092 | 0.7905 |
| ERCC-00046 | 522 | 1887850 | 3,616.5709 | 266.2018 |
| ERCC-00048 | 992 | 0 | 0 | 0 |
| ERCC-00051 | 274 | 16601 | 60.5876 | 6.0616 |
| ERCC-00053 | 1023 | 22750 | 22.2385 | 1.2083 |
| ERCC-00054 | 274 | 6999 | 25.5438 | 2.1918 |
| ERCC-00057 | 1021 | 0 | 0 | 0 |
| ERCC-00058 | 1136 | 0 | 0 | 0 |
| ERCC-00059 | 525 | 1033 | 1.9676 | 0.2836 |
| ERCC-00060 | 523 | 192579 | 368.2199 | 29.6735 |
| ERCC-00061 | 1136 | 0 | 0 | 0 |
| ERCC-00062 | 1023 | 71049 | 69.4516 | 15.175 |
| ERCC-00067 | 644 | 0 | 0 | 0 |
| ERCC-00069 | 1137 | 0 | 0 | 0 |
| ERCC-00071 | 642 | 68285 | 106.3629 | 6.426 |
| ERCC-00073 | 603 | 0 | 0 | 0 |
| ERCC-00074 | 522 | 2408421 | 4,613.8333 | 320.2724 |
| ERCC-00075 | 1023 | 0 | 0 | 0 |
| ERCC-00076 | 642 | 194018 | 302.2087 | 21.9742 |
| ERCC-00077 | 273 | 1887 | 6.9121 | 0.6311 |
| ERCC-00078 | 993 | 14940 | 15.0453 | 1.1656 |
| ERCC-00079 | 644 | 19672 | 30.5466 | 2.6234 |
| ERCC-00081 | 534 | 2812 | 5.2659 | 0.6684 |
| ERCC-00083 | 1022 | 0 | 0 | 0 |
| ERCC-00084 | 994 | 1952 | 1.9638 | 0.3628 |
| ERCC-00085 | 844 | 1665 | 1.9727 | 0.3089 |
| ERCC-00086 | 1020 | 0 | 0 | 0 |
| ERCC-00092 | 1124 | 14731 | 13.1059 | 1.1263 |
| ERCC-00095 | 521 | 23975 | 46.0173 | 3.7878 |
| ERCC-00096 | 1107 | 9938652 | 8,978.0054 | 561.2079 |
| ERCC-00097 | 523 | 523 | 1 | 0.28 |
| ERCC-00098 | 1143 | 0 | 0 | 0 |
| ERCC-00099 | 1350 | 391 | 0.2896 | 0.4156 |
| ERCC-00104 | 2022 | 0 | 0 | 0 |
| ERCC-00108 | 1022 | 342302 | 334.9335 | 26.5032 |
| ERCC-00109 | 536 | 536 | 1 | 0.1366 |
| ERCC-00111 | 994 | 989121 | 995.0915 | 54.6436 |
| ERCC-00112 | 1136 | 5157 | 4.5396 | 0.951 |
| ERCC-00113 | 840 | 2995262 | 3,565.7881 | 224.5355 |
| 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 | 7798 | 6.975 | 0.393 |
| ERCC-00130 | 1059 | 19942309 | 18,831.2644 | 1,317.2323 |
| ERCC-00131 | 771 | 6815 | 8.8392 | 0.8548 |
| ERCC-00134 | 274 | 1046 | 3.8175 | 0.6485 |
| ERCC-00136 | 1033 | 1764104 | 1,707.7483 | 89.4718 |
| ERCC-00137 | 537 | 1073 | 1.9981 | 0.1612 |
| ERCC-00138 | 1024 | 0 | 0 | 0 |
| ERCC-00142 | 493 | 0 | 0 | 0 |
| ERCC-00143 | 784 | 3106 | 3.9617 | 0.36 |
| ERCC-00144 | 538 | 10570 | 19.6468 | 2.3197 |
| ERCC-00145 | 1042 | 201712 | 193.5816 | 18.2058 |
| ERCC-00147 | 1023 | 0 | 0 | 0 |
| ERCC-00148 | 494 | 19769 | 40.0182 | 3.5975 |
| ERCC-00150 | 743 | 740 | 0.996 | 0.0896 |
| ERCC-00154 | 537 | 2118 | 3.9441 | 0.392 |
| ERCC-00156 | 494 | 494 | 1 | 0.09 |
| ERCC-00157 | 1019 | 11902 | 11.6801 | 1.3957 |
| ERCC-00158 | 1027 | 0 | 0 | 0 |
| ERCC-00160 | 743 | 16800 | 22.611 | 2.1831 |
| ERCC-00162 | 523 | 25225 | 48.2314 | 4.3988 |
| ERCC-00163 | 543 | 38362 | 70.6483 | 4.9878 |
| ERCC-00164 | 1022 | 0 | 0 | 0 |
| ERCC-00165 | 872 | 10840 | 12.4312 | 0.9591 |
| ERCC-00168 | 1024 | 0 | 0 | 0 |
| ERCC-00170 | 1023 | 5056 | 4.9423 | 0.5094 |
| ERCC-00171 | 505 | 1128208 | 2,234.0752 | 230.1898 |
| GL000008.2 | 209709 | 0 | 0 | 0 |
| GL000009.2 | 201709 | 0 | 0 | 0 |
| GL000194.1 | 191469 | 0 | 0 | 0 |
| GL000195.1 | 182896 | 0 | 0 | 0 |
| GL000205.2 | 185591 | 0 | 0 | 0 |
| GL000208.1 | 92689 | 0 | 0 | 0 |
| GL000213.1 | 164239 | 0 | 0 | 0 |
| GL000214.1 | 137718 | 24685 | 0.1792 | 0.1903 |
| GL000216.2 | 176608 | 0 | 0 | 0 |
| GL000218.1 | 161147 | 1453 | 0.009 | 0.1539 |
| GL000219.1 | 179198 | 0 | 0 | 0 |
| GL000220.1 | 161802 | 82691 | 0.5111 | 0.7385 |
| GL000221.1 | 155397 | 0 | 0 | 0 |
| GL000224.1 | 179693 | 0 | 0 | 0 |
| 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 | 19517 | 0.0498 | 0.0578 |
| 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 | 0 | 0 | 0 |
| 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 | 0 | 0 | 0 |
| KI270712.1 | 176043 | 463 | 0.0026 | 0.0499 |
| KI270713.1 | 40745 | 159 | 0.0039 | 0.061 |
| KI270714.1 | 41717 | 0 | 0 | 0 |
| KI270715.1 | 161471 | 0 | 0 | 0 |
| KI270716.1 | 153799 | 0 | 0 | 0 |
| KI270717.1 | 40062 | 0 | 0 | 0 |
| KI270718.1 | 38054 | 0 | 0 | 0 |
| KI270719.1 | 176845 | 0 | 0 | 0 |
| KI270720.1 | 39050 | 9743 | 0.2495 | 0.2643 |
| KI270721.1 | 100316 | 180669 | 1.801 | 2.7172 |
| KI270722.1 | 194050 | 267 | 0.0014 | 0.037 |
| 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 | 19460 | 0.0434 | 1.134 |
| KI270728.1 | 1872759 | 17745 | 0.0095 | 0.3252 |
| KI270729.1 | 280839 | 50215 | 0.1788 | 0.181 |
| KI270730.1 | 112551 | 0 | 0 | 0 |
| KI270731.1 | 150754 | 7474 | 0.0496 | 0.4456 |
| KI270732.1 | 41543 | 0 | 0 | 0 |
| KI270733.1 | 179772 | 500627 | 2.7848 | 3.0208 |
| KI270734.1 | 165050 | 930709 | 5.639 | 6.6267 |
| 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 | 0 | 0 | 0 |
| KI270742.1 | 186739 | 205 | 0.0011 | 0.033 |
| KI270743.1 | 210658 | 0 | 0 | 0 |
| KI270744.1 | 168472 | 891 | 0.0053 | 0.0814 |
| KI270745.1 | 41891 | 0 | 0 | 0 |
| 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 | 0 | 0 | 0 |
| KI270752.1 | 27745 | 52375130 | 1,887.7322 | 1,895.5628 |
| 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 | 64851418 | 280.719 | 374.1053 |
