Input data and parameters
QualiMap command line
| qualimap bamqc -bam output/mappings/longReadMapping/ont-Cshl-Smarter_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-Smarter_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 22:41:13 CET 2022 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | output/mappings/longReadMapping/ont-Cshl-Smarter_HpreCap_0+_Brain01Rep1.bam |
Summary
Globals
| Reference size | 3,110,632,377 |
| Number of reads | 6,556,308 |
| Mapped reads | 6,556,308 / 100% |
| Unmapped reads | 0 / 0% |
| Mapped paired reads | 0 / 0% |
| Secondary alignments | 0 |
| Read min/max/mean length | 110 / 223,815 / 832.03 |
| Duplicated reads (estimated) | 5,105,903 / 77.88% |
| Duplication rate | 26.06% |
| Clipped reads | 6,556,135 / 100% |
ACGT Content
| Number/percentage of A's | 1,260,527,842 / 29.22% |
| Number/percentage of C's | 874,740,804 / 20.28% |
| Number/percentage of T's | 1,299,347,206 / 30.12% |
| Number/percentage of G's | 879,657,970 / 20.39% |
| Number/percentage of N's | 0 / 0% |
| GC Percentage | 40.66% |
Coverage
| Mean | 9.3378 |
| Standard Deviation | 114.9601 |
Mapping Quality
| Mean Mapping Quality | 5.9 |
Mismatches and indels
| General error rate | 0.63% |
| Mismatches | 133,417,423 |
| Insertions | 27,661,305 |
| Mapped reads with at least one insertion | 83.85% |
| Deletions | 45,217,168 |
| Mapped reads with at least one deletion | 91.1% |
| Homopolymer indels | 36.69% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| chr1 | 248956422 | 2170737693 | 8.7193 | 49.4864 |
| chr10 | 133797422 | 943314507 | 7.0503 | 37.5176 |
| chr11 | 135086622 | 1073306045 | 7.9453 | 42.2916 |
| chr12 | 133275309 | 1443609813 | 10.8318 | 81.0647 |
| chr13 | 114364328 | 570268031 | 4.9864 | 45.3998 |
| chr14 | 107043718 | 930677832 | 8.6944 | 57.0267 |
| chr15 | 101991189 | 712035420 | 6.9813 | 38.4712 |
| chr16 | 90338345 | 883632884 | 9.7814 | 40.0591 |
| chr17 | 83257441 | 967337544 | 11.6186 | 58.8279 |
| chr18 | 80373285 | 1703750428 | 21.198 | 197.0462 |
| chr19 | 58617616 | 727276606 | 12.4071 | 107.1032 |
| chr2 | 242193529 | 2651213539 | 10.9467 | 74.1026 |
| chr20 | 64444167 | 794645673 | 12.3308 | 52.0374 |
| chr21 | 46709983 | 325965450 | 6.9785 | 34.4466 |
| chr22 | 50818468 | 403653709 | 7.9431 | 42.9203 |
| chr3 | 198295559 | 1943850967 | 9.8028 | 48.883 |
| chr4 | 190214555 | 1342402125 | 7.0573 | 51.3503 |
| chr5 | 181538259 | 1653676789 | 9.1092 | 44.5786 |
| chr6 | 170805979 | 1108595581 | 6.4904 | 42.6297 |
| chr7 | 159345973 | 1264462137 | 7.9353 | 47.4906 |
| chr8 | 145138636 | 1309704752 | 9.0238 | 57.6961 |
| chr9 | 138394717 | 718991242 | 5.1952 | 25.0232 |
| chrIS | 10567884 | 0 | 0 | 0 |
| chrM | 16569 | 419009081 | 25,288.7369 | 29,869.6341 |
| chrX | 156040895 | 1019538918 | 6.5338 | 44.7289 |
| chrY | 57227415 | 39972493 | 0.6985 | 2.7575 |
| 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 | 209450 | 0.9988 | 0.9878 |
| GL000009.2 | 201709 | 572 | 0.0028 | 0.0529 |
| GL000194.1 | 191469 | 1351796 | 7.0601 | 7.0221 |
| GL000195.1 | 182896 | 635982 | 3.4773 | 3.758 |
| GL000205.2 | 185591 | 70099 | 0.3777 | 0.5531 |
| GL000208.1 | 92689 | 0 | 0 | 0 |
| GL000213.1 | 164239 | 0 | 0 | 0 |
| GL000214.1 | 137718 | 1877 | 0.0136 | 0.1366 |
| GL000216.2 | 176608 | 0 | 0 | 0 |
| GL000218.1 | 161147 | 324596 | 2.0143 | 2.1707 |
| GL000219.1 | 179198 | 1271379 | 7.0948 | 7.887 |
| GL000220.1 | 161802 | 200409 | 1.2386 | 1.2146 |
| GL000221.1 | 155397 | 152778 | 0.9831 | 1.0652 |
| GL000224.1 | 179693 | 28461 | 0.1584 | 0.2076 |
| 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 | 467 | 0.2827 | 0.4494 |
| 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 | 60681 | 0.1548 | 0.1807 |
| 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 | 28603 | 0.1634 | 0.5551 |
| KI270707.1 | 32032 | 7659 | 0.2391 | 0.6257 |
| KI270708.1 | 127682 | 0 | 0 | 0 |
| KI270709.1 | 66860 | 194 | 0.0029 | 0.0538 |
| KI270710.1 | 40176 | 0 | 0 | 0 |
| KI270711.1 | 42210 | 112151 | 2.657 | 4.9784 |
| KI270712.1 | 176043 | 37486 | 0.2129 | 2.5784 |
| KI270713.1 | 40745 | 26534 | 0.6512 | 1.2208 |
| KI270714.1 | 41717 | 14553 | 0.3489 | 0.6162 |
| KI270715.1 | 161471 | 0 | 0 | 0 |
| KI270716.1 | 153799 | 0 | 0 | 0 |
| KI270717.1 | 40062 | 10780 | 0.2691 | 1.4297 |
| KI270718.1 | 38054 | 43573 | 1.145 | 1.6752 |
| KI270719.1 | 176845 | 734 | 0.0042 | 0.0748 |
| KI270720.1 | 39050 | 0 | 0 | 0 |
| KI270721.1 | 100316 | 447 | 0.0045 | 0.0665 |
| KI270722.1 | 194050 | 0 | 0 | 0 |
| KI270723.1 | 38115 | 0 | 0 | 0 |
| KI270724.1 | 39555 | 0 | 0 | 0 |
| KI270725.1 | 172810 | 555 | 0.0032 | 0.0363 |
| KI270726.1 | 43739 | 0 | 0 | 0 |
| KI270727.1 | 448248 | 20532 | 0.0458 | 0.348 |
| KI270728.1 | 1872759 | 16603 | 0.0089 | 0.1325 |
| KI270729.1 | 280839 | 585 | 0.0021 | 0.0785 |
| KI270730.1 | 112551 | 0 | 0 | 0 |
| KI270731.1 | 150754 | 3816 | 0.0253 | 0.1659 |
| KI270732.1 | 41543 | 0 | 0 | 0 |
| KI270733.1 | 179772 | 526374 | 2.928 | 2.8699 |
| KI270734.1 | 165050 | 986754 | 5.9785 | 13.9428 |
| 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 | 5122 | 0.0325 | 0.2525 |
| KI270742.1 | 186739 | 81432 | 0.4361 | 0.5257 |
| KI270743.1 | 210658 | 1384009 | 6.5699 | 6.5485 |
| KI270744.1 | 168472 | 29455 | 0.1748 | 1.1051 |
| KI270745.1 | 41891 | 16923 | 0.404 | 0.9606 |
| KI270746.1 | 66486 | 974 | 0.0146 | 0.0622 |
| KI270747.1 | 198735 | 0 | 0 | 0 |
| KI270748.1 | 93321 | 10150 | 0.1088 | 0.1662 |
| KI270749.1 | 158759 | 0 | 0 | 0 |
| KI270750.1 | 148850 | 0 | 0 | 0 |
| KI270751.1 | 150742 | 1390 | 0.0092 | 0.0952 |
| KI270752.1 | 27745 | 176 | 0.0063 | 0.0776 |
| KI270753.1 | 62944 | 0 | 0 | 0 |
| KI270754.1 | 40191 | 0 | 0 | 0 |
| KI270755.1 | 36723 | 898 | 0.0245 | 0.154 |
| KI270756.1 | 79590 | 0 | 0 | 0 |
| KI270757.1 | 71251 | 0 | 0 | 0 |
| SIRVome_isoforms | 231019 | 1917269604 | 8,299.1858 | 8,917.8985 |
