Input data and parameters
QualiMap command line
| qualimap bamqc -bam output/mappings/longReadMapping/pacBio-Cshl-Smarter_HpreCap_0+_Brain01Rep1.bam -nw 400 -hm 3 |
Alignment
| Command line: | minimap2 --MD -x splice:hq -t 12 --secondary=no -L -a genomes/hg38.sorted.fa fastqs/pacBio-Cshl-Smarter_HpreCap_0+_Brain01Rep1.fastq.gz |
| Draw chromosome limits: | no |
| Analyze overlapping paired-end reads: | no |
| Program: | minimap2 (2.22-r1101) |
| Analysis date: | Tue Nov 15 19:48:05 CET 2022 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | output/mappings/longReadMapping/pacBio-Cshl-Smarter_HpreCap_0+_Brain01Rep1.bam |
Summary
Globals
| Reference size | 3,110,632,377 |
| Number of reads | 500,453 |
| Mapped reads | 500,453 / 100% |
| Unmapped reads | 0 / 0% |
| Mapped paired reads | 0 / 0% |
| Secondary alignments | 0 |
| Read min/max/mean length | 214 / 11,066 / 1,288.33 |
| Duplicated reads (estimated) | 319,135 / 63.77% |
| Duplication rate | 22.28% |
| Clipped reads | 500,449 / 100% |
ACGT Content
| Number/percentage of A's | 164,583,702 / 28.66% |
| Number/percentage of C's | 121,812,642 / 21.21% |
| Number/percentage of T's | 166,221,157 / 28.94% |
| Number/percentage of G's | 121,715,934 / 21.19% |
| Number/percentage of N's | 0 / 0% |
| GC Percentage | 42.4% |
Coverage
| Mean | 1.5167 |
| Standard Deviation | 14.8107 |
Mapping Quality
| Mean Mapping Quality | 5.23 |
Mismatches and indels
| General error rate | 0.06% |
| Mismatches | 1,218,259 |
| Insertions | 869,159 |
| Mapped reads with at least one insertion | 28.9% |
| Deletions | 358,316 |
| Mapped reads with at least one deletion | 30.33% |
| Homopolymer indels | 41.01% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| chr1 | 248956422 | 339563924 | 1.3639 | 5.9263 |
| chr10 | 133797422 | 151956349 | 1.1357 | 4.6347 |
| chr11 | 135086622 | 179787166 | 1.3309 | 5.4929 |
| chr12 | 133275309 | 218880192 | 1.6423 | 11.2979 |
| chr13 | 114364328 | 85680024 | 0.7492 | 5.7879 |
| chr14 | 107043718 | 137657707 | 1.286 | 10.0112 |
| chr15 | 101991189 | 116088126 | 1.1382 | 3.9803 |
| chr16 | 90338345 | 123818701 | 1.3706 | 6.0851 |
| chr17 | 83257441 | 139693801 | 1.6779 | 8.0081 |
| chr18 | 80373285 | 485227939 | 6.0372 | 59.4696 |
| chr19 | 58617616 | 87667296 | 1.4956 | 12.32 |
| chr2 | 242193529 | 414691789 | 1.7122 | 9.3341 |
| chr20 | 64444167 | 169174555 | 2.6251 | 7.9311 |
| chr21 | 46709983 | 37121170 | 0.7947 | 3.4955 |
| chr22 | 50818468 | 53134482 | 1.0456 | 3.6319 |
| chr3 | 198295559 | 315399872 | 1.5906 | 6.3196 |
| chr4 | 190214555 | 250232187 | 1.3155 | 5.9054 |
| chr5 | 181538259 | 242741360 | 1.3371 | 7.1323 |
| chr6 | 170805979 | 171772380 | 1.0057 | 6.7715 |
| chr7 | 159345973 | 203392911 | 1.2764 | 4.623 |
| chr8 | 145138636 | 208953894 | 1.4397 | 10.9514 |
| chr9 | 138394717 | 110148850 | 0.7959 | 3.3537 |
| chrIS | 10567884 | 0 | 0 | 0 |
| chrM | 16569 | 31085892 | 1,876.1477 | 2,183.9759 |
| chrX | 156040895 | 189055492 | 1.2116 | 5.6591 |
| chrY | 57227415 | 4445419 | 0.0777 | 0.3431 |
| 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 | 0 | 0 | 0 |
| GL000009.2 | 201709 | 0 | 0 | 0 |
| GL000194.1 | 191469 | 160328 | 0.8374 | 0.8537 |
| GL000195.1 | 182896 | 102167 | 0.5586 | 0.6142 |
| GL000205.2 | 185591 | 5776 | 0.0311 | 0.2072 |
| GL000208.1 | 92689 | 0 | 0 | 0 |
| GL000213.1 | 164239 | 0 | 0 | 0 |
| GL000214.1 | 137718 | 477 | 0.0035 | 0.0588 |
| GL000216.2 | 176608 | 0 | 0 | 0 |
| GL000218.1 | 161147 | 51869 | 0.3219 | 0.331 |
| GL000219.1 | 179198 | 149992 | 0.837 | 0.9596 |
| GL000220.1 | 161802 | 45084 | 0.2786 | 0.2812 |
| GL000221.1 | 155397 | 15186 | 0.0977 | 0.1528 |
| 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 | 0 | 0 | 0 |
| 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 | 1034 | 0.0059 | 0.0766 |
| 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 | 11204 | 0.2654 | 0.8985 |
| KI270712.1 | 176043 | 893 | 0.0051 | 0.071 |
| KI270713.1 | 40745 | 4415 | 0.1084 | 0.3709 |
| 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 | 7470 | 0.1963 | 0.359 |
| KI270719.1 | 176845 | 0 | 0 | 0 |
| KI270720.1 | 39050 | 0 | 0 | 0 |
| KI270721.1 | 100316 | 0 | 0 | 0 |
| 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 | 1119 | 0.0025 | 0.035 |
| KI270728.1 | 1872759 | 92113 | 0.0492 | 0.0638 |
| KI270729.1 | 280839 | 0 | 0 | 0 |
| KI270730.1 | 112551 | 0 | 0 | 0 |
| KI270731.1 | 150754 | 0 | 0 | 0 |
| KI270732.1 | 41543 | 0 | 0 | 0 |
| KI270733.1 | 179772 | 350 | 0.0019 | 0.0441 |
| KI270734.1 | 165050 | 202587 | 1.2274 | 2.8189 |
| 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 | 2094 | 0.0133 | 0.1145 |
| KI270742.1 | 186739 | 0 | 0 | 0 |
| KI270743.1 | 210658 | 0 | 0 | 0 |
| KI270744.1 | 168472 | 6735 | 0.04 | 0.1605 |
| KI270745.1 | 41891 | 1211 | 0.0289 | 0.1675 |
| 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 | 27784 | 0.1867 | 0.1931 |
| KI270751.1 | 150742 | 0 | 0 | 0 |
| 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 | 249541347 | 1,080.1767 | 1,171.9134 |
