Input data and parameters
QualiMap command line
| qualimap bamqc -bam output/mappings/longReadMapping/ont-Crg-CapTrap_HpreCap_0+_Brain01Rep4.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+_Brain01Rep4.fastq.gz |
| Draw chromosome limits: | no |
| Analyze overlapping paired-end reads: | no |
| Program: | minimap2 (2.22-r1101) |
| Analysis date: | Tue Nov 15 20:16:08 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+_Brain01Rep4.bam |
Summary
Globals
| Reference size | 3,110,632,377 |
| Number of reads | 3,487,722 |
| Mapped reads | 3,487,722 / 100% |
| Unmapped reads | 0 / 0% |
| Mapped paired reads | 0 / 0% |
| Secondary alignments | 0 |
| Read min/max/mean length | 94 / 76,429 / 842.28 |
| Duplicated reads (estimated) | 3,124,622 / 89.59% |
| Duplication rate | 34.3% |
| Clipped reads | 3,487,457 / 99.99% |
ACGT Content
| Number/percentage of A's | 486,516,270 / 23.87% |
| Number/percentage of C's | 520,097,607 / 25.52% |
| Number/percentage of T's | 507,558,330 / 24.91% |
| Number/percentage of G's | 523,644,181 / 25.7% |
| Number/percentage of N's | 0 / 0% |
| GC Percentage | 51.22% |
Coverage
| Mean | 7.1096 |
| Standard Deviation | 83.7307 |
Mapping Quality
| Mean Mapping Quality | 7.68 |
Mismatches and indels
| General error rate | 0.48% |
| Mismatches | 75,997,876 |
| Insertions | 16,367,661 |
| Mapped reads with at least one insertion | 91.09% |
| Deletions | 25,271,979 |
| Mapped reads with at least one deletion | 96.02% |
| Homopolymer indels | 33.78% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| chr1 | 248956422 | 2390961065 | 9.6039 | 48.683 |
| chr10 | 133797422 | 538928254 | 4.0279 | 23.8338 |
| chr11 | 135086622 | 1391021374 | 10.2973 | 139.3696 |
| chr12 | 133275309 | 1053245509 | 7.9028 | 64.5317 |
| chr13 | 114364328 | 240033340 | 2.0988 | 12.4388 |
| chr14 | 107043718 | 887595770 | 8.2919 | 71.0201 |
| chr15 | 101991189 | 545875362 | 5.3522 | 89.9879 |
| chr16 | 90338345 | 819375038 | 9.0701 | 153.5709 |
| chr17 | 83257441 | 893363694 | 10.7301 | 84.3626 |
| chr18 | 80373285 | 635462644 | 7.9064 | 88.9867 |
| chr19 | 58617616 | 2272697253 | 38.7716 | 206.6955 |
| chr2 | 242193529 | 1589162478 | 6.5615 | 133.5344 |
| chr20 | 64444167 | 456338435 | 7.0811 | 70.1001 |
| chr21 | 46709983 | 502227420 | 10.752 | 126.7997 |
| chr22 | 50818468 | 421461620 | 8.2935 | 50.8675 |
| chr3 | 198295559 | 1459398309 | 7.3597 | 57.7751 |
| chr4 | 190214555 | 525858981 | 2.7646 | 31.7461 |
| chr5 | 181538259 | 1186213752 | 6.5342 | 65.6061 |
| chr6 | 170805979 | 950975004 | 5.5676 | 55.3664 |
| chr7 | 159345973 | 1026523030 | 6.4421 | 53.3682 |
| chr8 | 145138636 | 647603267 | 4.462 | 25.3942 |
| chr9 | 138394717 | 707323565 | 5.1109 | 80.7973 |
| chrIS | 10567884 | 0 | 0 | 0 |
| chrM | 16569 | 7456355 | 450.0184 | 635.3509 |
| chrX | 156040895 | 536512271 | 3.4383 | 46.1176 |
| chrY | 57227415 | 246851 | 0.0043 | 0.0291 |
| ERCC-00002 | 1061 | 15565318 | 14,670.4222 | 1,618.8219 |
| ERCC-00003 | 1023 | 132239 | 129.2659 | 13.5019 |
| ERCC-00004 | 523 | 2082262 | 3,981.3805 | 549.2032 |
| ERCC-00009 | 984 | 553349 | 562.3465 | 61.7475 |
| ERCC-00012 | 994 | 0 | 0 | 0 |
| ERCC-00013 | 808 | 2182 | 2.7005 | 0.6182 |
| ERCC-00014 | 1957 | 719 | 0.3674 | 0.481 |
| ERCC-00016 | 844 | 0 | 0 | 0 |
| ERCC-00017 | 1136 | 0 | 0 | 0 |
| ERCC-00019 | 644 | 20704 | 32.1491 | 3.6126 |
| ERCC-00022 | 751 | 83983 | 111.8282 | 13.4344 |
| ERCC-00024 | 536 | 526 | 0.9813 | 0.1951 |
| ERCC-00025 | 1994 | 1984 | 0.995 | 0.1046 |
| ERCC-00028 | 1130 | 0 | 0 | 0 |
| ERCC-00031 | 1138 | 0 | 0 | 0 |
| ERCC-00033 | 2022 | 0 | 0 | 0 |
| ERCC-00034 | 1019 | 5694 | 5.5878 | 0.7539 |
| ERCC-00035 | 1130 | 27232 | 24.0991 | 2.2408 |
| ERCC-00039 | 740 | 2179 | 2.9446 | 0.444 |
| ERCC-00040 | 744 | 132 | 0.1774 | 0.3797 |
| ERCC-00041 | 1122 | 0 | 0 | 0 |
| ERCC-00042 | 1023 | 50318 | 49.1867 | 4.8281 |
| ERCC-00043 | 1023 | 25074 | 24.5103 | 2.3945 |
| ERCC-00044 | 1156 | 12832 | 11.1003 | 1.1189 |
| ERCC-00046 | 522 | 7843018 | 15,024.9387 | 1,931.1332 |
| ERCC-00048 | 992 | 0 | 0 | 0 |
| ERCC-00051 | 274 | 9767 | 35.646 | 6.4115 |
| ERCC-00053 | 1023 | 11846 | 11.5797 | 1.4917 |
| ERCC-00054 | 274 | 2286 | 8.3431 | 1.6266 |
| ERCC-00057 | 1021 | 0 | 0 | 0 |
| ERCC-00058 | 1136 | 0 | 0 | 0 |
| ERCC-00059 | 525 | 15268 | 29.0819 | 3.9964 |
| ERCC-00060 | 523 | 253891 | 485.4512 | 69.2779 |
| ERCC-00061 | 1136 | 0 | 0 | 0 |
| ERCC-00062 | 1023 | 27291 | 26.6774 | 3.0269 |
| ERCC-00067 | 644 | 3752 | 5.8261 | 0.7632 |
| ERCC-00069 | 1137 | 0 | 0 | 0 |
| ERCC-00071 | 642 | 45493 | 70.8614 | 8.0791 |
| ERCC-00073 | 603 | 589 | 0.9768 | 0.1506 |
| ERCC-00074 | 522 | 18410015 | 35,268.228 | 4,471.4305 |
| ERCC-00075 | 1023 | 0 | 0 | 0 |
| ERCC-00076 | 642 | 162251 | 252.7274 | 28.7188 |
| ERCC-00077 | 273 | 0 | 0 | 0 |
| ERCC-00078 | 993 | 10226 | 10.2981 | 1.7058 |
| ERCC-00079 | 644 | 56949 | 88.4301 | 10.2829 |
| ERCC-00081 | 534 | 0 | 0 | 0 |
| ERCC-00083 | 1022 | 0 | 0 | 0 |
| ERCC-00084 | 994 | 1551 | 1.5604 | 1.0492 |
| ERCC-00085 | 844 | 0 | 0 | 0 |
| ERCC-00086 | 1020 | 0 | 0 | 0 |
| ERCC-00092 | 1124 | 143681 | 127.8301 | 20.3173 |
| ERCC-00095 | 521 | 71675 | 137.572 | 17.8427 |
| ERCC-00096 | 1107 | 13626826 | 12,309.6893 | 1,317.1968 |
| ERCC-00097 | 523 | 1034 | 1.9771 | 0.2608 |
| ERCC-00098 | 1143 | 0 | 0 | 0 |
| ERCC-00099 | 1350 | 5344 | 3.9585 | 0.4495 |
| ERCC-00104 | 2022 | 0 | 0 | 0 |
| ERCC-00108 | 1022 | 198423 | 194.1517 | 20.4883 |
| ERCC-00109 | 536 | 0 | 0 | 0 |
| ERCC-00111 | 994 | 174314 | 175.3662 | 17.1646 |
| ERCC-00112 | 1136 | 26600 | 23.4155 | 2.4744 |
| ERCC-00113 | 840 | 1998848 | 2,379.581 | 237.703 |
| ERCC-00116 | 1991 | 2078 | 1.0437 | 1.4058 |
| 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 | 5751928 | 5,431.4712 | 545.1141 |
| ERCC-00131 | 771 | 58019 | 75.2516 | 8.1962 |
| ERCC-00134 | 274 | 0 | 0 | 0 |
| ERCC-00136 | 1033 | 458819 | 444.1617 | 39.526 |
| ERCC-00137 | 537 | 1040 | 1.9367 | 0.3801 |
| ERCC-00138 | 1024 | 0 | 0 | 0 |
| ERCC-00142 | 493 | 0 | 0 | 0 |
| ERCC-00143 | 784 | 1381 | 1.7615 | 0.4655 |
| ERCC-00144 | 538 | 26002 | 48.3309 | 7.0038 |
| ERCC-00145 | 1042 | 131000 | 125.7198 | 13.577 |
| ERCC-00147 | 1023 | 0 | 0 | 0 |
| ERCC-00148 | 494 | 7060 | 14.2915 | 2.2258 |
| ERCC-00150 | 743 | 2884 | 3.8816 | 0.6142 |
| ERCC-00154 | 537 | 3165 | 5.8939 | 0.7821 |
| ERCC-00156 | 494 | 485 | 0.9818 | 0.1541 |
| ERCC-00157 | 1019 | 3246 | 3.1855 | 0.854 |
| ERCC-00158 | 1027 | 0 | 0 | 0 |
| ERCC-00160 | 743 | 15393 | 20.7174 | 2.6036 |
| ERCC-00162 | 523 | 17685 | 33.8145 | 4.3474 |
| ERCC-00163 | 543 | 19028 | 35.0424 | 4.897 |
| ERCC-00164 | 1022 | 0 | 0 | 0 |
| ERCC-00165 | 872 | 43620 | 50.0229 | 5.6504 |
| ERCC-00168 | 1024 | 0 | 0 | 0 |
| ERCC-00170 | 1023 | 8091 | 7.9091 | 1.1035 |
| ERCC-00171 | 505 | 3197359 | 6,331.404 | 940.5637 |
| GL000008.2 | 209709 | 716066 | 3.4146 | 3.3994 |
| GL000009.2 | 201709 | 0 | 0 | 0 |
| GL000194.1 | 191469 | 1513591 | 7.9051 | 7.901 |
| GL000195.1 | 182896 | 113296 | 0.6195 | 0.8629 |
| GL000205.2 | 185591 | 214583 | 1.1562 | 1.7082 |
| GL000208.1 | 92689 | 0 | 0 | 0 |
| GL000213.1 | 164239 | 0 | 0 | 0 |
| GL000214.1 | 137718 | 8501 | 0.0617 | 0.1003 |
| GL000216.2 | 176608 | 0 | 0 | 0 |
| GL000218.1 | 161147 | 518571 | 3.218 | 3.2452 |
| GL000219.1 | 179198 | 290777 | 1.6227 | 2.505 |
| GL000220.1 | 161802 | 180573 | 1.116 | 1.7825 |
| GL000221.1 | 155397 | 563 | 0.0036 | 0.0594 |
| GL000224.1 | 179693 | 409486 | 2.2788 | 3.5361 |
| 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 | 76120 | 0.6766 | 0.6766 |
| 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 | 278 | 0.0123 | 0.109 |
| 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 | 361 | 0.0021 | 0.0451 |
| 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 | 8777 | 0.2079 | 0.3737 |
| KI270712.1 | 176043 | 8313 | 0.0472 | 0.1148 |
| KI270713.1 | 40745 | 27067 | 0.6643 | 0.8079 |
| KI270714.1 | 41717 | 779 | 0.0187 | 0.1342 |
| KI270715.1 | 161471 | 0 | 0 | 0 |
| KI270716.1 | 153799 | 0 | 0 | 0 |
| KI270717.1 | 40062 | 0 | 0 | 0 |
| KI270718.1 | 38054 | 3108 | 0.0817 | 0.1211 |
| KI270719.1 | 176845 | 0 | 0 | 0 |
| KI270720.1 | 39050 | 0 | 0 | 0 |
| KI270721.1 | 100316 | 611 | 0.0061 | 0.1329 |
| 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 | 260 | 0.0006 | 0.0233 |
| KI270728.1 | 1872759 | 13419 | 0.0072 | 0.0803 |
| 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 | 327072 | 1.8194 | 3.0486 |
| KI270734.1 | 165050 | 1340509 | 8.1218 | 22.4688 |
| 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 | 467221 | 2.9678 | 3.068 |
| KI270742.1 | 186739 | 1241251 | 6.647 | 6.6292 |
| KI270743.1 | 210658 | 4007651 | 19.0244 | 18.9891 |
| KI270744.1 | 168472 | 6906 | 0.041 | 0.0649 |
| KI270745.1 | 41891 | 0 | 0 | 0 |
| KI270746.1 | 66486 | 0 | 0 | 0 |
| KI270747.1 | 198735 | 0 | 0 | 0 |
| KI270748.1 | 93321 | 8948 | 0.0959 | 0.1234 |
| KI270749.1 | 158759 | 0 | 0 | 0 |
| KI270750.1 | 148850 | 0 | 0 | 0 |
| KI270751.1 | 150742 | 37946 | 0.2517 | 0.2601 |
| KI270752.1 | 27745 | 206405 | 7.4394 | 7.3981 |
| KI270753.1 | 62944 | 0 | 0 | 0 |
| KI270754.1 | 40191 | 0 | 0 | 0 |
| KI270755.1 | 36723 | 388 | 0.0106 | 0.1007 |
| KI270756.1 | 79590 | 67131 | 0.8435 | 0.8401 |
| KI270757.1 | 71251 | 0 | 0 | 0 |
| SIRVome_isoforms | 231019 | 346353860 | 1,499.244 | 1,520.954 |
