Input data and parameters
QualiMap command line
| qualimap bamqc -bam output/mappings/longReadMapping/ont-Crg-CapTrap_HpreCap_0+_Brain01Rep3.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+_Brain01Rep3.fastq.gz |
| Draw chromosome limits: | no |
| Analyze overlapping paired-end reads: | no |
| Program: | minimap2 (2.22-r1101) |
| Analysis date: | Tue Nov 15 22:04:35 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+_Brain01Rep3.bam |
Summary
Globals
| Reference size | 3,110,632,377 |
| Number of reads | 12,416,052 |
| Mapped reads | 12,416,052 / 100% |
| Unmapped reads | 0 / 0% |
| Mapped paired reads | 0 / 0% |
| Secondary alignments | 0 |
| Read min/max/mean length | 104 / 17,336 / 863.19 |
| Duplicated reads (estimated) | 11,502,821 / 92.64% |
| Duplication rate | 36.98% |
| Clipped reads | 12,415,857 / 100% |
ACGT Content
| Number/percentage of A's | 1,839,626,193 / 25.23% |
| Number/percentage of C's | 1,784,780,232 / 24.47% |
| Number/percentage of T's | 1,864,323,474 / 25.56% |
| Number/percentage of G's | 1,803,818,645 / 24.74% |
| Number/percentage of N's | 0 / 0% |
| GC Percentage | 49.21% |
Coverage
| Mean | 31.243 |
| Standard Deviation | 267.1754 |
Mapping Quality
| Mean Mapping Quality | 5.85 |
Mismatches and indels
| General error rate | 0.35% |
| Mismatches | 248,677,335 |
| Insertions | 50,254,993 |
| Mapped reads with at least one insertion | 89.81% |
| Deletions | 79,904,469 |
| Mapped reads with at least one deletion | 95.23% |
| Homopolymer indels | 33.89% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| chr1 | 248956422 | 9448813640 | 37.9537 | 183.6849 |
| chr10 | 133797422 | 2836111022 | 21.1971 | 123.2366 |
| chr11 | 135086622 | 4502077630 | 33.3273 | 288.4949 |
| chr12 | 133275309 | 4368169606 | 32.7755 | 199.6651 |
| chr13 | 114364328 | 1490602569 | 13.0338 | 117.7213 |
| chr14 | 107043718 | 4562540053 | 42.6231 | 427.3256 |
| chr15 | 101991189 | 2664073825 | 26.1206 | 281.0395 |
| chr16 | 90338345 | 2897769901 | 32.0769 | 372.3345 |
| chr17 | 83257441 | 3875204836 | 46.5448 | 326.6151 |
| chr18 | 80373285 | 2267370093 | 28.2105 | 201.2703 |
| chr19 | 58617616 | 6081394523 | 103.7469 | 472.4586 |
| chr2 | 242193529 | 8553743078 | 35.3178 | 467.2092 |
| chr20 | 64444167 | 2136775856 | 33.157 | 268.1143 |
| chr21 | 46709983 | 3070085661 | 65.7265 | 373.8031 |
| chr22 | 50818468 | 1645022744 | 32.3706 | 192.0296 |
| chr3 | 198295559 | 6654791255 | 33.56 | 224.5486 |
| chr4 | 190214555 | 3955694249 | 20.796 | 205.4204 |
| chr5 | 181538259 | 6352459043 | 34.9924 | 222.5867 |
| chr6 | 170805979 | 4441969885 | 26.0059 | 237.1229 |
| chr7 | 159345973 | 5008291877 | 31.4303 | 261.7086 |
| chr8 | 145138636 | 4830729131 | 33.2836 | 183.818 |
| chr9 | 138394717 | 2740484162 | 19.8019 | 208.0316 |
| chrIS | 10567884 | 0 | 0 | 0 |
| chrM | 16569 | 53801287 | 3,247.1053 | 3,470.5361 |
| chrX | 156040895 | 2529466121 | 16.2103 | 158.6914 |
| chrY | 57227415 | 167007252 | 2.9183 | 11.3993 |
| ERCC-00002 | 1061 | 1213176 | 1,143.427 | 381.7044 |
| ERCC-00003 | 1023 | 21507 | 21.0235 | 5.7225 |
| ERCC-00004 | 523 | 161914 | 309.587 | 57.27 |
| ERCC-00009 | 984 | 42192 | 42.878 | 9.1584 |
| 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 | 3158 | 4.9037 | 0.6115 |
| ERCC-00022 | 751 | 4581 | 6.0999 | 1.5041 |
| ERCC-00024 | 536 | 0 | 0 | 0 |
| ERCC-00025 | 1994 | 1431 | 0.7177 | 0.9025 |
| 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 | 1825 | 1.615 | 0.8588 |
| ERCC-00039 | 740 | 0 | 0 | 0 |
| ERCC-00040 | 744 | 730 | 0.9812 | 0.1979 |
| ERCC-00041 | 1122 | 0 | 0 | 0 |
| ERCC-00042 | 1023 | 5113 | 4.998 | 3.2482 |
| ERCC-00043 | 1023 | 10835 | 10.5914 | 1.5157 |
| ERCC-00044 | 1156 | 3634 | 3.1436 | 2.0121 |
| ERCC-00046 | 522 | 333824 | 639.5096 | 89.0386 |
| ERCC-00048 | 992 | 0 | 0 | 0 |
| ERCC-00051 | 274 | 0 | 0 | 0 |
| ERCC-00053 | 1023 | 2288 | 2.2366 | 0.9645 |
| ERCC-00054 | 274 | 0 | 0 | 0 |
| ERCC-00057 | 1021 | 0 | 0 | 0 |
| ERCC-00058 | 1136 | 0 | 0 | 0 |
| ERCC-00059 | 525 | 502 | 0.9562 | 0.2287 |
| ERCC-00060 | 523 | 28065 | 53.6616 | 8.3284 |
| ERCC-00061 | 1136 | 0 | 0 | 0 |
| ERCC-00062 | 1023 | 3898 | 3.8104 | 1.787 |
| ERCC-00067 | 644 | 0 | 0 | 0 |
| ERCC-00069 | 1137 | 1316 | 1.1574 | 0.9796 |
| ERCC-00071 | 642 | 5543 | 8.634 | 1.1346 |
| ERCC-00073 | 603 | 0 | 0 | 0 |
| ERCC-00074 | 522 | 1074434 | 2,058.3027 | 291.0171 |
| ERCC-00075 | 1023 | 0 | 0 | 0 |
| ERCC-00076 | 642 | 9883 | 15.3941 | 2.1898 |
| ERCC-00077 | 273 | 0 | 0 | 0 |
| ERCC-00078 | 993 | 377 | 0.3797 | 0.4851 |
| ERCC-00079 | 644 | 5086 | 7.8975 | 1.3936 |
| ERCC-00081 | 534 | 0 | 0 | 0 |
| ERCC-00083 | 1022 | 0 | 0 | 0 |
| ERCC-00084 | 994 | 0 | 0 | 0 |
| ERCC-00085 | 844 | 720 | 0.8531 | 0.3911 |
| ERCC-00086 | 1020 | 0 | 0 | 0 |
| ERCC-00092 | 1124 | 15822 | 14.0765 | 4.9095 |
| ERCC-00095 | 521 | 1807 | 3.4683 | 1.5143 |
| ERCC-00096 | 1107 | 1205666 | 1,089.1292 | 318.2301 |
| 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 | 23791 | 23.2789 | 8.3339 |
| ERCC-00109 | 536 | 0 | 0 | 0 |
| ERCC-00111 | 994 | 16672 | 16.7726 | 6.88 |
| ERCC-00112 | 1136 | 3516 | 3.0951 | 1.6898 |
| ERCC-00113 | 840 | 124637 | 148.3774 | 25.1415 |
| ERCC-00116 | 1991 | 6715 | 3.3727 | 1.4383 |
| 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 | 753360 | 711.3881 | 310.66 |
| ERCC-00131 | 771 | 3595 | 4.6628 | 2.2724 |
| ERCC-00134 | 274 | 0 | 0 | 0 |
| ERCC-00136 | 1033 | 39014 | 37.7677 | 11.7853 |
| 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 | 2070 | 3.8476 | 0.6998 |
| ERCC-00145 | 1042 | 24530 | 23.5413 | 10.6891 |
| 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 | 2167 | 4.1434 | 1.4678 |
| ERCC-00163 | 543 | 0 | 0 | 0 |
| ERCC-00164 | 1022 | 0 | 0 | 0 |
| ERCC-00165 | 872 | 3865 | 4.4323 | 1.7995 |
| ERCC-00168 | 1024 | 0 | 0 | 0 |
| ERCC-00170 | 1023 | 0 | 0 | 0 |
| ERCC-00171 | 505 | 158365 | 313.5941 | 50.3568 |
| GL000008.2 | 209709 | 0 | 0 | 0 |
| GL000009.2 | 201709 | 115221 | 0.5712 | 0.5706 |
| GL000194.1 | 191469 | 6896513 | 36.019 | 35.8282 |
| GL000195.1 | 182896 | 1354036 | 7.4033 | 7.306 |
| GL000205.2 | 185591 | 536451 | 2.8905 | 4.0131 |
| GL000208.1 | 92689 | 0 | 0 | 0 |
| GL000213.1 | 164239 | 0 | 0 | 0 |
| GL000214.1 | 137718 | 1816 | 0.0132 | 0.1558 |
| GL000216.2 | 176608 | 19128 | 0.1083 | 0.1178 |
| GL000218.1 | 161147 | 2891662 | 17.9442 | 17.9703 |
| GL000219.1 | 179198 | 3334851 | 18.6099 | 22.4856 |
| GL000220.1 | 161802 | 773729 | 4.7819 | 13.2238 |
| GL000221.1 | 155397 | 259702 | 1.6712 | 1.6683 |
| GL000224.1 | 179693 | 360125 | 2.0041 | 3.7688 |
| GL000225.1 | 211173 | 241 | 0.0011 | 0.0336 |
| 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 | 1133 | 0.0101 | 0.0998 |
| KI270442.1 | 392061 | 63583 | 0.1622 | 0.1855 |
| 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 | 331 | 0.0019 | 0.0434 |
| KI270707.1 | 32032 | 0 | 0 | 0 |
| KI270708.1 | 127682 | 0 | 0 | 0 |
| KI270709.1 | 66860 | 5350 | 0.08 | 0.1165 |
| KI270710.1 | 40176 | 0 | 0 | 0 |
| KI270711.1 | 42210 | 19590 | 0.4641 | 1.3297 |
| KI270712.1 | 176043 | 37078 | 0.2106 | 0.7943 |
| KI270713.1 | 40745 | 19505 | 0.4787 | 2.5217 |
| KI270714.1 | 41717 | 11498 | 0.2756 | 0.3175 |
| KI270715.1 | 161471 | 0 | 0 | 0 |
| KI270716.1 | 153799 | 0 | 0 | 0 |
| KI270717.1 | 40062 | 36574 | 0.9129 | 0.9242 |
| KI270718.1 | 38054 | 3351 | 0.0881 | 0.1708 |
| KI270719.1 | 176845 | 20906 | 0.1182 | 0.1278 |
| KI270720.1 | 39050 | 0 | 0 | 0 |
| KI270721.1 | 100316 | 125103 | 1.2471 | 1.3601 |
| KI270722.1 | 194050 | 0 | 0 | 0 |
| KI270723.1 | 38115 | 0 | 0 | 0 |
| KI270724.1 | 39555 | 0 | 0 | 0 |
| KI270725.1 | 172810 | 8940 | 0.0517 | 0.0673 |
| KI270726.1 | 43739 | 0 | 0 | 0 |
| KI270727.1 | 448248 | 70461 | 0.1572 | 0.1695 |
| KI270728.1 | 1872759 | 7238 | 0.0039 | 0.0428 |
| KI270729.1 | 280839 | 29196 | 0.104 | 0.1074 |
| KI270730.1 | 112551 | 0 | 0 | 0 |
| KI270731.1 | 150754 | 2128 | 0.0141 | 0.2355 |
| KI270732.1 | 41543 | 0 | 0 | 0 |
| KI270733.1 | 179772 | 1135456 | 6.3161 | 16.6386 |
| KI270734.1 | 165050 | 4547183 | 27.5503 | 76.5277 |
| KI270735.1 | 42811 | 0 | 0 | 0 |
| KI270736.1 | 181920 | 5214 | 0.0287 | 0.0387 |
| 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 | 120362 | 0.7645 | 1.1685 |
| KI270742.1 | 186739 | 5594201 | 29.9573 | 29.8936 |
| KI270743.1 | 210658 | 2626116 | 12.4663 | 12.4391 |
| KI270744.1 | 168472 | 1303 | 0.0077 | 0.0995 |
| KI270745.1 | 41891 | 999 | 0.0238 | 0.1517 |
| KI270746.1 | 66486 | 4786 | 0.072 | 0.1259 |
| KI270747.1 | 198735 | 913 | 0.0046 | 0.0676 |
| KI270748.1 | 93321 | 9179 | 0.0984 | 0.1497 |
| KI270749.1 | 158759 | 0 | 0 | 0 |
| KI270750.1 | 148850 | 0 | 0 | 0 |
| KI270751.1 | 150742 | 816 | 0.0054 | 0.0566 |
| KI270752.1 | 27745 | 399975 | 14.4161 | 14.7267 |
| KI270753.1 | 62944 | 0 | 0 | 0 |
| KI270754.1 | 40191 | 0 | 0 | 0 |
| KI270755.1 | 36723 | 1863 | 0.0507 | 0.2575 |
| KI270756.1 | 79590 | 0 | 0 | 0 |
| KI270757.1 | 71251 | 0 | 0 | 0 |
| SIRVome_isoforms | 231019 | 14242725 | 61.6517 | 63.2148 |
