Input data and parameters
QualiMap command line
| qualimap bamqc -bam output/mappings/longReadMapping/ont-Crg-Telop_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-Telop_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 21:37:26 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+_Brain01Rep3.bam |
Summary
Globals
| Reference size | 3,110,632,377 |
| Number of reads | 8,011,206 |
| Mapped reads | 8,011,206 / 100% |
| Unmapped reads | 0 / 0% |
| Mapped paired reads | 0 / 0% |
| Secondary alignments | 0 |
| Read min/max/mean length | 105 / 79,522 / 1,035.74 |
| Duplicated reads (estimated) | 7,362,649 / 91.9% |
| Duplication rate | 42.87% |
| Clipped reads | 8,010,011 / 99.99% |
ACGT Content
| Number/percentage of A's | 1,629,817,203 / 27.11% |
| Number/percentage of C's | 1,380,762,408 / 22.97% |
| Number/percentage of T's | 1,649,357,086 / 27.44% |
| Number/percentage of G's | 1,351,474,491 / 22.48% |
| Number/percentage of N's | 0 / 0% |
| GC Percentage | 45.45% |
Coverage
| Mean | 21.9002 |
| Standard Deviation | 346.9719 |
Mapping Quality
| Mean Mapping Quality | 8.99 |
Mismatches and indels
| General error rate | 0.49% |
| Mismatches | 238,430,390 |
| Insertions | 47,573,857 |
| Mapped reads with at least one insertion | 93.22% |
| Deletions | 81,200,946 |
| Mapped reads with at least one deletion | 97.32% |
| Homopolymer indels | 35.32% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| chr1 | 248956422 | 6519564835 | 26.1876 | 305.7845 |
| chr10 | 133797422 | 1914974977 | 14.3125 | 55.1269 |
| chr11 | 135086622 | 3019943885 | 22.3556 | 152.2718 |
| chr12 | 133275309 | 3003498947 | 22.536 | 136.8439 |
| chr13 | 114364328 | 976097864 | 8.535 | 48.7053 |
| chr14 | 107043718 | 2190989328 | 20.4682 | 69.3681 |
| chr15 | 101991189 | 2467568776 | 24.1939 | 162.4888 |
| chr16 | 90338345 | 1407893245 | 15.5847 | 56.9998 |
| chr17 | 83257441 | 3124851007 | 37.5324 | 128.7404 |
| chr18 | 80373285 | 1707008236 | 21.2385 | 151.3941 |
| chr19 | 58617616 | 1925757524 | 32.8529 | 158.6235 |
| chr2 | 242193529 | 8123205202 | 33.5401 | 116.9756 |
| chr20 | 64444167 | 4431536440 | 68.7655 | 231.9681 |
| chr21 | 46709983 | 1358738121 | 29.0888 | 125.7541 |
| chr22 | 50818468 | 1272239151 | 25.035 | 84.8594 |
| chr3 | 198295559 | 5204102156 | 26.2442 | 88.109 |
| chr4 | 190214555 | 3249429230 | 17.083 | 100.0735 |
| chr5 | 181538259 | 2892330390 | 15.9323 | 59.7597 |
| chr6 | 170805979 | 2149716161 | 12.5857 | 147.5154 |
| chr7 | 159345973 | 2661385846 | 16.7019 | 117.1042 |
| chr8 | 145138636 | 2870031040 | 19.7744 | 52.5447 |
| chr9 | 138394717 | 1732585259 | 12.5192 | 64.5506 |
| chrIS | 10567884 | 0 | 0 | 0 |
| chrM | 16569 | 1370405678 | 82,709.0155 | 115,032.764 |
| chrX | 156040895 | 1936349381 | 12.4092 | 69.118 |
| chrY | 57227415 | 138495555 | 2.4201 | 12.4259 |
| ERCC-00002 | 1061 | 14739689 | 13,892.2611 | 882.4501 |
| ERCC-00003 | 1023 | 1255120 | 1,226.9013 | 99.8252 |
| ERCC-00004 | 523 | 7388385 | 14,126.9312 | 1,360.9667 |
| ERCC-00009 | 984 | 3593182 | 3,651.6077 | 285.8688 |
| ERCC-00012 | 994 | 983 | 0.9889 | 0.1721 |
| ERCC-00013 | 808 | 4182 | 5.1757 | 0.7105 |
| ERCC-00014 | 1957 | 13628 | 6.9637 | 0.7361 |
| ERCC-00016 | 844 | 4166 | 4.936 | 0.51 |
| ERCC-00017 | 1136 | 0 | 0 | 0 |
| ERCC-00019 | 644 | 103569 | 160.8214 | 13.0105 |
| ERCC-00022 | 751 | 216037 | 287.6658 | 24.6853 |
| ERCC-00024 | 536 | 0 | 0 | 0 |
| ERCC-00025 | 1994 | 40763 | 20.4428 | 2.0256 |
| ERCC-00028 | 1130 | 0 | 0 | 0 |
| ERCC-00031 | 1138 | 0 | 0 | 0 |
| ERCC-00033 | 2022 | 18079 | 8.9411 | 0.7945 |
| ERCC-00034 | 1019 | 73005 | 71.6438 | 5.3282 |
| ERCC-00035 | 1130 | 18906 | 16.731 | 1.6483 |
| ERCC-00039 | 740 | 9534 | 12.8838 | 1.0327 |
| ERCC-00040 | 744 | 3697 | 4.9691 | 0.4412 |
| ERCC-00041 | 1122 | 5578 | 4.9715 | 0.3344 |
| ERCC-00042 | 1023 | 2018776 | 1,973.3881 | 114.8854 |
| ERCC-00043 | 1023 | 200774 | 196.26 | 14.012 |
| ERCC-00044 | 1156 | 97862 | 84.6557 | 4.9608 |
| ERCC-00046 | 522 | 13723474 | 26,290.1801 | 2,090.1603 |
| ERCC-00048 | 992 | 0 | 0 | 0 |
| ERCC-00051 | 274 | 158450 | 578.2847 | 57.83 |
| ERCC-00053 | 1023 | 107134 | 104.7253 | 7.0882 |
| ERCC-00054 | 274 | 24647 | 89.9526 | 9.0111 |
| ERCC-00057 | 1021 | 0 | 0 | 0 |
| ERCC-00058 | 1136 | 7883 | 6.9393 | 0.706 |
| ERCC-00059 | 525 | 6211 | 11.8305 | 1.1463 |
| ERCC-00060 | 523 | 1085192 | 2,074.9369 | 186.8198 |
| ERCC-00061 | 1136 | 0 | 0 | 0 |
| ERCC-00062 | 1023 | 429466 | 419.8104 | 26.6281 |
| ERCC-00067 | 644 | 9352 | 14.5217 | 1.3745 |
| ERCC-00069 | 1137 | 0 | 0 | 0 |
| ERCC-00071 | 642 | 202877 | 316.0078 | 20.3737 |
| ERCC-00073 | 603 | 6556 | 10.8723 | 1.0266 |
| ERCC-00074 | 522 | 11493096 | 22,017.4253 | 1,572.5082 |
| ERCC-00075 | 1023 | 0 | 0 | 0 |
| ERCC-00076 | 642 | 958688 | 1,493.2835 | 115.3765 |
| ERCC-00077 | 273 | 6108 | 22.3736 | 2.1393 |
| ERCC-00078 | 993 | 54074 | 54.4552 | 4.4571 |
| ERCC-00079 | 644 | 278882 | 433.0466 | 31.5833 |
| ERCC-00081 | 534 | 0 | 0 | 0 |
| ERCC-00083 | 1022 | 0 | 0 | 0 |
| ERCC-00084 | 994 | 0 | 0 | 0 |
| ERCC-00085 | 844 | 16643 | 19.7192 | 1.8693 |
| ERCC-00086 | 1020 | 0 | 0 | 0 |
| ERCC-00092 | 1124 | 252110 | 224.2972 | 16.9426 |
| ERCC-00095 | 521 | 70879 | 136.0441 | 12.5078 |
| ERCC-00096 | 1107 | 42549730 | 38,436.9738 | 2,572.4727 |
| ERCC-00097 | 523 | 2069 | 3.956 | 0.4723 |
| ERCC-00098 | 1143 | 0 | 0 | 0 |
| ERCC-00099 | 1350 | 41677 | 30.8719 | 2.3389 |
| ERCC-00104 | 2022 | 0 | 0 | 0 |
| ERCC-00108 | 1022 | 2093341 | 2,048.2789 | 170.4493 |
| ERCC-00109 | 536 | 2677 | 4.9944 | 0.3674 |
| ERCC-00111 | 994 | 2849934 | 2,867.1368 | 175.6874 |
| ERCC-00112 | 1136 | 59082 | 52.0088 | 3.8254 |
| ERCC-00113 | 840 | 12893188 | 15,349.0333 | 1,011.2549 |
| ERCC-00116 | 1991 | 19942 | 10.0161 | 0.7636 |
| ERCC-00117 | 1136 | 0 | 0 | 0 |
| ERCC-00120 | 536 | 533 | 0.9944 | 0.0962 |
| ERCC-00123 | 1022 | 0 | 0 | 0 |
| ERCC-00126 | 1118 | 7676 | 6.8658 | 0.8388 |
| ERCC-00130 | 1059 | 106204810 | 100,287.8281 | 7,510.1472 |
| ERCC-00131 | 771 | 203444 | 263.8703 | 18.932 |
| ERCC-00134 | 274 | 1607 | 5.865 | 0.714 |
| ERCC-00136 | 1033 | 10161084 | 9,836.4802 | 554.8556 |
| ERCC-00137 | 537 | 12621 | 23.5028 | 2.5213 |
| ERCC-00138 | 1024 | 0 | 0 | 0 |
| ERCC-00142 | 493 | 0 | 0 | 0 |
| ERCC-00143 | 784 | 5414 | 6.9056 | 0.6559 |
| ERCC-00144 | 538 | 34905 | 64.8792 | 7.1772 |
| ERCC-00145 | 1042 | 1356575 | 1,301.8954 | 118.9058 |
| ERCC-00147 | 1023 | 2019 | 1.9736 | 0.3027 |
| ERCC-00148 | 494 | 63462 | 128.4656 | 12.1454 |
| ERCC-00150 | 743 | 10907 | 14.6797 | 1.1822 |
| ERCC-00154 | 537 | 12343 | 22.9851 | 2.1431 |
| ERCC-00156 | 494 | 2934 | 5.9393 | 0.492 |
| ERCC-00157 | 1019 | 42511 | 41.7184 | 2.6624 |
| ERCC-00158 | 1027 | 0 | 0 | 0 |
| ERCC-00160 | 743 | 34203 | 46.0336 | 4.7159 |
| ERCC-00162 | 523 | 39058 | 74.6807 | 6.847 |
| ERCC-00163 | 543 | 74418 | 137.0497 | 9.5529 |
| ERCC-00164 | 1022 | 0 | 0 | 0 |
| ERCC-00165 | 872 | 414053 | 474.8314 | 35.0467 |
| ERCC-00168 | 1024 | 0 | 0 | 0 |
| ERCC-00170 | 1023 | 25872 | 25.2903 | 1.8661 |
| ERCC-00171 | 505 | 8089223 | 16,018.2634 | 1,754.4542 |
| GL000008.2 | 209709 | 0 | 0 | 0 |
| GL000009.2 | 201709 | 229 | 0.0011 | 0.0328 |
| GL000194.1 | 191469 | 7576924 | 39.5726 | 39.5305 |
| GL000195.1 | 182896 | 981556 | 5.3667 | 5.5464 |
| GL000205.2 | 185591 | 158173 | 0.8523 | 1.444 |
| GL000208.1 | 92689 | 0 | 0 | 0 |
| GL000213.1 | 164239 | 0 | 0 | 0 |
| GL000214.1 | 137718 | 1025 | 0.0074 | 0.1056 |
| GL000216.2 | 176608 | 0 | 0 | 0 |
| GL000218.1 | 161147 | 2715044 | 16.8482 | 16.8584 |
| GL000219.1 | 179198 | 4251467 | 23.725 | 25.5305 |
| GL000220.1 | 161802 | 753402 | 4.6563 | 9.2178 |
| GL000221.1 | 155397 | 32936 | 0.2119 | 0.2218 |
| GL000224.1 | 179693 | 1833933 | 10.2059 | 21.1074 |
| 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 | 34616 | 0.0883 | 0.1224 |
| 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 | 2787 | 0.0159 | 0.2263 |
| KI270707.1 | 32032 | 0 | 0 | 0 |
| KI270708.1 | 127682 | 0 | 0 | 0 |
| KI270709.1 | 66860 | 456 | 0.0068 | 0.082 |
| KI270710.1 | 40176 | 0 | 0 | 0 |
| KI270711.1 | 42210 | 62080 | 1.4707 | 4.997 |
| KI270712.1 | 176043 | 41855 | 0.2378 | 1.5216 |
| KI270713.1 | 40745 | 17760 | 0.4359 | 1.8479 |
| KI270714.1 | 41717 | 16888 | 0.4048 | 0.5613 |
| KI270715.1 | 161471 | 0 | 0 | 0 |
| KI270716.1 | 153799 | 0 | 0 | 0 |
| KI270717.1 | 40062 | 4871 | 0.1216 | 0.7534 |
| KI270718.1 | 38054 | 4864 | 0.1278 | 0.3054 |
| KI270719.1 | 176845 | 0 | 0 | 0 |
| KI270720.1 | 39050 | 0 | 0 | 0 |
| KI270721.1 | 100316 | 170943 | 1.704 | 2.1334 |
| 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 | 6991 | 0.0156 | 0.3371 |
| KI270728.1 | 1872759 | 6601 | 0.0035 | 0.0572 |
| KI270729.1 | 280839 | 8390 | 0.0299 | 0.038 |
| KI270730.1 | 112551 | 0 | 0 | 0 |
| KI270731.1 | 150754 | 334 | 0.0022 | 0.046 |
| KI270732.1 | 41543 | 0 | 0 | 0 |
| KI270733.1 | 179772 | 630699 | 3.5083 | 8.6958 |
| KI270734.1 | 165050 | 279291 | 1.6922 | 3.6906 |
| KI270735.1 | 42811 | 0 | 0 | 0 |
| KI270736.1 | 181920 | 0 | 0 | 0 |
| KI270737.1 | 103838 | 0 | 0 | 0 |
| KI270738.1 | 99375 | 1559 | 0.0157 | 0.2526 |
| KI270739.1 | 73985 | 0 | 0 | 0 |
| KI270740.1 | 37240 | 0 | 0 | 0 |
| KI270741.1 | 157432 | 502541 | 3.1921 | 3.6979 |
| KI270742.1 | 186739 | 2112194 | 11.3109 | 11.2946 |
| KI270743.1 | 210658 | 0 | 0 | 0 |
| KI270744.1 | 168472 | 4529 | 0.0269 | 0.667 |
| KI270745.1 | 41891 | 6068 | 0.1449 | 1.286 |
| KI270746.1 | 66486 | 0 | 0 | 0 |
| KI270747.1 | 198735 | 0 | 0 | 0 |
| KI270748.1 | 93321 | 334 | 0.0036 | 0.0585 |
| KI270749.1 | 158759 | 561 | 0.0035 | 0.0581 |
| KI270750.1 | 148850 | 0 | 0 | 0 |
| KI270751.1 | 150742 | 876 | 0.0058 | 0.1051 |
| KI270752.1 | 27745 | 150301 | 5.4172 | 5.357 |
| 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 | 206320616 | 893.0894 | 1,187.1075 |
