Input data and parameters
QualiMap command line
| qualimap bamqc -bam output/mappings/longReadMapping/pacBioSII-Cshl-CapTrap_HpreCap_0+_Brain03Rep1.bam -nw 400 -hm 3 |
Alignment
| Command line: | minimap2 --MD -x splice:hq -t 12 --secondary=no -L -a genomes/hg38.sorted.fa fastqs/pacBioSII-Cshl-CapTrap_HpreCap_0+_Brain03Rep1.fastq.gz |
| Draw chromosome limits: | no |
| Analyze overlapping paired-end reads: | no |
| Program: | minimap2 (2.22-r1101) |
| Analysis date: | Tue Nov 15 19:47:13 CET 2022 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | output/mappings/longReadMapping/pacBioSII-Cshl-CapTrap_HpreCap_0+_Brain03Rep1.bam |
Summary
Globals
| Reference size | 3,110,632,377 |
| Number of reads | 1,683,773 |
| Mapped reads | 1,683,773 / 100% |
| Unmapped reads | 0 / 0% |
| Mapped paired reads | 0 / 0% |
| Secondary alignments | 0 |
| Read min/max/mean length | 119 / 6,379 / 959.13 |
| Duplicated reads (estimated) | 1,498,236 / 88.98% |
| Duplication rate | 36.53% |
| Clipped reads | 1,683,578 / 99.99% |
ACGT Content
| Number/percentage of A's | 367,712,498 / 26.25% |
| Number/percentage of C's | 347,928,380 / 24.83% |
| Number/percentage of T's | 318,654,421 / 22.75% |
| Number/percentage of G's | 366,681,371 / 26.17% |
| Number/percentage of N's | 0 / 0% |
| GC Percentage | 51.01% |
Coverage
| Mean | 5.9837 |
| Standard Deviation | 36.9443 |
Mapping Quality
| Mean Mapping Quality | 7.13 |
Mismatches and indels
| General error rate | 0.02% |
| Mismatches | 2,602,049 |
| Insertions | 857,633 |
| Mapped reads with at least one insertion | 19.85% |
| Deletions | 353,554 |
| Mapped reads with at least one deletion | 12.63% |
| Homopolymer indels | 46.39% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| chr1 | 248956422 | 1791540608 | 7.1962 | 27.7444 |
| chr10 | 133797422 | 570769052 | 4.2659 | 16.7958 |
| chr11 | 135086622 | 938068070 | 6.9442 | 42.2448 |
| chr12 | 133275309 | 1102616746 | 8.2732 | 56.3637 |
| chr13 | 114364328 | 214703334 | 1.8774 | 9.8625 |
| chr14 | 107043718 | 684055092 | 6.3904 | 54.8733 |
| chr15 | 101991189 | 582745382 | 5.7137 | 31.4033 |
| chr16 | 90338345 | 709986493 | 7.8592 | 64.5351 |
| chr17 | 83257441 | 667839151 | 8.0214 | 44.423 |
| chr18 | 80373285 | 635101903 | 7.9019 | 57.8715 |
| chr19 | 58617616 | 1233218562 | 21.0384 | 80.2159 |
| chr2 | 242193529 | 1491133573 | 6.1568 | 30.0608 |
| chr20 | 64444167 | 641949778 | 9.9613 | 26.3596 |
| chr21 | 46709983 | 303716626 | 6.5022 | 37.3 |
| chr22 | 50818468 | 398019095 | 7.8322 | 42.2422 |
| chr3 | 198295559 | 1345457157 | 6.7851 | 25.1349 |
| chr4 | 190214555 | 592011172 | 3.1123 | 14.507 |
| chr5 | 181538259 | 954409891 | 5.2573 | 21.5737 |
| chr6 | 170805979 | 705098837 | 4.1281 | 27.3356 |
| chr7 | 159345973 | 915615198 | 5.7461 | 36.095 |
| chr8 | 145138636 | 788407361 | 5.4321 | 24.4081 |
| chr9 | 138394717 | 523252559 | 3.7809 | 36.6868 |
| chrIS | 10567884 | 0 | 0 | 0 |
| chrM | 16569 | 4194638 | 253.1618 | 231.1603 |
| chrX | 156040895 | 629687925 | 4.0354 | 29.6624 |
| chrY | 57227415 | 20947910 | 0.366 | 1.7874 |
| ERCC-00002 | 1061 | 12864038 | 12,124.4467 | 1,054.8922 |
| ERCC-00003 | 1023 | 17147 | 16.7615 | 1.5907 |
| ERCC-00004 | 523 | 66523 | 127.195 | 14.8382 |
| ERCC-00009 | 984 | 359592 | 365.439 | 30.8838 |
| 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 | 9330 | 14.4876 | 1.7854 |
| ERCC-00022 | 751 | 37218 | 49.5579 | 4.7379 |
| ERCC-00024 | 536 | 0 | 0 | 0 |
| ERCC-00025 | 1994 | 834 | 0.4183 | 0.4933 |
| ERCC-00028 | 1130 | 0 | 0 | 0 |
| ERCC-00031 | 1138 | 1130 | 0.993 | 0.0933 |
| ERCC-00033 | 2022 | 0 | 0 | 0 |
| ERCC-00034 | 1019 | 5065 | 4.9706 | 0.3361 |
| ERCC-00035 | 1130 | 21322 | 18.869 | 1.4829 |
| ERCC-00039 | 740 | 0 | 0 | 0 |
| ERCC-00040 | 744 | 0 | 0 | 0 |
| ERCC-00041 | 1122 | 0 | 0 | 0 |
| ERCC-00042 | 1023 | 6899 | 6.7439 | 0.6445 |
| ERCC-00043 | 1023 | 19782 | 19.3372 | 1.1311 |
| ERCC-00044 | 1156 | 19581 | 16.9386 | 0.8115 |
| ERCC-00046 | 522 | 262138 | 502.1801 | 58.7437 |
| ERCC-00048 | 992 | 0 | 0 | 0 |
| ERCC-00051 | 274 | 266 | 0.9708 | 0.1684 |
| ERCC-00053 | 1023 | 2029 | 1.9834 | 0.1788 |
| ERCC-00054 | 274 | 538 | 1.9635 | 0.1875 |
| ERCC-00057 | 1021 | 0 | 0 | 0 |
| ERCC-00058 | 1136 | 0 | 0 | 0 |
| ERCC-00059 | 525 | 6203 | 11.8152 | 1.435 |
| ERCC-00060 | 523 | 4771 | 9.1224 | 1.2908 |
| ERCC-00061 | 1136 | 0 | 0 | 0 |
| ERCC-00062 | 1023 | 12190 | 11.9159 | 0.9292 |
| ERCC-00067 | 644 | 0 | 0 | 0 |
| ERCC-00069 | 1137 | 0 | 0 | 0 |
| ERCC-00071 | 642 | 24112 | 37.5576 | 3.8444 |
| ERCC-00073 | 603 | 0 | 0 | 0 |
| ERCC-00074 | 522 | 486817 | 932.5996 | 111.0248 |
| ERCC-00075 | 1023 | 0 | 0 | 0 |
| ERCC-00076 | 642 | 73761 | 114.8925 | 12.2654 |
| ERCC-00077 | 273 | 0 | 0 | 0 |
| ERCC-00078 | 993 | 13396 | 13.4904 | 1.1976 |
| ERCC-00079 | 644 | 27350 | 42.4689 | 4.5138 |
| ERCC-00081 | 534 | 0 | 0 | 0 |
| ERCC-00083 | 1022 | 0 | 0 | 0 |
| ERCC-00084 | 994 | 4243 | 4.2686 | 0.4432 |
| ERCC-00085 | 844 | 844 | 1 | 0 |
| ERCC-00086 | 1020 | 0 | 0 | 0 |
| ERCC-00092 | 1124 | 126640 | 112.669 | 8.8318 |
| ERCC-00095 | 521 | 1544 | 2.9635 | 0.3229 |
| ERCC-00096 | 1107 | 10857939 | 9,808.4363 | 817.4889 |
| ERCC-00097 | 523 | 0 | 0 | 0 |
| ERCC-00098 | 1143 | 0 | 0 | 0 |
| ERCC-00099 | 1350 | 2682 | 1.9867 | 0.1604 |
| ERCC-00104 | 2022 | 0 | 0 | 0 |
| ERCC-00108 | 1022 | 229312 | 224.3757 | 18.9114 |
| ERCC-00109 | 536 | 531 | 0.9907 | 0.0961 |
| ERCC-00111 | 994 | 168538 | 169.5553 | 14.3906 |
| ERCC-00112 | 1136 | 37056 | 32.6197 | 2.5165 |
| ERCC-00113 | 840 | 1388190 | 1,652.6071 | 142.1912 |
| ERCC-00116 | 1991 | 27037 | 13.5796 | 0.8216 |
| ERCC-00117 | 1136 | 0 | 0 | 0 |
| ERCC-00120 | 536 | 528 | 0.9851 | 0.1213 |
| ERCC-00123 | 1022 | 0 | 0 | 0 |
| ERCC-00126 | 1118 | 6679 | 5.9741 | 0.383 |
| ERCC-00130 | 1059 | 4934908 | 4,659.9698 | 334.2098 |
| ERCC-00131 | 771 | 43172 | 55.9948 | 5.4368 |
| ERCC-00134 | 274 | 0 | 0 | 0 |
| ERCC-00136 | 1033 | 401675 | 388.8432 | 27.5504 |
| ERCC-00137 | 537 | 0 | 0 | 0 |
| ERCC-00138 | 1024 | 0 | 0 | 0 |
| ERCC-00142 | 493 | 0 | 0 | 0 |
| ERCC-00143 | 784 | 1548 | 1.9745 | 0.2187 |
| ERCC-00144 | 538 | 9533 | 17.7193 | 2.0805 |
| ERCC-00145 | 1042 | 117286 | 112.5585 | 9.8974 |
| ERCC-00147 | 1023 | 0 | 0 | 0 |
| ERCC-00148 | 494 | 3405 | 6.8927 | 0.8189 |
| ERCC-00150 | 743 | 0 | 0 | 0 |
| ERCC-00154 | 537 | 528 | 0.9832 | 0.1284 |
| ERCC-00156 | 494 | 0 | 0 | 0 |
| ERCC-00157 | 1019 | 0 | 0 | 0 |
| ERCC-00158 | 1027 | 0 | 0 | 0 |
| ERCC-00160 | 743 | 5145 | 6.9246 | 0.6997 |
| ERCC-00162 | 523 | 513 | 0.9809 | 0.1369 |
| ERCC-00163 | 543 | 4816 | 8.8692 | 1.037 |
| ERCC-00164 | 1022 | 0 | 0 | 0 |
| ERCC-00165 | 872 | 32828 | 37.6468 | 3.532 |
| ERCC-00168 | 1024 | 0 | 0 | 0 |
| ERCC-00170 | 1023 | 1015 | 0.9922 | 0.0934 |
| ERCC-00171 | 505 | 1010567 | 2,001.1228 | 241.5582 |
| GL000008.2 | 209709 | 0 | 0 | 0 |
| GL000009.2 | 201709 | 0 | 0 | 0 |
| GL000194.1 | 191469 | 1719115 | 8.9786 | 8.9508 |
| GL000195.1 | 182896 | 122843 | 0.6717 | 0.7045 |
| GL000205.2 | 185591 | 29057 | 0.1566 | 0.3016 |
| GL000208.1 | 92689 | 0 | 0 | 0 |
| GL000213.1 | 164239 | 0 | 0 | 0 |
| GL000214.1 | 137718 | 0 | 0 | 0 |
| GL000216.2 | 176608 | 0 | 0 | 0 |
| GL000218.1 | 161147 | 605395 | 3.7568 | 3.7481 |
| GL000219.1 | 179198 | 744321 | 4.1536 | 4.8403 |
| GL000220.1 | 161802 | 47934 | 0.2963 | 0.6142 |
| GL000221.1 | 155397 | 0 | 0 | 0 |
| GL000224.1 | 179693 | 32045 | 0.1783 | 0.3828 |
| 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 | 0 | 0 | 0 |
| 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 | 431 | 0.0102 | 0.1005 |
| KI270712.1 | 176043 | 1053 | 0.006 | 0.1226 |
| KI270713.1 | 40745 | 7769 | 0.1907 | 0.4941 |
| 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 | 0 | 0 | 0 |
| KI270719.1 | 176845 | 0 | 0 | 0 |
| KI270720.1 | 39050 | 0 | 0 | 0 |
| KI270721.1 | 100316 | 6298 | 0.0628 | 0.1358 |
| 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 | 88 | 0.0002 | 0.014 |
| KI270728.1 | 1872759 | 0 | 0 | 0 |
| 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 | 37121 | 0.2065 | 0.7828 |
| KI270734.1 | 165050 | 2134227 | 12.9308 | 32.2529 |
| 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 | 13750 | 0.0873 | 0.1473 |
| KI270742.1 | 186739 | 528599 | 2.8307 | 2.8212 |
| KI270743.1 | 210658 | 138200 | 0.656 | 0.6555 |
| KI270744.1 | 168472 | 0 | 0 | 0 |
| KI270745.1 | 41891 | 0 | 0 | 0 |
| 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 | 0 | 0 | 0 |
| 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 | 128565283 | 556.5139 | 631.6651 |
