Input data and parameters
QualiMap command line
qualimap bamqc -bam output/mappings/longReadMapping/ont-Crg-CapTrap_HpreCap_0+_Brain01Rep5.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+_Brain01Rep5.fastq.gz |
Draw chromosome limits: | no |
Analyze overlapping paired-end reads: | no |
Program: | minimap2 (2.22-r1101) |
Analysis date: | Tue Nov 15 22:13:15 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+_Brain01Rep5.bam |
Summary
Globals
Reference size | 3,110,632,377 |
Number of reads | 13,811,609 |
Mapped reads | 13,811,609 / 100% |
Unmapped reads | 0 / 0% |
Mapped paired reads | 0 / 0% |
Secondary alignments | 0 |
Read min/max/mean length | 102 / 9,360 / 779.41 |
Duplicated reads (estimated) | 12,806,986 / 92.73% |
Duplication rate | 37.79% |
Clipped reads | 13,811,487 / 100% |
ACGT Content
Number/percentage of A's | 1,926,397,552 / 25.39% |
Number/percentage of C's | 1,839,015,808 / 24.24% |
Number/percentage of T's | 1,968,762,278 / 25.95% |
Number/percentage of G's | 1,851,637,071 / 24.41% |
Number/percentage of N's | 0 / 0% |
GC Percentage | 48.65% |
Coverage
Mean | 30.5097 |
Standard Deviation | 279.8753 |
Mapping Quality
Mean Mapping Quality | 8.58 |
Mismatches and indels
General error rate | 0.34% |
Mismatches | 238,567,308 |
Insertions | 49,662,015 |
Mapped reads with at least one insertion | 87.32% |
Deletions | 78,325,343 |
Mapped reads with at least one deletion | 93.48% |
Homopolymer indels | 33.87% |
Chromosome stats
Name | Length | Mapped bases | Mean coverage | Standard deviation |
chr1 | 248956422 | 9106852747 | 36.5801 | 183.4788 |
chr10 | 133797422 | 2762495838 | 20.6469 | 133.5174 |
chr11 | 135086622 | 4288963449 | 31.7497 | 301.7844 |
chr12 | 133275309 | 4103521558 | 30.7898 | 212.359 |
chr13 | 114364328 | 1448185265 | 12.6629 | 122.4177 |
chr14 | 107043718 | 4325755976 | 40.4111 | 390.0244 |
chr15 | 101991189 | 2449237861 | 24.0142 | 287.3811 |
chr16 | 90338345 | 2761402110 | 30.5673 | 406.2656 |
chr17 | 83257441 | 3900917018 | 46.8537 | 350.6276 |
chr18 | 80373285 | 2025942822 | 25.2067 | 174.9815 |
chr19 | 58617616 | 6122187765 | 104.4428 | 491.4003 |
chr2 | 242193529 | 8122980336 | 33.5392 | 466.501 |
chr20 | 64444167 | 2025251084 | 31.4264 | 301.7814 |
chr21 | 46709983 | 3030258100 | 64.8739 | 348.3958 |
chr22 | 50818468 | 1596101571 | 31.4079 | 203.8281 |
chr3 | 198295559 | 6355165471 | 32.049 | 232.3332 |
chr4 | 190214555 | 3724272345 | 19.5793 | 215.1991 |
chr5 | 181538259 | 6243915382 | 34.3945 | 239.9862 |
chr6 | 170805979 | 4246812448 | 24.8634 | 243.0536 |
chr7 | 159345973 | 4931211651 | 30.9466 | 285.4814 |
chr8 | 145138636 | 4746358830 | 32.7022 | 196.0967 |
chr9 | 138394717 | 2616378204 | 18.9052 | 219.2689 |
chrIS | 10567884 | 0 | 0 | 0 |
chrM | 16569 | 102978756 | 6,215.1461 | 6,992.0877 |
chrX | 156040895 | 2365456205 | 15.1592 | 160.5447 |
chrY | 57227415 | 177424673 | 3.1003 | 11.881 |
ERCC-00002 | 1061 | 37512484 | 35,355.7813 | 4,756.5453 |
ERCC-00003 | 1023 | 717103 | 700.9804 | 74.6404 |
ERCC-00004 | 523 | 9732092 | 18,608.2065 | 2,573.8754 |
ERCC-00009 | 984 | 1224215 | 1,244.1209 | 150.4281 |
ERCC-00012 | 994 | 0 | 0 | 0 |
ERCC-00013 | 808 | 0 | 0 | 0 |
ERCC-00014 | 1957 | 385 | 0.1967 | 0.3971 |
ERCC-00016 | 844 | 827 | 0.9799 | 0.1858 |
ERCC-00017 | 1136 | 0 | 0 | 0 |
ERCC-00019 | 644 | 54107 | 84.0171 | 10.1962 |
ERCC-00022 | 751 | 225381 | 300.1079 | 34.9137 |
ERCC-00024 | 536 | 524 | 0.9776 | 0.1703 |
ERCC-00025 | 1994 | 1795 | 0.9002 | 0.3173 |
ERCC-00028 | 1130 | 1121 | 0.992 | 0.1478 |
ERCC-00031 | 1138 | 591 | 0.5193 | 0.4998 |
ERCC-00033 | 2022 | 2011 | 0.9946 | 0.0914 |
ERCC-00034 | 1019 | 24396 | 23.9411 | 2.5316 |
ERCC-00035 | 1130 | 46815 | 41.4292 | 3.715 |
ERCC-00039 | 740 | 2915 | 3.9392 | 0.5207 |
ERCC-00040 | 744 | 4393 | 5.9046 | 0.7747 |
ERCC-00041 | 1122 | 0 | 0 | 0 |
ERCC-00042 | 1023 | 197818 | 193.3705 | 18.9721 |
ERCC-00043 | 1023 | 269105 | 263.0547 | 22.6039 |
ERCC-00044 | 1156 | 34872 | 30.1661 | 4.0204 |
ERCC-00046 | 522 | 17812480 | 34,123.5249 | 4,569.1323 |
ERCC-00048 | 992 | 0 | 0 | 0 |
ERCC-00051 | 274 | 32602 | 118.9854 | 19.9112 |
ERCC-00053 | 1023 | 40381 | 39.4731 | 3.647 |
ERCC-00054 | 274 | 14872 | 54.2774 | 10.789 |
ERCC-00057 | 1021 | 0 | 0 | 0 |
ERCC-00058 | 1136 | 0 | 0 | 0 |
ERCC-00059 | 525 | 54305 | 103.4381 | 13.2118 |
ERCC-00060 | 523 | 1301031 | 2,487.631 | 350.4327 |
ERCC-00061 | 1136 | 0 | 0 | 0 |
ERCC-00062 | 1023 | 113941 | 111.3793 | 10.8464 |
ERCC-00067 | 644 | 7100 | 11.0248 | 2.21 |
ERCC-00069 | 1137 | 0 | 0 | 0 |
ERCC-00071 | 642 | 118681 | 184.8614 | 20.8001 |
ERCC-00073 | 603 | 1183 | 1.9619 | 0.3186 |
ERCC-00074 | 522 | 54679628 | 104,750.2452 | 13,666.2754 |
ERCC-00075 | 1023 | 0 | 0 | 0 |
ERCC-00076 | 642 | 391245 | 609.4159 | 70.9711 |
ERCC-00077 | 273 | 1837 | 6.7289 | 1.2215 |
ERCC-00078 | 993 | 32422 | 32.6506 | 8.3192 |
ERCC-00079 | 644 | 166398 | 258.382 | 30.6914 |
ERCC-00081 | 534 | 0 | 0 | 0 |
ERCC-00083 | 1022 | 0 | 0 | 0 |
ERCC-00084 | 994 | 4326 | 4.3521 | 3.2552 |
ERCC-00085 | 844 | 5886 | 6.9739 | 0.38 |
ERCC-00086 | 1020 | 0 | 0 | 0 |
ERCC-00092 | 1124 | 303468 | 269.9893 | 39.6148 |
ERCC-00095 | 521 | 275585 | 528.9539 | 65.3391 |
ERCC-00096 | 1107 | 26085726 | 23,564.3415 | 2,664.8628 |
ERCC-00097 | 523 | 2496 | 4.7725 | 0.6803 |
ERCC-00098 | 1143 | 0 | 0 | 0 |
ERCC-00099 | 1350 | 21454 | 15.8919 | 2.1394 |
ERCC-00104 | 2022 | 0 | 0 | 0 |
ERCC-00108 | 1022 | 731999 | 716.2417 | 72.132 |
ERCC-00109 | 536 | 2100 | 3.9179 | 0.553 |
ERCC-00111 | 994 | 517903 | 521.0292 | 50.7803 |
ERCC-00112 | 1136 | 125949 | 110.8706 | 10.813 |
ERCC-00113 | 840 | 5375357 | 6,399.2345 | 625.8343 |
ERCC-00116 | 1991 | 21143 | 10.6193 | 2.741 |
ERCC-00117 | 1136 | 0 | 0 | 0 |
ERCC-00120 | 536 | 519 | 0.9683 | 0.2155 |
ERCC-00123 | 1022 | 0 | 0 | 0 |
ERCC-00126 | 1118 | 2206 | 1.9732 | 0.2335 |
ERCC-00130 | 1059 | 14771799 | 13,948.8187 | 1,367.7153 |
ERCC-00131 | 771 | 143693 | 186.3722 | 23.5968 |
ERCC-00134 | 274 | 526 | 1.9197 | 0.3872 |
ERCC-00136 | 1033 | 1247900 | 1,208.0348 | 105.9301 |
ERCC-00137 | 537 | 1042 | 1.9404 | 0.3255 |
ERCC-00138 | 1024 | 0 | 0 | 0 |
ERCC-00142 | 493 | 973 | 1.9736 | 0.2348 |
ERCC-00143 | 784 | 9993 | 12.7462 | 1.4966 |
ERCC-00144 | 538 | 59181 | 110.0019 | 14.9005 |
ERCC-00145 | 1042 | 397170 | 381.1612 | 41.2672 |
ERCC-00147 | 1023 | 3042 | 2.9736 | 0.2537 |
ERCC-00148 | 494 | 20651 | 41.8036 | 6.088 |
ERCC-00150 | 743 | 4056 | 5.459 | 1.0554 |
ERCC-00154 | 537 | 7895 | 14.702 | 1.821 |
ERCC-00156 | 494 | 0 | 0 | 0 |
ERCC-00157 | 1019 | 12416 | 12.1845 | 1.3094 |
ERCC-00158 | 1027 | 1010 | 0.9834 | 0.1689 |
ERCC-00160 | 743 | 23763 | 31.9825 | 3.8334 |
ERCC-00162 | 523 | 90554 | 173.1434 | 22.6351 |
ERCC-00163 | 543 | 50051 | 92.175 | 12.1095 |
ERCC-00164 | 1022 | 0 | 0 | 0 |
ERCC-00165 | 872 | 89151 | 102.2374 | 11.0471 |
ERCC-00168 | 1024 | 2009 | 1.9619 | 0.3257 |
ERCC-00170 | 1023 | 23451 | 22.9238 | 2.5913 |
ERCC-00171 | 505 | 8899547 | 17,622.8653 | 2,567.7617 |
GL000008.2 | 209709 | 233219 | 1.1121 | 1.1109 |
GL000009.2 | 201709 | 4622 | 0.0229 | 0.0561 |
GL000194.1 | 191469 | 6711683 | 35.0536 | 34.8874 |
GL000195.1 | 182896 | 901219 | 4.9275 | 4.9987 |
GL000205.2 | 185591 | 678391 | 3.6553 | 4.969 |
GL000208.1 | 92689 | 0 | 0 | 0 |
GL000213.1 | 164239 | 0 | 0 | 0 |
GL000214.1 | 137718 | 1623 | 0.0118 | 0.1068 |
GL000216.2 | 176608 | 24408 | 0.1382 | 0.1458 |
GL000218.1 | 161147 | 2044872 | 12.6895 | 12.7389 |
GL000219.1 | 179198 | 3147356 | 17.5636 | 20.9946 |
GL000220.1 | 161802 | 749422 | 4.6317 | 20.5907 |
GL000221.1 | 155397 | 13852 | 0.0891 | 0.2747 |
GL000224.1 | 179693 | 305634 | 1.7009 | 2.5636 |
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 | 31921 | 0.0814 | 0.0946 |
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 | 23533 | 0.1344 | 0.1546 |
KI270707.1 | 32032 | 0 | 0 | 0 |
KI270708.1 | 127682 | 26532 | 0.2078 | 0.2113 |
KI270709.1 | 66860 | 0 | 0 | 0 |
KI270710.1 | 40176 | 0 | 0 | 0 |
KI270711.1 | 42210 | 13859 | 0.3283 | 1.5375 |
KI270712.1 | 176043 | 71409 | 0.4056 | 0.938 |
KI270713.1 | 40745 | 16395 | 0.4024 | 1.9533 |
KI270714.1 | 41717 | 5959 | 0.1428 | 0.1747 |
KI270715.1 | 161471 | 0 | 0 | 0 |
KI270716.1 | 153799 | 0 | 0 | 0 |
KI270717.1 | 40062 | 12080 | 0.3015 | 0.3062 |
KI270718.1 | 38054 | 17335 | 0.4555 | 0.5084 |
KI270719.1 | 176845 | 149 | 0.0008 | 0.0288 |
KI270720.1 | 39050 | 0 | 0 | 0 |
KI270721.1 | 100316 | 124597 | 1.242 | 1.4575 |
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 | 55137 | 0.123 | 0.2117 |
KI270728.1 | 1872759 | 21278 | 0.0114 | 0.0665 |
KI270729.1 | 280839 | 1303 | 0.0046 | 0.0244 |
KI270730.1 | 112551 | 0 | 0 | 0 |
KI270731.1 | 150754 | 6089 | 0.0404 | 0.5209 |
KI270732.1 | 41543 | 0 | 0 | 0 |
KI270733.1 | 179772 | 1136727 | 6.3232 | 21.5124 |
KI270734.1 | 165050 | 3519631 | 21.3246 | 62.4598 |
KI270735.1 | 42811 | 0 | 0 | 0 |
KI270736.1 | 181920 | 0 | 0 | 0 |
KI270737.1 | 103838 | 0 | 0 | 0 |
KI270738.1 | 99375 | 221 | 0.0022 | 0.0471 |
KI270739.1 | 73985 | 0 | 0 | 0 |
KI270740.1 | 37240 | 0 | 0 | 0 |
KI270741.1 | 157432 | 333892 | 2.1209 | 2.6316 |
KI270742.1 | 186739 | 4117413 | 22.049 | 21.9913 |
KI270743.1 | 210658 | 3180646 | 15.0986 | 15.0675 |
KI270744.1 | 168472 | 1913 | 0.0114 | 0.1662 |
KI270745.1 | 41891 | 1159 | 0.0277 | 0.1959 |
KI270746.1 | 66486 | 26191 | 0.3939 | 0.396 |
KI270747.1 | 198735 | 0 | 0 | 0 |
KI270748.1 | 93321 | 19088 | 0.2045 | 0.3769 |
KI270749.1 | 158759 | 0 | 0 | 0 |
KI270750.1 | 148850 | 0 | 0 | 0 |
KI270751.1 | 150742 | 0 | 0 | 0 |
KI270752.1 | 27745 | 76728 | 2.7655 | 2.7406 |
KI270753.1 | 62944 | 0 | 0 | 0 |
KI270754.1 | 40191 | 0 | 0 | 0 |
KI270755.1 | 36723 | 2484 | 0.0676 | 0.2708 |
KI270756.1 | 79590 | 0 | 0 | 0 |
KI270757.1 | 71251 | 0 | 0 | 0 |
SIRVome_isoforms | 231019 | 1112551451 | 4,815.8439 | 4,860.542 |