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

Coverage across reference 

Coverage Histogram 

Coverage Histogram (0-50X) 

Genome Fraction Coverage 

Duplication Rate Histogram 

Mapped Reads Nucleotide Content 

Mapped Reads GC-content Distribution 

Mapped Reads Clipping Profile 

Homopolymer Indels 

Mapping Quality Across Reference 

Mapping Quality Histogram