Qualimap Report: BAM QC

Input data and parameters 

QualiMap command line

qualimap bamqc -bam output/mappings/longReadMapping/pacBio-Cshl-Smarter_HpreCap_0+_Heart01Rep1.bam -nw 400 -hm 3

Alignment

Command line: minimap2 --MD -x splice:hq -t 12 --secondary=no -L -a genomes/hg38.sorted.fa fastqs/pacBio-Cshl-Smarter_HpreCap_0+_Heart01Rep1.fastq.gz
Draw chromosome limits: no
Analyze overlapping paired-end reads: no
Program: minimap2 (2.22-r1101)
Analysis date: Tue Nov 15 19:21:14 CET 2022
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: output/mappings/longReadMapping/pacBio-Cshl-Smarter_HpreCap_0+_Heart01Rep1.bam

Summary 

Globals

Reference size 3,110,632,377
Number of reads 502,412
Mapped reads 502,412 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 0 / 0%
Secondary alignments 0
Read min/max/mean length 202 / 11,417 / 1,195.93
Duplicated reads (estimated) 367,193 / 73.09%
Duplication rate 27.34%
Clipped reads 502,409 / 100%

ACGT Content

Number/percentage of A's 145,736,287 / 27.46%
Number/percentage of C's 119,056,634 / 22.43%
Number/percentage of T's 147,158,008 / 27.73%
Number/percentage of G's 118,786,824 / 22.38%
Number/percentage of N's 0 / 0%
GC Percentage 44.81%

Coverage

Mean 1.6218
Standard Deviation 15.3986

Mapping Quality

Mean Mapping Quality 4.59

Mismatches and indels

General error rate 0.04%
Mismatches 852,925
Insertions 690,452
Mapped reads with at least one insertion 24.8%
Deletions 243,409
Mapped reads with at least one deletion 21.9%
Homopolymer indels 39.53%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
chr1 248956422 569327273 2.2869 24.1512
chr10 133797422 212016336 1.5846 5.7279
chr11 135086622 204766855 1.5158 7.9592
chr12 133275309 348188304 2.6125 26.8561
chr13 114364328 77290910 0.6758 2.8561
chr14 107043718 145563311 1.3598 16.0899
chr15 101991189 239844240 2.3516 24.9533
chr16 90338345 133362712 1.4763 13.6187
chr17 83257441 137998524 1.6575 7.3094
chr18 80373285 119604257 1.4881 23.1686
chr19 58617616 186005025 3.1732 23.3473
chr2 242193529 443367198 1.8306 9.0051
chr20 64444167 78353439 1.2158 3.4299
chr21 46709983 42784197 0.916 4.8071
chr22 50818468 76955787 1.5143 4.9886
chr3 198295559 292703556 1.4761 9.853
chr4 190214555 301305119 1.584 6.4189
chr5 181538259 315282478 1.7367 6.0909
chr6 170805979 277622491 1.6254 6.0315
chr7 159345973 254092798 1.5946 5.6512
chr8 145138636 198628263 1.3685 3.9333
chr9 138394717 102172796 0.7383 3.0152
chrIS 10567884 0 0 0
chrM 16569 44951483 2,712.9871 2,544.2104
chrX 156040895 122958771 0.788 3.5245
chrY 57227415 7936616 0.1387 0.9356
ERCC-00002 1061 0 0 0
ERCC-00003 1023 0 0 0
ERCC-00004 523 0 0 0
ERCC-00009 984 0 0 0
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 0 0 0
ERCC-00022 751 0 0 0
ERCC-00024 536 0 0 0
ERCC-00025 1994 0 0 0
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 0 0 0
ERCC-00039 740 0 0 0
ERCC-00040 744 0 0 0
ERCC-00041 1122 0 0 0
ERCC-00042 1023 0 0 0
ERCC-00043 1023 0 0 0
ERCC-00044 1156 0 0 0
ERCC-00046 522 0 0 0
ERCC-00048 992 0 0 0
ERCC-00051 274 0 0 0
ERCC-00053 1023 0 0 0
ERCC-00054 274 0 0 0
ERCC-00057 1021 0 0 0
ERCC-00058 1136 0 0 0
ERCC-00059 525 0 0 0
ERCC-00060 523 0 0 0
ERCC-00061 1136 0 0 0
ERCC-00062 1023 0 0 0
ERCC-00067 644 0 0 0
ERCC-00069 1137 0 0 0
ERCC-00071 642 0 0 0
ERCC-00073 603 0 0 0
ERCC-00074 522 0 0 0
ERCC-00075 1023 0 0 0
ERCC-00076 642 0 0 0
ERCC-00077 273 0 0 0
ERCC-00078 993 0 0 0
ERCC-00079 644 0 0 0
ERCC-00081 534 0 0 0
ERCC-00083 1022 0 0 0
ERCC-00084 994 0 0 0
ERCC-00085 844 0 0 0
ERCC-00086 1020 0 0 0
ERCC-00092 1124 0 0 0
ERCC-00095 521 0 0 0
ERCC-00096 1107 0 0 0
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 0 0 0
ERCC-00109 536 0 0 0
ERCC-00111 994 0 0 0
ERCC-00112 1136 0 0 0
ERCC-00113 840 0 0 0
ERCC-00116 1991 0 0 0
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 0 0 0
ERCC-00131 771 0 0 0
ERCC-00134 274 0 0 0
ERCC-00136 1033 0 0 0
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 0 0 0
ERCC-00145 1042 0 0 0
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 0 0 0
ERCC-00163 543 0 0 0
ERCC-00164 1022 0 0 0
ERCC-00165 872 0 0 0
ERCC-00168 1024 0 0 0
ERCC-00170 1023 0 0 0
ERCC-00171 505 0 0 0
GL000008.2 209709 1442 0.0069 0.0826
GL000009.2 201709 860 0.0043 0.0416
GL000194.1 191469 334435 1.7467 1.7721
GL000195.1 182896 50166 0.2743 0.3388
GL000205.2 185591 48820 0.2631 0.2942
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 15458 0.0959 0.239
GL000219.1 179198 118409 0.6608 0.691
GL000220.1 161802 0 0 0
GL000221.1 155397 0 0 0
GL000224.1 179693 0 0 0
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 1613 0.0092 0.0829
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 1581 0.0375 0.1899
KI270712.1 176043 0 0 0
KI270713.1 40745 0 0 0
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 5685 0.0567 0.4738
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 0 0 0
KI270728.1 1872759 27594 0.0147 0.0476
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 0 0 0
KI270734.1 165050 222061 1.3454 3.2051
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 17500 0.1112 0.1236
KI270742.1 186739 56471 0.3024 0.3302
KI270743.1 210658 0 0 0
KI270744.1 168472 872 0.0052 0.0854
KI270745.1 41891 653 0.0156 0.1239
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 2855 0.0189 0.0702
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 110723048 479.2811 524.1144

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 

Contents

  • Input data & parameters
  • Summary
  • 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
    • 2022/11/15 19:21:15
    Generated by QualiMap v.2.2.2-dev