BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR8617705.sorted.bam
outfile = /mainsd2/zhouyj/SRP186739/SRP186739.result/quality.files/genome_results.txt
>>>>>>> Reference
number of bases = 3,095,693,983 bp
number of contigs = 25
>>>>>>> Globals
number of windows = 424
number of reads = 32,640,674
number of mapped reads = 31,830,275 (97.52%)
number of supplementary alignments = 2,380,856 (7.29%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 16,097,895
number of mapped paired reads (second in pair) = 15,732,380
number of mapped paired reads (both in pair) = 31,317,238
number of mapped paired reads (singletons) = 513,037
number of mapped bases = 4,228,675,815 bp
number of sequenced bases = 4,225,670,601 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 9,538,444
duplication rate = 21.97%
>>>>>>> Insert size
mean insert size = 565,869.4231
std insert size = 7,414,228.5866
median insert size = 252
>>>>>>> Mapping quality
mean mapping quality = 52.385
>>>>>>> ACTG content
number of A's = 1,241,418,847 bp (29.38%)
number of C's = 788,315,424 bp (18.66%)
number of T's = 1,288,594,172 bp (30.49%)
number of G's = 907,184,040 bp (21.47%)
number of N's = 158,118 bp (0%)
GC percentage = 40.12%
>>>>>>> Mismatches and indels
general error rate = 0.0121
number of mismatches = 49,185,964
number of insertions = 739,705
mapped reads with insertion percentage = 2.2%
number of deletions = 1,521,834
mapped reads with deletion percentage = 4.6%
homopolymer indels = 46.5%
>>>>>>> Coverage
mean coverageData = 1.366X
std coverageData = 15.9194X
There is a 39.1% of reference with a coverageData >= 1X
There is a 25.6% of reference with a coverageData >= 2X
There is a 17% of reference with a coverageData >= 3X
There is a 11.96% of reference with a coverageData >= 4X
There is a 8.49% of reference with a coverageData >= 5X
There is a 6.2% of reference with a coverageData >= 6X
There is a 4.57% of reference with a coverageData >= 7X
There is a 3.44% of reference with a coverageData >= 8X
There is a 2.61% of reference with a coverageData >= 9X
There is a 2.01% of reference with a coverageData >= 10X
There is a 1.56% of reference with a coverageData >= 11X
There is a 1.22% of reference with a coverageData >= 12X
There is a 0.97% of reference with a coverageData >= 13X
There is a 0.78% of reference with a coverageData >= 14X
There is a 0.62% of reference with a coverageData >= 15X
There is a 0.51% of reference with a coverageData >= 16X
There is a 0.42% of reference with a coverageData >= 17X
There is a 0.34% of reference with a coverageData >= 18X
There is a 0.28% of reference with a coverageData >= 19X
There is a 0.24% of reference with a coverageData >= 20X
There is a 0.2% of reference with a coverageData >= 21X
There is a 0.17% of reference with a coverageData >= 22X
There is a 0.15% of reference with a coverageData >= 23X
There is a 0.13% of reference with a coverageData >= 24X
There is a 0.11% of reference with a coverageData >= 25X
There is a 0.1% of reference with a coverageData >= 26X
There is a 0.08% of reference with a coverageData >= 27X
There is a 0.07% of reference with a coverageData >= 28X
There is a 0.07% of reference with a coverageData >= 29X
There is a 0.06% of reference with a coverageData >= 30X
There is a 0.05% of reference with a coverageData >= 31X
There is a 0.05% of reference with a coverageData >= 32X
There is a 0.04% of reference with a coverageData >= 33X
There is a 0.04% of reference with a coverageData >= 34X
There is a 0.04% of reference with a coverageData >= 35X
There is a 0.04% of reference with a coverageData >= 36X
There is a 0.03% of reference with a coverageData >= 37X
There is a 0.03% of reference with a coverageData >= 38X
There is a 0.03% of reference with a coverageData >= 39X
There is a 0.03% of reference with a coverageData >= 40X
There is a 0.03% of reference with a coverageData >= 41X
There is a 0.02% of reference with a coverageData >= 42X
There is a 0.02% of reference with a coverageData >= 43X
There is a 0.02% of reference with a coverageData >= 44X
There is a 0.02% of reference with a coverageData >= 45X
There is a 0.02% of reference with a coverageData >= 46X
There is a 0.02% of reference with a coverageData >= 47X
There is a 0.02% of reference with a coverageData >= 48X
There is a 0.02% of reference with a coverageData >= 49X
There is a 0.02% of reference with a coverageData >= 50X
There is a 0.02% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 365842278 1.4677687723795079 15.816610329476395
chr2 243199373 455669454 1.873645677532236 16.511804960078802
chr3 198022430 245092516 1.2377007796541029 2.941750373274514
chr4 191154276 234041896 1.224361290249139 14.713240808760597
chr5 180915260 173441092 0.9586869123146383 2.345296871738378
chr6 171115067 272651313 1.5933799272041895 6.6569985294935075
chr7 159138663 250724680 1.575510785835872 15.861888887663811
chr8 146364022 237211316 1.6206941621213442 5.251217002279975
chr9 141213431 206864252 1.4649049352819705 28.859411579347046
chr10 135534747 190575159 1.40609816462785 42.263243651949004
chr11 135006516 154059683 1.1411277586038884 6.044533504025619
chr12 133851895 203056900 1.5170267107537028 7.145115001239036
chr13 115169878 118879118 1.0322066851542553 2.3678937275556544
chr14 107349540 134546588 1.2533503916272022 2.9981635128122424
chr15 102531392 137211723 1.3382411018081175 4.005986576001368
chr16 90354753 158604792 1.7553563784298098 34.12438453653969
chr17 81195210 70086052 0.8631796383062499 7.2251378847488255
chr18 78077248 145632458 1.8652355421133695 22.36406847138682
chr19 59128983 43400001 0.7339886261869243 8.154450724299096
chr20 63025520 90339353 1.4333773525390985 5.17710894564383
chr21 48129895 55993344 1.163379724805134 7.450438380220511
chr22 51304566 35155241 0.6852263597746836 2.0992511561118037
chrMT 16571 203651 12.28960231730131 8.15176119334015
chrX 155270560 233508715 1.503882738620895 5.272272121287389
chrY 59373566 15884240 0.2675305033893366 19.992934093195544