BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524321.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,626,706
number of mapped reads = 1,478,442 (90.89%)
number of supplementary alignments = 7,980 (0.49%)
number of secondary alignments = 0
number of mapped bases = 85,401,545 bp
number of sequenced bases = 85,379,150 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 45,189
duplication rate = 2.16%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 43.8694
>>>>>>> ACTG content
number of A's = 21,304,018 bp (24.95%)
number of C's = 16,888,202 bp (19.78%)
number of T's = 26,580,132 bp (31.13%)
number of G's = 20,594,954 bp (24.12%)
number of N's = 11,844 bp (0.01%)
GC percentage = 43.9%
>>>>>>> Mismatches and indels
general error rate = 0.0052
number of mismatches = 438,135
number of insertions = 4,663
mapped reads with insertion percentage = 0.31%
number of deletions = 13,761
mapped reads with deletion percentage = 0.92%
homopolymer indels = 43.9%
>>>>>>> Coverage
mean coverageData = 0.0276X
std coverageData = 0.2616X
There is a 2.51% of reference with a coverageData >= 1X
There is a 0.18% of reference with a coverageData >= 2X
There is a 0.02% of reference with a coverageData >= 3X
There is a 0.01% of reference with a coverageData >= 4X
There is a 0% of reference with a coverageData >= 5X
There is a 0% of reference with a coverageData >= 6X
There is a 0% of reference with a coverageData >= 7X
There is a 0% of reference with a coverageData >= 8X
There is a 0% of reference with a coverageData >= 9X
There is a 0% of reference with a coverageData >= 10X
There is a 0% of reference with a coverageData >= 11X
There is a 0% of reference with a coverageData >= 12X
There is a 0% of reference with a coverageData >= 13X
There is a 0% of reference with a coverageData >= 14X
There is a 0% of reference with a coverageData >= 15X
There is a 0% of reference with a coverageData >= 16X
There is a 0% of reference with a coverageData >= 17X
There is a 0% of reference with a coverageData >= 18X
There is a 0% of reference with a coverageData >= 19X
There is a 0% of reference with a coverageData >= 20X
There is a 0% of reference with a coverageData >= 21X
There is a 0% of reference with a coverageData >= 22X
There is a 0% of reference with a coverageData >= 23X
There is a 0% of reference with a coverageData >= 24X
There is a 0% of reference with a coverageData >= 25X
There is a 0% of reference with a coverageData >= 26X
There is a 0% of reference with a coverageData >= 27X
There is a 0% of reference with a coverageData >= 28X
There is a 0% of reference with a coverageData >= 29X
There is a 0% of reference with a coverageData >= 30X
There is a 0% of reference with a coverageData >= 31X
There is a 0% of reference with a coverageData >= 32X
There is a 0% of reference with a coverageData >= 33X
There is a 0% of reference with a coverageData >= 34X
There is a 0% of reference with a coverageData >= 35X
There is a 0% of reference with a coverageData >= 36X
There is a 0% of reference with a coverageData >= 37X
There is a 0% of reference with a coverageData >= 38X
There is a 0% of reference with a coverageData >= 39X
There is a 0% of reference with a coverageData >= 40X
There is a 0% of reference with a coverageData >= 41X
There is a 0% of reference with a coverageData >= 42X
There is a 0% of reference with a coverageData >= 43X
There is a 0% of reference with a coverageData >= 44X
There is a 0% of reference with a coverageData >= 45X
There is a 0% of reference with a coverageData >= 46X
There is a 0% of reference with a coverageData >= 47X
There is a 0% of reference with a coverageData >= 48X
There is a 0% of reference with a coverageData >= 49X
There is a 0% of reference with a coverageData >= 50X
There is a 0% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 7240032 0.029047197439078798 0.48345366797330136
chr2 243199373 5572664 0.022913973548772264 0.3514861059925931
chr3 198022430 5962582 0.030110639486648053 0.18688012157678507
chr4 191154276 4415160 0.023097364560131523 0.18336572938733975
chr5 180915260 5015565 0.027723283265325433 0.1798002794674213
chr6 171115067 5377644 0.03142706305342475 0.20613956829929958
chr7 159138663 3883288 0.024401914197306033 0.30498711040757875
chr8 146364022 8813716 0.06021777674297581 0.32706330000373884
chr9 141213431 3558743 0.025201165178119638 0.20406057237852898
chr10 135534747 4366552 0.032217214379719174 0.256434017232774
chr11 135006516 4086942 0.03027218330706349 0.219947246862614
chr12 133851895 3415946 0.025520340970891744 0.17540156046416708
chr13 115169878 2146454 0.018637286391846312 0.1464806527436991
chr14 107349540 1781134 0.01659191087358176 0.14395193770440515
chr15 102531392 2633747 0.02568722562549429 0.1764721872643102
chr16 90354753 2736240 0.030283298987049415 0.19654433428631657
chr17 81195210 2668729 0.032868059581347225 0.20856334198031246
chr18 78077248 1974933 0.025294603108962036 0.32817123466103804
chr19 59128983 1562009 0.026416977271535347 0.32389383784194115
chr20 63025520 1951129 0.03095776123703541 0.19313397845790994
chr21 48129895 1217770 0.02530173814008944 0.18292973985845684
chr22 51304566 654240 0.012752081364453995 0.12248018344174777
chrMT 16571 11827 0.7137167340534669 0.9709926573898336
chrX 155270560 4105750 0.026442552921815958 0.19421044506983887
chrY 59373566 248749 0.004189558026546696 0.12207890994722673