BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524656.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 = 3,270,729
number of mapped reads = 3,025,529 (92.5%)
number of supplementary alignments = 11,350 (0.35%)
number of secondary alignments = 0
number of mapped bases = 176,521,963 bp
number of sequenced bases = 176,464,412 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 244,193
duplication rate = 6.07%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.999
>>>>>>> ACTG content
number of A's = 43,541,861 bp (24.67%)
number of C's = 36,034,993 bp (20.42%)
number of T's = 53,814,931 bp (30.5%)
number of G's = 43,071,113 bp (24.41%)
number of N's = 1,514 bp (0%)
GC percentage = 44.83%
>>>>>>> Mismatches and indels
general error rate = 0.0052
number of mismatches = 897,437
number of insertions = 12,042
mapped reads with insertion percentage = 0.4%
number of deletions = 34,269
mapped reads with deletion percentage = 1.12%
homopolymer indels = 42.91%
>>>>>>> Coverage
mean coverageData = 0.057X
std coverageData = 0.4827X
There is a 4.58% of reference with a coverageData >= 1X
There is a 0.77% of reference with a coverageData >= 2X
There is a 0.17% of reference with a coverageData >= 3X
There is a 0.05% of reference with a coverageData >= 4X
There is a 0.02% of reference with a coverageData >= 5X
There is a 0.01% of reference with a coverageData >= 6X
There is a 0.01% of reference with a coverageData >= 7X
There is a 0.01% 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 17464089 0.07006638109840456 0.9371119439362564
chr2 243199373 15659250 0.0643885294885197 0.5948774342618605
chr3 198022430 11152143 0.056317574731306955 0.28700841577379743
chr4 191154276 8046967 0.04209671459298143 0.3356675539218711
chr5 180915260 10949493 0.0605227718214594 0.2960993432708521
chr6 171115067 11215119 0.06554138800646936 0.3419931808092501
chr7 159138663 10787319 0.06778565809617239 0.6312063559787389
chr8 146364022 15521910 0.10605003735139228 0.6221708570693486
chr9 141213431 6454942 0.04571053868098425 0.3762536851659593
chr10 135534747 7816647 0.05767264242578326 0.5309092001918466
chr11 135006516 9096579 0.06737881451588604 0.4023337714779016
chr12 133851895 5924213 0.04425946304308953 0.2699649058812616
chr13 115169878 4247657 0.03688166622873387 0.233952719464626
chr14 107349540 3258787 0.030356785879101112 0.22349132248729936
chr15 102531392 4490671 0.04379801066194439 0.2545254579842158
chr16 90354753 5265439 0.05827517452236298 0.3208356769879936
chr17 81195210 3991666 0.04916134831106416 0.2845450594529524
chr18 78077248 4625300 0.05924004903451515 0.6706113529170917
chr19 59128983 3676735 0.06218160390142344 0.6536169715137403
chr20 63025520 3378063 0.05359833603911558 0.29428965914529853
chr21 48129895 1588147 0.032997100866311885 0.287413538113467
chr22 51304566 3294755 0.0642195277511947 0.31113299801250327
chrMT 16571 175963 10.618731518918592 6.627201869360208
chrX 155270560 7942153 0.05115041125632573 0.31368030988696083
chrY 59373566 497956 0.00838682992360607 0.29084344617765534