BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524525.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 = 1,911,501
number of mapped reads = 1,752,485 (91.68%)
number of supplementary alignments = 7,621 (0.4%)
number of secondary alignments = 0
number of mapped bases = 101,946,456 bp
number of sequenced bases = 101,915,452 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 127,150
duplication rate = 5.63%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.6797
>>>>>>> ACTG content
number of A's = 24,926,602 bp (24.46%)
number of C's = 20,118,318 bp (19.74%)
number of T's = 31,798,859 bp (31.2%)
number of G's = 25,070,119 bp (24.6%)
number of N's = 1,554 bp (0%)
GC percentage = 44.34%
>>>>>>> Mismatches and indels
general error rate = 0.0053
number of mismatches = 525,619
number of insertions = 6,475
mapped reads with insertion percentage = 0.37%
number of deletions = 18,484
mapped reads with deletion percentage = 1.05%
homopolymer indels = 43.24%
>>>>>>> Coverage
mean coverageData = 0.0329X
std coverageData = 0.3254X
There is a 2.73% of reference with a coverageData >= 1X
There is a 0.4% of reference with a coverageData >= 2X
There is a 0.08% of reference with a coverageData >= 3X
There is a 0.02% of reference with a coverageData >= 4X
There is a 0.01% of reference with a coverageData >= 5X
There is a 0.01% 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 10094471 0.04049928124351594 0.6365839583339501
chr2 243199373 7915298 0.03254653950115242 0.3934574220957008
chr3 198022430 5502715 0.027788341957019718 0.1952678642004709
chr4 191154276 5658371 0.029601069452403983 0.25027709439013685
chr5 180915260 5533546 0.030586397189490813 0.2054779140930358
chr6 171115067 4329077 0.025299215761052766 0.23224751929521473
chr7 159138663 5123721 0.03219658192051042 0.3709165010075165
chr8 146364022 9292723 0.06349048675363676 0.3576326278059037
chr9 141213431 4342947 0.030754489634912986 0.25022501383686735
chr10 135534747 5420086 0.039990379736349085 0.3608696142112707
chr11 135006516 3531024 0.026154470944202427 0.2534685974912654
chr12 133851895 4784793 0.0357469201313885 0.22310122516268588
chr13 115169878 2217206 0.019251613690169925 0.16272777498042126
chr14 107349540 2410505 0.02245473059316323 0.18013190672776494
chr15 102531392 2697958 0.026313482606380688 0.1914795614979405
chr16 90354753 3182477 0.035222020915712096 0.23206106686786152
chr17 81195210 3622873 0.04461929466036235 0.26189034190224864
chr18 78077248 2389343 0.030602295306309975 0.4659835252786142
chr19 59128983 2213970 0.037443059015576166 0.4364432625557828
chr20 63025520 2955462 0.046893099810997194 0.2584092716510747
chr21 48129895 1414870 0.029396906018598214 0.23283035480681258
chr22 51304566 855090 0.01666693759771791 0.15174615193382288
chrMT 16571 58705 3.5426347233118096 2.7381570598716154
chrX 155270560 6006932 0.03868687019612733 0.24883226999011787
chrY 59373566 392293 0.00660719957430214 0.22750771185563634