BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524652.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 = 4,196,333
number of mapped reads = 3,867,882 (92.17%)
number of supplementary alignments = 15,310 (0.36%)
number of secondary alignments = 0
number of mapped bases = 224,963,376 bp
number of sequenced bases = 224,891,170 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 445,274
duplication rate = 8.4%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.7772
>>>>>>> ACTG content
number of A's = 56,971,585 bp (25.33%)
number of C's = 41,915,667 bp (18.64%)
number of T's = 72,746,570 bp (32.35%)
number of G's = 53,255,534 bp (23.68%)
number of N's = 1,814 bp (0%)
GC percentage = 42.32%
>>>>>>> Mismatches and indels
general error rate = 0.0052
number of mismatches = 1,150,002
number of insertions = 14,381
mapped reads with insertion percentage = 0.37%
number of deletions = 43,138
mapped reads with deletion percentage = 1.11%
homopolymer indels = 43.51%
>>>>>>> Coverage
mean coverageData = 0.0727X
std coverageData = 0.6023X
There is a 5.31% of reference with a coverageData >= 1X
There is a 1.26% of reference with a coverageData >= 2X
There is a 0.36% of reference with a coverageData >= 3X
There is a 0.12% of reference with a coverageData >= 4X
There is a 0.05% of reference with a coverageData >= 5X
There is a 0.02% 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 0.01% of reference with a coverageData >= 9X
There is a 0.01% 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 24540481 0.09845705058443967 1.1455014345522052
chr2 243199373 18553261 0.07628827645044957 0.8025578631677746
chr3 198022430 14230455 0.07186284402226556 0.3539529080682218
chr4 191154276 10359357 0.05419369745095318 0.45376248614521714
chr5 180915260 13589547 0.07511553751739904 0.3611590441817075
chr6 171115067 14658633 0.0856653552314011 0.4193607246180667
chr7 159138663 13335937 0.08380073546300938 0.7008491582867966
chr8 146364022 19958556 0.13636244568354372 0.832472741614138
chr9 141213431 7933757 0.05618273661235524 0.47348832547995495
chr10 135534747 9788218 0.07221925164327049 0.6698335913822949
chr11 135006516 11366554 0.08419263259856287 0.5010207530335338
chr12 133851895 7454722 0.05569380993821567 0.33037866918765235
chr13 115169878 5578119 0.04843383614594087 0.2916032202938739
chr14 107349540 3988383 0.0371532379179268 0.2734512436462762
chr15 102531392 5795828 0.05652735115504918 0.31298944797754424
chr16 90354753 6806505 0.07533090151881662 0.39270680934018215
chr17 81195210 4865968 0.059929249521000066 0.34862759034387886
chr18 78077248 6094170 0.07805308404312611 0.8174891951749663
chr19 59128983 4511981 0.07630743454525507 0.8000753706436315
chr20 63025520 4363253 0.06922994050663922 0.36718956734234626
chr21 48129895 2138209 0.0444257981447913 0.3924420489511216
chr22 51304566 4196191 0.08178981574466491 0.38248626569633526
chrMT 16571 24247 1.4632188763502505 1.8370361661122576
chrX 155270560 10163552 0.06545704478685464 0.40097559697357515
chrY 59373566 667492 0.011242242044212066 0.39326859179630846