BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6068958.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,192,268
number of mapped reads = 2,631,619 (82.44%)
number of supplementary alignments = 14,509 (0.45%)
number of secondary alignments = 0
number of mapped bases = 167,118,384 bp
number of sequenced bases = 167,041,870 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 122,563
duplication rate = 2.82%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 43.7713
>>>>>>> ACTG content
number of A's = 43,572,959 bp (26.09%)
number of C's = 28,281,728 bp (16.93%)
number of T's = 55,567,940 bp (33.27%)
number of G's = 39,234,966 bp (23.49%)
number of N's = 384,277 bp (0.23%)
GC percentage = 40.42%
>>>>>>> Mismatches and indels
general error rate = 0.0097
number of mismatches = 1,592,394
number of insertions = 15,872
mapped reads with insertion percentage = 0.6%
number of deletions = 46,723
mapped reads with deletion percentage = 1.76%
homopolymer indels = 47.61%
>>>>>>> Coverage
mean coverageData = 0.054X
std coverageData = 0.6517X
There is a 4.66% of reference with a coverageData >= 1X
There is a 0.46% of reference with a coverageData >= 2X
There is a 0.07% 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 0.01% 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% 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 19096510 0.07661569677694002 1.4481267440992032
chr2 243199373 11760936 0.04835923651826191 0.5829212785908258
chr3 198022430 9859694 0.04979079390147874 0.2861647713281192
chr4 191154276 6481342 0.03390634065648628 0.26263112236994984
chr5 180915260 9151633 0.05058519109996581 0.25621852467597006
chr6 171115067 11218786 0.06556281803051277 0.3821103010104938
chr7 159138663 11101889 0.06976236189693262 0.8995479351660312
chr8 146364022 10335046 0.07061192948086654 0.7430081289033679
chr9 141213431 8292699 0.058724576984465454 0.6342734842596893
chr10 135534747 10740483 0.07924523590987335 0.9255705217732677
chr11 135006516 5511862 0.04082663684173585 0.47604682971157797
chr12 133851895 9143454 0.06831023199185936 0.30625705503455863
chr13 115169878 3563855 0.03094433251027669 0.19261475941597553
chr14 107349540 4627290 0.04310488894502948 0.28523302220879543
chr15 102531392 3310178 0.03228453194120295 0.20013759534820544
chr16 90354753 3029775 0.033531993607464124 0.2974015103928648
chr17 81195210 4012026 0.04941210201931863 0.29497807929211023
chr18 78077248 3781780 0.04843638956127142 1.0076414148972035
chr19 59128983 3080475 0.05209754749206493 1.0055531888423017
chr20 63025520 2261806 0.035887145397610364 0.24338651773527692
chr21 48129895 2253987 0.04683133009120423 0.2880001822015402
chr22 51304566 1272376 0.024800443687604725 0.17719168969939558
chrMT 16571 234608 14.157745458934283 8.77830492123239
chrX 155270560 12477758 0.08036138982174083 0.431160381593346
chrY 59373566 518136 0.008726711816500966 0.2079193260314154