BamQC report ----------------------------------- >>>>>>> Input bam file = SRR053633.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 15,100,758 number of mapped reads = 12,241,969 (81.07%) number of supplementary alignments = 357 (0%) number of secondary alignments = 0 number of mapped bases = 579,956,379 bp number of sequenced bases = 579,842,102 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,836,378 duplication rate = 16.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0301 >>>>>>> ACTG content number of A's = 170,443,919 bp (29.39%) number of C's = 109,876,529 bp (18.95%) number of T's = 172,893,795 bp (29.82%) number of G's = 126,622,215 bp (21.84%) number of N's = 5,644 bp (0%) GC percentage = 40.79% >>>>>>> Mismatches and indels general error rate = 0.0046 number of mismatches = 2,631,742 number of insertions = 23,120 mapped reads with insertion percentage = 0.19% number of deletions = 76,685 mapped reads with deletion percentage = 0.62% homopolymer indels = 48.57% >>>>>>> Coverage mean coverageData = 0.1873X std coverageData = 1.2207X There is a 7.57% of reference with a coverageData >= 1X There is a 3.5% of reference with a coverageData >= 2X There is a 2.09% of reference with a coverageData >= 3X There is a 1.37% of reference with a coverageData >= 4X There is a 0.94% of reference with a coverageData >= 5X There is a 0.67% of reference with a coverageData >= 6X There is a 0.5% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.29% of reference with a coverageData >= 9X There is a 0.22% of reference with a coverageData >= 10X There is a 0.18% of reference with a coverageData >= 11X There is a 0.14% of reference with a coverageData >= 12X There is a 0.12% of reference with a coverageData >= 13X There is a 0.09% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% 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 46195579 0.18533786922841808 1.2490821445526845 chr2 243199373 49509141 0.20357429539919086 1.5298083912711815 chr3 198022430 39836769 0.20117301358235024 1.0822676507707476 chr4 191154276 37776120 0.1976211089308826 1.1201428497753319 chr5 180915260 35998055 0.19897743838745277 1.0871143665477614 chr6 171115067 34255880 0.20019207309196216 1.2039367831688472 chr7 159138663 31443845 0.19758771631756136 1.6338073365938706 chr8 146364022 29480189 0.20141690968290007 1.2155995011640044 chr9 141213431 23837652 0.16880584113843958 1.2555455011439483 chr10 135534747 26683092 0.1968727030567298 1.2131601493646675 chr11 135006516 26495064 0.196250260987403 1.3369479172816272 chr12 133851895 26389808 0.1971567754046366 1.0846365686109776 chr13 115169878 18773833 0.16300992348016555 0.9744717268949225 chr14 107349540 17473720 0.16277405566898565 1.1957947144868124 chr15 102531392 16673646 0.16261991254346767 0.987277016960462 chr16 90354753 16469352 0.18227432927629164 1.0785277176519112 chr17 81195210 14740490 0.18154383737661373 1.0428033900218299 chr18 78077248 15556086 0.1992396811936814 1.3903537509603898 chr19 59128983 10119758 0.17114716821698084 1.211673622472225 chr20 63025520 12298699 0.19513839790611803 1.1233888907620857 chr21 48129895 7413297 0.15402686833204185 1.0641610024407482 chr22 51304566 6229813 0.121428042096682 0.825452628105135 chrMT 16571 91978 5.550540100175004 9.591526279227617 chrX 155270560 34786748 0.22403956036482384 1.3418255390913696 chrY 59373566 1427765 0.02404714919767494 0.45154891173572925