BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082425.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,062,896 number of mapped reads = 2,761,860 (90.17%) number of supplementary alignments = 24,941 (0.81%) number of secondary alignments = 0 number of mapped bases = 185,843,726 bp number of sequenced bases = 185,775,594 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 112,765 duplication rate = 3.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1185 >>>>>>> ACTG content number of A's = 52,196,887 bp (28.1%) number of C's = 34,699,765 bp (18.68%) number of T's = 58,060,056 bp (31.25%) number of G's = 40,814,951 bp (21.97%) number of N's = 3,935 bp (0%) GC percentage = 40.65% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,540,326 number of insertions = 14,943 mapped reads with insertion percentage = 0.54% number of deletions = 42,376 mapped reads with deletion percentage = 1.52% homopolymer indels = 47.51% >>>>>>> Coverage mean coverageData = 0.06X std coverageData = 0.4837X There is a 5.15% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.09% 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 14584335 0.058512732852930384 0.8026861981713888 chr2 243199373 15988692 0.0657431464677337 0.6189107076940311 chr3 198022430 12586400 0.0635604764571367 0.2830972595130956 chr4 191154276 12545785 0.06563172565389017 0.30291450474302045 chr5 180915260 11475170 0.06342842499853246 0.2849356269267778 chr6 171115067 10963265 0.06406954800771576 0.34717223075139125 chr7 159138663 10225835 0.064257389167584 0.6233221386488786 chr8 146364022 9532766 0.06513052777410011 0.8544502584171968 chr9 141213431 7991654 0.05659273302409882 0.4464961876250742 chr10 135534747 8477887 0.06255139134173468 0.4107161771662734 chr11 135006516 8383078 0.06209387700961041 0.4041189893837543 chr12 133851895 8457625 0.06318644199994329 0.28863090987136714 chr13 115169878 6193495 0.053777038819125954 0.26027921711565355 chr14 107349540 5717977 0.05326503495031278 0.28237311294397044 chr15 102531392 5317684 0.0518639598689931 0.2710704530864607 chr16 90354753 5062010 0.05602372683150382 0.3027409178928166 chr17 81195210 4509583 0.055540012766762965 0.2937455018442758 chr18 78077248 5098811 0.06530469670242475 0.8524381699713409 chr19 59128983 3328347 0.05628960335746008 0.6091183637385895 chr20 63025520 3669227 0.0582181154554536 0.28005673422839206 chr21 48129895 2460719 0.05112662306867696 0.2749055401374914 chr22 51304566 1981585 0.03862395015679501 0.21872675916242795 chrMT 16571 107597 6.493090338543238 3.966713224284733 chrX 155270560 10743991 0.06919528724569551 0.33612089542597146 chrY 59373566 440208 0.007414208538527061 0.14874104282486927