BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081249.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 = 4,526,553 number of mapped reads = 3,904,857 (86.27%) number of supplementary alignments = 38,545 (0.85%) number of secondary alignments = 0 number of mapped bases = 261,737,771 bp number of sequenced bases = 261,626,603 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 227,042 duplication rate = 4.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2607 >>>>>>> ACTG content number of A's = 71,571,981 bp (27.36%) number of C's = 47,865,959 bp (18.3%) number of T's = 83,662,862 bp (31.98%) number of G's = 58,455,946 bp (22.34%) number of N's = 69,855 bp (0.03%) GC percentage = 40.64% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 2,213,267 number of insertions = 21,578 mapped reads with insertion percentage = 0.55% number of deletions = 65,147 mapped reads with deletion percentage = 1.65% homopolymer indels = 49.47% >>>>>>> Coverage mean coverageData = 0.0845X std coverageData = 0.6853X There is a 6.45% of reference with a coverageData >= 1X There is a 1.36% of reference with a coverageData >= 2X There is a 0.33% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.03% 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 26511124 0.1063633217587851 1.2795317054890838 chr2 243199373 16329227 0.06714337622901684 0.7194018712727253 chr3 198022430 16407023 0.08285436654827436 0.373636713569219 chr4 191154276 11073551 0.05792991520629128 0.3968216505800965 chr5 180915260 18930069 0.10463500425558353 0.4051993491533198 chr6 171115067 17209552 0.10057297876638766 0.512435183397376 chr7 159138663 16280285 0.10230251211800115 1.0329281127740102 chr8 146364022 15073287 0.10298491934035538 0.8323509046189723 chr9 141213431 12534418 0.0887622226245604 0.6509720377986996 chr10 135534747 7873139 0.058089450670535434 0.8121478062789402 chr11 135006516 13464009 0.09972858643356147 0.7375057241141154 chr12 133851895 7467101 0.055786292752896774 0.3049397913362659 chr13 115169878 8083728 0.07018960287515456 0.3257435272989185 chr14 107349540 9524909 0.08872799082324899 0.4140606452915993 chr15 102531392 8697121 0.08482398249308856 0.36334372242527824 chr16 90354753 8122672 0.08989756189140377 0.4268473811437345 chr17 81195210 4075879 0.05019851540503436 0.39636458401388647 chr18 78077248 8046586 0.10305929327836964 0.9963214489484438 chr19 59128983 6451233 0.10910441331284186 1.0245068190458193 chr20 63025520 6017136 0.09547142173519552 0.40682636106553327 chr21 48129895 3796062 0.07887118806305311 0.4306385143116075 chr22 51304566 1802599 0.035135254823128216 0.22745553871986637 chrMT 16571 246590 14.880815883169392 7.684806843895923 chrX 155270560 16967269 0.10927550592977832 0.46318704138172384 chrY 59373566 753202 0.012685813750853368 0.34139729377925593