BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013364.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 = 2,299,926 number of mapped reads = 1,890,580 (82.2%) number of supplementary alignments = 25,766 (1.12%) number of secondary alignments = 0 number of mapped bases = 125,308,410 bp number of sequenced bases = 125,259,513 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 218,183 duplication rate = 8.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.651 >>>>>>> ACTG content number of A's = 34,410,959 bp (27.47%) number of C's = 23,693,117 bp (18.92%) number of T's = 39,008,233 bp (31.14%) number of G's = 28,132,426 bp (22.46%) number of N's = 14,778 bp (0.01%) GC percentage = 41.37% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 930,229 number of insertions = 8,804 mapped reads with insertion percentage = 0.46% number of deletions = 28,502 mapped reads with deletion percentage = 1.49% homopolymer indels = 46.88% >>>>>>> Coverage mean coverageData = 0.0405X std coverageData = 0.4379X There is a 2.17% of reference with a coverageData >= 1X There is a 0.9% of reference with a coverageData >= 2X There is a 0.43% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.11% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% 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 0.01% 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 9968260 0.03999291941583568 0.6871465272258817 chr2 243199373 11384620 0.04681188055530061 0.5183184715503766 chr3 198022430 8429365 0.0425677283123937 0.35267572505074224 chr4 191154276 8019722 0.041954185738434645 0.3614434402250706 chr5 180915260 8061233 0.044558059944749824 0.36004729994983636 chr6 171115067 7127774 0.041654859066267966 0.3867630052393032 chr7 159138663 7579517 0.04762838179682331 0.6166254120366444 chr8 146364022 6634324 0.04532756007483861 0.4530175909677578 chr9 141213431 5715513 0.040474287463492055 0.4224449351505015 chr10 135534747 5183812 0.03824710721598204 0.4261466292130847 chr11 135006516 5529604 0.04095805272095163 0.3680684014237204 chr12 133851895 6228590 0.04653344653805611 0.3762885048694676 chr13 115169878 3582312 0.031104591427977373 0.3085525141812719 chr14 107349540 3602671 0.03356019038367561 0.3364062241024888 chr15 102531392 3682194 0.035912845111865835 0.35068007853916283 chr16 90354753 3342395 0.03699191120582223 0.34984943824027254 chr17 81195210 3015148 0.03713455510491321 0.33492087137277454 chr18 78077248 2822935 0.03615566726942015 0.5294792618043497 chr19 59128983 2192397 0.03707821255779082 0.4987935031175419 chr20 63025520 2796421 0.04436966168625027 0.3752537031070474 chr21 48129895 1515472 0.03148712458234118 0.310529608025229 chr22 51304566 1380543 0.026908774552346863 0.27459899072408456 chrMT 16571 22194 1.3393277412346871 2.3056838951385585 chrX 155270560 7176975 0.04622238111332889 0.3809001407652082 chrY 59373566 314419 0.005295605791978201 0.16923455300996756