BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013206.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 = 2,418,627 number of mapped reads = 2,171,142 (89.77%) number of supplementary alignments = 16,745 (0.69%) number of secondary alignments = 0 number of mapped bases = 147,887,756 bp number of sequenced bases = 147,828,141 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 124,188 duplication rate = 4.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7255 >>>>>>> ACTG content number of A's = 42,098,409 bp (28.48%) number of C's = 27,080,167 bp (18.32%) number of T's = 47,351,357 bp (32.03%) number of G's = 31,266,235 bp (21.15%) number of N's = 31,973 bp (0.02%) GC percentage = 39.47% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,175,478 number of insertions = 11,294 mapped reads with insertion percentage = 0.52% number of deletions = 33,715 mapped reads with deletion percentage = 1.53% homopolymer indels = 47.3% >>>>>>> Coverage mean coverageData = 0.0478X std coverageData = 0.5413X There is a 3.86% of reference with a coverageData >= 1X There is a 0.64% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% 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% 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 12518230 0.050223465641836856 0.9840522712710122 chr2 243199373 22116204 0.09093857326679868 0.6255707293797965 chr3 198022430 10442995 0.05273642485853749 0.27008806714023914 chr4 191154276 11527710 0.06030579195623121 0.3543553078668691 chr5 180915260 6990210 0.038638034182412254 0.23457401066387754 chr6 171115067 4789105 0.02798762893275786 0.22549683576371354 chr7 159138663 10758115 0.06760214518077232 0.9476664793800865 chr8 146364022 8302025 0.05672176048838013 0.9332462443965878 chr9 141213431 6230266 0.04411950021949399 0.4572433709326349 chr10 135534747 5314144 0.03920872040289417 0.5557473004816696 chr11 135006516 6922308 0.05127388073624535 0.3651173792049782 chr12 133851895 6923004 0.051721374583452856 0.2804214451736185 chr13 115169878 2435236 0.021144730221907503 0.17065436033834505 chr14 107349540 3894835 0.03628180428160195 0.2446754509252198 chr15 102531392 3702585 0.03611172078888776 0.2203772860667486 chr16 90354753 2478180 0.02742722344667358 0.25514628293462605 chr17 81195210 4909560 0.060466128482209724 0.31964969821778494 chr18 78077248 3803951 0.04872035192633839 0.8476550464004207 chr19 59128983 1736290 0.029364448903171563 0.6488856415437849 chr20 63025520 2443198 0.03876521764516977 0.2481285021478331 chr21 48129895 2486259 0.05165727039296471 0.3147149907867466 chr22 51304566 1025767 0.019993678535356874 0.16197178472162446 chrMT 16571 347974 20.998974111399434 12.000160450575747 chrX 155270560 5477869 0.03527950823388542 0.2562605134890901 chrY 59373566 311736 0.005250417332184495 0.1948724057226493