BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514747.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 33,016,483 number of mapped reads = 30,318,387 (91.83%) number of supplementary alignments = 4,943,434 (14.97%) number of secondary alignments = 0 number of mapped bases = 2,832,389,481 bp number of sequenced bases = 2,828,822,676 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,527,676 duplication rate = 39.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3763 >>>>>>> ACTG content number of A's = 861,292,221 bp (30.45%) number of C's = 530,505,993 bp (18.75%) number of T's = 865,266,185 bp (30.59%) number of G's = 571,568,494 bp (20.21%) number of N's = 189,783 bp (0.01%) GC percentage = 38.96% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 19,176,814 number of insertions = 2,088,665 mapped reads with insertion percentage = 6.5% number of deletions = 1,025,067 mapped reads with deletion percentage = 3.12% homopolymer indels = 43.83% >>>>>>> Coverage mean coverageData = 0.9149X std coverageData = 98.7938X There is a 4.04% of reference with a coverageData >= 1X There is a 2.46% of reference with a coverageData >= 2X There is a 1.95% of reference with a coverageData >= 3X There is a 1.67% of reference with a coverageData >= 4X There is a 1.49% of reference with a coverageData >= 5X There is a 1.35% of reference with a coverageData >= 6X There is a 1.24% of reference with a coverageData >= 7X There is a 1.15% of reference with a coverageData >= 8X There is a 1.08% of reference with a coverageData >= 9X There is a 1.01% of reference with a coverageData >= 10X There is a 0.96% of reference with a coverageData >= 11X There is a 0.91% of reference with a coverageData >= 12X There is a 0.87% of reference with a coverageData >= 13X There is a 0.83% of reference with a coverageData >= 14X There is a 0.79% of reference with a coverageData >= 15X There is a 0.76% of reference with a coverageData >= 16X There is a 0.73% of reference with a coverageData >= 17X There is a 0.7% of reference with a coverageData >= 18X There is a 0.68% of reference with a coverageData >= 19X There is a 0.66% of reference with a coverageData >= 20X There is a 0.63% of reference with a coverageData >= 21X There is a 0.61% of reference with a coverageData >= 22X There is a 0.59% of reference with a coverageData >= 23X There is a 0.58% of reference with a coverageData >= 24X There is a 0.56% of reference with a coverageData >= 25X There is a 0.54% of reference with a coverageData >= 26X There is a 0.53% of reference with a coverageData >= 27X There is a 0.51% of reference with a coverageData >= 28X There is a 0.5% of reference with a coverageData >= 29X There is a 0.49% of reference with a coverageData >= 30X There is a 0.48% of reference with a coverageData >= 31X There is a 0.47% of reference with a coverageData >= 32X There is a 0.45% of reference with a coverageData >= 33X There is a 0.44% of reference with a coverageData >= 34X There is a 0.43% of reference with a coverageData >= 35X There is a 0.42% of reference with a coverageData >= 36X There is a 0.41% of reference with a coverageData >= 37X There is a 0.41% of reference with a coverageData >= 38X There is a 0.4% of reference with a coverageData >= 39X There is a 0.39% of reference with a coverageData >= 40X There is a 0.38% of reference with a coverageData >= 41X There is a 0.37% of reference with a coverageData >= 42X There is a 0.37% of reference with a coverageData >= 43X There is a 0.36% of reference with a coverageData >= 44X There is a 0.35% of reference with a coverageData >= 45X There is a 0.35% of reference with a coverageData >= 46X There is a 0.34% of reference with a coverageData >= 47X There is a 0.33% of reference with a coverageData >= 48X There is a 0.33% of reference with a coverageData >= 49X There is a 0.32% of reference with a coverageData >= 50X There is a 0.32% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 199206486 0.7992216236042998 27.491623518263598 chr2 243199373 205062880 0.843188358055512 30.4598993525855 chr3 198022430 214306193 1.0822319118091823 18.87046306271626 chr4 191154276 239629935 1.253594426524887 93.14788661952886 chr5 180915260 403529424 2.230488594494461 367.6571391459358 chr6 171115067 175217044 1.0239720386516284 29.149264836304873 chr7 159138663 148521799 0.9332854518200897 22.88281156369796 chr8 146364022 101044718 0.6903658195454618 18.985050372316945 chr9 141213431 98026071 0.6941696006238953 17.226834641562462 chr10 135534747 130078628 0.9597437622398041 18.757932682560025 chr11 135006516 82392204 0.6102831658880821 54.30903857127643 chr12 133851895 128354609 0.9589300846282378 60.773632487031385 chr13 115169878 102018544 0.8858092564793721 68.93465315946335 chr14 107349540 71542212 0.6664417192658674 14.359916309790375 chr15 102531392 60701912 0.5920324577276782 20.401167644877923 chr16 90354753 93095971 1.0303383929343484 111.86219643049223 chr17 81195210 32983535 0.4062251332313815 8.552008194781179 chr18 78077248 46062909 0.5899658374229584 16.1425660887254 chr19 59128983 15120533 0.2557211748424626 7.761397982985716 chr20 63025520 61272096 0.9721791426710957 21.263951022729717 chr21 48129895 62527155 1.2991334180138976 19.35772218607053 chr22 51304566 35221721 0.6865221508744466 43.84688232977679 chrMT 16571 46894897 2829.9376621809183 3064.3551207422624 chrX 155270560 53250652 0.34295395083266267 22.270478555217707 chrY 59373566 26327353 0.4434187597894996 34.29677409623171