BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514758.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 = 60,420,432 number of mapped reads = 57,374,682 (94.96%) number of supplementary alignments = 8,078,765 (13.37%) number of secondary alignments = 0 number of mapped bases = 5,473,107,806 bp number of sequenced bases = 5,469,417,610 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 45,654,916 duplication rate = 46.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7646 >>>>>>> ACTG content number of A's = 1,715,597,060 bp (31.37%) number of C's = 1,023,431,848 bp (18.71%) number of T's = 1,685,358,133 bp (30.81%) number of G's = 1,044,653,959 bp (19.1%) number of N's = 376,610 bp (0.01%) GC percentage = 37.81% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 29,038,783 number of insertions = 3,546,228 mapped reads with insertion percentage = 5.92% number of deletions = 1,361,175 mapped reads with deletion percentage = 2.23% homopolymer indels = 52.25% >>>>>>> Coverage mean coverageData = 1.768X std coverageData = 61.2232X There is a 4.97% of reference with a coverageData >= 1X There is a 3.32% of reference with a coverageData >= 2X There is a 2.73% of reference with a coverageData >= 3X There is a 2.4% of reference with a coverageData >= 4X There is a 2.17% of reference with a coverageData >= 5X There is a 2.01% of reference with a coverageData >= 6X There is a 1.88% of reference with a coverageData >= 7X There is a 1.77% of reference with a coverageData >= 8X There is a 1.68% of reference with a coverageData >= 9X There is a 1.6% of reference with a coverageData >= 10X There is a 1.53% of reference with a coverageData >= 11X There is a 1.47% of reference with a coverageData >= 12X There is a 1.41% of reference with a coverageData >= 13X There is a 1.36% of reference with a coverageData >= 14X There is a 1.31% of reference with a coverageData >= 15X There is a 1.27% of reference with a coverageData >= 16X There is a 1.23% of reference with a coverageData >= 17X There is a 1.2% of reference with a coverageData >= 18X There is a 1.16% of reference with a coverageData >= 19X There is a 1.13% of reference with a coverageData >= 20X There is a 1.1% of reference with a coverageData >= 21X There is a 1.07% of reference with a coverageData >= 22X There is a 1.05% of reference with a coverageData >= 23X There is a 1.02% of reference with a coverageData >= 24X There is a 1% of reference with a coverageData >= 25X There is a 0.98% of reference with a coverageData >= 26X There is a 0.95% of reference with a coverageData >= 27X There is a 0.93% of reference with a coverageData >= 28X There is a 0.91% of reference with a coverageData >= 29X There is a 0.9% of reference with a coverageData >= 30X There is a 0.88% of reference with a coverageData >= 31X There is a 0.86% of reference with a coverageData >= 32X There is a 0.85% of reference with a coverageData >= 33X There is a 0.83% of reference with a coverageData >= 34X There is a 0.81% of reference with a coverageData >= 35X There is a 0.8% of reference with a coverageData >= 36X There is a 0.79% of reference with a coverageData >= 37X There is a 0.77% of reference with a coverageData >= 38X There is a 0.76% of reference with a coverageData >= 39X There is a 0.75% of reference with a coverageData >= 40X There is a 0.73% of reference with a coverageData >= 41X There is a 0.72% of reference with a coverageData >= 42X There is a 0.71% of reference with a coverageData >= 43X There is a 0.7% of reference with a coverageData >= 44X There is a 0.69% of reference with a coverageData >= 45X There is a 0.68% of reference with a coverageData >= 46X There is a 0.67% of reference with a coverageData >= 47X There is a 0.66% of reference with a coverageData >= 48X There is a 0.65% of reference with a coverageData >= 49X There is a 0.64% of reference with a coverageData >= 50X There is a 0.63% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 371233121 1.4893969752637046 69.1207262443188 chr2 243199373 522443014 2.148208720916398 43.673711558860155 chr3 198022430 415727429 2.0993956543205736 33.311205906678474 chr4 191154276 438495639 2.2939358102562144 93.76856132154583 chr5 180915260 233369118 1.2899360617783155 26.171858231993834 chr6 171115067 358730379 2.096427773949327 41.43461678538204 chr7 159138663 176455955 1.1088188858291463 21.549619575218568 chr8 146364022 309025826 2.1113510122043517 38.34881821349858 chr9 141213431 168859329 1.195773856666651 26.78297966773068 chr10 135534747 256490001 1.8924298504795969 72.15635484590732 chr11 135006516 553831816 4.102259893885418 44.573902193963946 chr12 133851895 257822258 1.9261756286677898 29.357471987782308 chr13 115169878 217915674 1.8921238589833358 31.86705300394319 chr14 107349540 139895402 1.303176538995882 25.878611224301046 chr15 102531392 149392580 1.457042346601517 27.627014409700145 chr16 90354753 115910823 1.2828414571616393 31.348515127164028 chr17 81195210 54628254 0.6728014374246953 14.84103791052504 chr18 78077248 140077494 1.7940885160296633 48.85378800275234 chr19 59128983 61661727 1.042834222262879 118.0942877256581 chr20 63025520 93350459 1.4811533328086781 44.844964868576454 chr21 48129895 49944513 1.0377025131677515 18.707131926105795 chr22 51304566 13812430 0.2692241856212174 11.100382302428407 chrMT 16571 202446389 12216.908394182608 11178.159909355938 chrX 155270560 137135279 0.8832020635463671 19.518243768725846 chrY 59373566 34452897 0.5802733324119357 15.076761493019887