BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708552.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 4,236,934 number of mapped reads = 3,484,882 (82.25%) number of supplementary alignments = 75 (0%) number of secondary alignments = 0 number of mapped bases = 173,777,421 bp number of sequenced bases = 173,762,020 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,060 duplication rate = 0.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4761 >>>>>>> ACTG content number of A's = 53,695,519 bp (30.9%) number of C's = 33,094,507 bp (19.05%) number of T's = 53,598,324 bp (30.85%) number of G's = 33,366,289 bp (19.2%) number of N's = 7,381 bp (0%) GC percentage = 38.25% >>>>>>> Mismatches and indels general error rate = 0.0017 number of mismatches = 275,330 number of insertions = 11,477 mapped reads with insertion percentage = 0.33% number of deletions = 9,204 mapped reads with deletion percentage = 0.26% homopolymer indels = 46.93% >>>>>>> Coverage mean coverageData = 0.0561X std coverageData = 0.2457X There is a 5.27% of reference with a coverageData >= 1X There is a 0.32% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 12304157 0.049364599175863236 0.23132132734595154 chr2 243199373 13482923 0.055439793424138475 0.24330407040794894 chr3 198022430 14376734 0.07260154316861983 0.2780673054286011 chr4 191154276 12612340 0.06597989992125523 0.2655494699662561 chr5 180915260 11736393 0.06487232199207518 0.2629169405224983 chr6 171115067 11486346 0.06712644421896524 0.26762715985688196 chr7 159138663 11273441 0.07084036517260422 0.27617024170417137 chr8 146364022 8362651 0.05713597430384907 0.2464767077280124 chr9 141213431 8353304 0.059153750042373804 0.2526875975729215 chr10 135534747 6507747 0.048015340302365414 0.22585225232760214 chr11 135006516 6136437 0.045452895029155484 0.2205185904808513 chr12 133851895 9836972 0.07349146607151136 0.281431163411666 chr13 115169878 8012468 0.06957086470127198 0.274059496657391 chr14 107349540 4060903 0.037828788087960134 0.20190688372421847 chr15 102531392 5914678 0.05768650834273273 0.25025467979364185 chr16 90354753 3771346 0.04173932056457506 0.21134575943475997 chr17 81195210 4100691 0.05050409993397394 0.23310626485208327 chr18 78077248 4047080 0.05183430645506358 0.23483614328093733 chr19 59128983 1600285 0.02706430787081185 0.16895232163030338 chr20 63025520 3206834 0.05088151593195899 0.23343541207242846 chr21 48129895 2311941 0.04803544657639498 0.22903732774839086 chr22 51304566 1138334 0.022187771747255402 0.1528557690471537 chrMT 16571 150 0.009051958240299317 0.09471019106894038 chrX 155270560 8928751 0.05750446832934717 0.24832370049715288 chrY 59373566 214515 0.0036129714694919956 0.06219818069403974