BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549135.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 9,716,164 number of mapped reads = 8,478,928 (87.27%) number of secondary alignments = 0 number of mapped bases = 336,696,548 bp number of sequenced bases = 336,664,960 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 372,876 duplication rate = 3.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6875 >>>>>>> ACTG content number of A's = 98,713,947 bp (29.32%) number of C's = 69,450,898 bp (20.63%) number of T's = 99,298,303 bp (29.49%) number of G's = 69,127,773 bp (20.53%) number of N's = 74,039 bp (0.02%) GC percentage = 41.16% >>>>>>> Mismatches and indels general error rate = 0.0032 number of mismatches = 1,067,828 number of insertions = 8,375 mapped reads with insertion percentage = 0.1% number of deletions = 25,092 mapped reads with deletion percentage = 0.3% homopolymer indels = 46.02% >>>>>>> Coverage mean coverageData = 0.1088X std coverageData = 0.7203X There is a 8.17% of reference with a coverageData >= 1X There is a 1.9% of reference with a coverageData >= 2X There is a 0.47% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 27510682 0.11037357455570793 1.2520712655554633 chr2 243199373 29159605 0.11990000072903148 0.5967111405262729 chr3 198022430 23572392 0.1190389997739145 0.43523222367273684 chr4 191154276 22513335 0.11777573314656063 0.4484631790826584 chr5 180915260 21273588 0.11758868765409838 0.4466642673802501 chr6 171115067 19898446 0.11628693106259311 0.4820583849826989 chr7 159138663 18728210 0.11768485198345546 0.9017537508145301 chr8 146364022 17478496 0.11941798101175438 1.592453059761697 chr9 141213431 14393147 0.10192477371362785 0.5478281514372688 chr10 135534747 16156330 0.1192043395336843 0.5960623370556963 chr11 135006516 15598860 0.1155415343063886 0.5544922046961182 chr12 133851895 15462612 0.11552030697809695 0.44807796349437934 chr13 115169878 10960944 0.09517196848988588 0.38605808368422084 chr14 107349540 10590697 0.09865619358965115 0.5100271030453104 chr15 102531392 9873388 0.09629624456868781 0.3872456401672958 chr16 90354753 9372841 0.1037337902965658 0.44213524916926683 chr17 81195210 8743350 0.10768307637852036 0.44056524514798073 chr18 78077248 9191502 0.11772318102195405 1.08933417455657 chr19 59128983 6401474 0.10826288015134643 1.0284393708571504 chr20 63025520 7163794 0.11366497253810837 0.4501659638841192 chr21 48129895 4498572 0.09346731381815813 0.4459612383722086 chr22 51304566 3922769 0.07646042654371153 0.3698844208984285 chrMT 16571 107423 6.482590066984491 8.279053088631972 chrX 155270560 11312350 0.0728557300237727 0.41503217921830915 chrY 59373566 2811741 0.047356781635787215 0.40813319669713505