BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716830.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,475,134 number of mapped reads = 1,094,126 (74.17%) number of supplementary alignments = 1,203 (0.08%) number of secondary alignments = 0 number of mapped bases = 56,885,711 bp number of sequenced bases = 56,870,404 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 89,798 duplication rate = 6.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.6159 >>>>>>> ACTG content number of A's = 10,970,161 bp (19.29%) number of C's = 10,335,014 bp (18.17%) number of T's = 19,664,305 bp (34.58%) number of G's = 15,899,981 bp (27.96%) number of N's = 943 bp (0%) GC percentage = 46.13% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 387,982 number of insertions = 3,521 mapped reads with insertion percentage = 0.32% number of deletions = 9,078 mapped reads with deletion percentage = 0.82% homopolymer indels = 40.23% >>>>>>> Coverage mean coverageData = 0.0184X std coverageData = 0.1866X There is a 1.56% of reference with a coverageData >= 1X There is a 0.19% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 5477481 0.021975796802528327 0.20734946312598243 chr2 243199373 4828580 0.01985440973978169 0.2882167230586392 chr3 198022430 3717802 0.018774650932220152 0.1589674782673006 chr4 191154276 3543225 0.018535944233860614 0.1763403485328546 chr5 180915260 3410316 0.018850350158411182 0.15999503701982964 chr6 171115067 2353185 0.01375206193853169 0.16915262480935128 chr7 159138663 3206738 0.02015059030626643 0.19364503745764697 chr8 146364022 3461030 0.023646726515892 0.19027293581805757 chr9 141213431 2494805 0.01766691016805618 0.17694860344340166 chr10 135534747 2848695 0.02101818952744273 0.19622159472639003 chr11 135006516 2399074 0.01777006081691642 0.1744085035873081 chr12 133851895 2666987 0.01992491028983938 0.1694388453186282 chr13 115169878 952900 0.008273864803434106 0.10810730604884583 chr14 107349540 2581752 0.0240499586677316 0.18505631210172335 chr15 102531392 1104259 0.010769960091832167 0.12117328325570637 chr16 90354753 1498825 0.016588225303432572 0.16297591030629083 chr17 81195210 2263416 0.027876225703462064 0.20531086265666643 chr18 78077248 1504889 0.019274360182367084 0.1961343081330396 chr19 59128983 1575230 0.02664057320248515 0.24504790660324707 chr20 63025520 1498636 0.023778240941129878 0.19249592594305714 chr21 48129895 805885 0.016743959237808435 0.16342554617350474 chr22 51304566 671417 0.013086885872887026 0.14318992337278336 chrMT 16571 98882 5.9671715647818475 4.884532067104767 chrX 155270560 1746627 0.011248925746129852 0.12720552752864728 chrY 59373566 175075 0.002948702794775709 0.08734638751871222