BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716771.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 = 619,782 number of mapped reads = 576,132 (92.96%) number of supplementary alignments = 14,115 (2.28%) number of secondary alignments = 0 number of mapped bases = 44,182,659 bp number of sequenced bases = 44,164,141 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,909 duplication rate = 1.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8278 >>>>>>> ACTG content number of A's = 11,497,118 bp (26.03%) number of C's = 8,904,160 bp (20.16%) number of T's = 12,906,357 bp (29.22%) number of G's = 10,854,801 bp (24.58%) number of N's = 1,705 bp (0%) GC percentage = 44.74% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 290,322 number of insertions = 4,454 mapped reads with insertion percentage = 0.76% number of deletions = 8,830 mapped reads with deletion percentage = 1.51% homopolymer indels = 38.25% >>>>>>> Coverage mean coverageData = 0.0143X std coverageData = 0.1525X There is a 1.32% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% 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 4892178 0.0196275458828245 0.2394318345254696 chr2 243199373 4114934 0.016920002503460402 0.16717380739659646 chr3 198022430 2809956 0.014190089476227517 0.12580078379068685 chr4 191154276 2122027 0.011101122320695562 0.13702787947977912 chr5 180915260 2649785 0.014646553308991181 0.12943245794009733 chr6 171115067 2695740 0.01575396046217251 0.1373228896442569 chr7 159138663 2782787 0.017486555105719344 0.18480745313157929 chr8 146364022 2697826 0.018432302987683682 0.16870388123383417 chr9 141213431 1335770 0.00945922771326192 0.1159928374739694 chr10 135534747 2321557 0.017128869543689782 0.2007197059446053 chr11 135006516 1327488 0.009832769849419713 0.12234849684251353 chr12 133851895 1566988 0.011706879458075659 0.11444738775023476 chr13 115169878 840620 0.007298957110990428 0.08962668088610615 chr14 107349540 843691 0.007859288451538778 0.09779332249180979 chr15 102531392 944126 0.009208165241724213 0.10166283620858477 chr16 90354753 1385325 0.015332065597036162 0.1343250154223775 chr17 81195210 819830 0.010097024196378087 0.1112478941608875 chr18 78077248 1323745 0.01695429890151866 0.1685922837252299 chr19 59128983 1123800 0.019005907813432206 0.1899577444044786 chr20 63025520 1199631 0.019034051603223582 0.1500335592323841 chr21 48129895 770210 0.016002735929509092 0.14822007281313676 chr22 51304566 713926 0.013915447603630445 0.1254004808029601 chrMT 16571 22029 1.3293705871703578 1.4323451223637766 chrX 155270560 2733499 0.01760474748078451 0.14325176882660234 chrY 59373566 145191 0.0024453811650794227 0.10037554681071831