BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716522.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 = 871,726 number of mapped reads = 717,961 (82.36%) number of supplementary alignments = 3,050 (0.35%) number of secondary alignments = 0 number of mapped bases = 39,410,064 bp number of sequenced bases = 39,398,789 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,408 duplication rate = 1.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.1873 >>>>>>> ACTG content number of A's = 9,001,354 bp (22.85%) number of C's = 8,087,847 bp (20.53%) number of T's = 11,418,945 bp (28.98%) number of G's = 10,889,623 bp (27.64%) number of N's = 1,020 bp (0%) GC percentage = 48.17% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 213,018 number of insertions = 3,024 mapped reads with insertion percentage = 0.42% number of deletions = 6,568 mapped reads with deletion percentage = 0.91% homopolymer indels = 33.27% >>>>>>> Coverage mean coverageData = 0.0127X std coverageData = 0.1349X There is a 1.17% of reference with a coverageData >= 1X There is a 0.07% 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 3811815 0.015293101315883984 0.15483944606905325 chr2 243199373 3414946 0.014041754951399484 0.1604303006103112 chr3 198022430 2613176 0.013196363664459627 0.12793365021284114 chr4 191154276 2493453 0.013044191593182044 0.1352244315482415 chr5 180915260 2336500 0.012914886229055525 0.12234017609689754 chr6 171115067 1720394 0.010054018212201032 0.10865879598585522 chr7 159138663 2286495 0.014367941497661067 0.15163324276827259 chr8 146364022 2365789 0.01616373318847442 0.14144287290769786 chr9 141213431 1723926 0.012207946424019681 0.12609778501758592 chr10 135534747 2048764 0.015116153203133954 0.18192266096602713 chr11 135006516 1679028 0.012436644169085883 0.14057754478783202 chr12 133851895 1914118 0.01430026821809284 0.12952129406876392 chr13 115169878 712704 0.006188284752719804 0.08535071905458493 chr14 107349540 1242832 0.01157743200390053 0.1161846192058882 chr15 102531392 808352 0.00788394641126105 0.09831076440644938 chr16 90354753 1088868 0.012051031781360744 0.1256256568114438 chr17 81195210 1589091 0.019571240717278764 0.15446522661282341 chr18 78077248 1045977 0.01339669400232959 0.14368216711876047 chr19 59128983 1098275 0.01857422442053502 0.16589084213565833 chr20 63025520 1018865 0.01616591184015618 0.14248933817940335 chr21 48129895 555483 0.011541329977968993 0.12462950354346822 chr22 51304566 461394 0.008993234637244569 0.10452968719722547 chrMT 16571 1768 0.10669241445899463 0.328054578329143 chrX 155270560 1249148 0.008044976459156198 0.10173380883684958 chrY 59373566 128903 0.0021710503290302626 0.07307847645757246