BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716128.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 = 453,207 number of mapped reads = 422,779 (93.29%) number of supplementary alignments = 8,865 (1.96%) number of secondary alignments = 0 number of mapped bases = 33,612,082 bp number of sequenced bases = 33,596,299 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,441 duplication rate = 1.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5196 >>>>>>> ACTG content number of A's = 8,630,198 bp (25.69%) number of C's = 6,367,550 bp (18.95%) number of T's = 10,478,797 bp (31.19%) number of G's = 8,117,395 bp (24.16%) number of N's = 2,359 bp (0.01%) GC percentage = 43.11% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 214,244 number of insertions = 2,771 mapped reads with insertion percentage = 0.64% number of deletions = 8,205 mapped reads with deletion percentage = 1.91% homopolymer indels = 44.69% >>>>>>> Coverage mean coverageData = 0.0109X std coverageData = 0.1398X There is a 1.02% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0% 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 3358705 0.01347521216406518 0.2549614790232474 chr2 243199373 2706050 0.01112687901543233 0.14067839799851298 chr3 198022430 2143769 0.010825889774203862 0.107281014162499 chr4 191154276 2205706 0.011538878680380657 0.12308672229398152 chr5 180915260 1958903 0.010827737803875692 0.10769578207919726 chr6 171115067 1827729 0.010681286178031301 0.10932520309970557 chr7 159138663 1755272 0.011029827490758799 0.15499522137913493 chr8 146364022 1651280 0.011282007541443484 0.14876614293416018 chr9 141213431 1339780 0.009487624445581242 0.1168501997121454 chr10 135534747 1534103 0.011318890793369762 0.14356422470859762 chr11 135006516 1865087 0.013814792465276268 0.14966902500344467 chr12 133851895 1461883 0.010921645898251944 0.1079481069735898 chr13 115169878 1190475 0.010336687167455366 0.1051140490443622 chr14 107349540 958662 0.008930285122786739 0.09923719792192695 chr15 102531392 927170 0.009042791499407322 0.09761461362531686 chr16 90354753 750987 0.008311538409053036 0.09989080893871399 chr17 81195210 1002039 0.012341109777288587 0.12192155188748018 chr18 78077248 859849 0.011012798504373514 0.16564824055776112 chr19 59128983 640002 0.010823828984171772 0.17855516632547166 chr20 63025520 687334 0.010905645839970857 0.11000998494499778 chr21 48129895 453230 0.00941680840982512 0.10961842746721304 chr22 51304566 373742 0.007284770716119107 0.08817383111908053 chrMT 16571 8476 0.5114959869651802 0.7398501952512904 chrX 155270560 1840417 0.011852968135105587 0.1189529426383945 chrY 59373566 111432 0.0018767948012420206 0.07976021584450135