BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231757.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 5,873,475 number of mapped reads = 5,414,405 (92.18%) number of supplementary alignments = 32,018 (0.55%) number of secondary alignments = 0 number of mapped bases = 376,099,403 bp number of sequenced bases = 375,968,708 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 802,595 duplication rate = 6.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9439 >>>>>>> ACTG content number of A's = 95,401,489 bp (25.37%) number of C's = 68,588,573 bp (18.24%) number of T's = 102,791,395 bp (27.34%) number of G's = 109,104,563 bp (29.02%) number of N's = 82,688 bp (0.02%) GC percentage = 47.26% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 2,218,335 number of insertions = 23,342 mapped reads with insertion percentage = 0.43% number of deletions = 77,154 mapped reads with deletion percentage = 1.41% homopolymer indels = 48.14% >>>>>>> Coverage mean coverageData = 0.1215X std coverageData = 64.5799X There is a 6.45% of reference with a coverageData >= 1X There is a 2.44% of reference with a coverageData >= 2X There is a 1.05% of reference with a coverageData >= 3X There is a 0.48% of reference with a coverageData >= 4X There is a 0.24% of reference with a coverageData >= 5X There is a 0.13% of reference with a coverageData >= 6X There is a 0.07% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 30732137 0.12329813613583734 1.1269123015129725 chr2 243199373 59620310 0.24514993301401317 230.39189106346868 chr3 198022430 20757628 0.10482463021992004 0.5065843151044682 chr4 191154276 21793747 0.11401129734602432 0.577903907408183 chr5 180915260 15685345 0.0866999555482495 0.46307085226346517 chr6 171115067 23218635 0.13569018443010633 0.6595721447405735 chr7 159138663 20915050 0.1314265785932863 1.1155347508032805 chr8 146364022 20617417 0.14086396860561812 0.7822073270556404 chr9 141213431 11197817 0.07929711020193256 0.704314869105348 chr10 135534747 10673218 0.07874894251287458 0.6091073893741114 chr11 135006516 17190425 0.1273303356706131 0.9690963933190745 chr12 133851895 14610506 0.10915427084539969 0.5303426358855047 chr13 115169878 11055762 0.09599525667640284 0.4878861633605254 chr14 107349540 12318830 0.11475438087578205 0.6523807793570342 chr15 102531392 11341097 0.1106109726862969 0.5340073050266423 chr16 90354753 11216084 0.12413385713090268 0.609367895725346 chr17 81195210 6364735 0.07838806008383992 0.5971314482077 chr18 78077248 11212089 0.14360251273200614 1.65120212835907 chr19 59128983 6337180 0.1071755284544637 0.871151324772384 chr20 63025520 5081020 0.08061845423885436 0.4926796495587246 chr21 48129895 4598622 0.09554606341858839 0.5863910415093453 chr22 51304566 5528958 0.10776736713843364 0.5465888232210708 chrMT 16571 7537 0.4548307283809064 0.9707834575704092 chrX 155270560 23133615 0.14898906141640758 0.6900947986177478 chrY 59373566 891639 0.01501744058963883 0.28145691871648726