BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716956.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 = 1,427,563 number of mapped reads = 1,321,784 (92.59%) number of supplementary alignments = 4,761 (0.33%) number of secondary alignments = 0 number of mapped bases = 77,611,526 bp number of sequenced bases = 77,587,375 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 46,286 duplication rate = 2.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8484 >>>>>>> ACTG content number of A's = 19,172,508 bp (24.71%) number of C's = 15,281,065 bp (19.7%) number of T's = 24,231,860 bp (31.23%) number of G's = 18,900,404 bp (24.36%) number of N's = 1,538 bp (0%) GC percentage = 44.06% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 386,144 number of insertions = 4,756 mapped reads with insertion percentage = 0.36% number of deletions = 14,862 mapped reads with deletion percentage = 1.12% homopolymer indels = 43.93% >>>>>>> Coverage mean coverageData = 0.0251X std coverageData = 0.2469X There is a 2.27% of reference with a coverageData >= 1X There is a 0.17% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 6555896 0.026302425942601765 0.37479034822027835 chr2 243199373 6024576 0.02477216912890643 0.35294517880840165 chr3 198022430 4425435 0.022348150156525196 0.16133286094254692 chr4 191154276 4752771 0.024863534834031125 0.20387283881087762 chr5 180915260 4416310 0.02441093139406814 0.1675925188556223 chr6 171115067 4083334 0.023863088573024372 0.19187349602793308 chr7 159138663 4421567 0.027784366895177447 0.3190917226308253 chr8 146364022 4154673 0.0283858898056245 0.32723092954436533 chr9 141213431 2561376 0.01813833133195383 0.176096303746413 chr10 135534747 3423316 0.025257847716349816 0.26173988618440136 chr11 135006516 2757694 0.02042637704983069 0.19577364721531915 chr12 133851895 3819912 0.02853834829906592 0.18387485060066108 chr13 115169878 2322586 0.020166609883879534 0.15314715450256766 chr14 107349540 2630310 0.024502294094599752 0.1705795290288404 chr15 102531392 2863182 0.02792493054224798 0.180567911771081 chr16 90354753 2705405 0.02994203304390639 0.19398771314632487 chr17 81195210 3345735 0.041206063756716683 0.22728745448553903 chr18 78077248 1460765 0.018709227558840188 0.27824121590595663 chr19 59128983 1997606 0.03378387211564251 0.30427853998019794 chr20 63025520 2584748 0.04101113326792068 0.22572880915622612 chr21 48129895 999505 0.0207668227823892 0.18773565337872256 chr22 51304566 730230 0.014233236082729946 0.12891829243055244 chrMT 16571 107992 6.51692716190936 4.46097909005796 chrX 155270560 4175018 0.026888664534989764 0.1868533245818947 chrY 59373566 291584 0.004911007029626619 0.229536911355041