BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237303.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 = 2,687,382 number of mapped reads = 1,964,804 (73.11%) number of supplementary alignments = 22,192 (0.83%) number of secondary alignments = 0 number of mapped bases = 123,138,348 bp number of sequenced bases = 123,079,733 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 606,537 duplication rate = 20.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.1373 >>>>>>> ACTG content number of A's = 32,065,689 bp (26.05%) number of C's = 21,446,536 bp (17.42%) number of T's = 40,970,925 bp (33.29%) number of G's = 28,582,965 bp (23.22%) number of N's = 13,618 bp (0.01%) GC percentage = 40.65% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 740,347 number of insertions = 8,469 mapped reads with insertion percentage = 0.43% number of deletions = 34,026 mapped reads with deletion percentage = 1.71% homopolymer indels = 42.45% >>>>>>> Coverage mean coverageData = 0.0398X std coverageData = 0.6105X There is a 1.49% of reference with a coverageData >= 1X There is a 0.84% of reference with a coverageData >= 2X There is a 0.55% of reference with a coverageData >= 3X There is a 0.36% of reference with a coverageData >= 4X There is a 0.23% of reference with a coverageData >= 5X There is a 0.15% of reference with a coverageData >= 6X There is a 0.1% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% 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 7489815 0.030049333357528525 0.41128426112526256 chr2 243199373 9714658 0.03994524278646064 0.932205680088337 chr3 198022430 6260474 0.03161497412187094 0.3733264739645331 chr4 191154276 9341191 0.048867287698026694 0.48292695418904047 chr5 180915260 3447962 0.01905843652989803 0.2841831111430858 chr6 171115067 13042829 0.07622256314810665 0.7883316141640287 chr7 159138663 3444439 0.02164426252594569 0.3531408852235558 chr8 146364022 12340457 0.0843134592188236 1.5209543481582195 chr9 141213431 5363858 0.037984049831633934 0.5217507531870343 chr10 135534747 3035398 0.02239571819911244 0.4064379216974598 chr11 135006516 6272260 0.04645894276688097 0.5094030047942252 chr12 133851895 3279429 0.02450043012091835 0.3460207752228885 chr13 115169878 1943869 0.01687827610618811 0.2854922539591796 chr14 107349540 4470947 0.04164849704991749 0.42903666464312123 chr15 102531392 2580881 0.025171617683684623 0.3426120435433431 chr16 90354753 1662316 0.018397659722449798 0.2876882357367021 chr17 81195210 2722805 0.03353405945991149 0.4125336468807461 chr18 78077248 5329040 0.06825343024385286 0.8823698638341889 chr19 59128983 2586249 0.04373910845041931 0.5433521183304385 chr20 63025520 1970574 0.03126628705324446 0.38418616231164826 chr21 48129895 5513469 0.11455393783842661 0.7296523752330106 chr22 51304566 905908 0.017657453724489163 0.2668785611777095 chrMT 16571 46709 2.818719449640939 4.10372504410792 chrX 155270560 9938832 0.06400976463278035 0.5868750281436084 chrY 59373566 433979 0.007309296531052219 0.18943416445842134