BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716896.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 = 1,369,528 number of mapped reads = 1,269,075 (92.67%) number of supplementary alignments = 29,767 (2.17%) number of secondary alignments = 0 number of mapped bases = 95,571,276 bp number of sequenced bases = 95,538,684 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 30,483 duplication rate = 1.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2217 >>>>>>> ACTG content number of A's = 24,812,733 bp (25.97%) number of C's = 19,692,874 bp (20.61%) number of T's = 27,766,677 bp (29.06%) number of G's = 23,255,030 bp (24.34%) number of N's = 11,370 bp (0.01%) GC percentage = 44.95% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 694,530 number of insertions = 7,396 mapped reads with insertion percentage = 0.57% number of deletions = 18,932 mapped reads with deletion percentage = 1.47% homopolymer indels = 40.56% >>>>>>> Coverage mean coverageData = 0.0309X std coverageData = 0.2547X There is a 2.76% of reference with a coverageData >= 1X There is a 0.24% of reference with a coverageData >= 2X There is a 0.03% 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 7605198 0.03051225296646302 0.28309759325391326 chr2 243199373 8068684 0.03317724014033539 0.3521547965766821 chr3 198022430 6472327 0.032684817573443575 0.19663703971649127 chr4 191154276 5935908 0.03105297001046422 0.2041116933336904 chr5 180915260 5800733 0.03206325989305711 0.19587287992374233 chr6 171115067 5579514 0.032606795519648776 0.21423794044822989 chr7 159138663 5310501 0.03337027533026339 0.31571641956313135 chr8 146364022 4859667 0.033202606307170215 0.318682161601553 chr9 141213431 4040766 0.02861460111396911 0.2587425375781327 chr10 135534747 4531303 0.033432777205095604 0.2635359254776644 chr11 135006516 4308823 0.03191566694454955 0.2669495437750424 chr12 133851895 4323155 0.03229804852594728 0.1986591780192844 chr13 115169878 2983654 0.02590654823824681 0.17482242236960938 chr14 107349540 2800173 0.026084629705912108 0.2007196485489614 chr15 102531392 2757740 0.026896543060685257 0.17899115488004883 chr16 90354753 2893847 0.03202761231608923 0.2117345352855739 chr17 81195210 2746521 0.03382614565563658 0.21711948963968541 chr18 78077248 2619195 0.03354620029640389 0.4736045982933915 chr19 59128983 1991682 0.0336836843616945 0.2684466505821761 chr20 63025520 2015302 0.03197596783017419 0.20067969381606926 chr21 48129895 1243974 0.025846181463724364 0.18938835075366628 chr22 51304566 1117765 0.021786852265741806 0.1613447673520454 chrMT 16571 10614 0.6405165650835798 0.9638896360178425 chrX 155270560 5313204 0.03421900455566078 0.23350127108903865 chrY 59373566 241026 0.004059483306089447 0.11599062386987216