BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716997.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 = 3,102,307 number of mapped reads = 2,744,926 (88.48%) number of supplementary alignments = 10,255 (0.33%) number of secondary alignments = 0 number of mapped bases = 157,761,171 bp number of sequenced bases = 157,714,600 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 129,365 duplication rate = 3.54% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0149 >>>>>>> ACTG content number of A's = 41,143,351 bp (26.09%) number of C's = 29,165,212 bp (18.49%) number of T's = 48,650,082 bp (30.85%) number of G's = 38,754,796 bp (24.57%) number of N's = 1,159 bp (0%) GC percentage = 43.07% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 823,380 number of insertions = 10,933 mapped reads with insertion percentage = 0.4% number of deletions = 29,032 mapped reads with deletion percentage = 1.05% homopolymer indels = 40.41% >>>>>>> Coverage mean coverageData = 0.051X std coverageData = 0.3792X There is a 4.27% of reference with a coverageData >= 1X There is a 0.59% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 12559781 0.05039016933883587 0.48006843022369783 chr2 243199373 13104870 0.05388529517302662 0.626329122677543 chr3 198022430 10389081 0.052464162771863776 0.27160672319262286 chr4 191154276 10057789 0.05261608168263 0.3186850954444025 chr5 180915260 9316676 0.05149745798115648 0.26478056536908495 chr6 171115067 8927981 0.0521753061055693 0.3152054884681615 chr7 159138663 8727827 0.05484416442533516 0.4666857653783893 chr8 146364022 7980718 0.0545265010550202 0.3851851143202967 chr9 141213431 6637789 0.047005365941430885 0.32415312686156944 chr10 135534747 7739718 0.057105046280124756 0.47908534591216717 chr11 135006516 7011041 0.05193113049447184 0.34074307134443915 chr12 133851895 7225476 0.05398112593026793 0.2750485348207321 chr13 115169878 4819548 0.04184729621750576 0.23831923532042731 chr14 107349540 4841921 0.04510425475507394 0.26736357547807904 chr15 102531392 4637038 0.04522554419235818 0.2556956035888462 chr16 90354753 4808843 0.053221804502083025 0.3031734726807833 chr17 81195210 4587526 0.056499958556668554 0.29275977935458747 chr18 78077248 4076849 0.05221558270086569 0.5338900623679688 chr19 59128983 3585815 0.06064394850153266 0.44147549261099084 chr20 63025520 3458881 0.054880642000256406 0.28859326719768813 chr21 48129895 2101499 0.04366307053028061 0.2888252072542834 chr22 51304566 1991793 0.03882291880219784 0.2335141512870893 chrMT 16571 23823 1.4376320077243376 1.542672301541341 chrX 155270560 8657669 0.05575859969848759 0.3083711939576101 chrY 59373566 491219 0.00827336192001673 0.2373403756089826