BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472377.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 16,135,524 number of mapped reads = 16,005,609 (99.19%) number of supplementary alignments = 62,004 (0.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,025,758 number of mapped paired reads (second in pair) = 7,979,851 number of mapped paired reads (both in pair) = 15,934,504 number of mapped paired reads (singletons) = 71,105 number of mapped bases = 1,565,914,846 bp number of sequenced bases = 1,565,721,483 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,896,579 duplication rate = 47.44% >>>>>>> Insert size mean insert size = 16,474.852 std insert size = 1,274,648.4626 median insert size = 206 >>>>>>> Mapping quality mean mapping quality = 54.966 >>>>>>> ACTG content number of A's = 424,091,990 bp (27.09%) number of C's = 359,781,722 bp (22.98%) number of T's = 425,188,340 bp (27.16%) number of G's = 356,470,258 bp (22.77%) number of N's = 189,173 bp (0.01%) GC percentage = 45.75% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 7,851,943 number of insertions = 90,717 mapped reads with insertion percentage = 0.56% number of deletions = 76,831 mapped reads with deletion percentage = 0.47% homopolymer indels = 45.35% >>>>>>> Coverage mean coverageData = 0.5058X std coverageData = 16.7735X There is a 4.41% of reference with a coverageData >= 1X There is a 1.99% of reference with a coverageData >= 2X There is a 0.84% of reference with a coverageData >= 3X There is a 0.64% of reference with a coverageData >= 4X There is a 0.48% of reference with a coverageData >= 5X There is a 0.44% of reference with a coverageData >= 6X There is a 0.4% of reference with a coverageData >= 7X There is a 0.38% of reference with a coverageData >= 8X There is a 0.36% of reference with a coverageData >= 9X There is a 0.35% of reference with a coverageData >= 10X There is a 0.34% of reference with a coverageData >= 11X There is a 0.33% of reference with a coverageData >= 12X There is a 0.32% of reference with a coverageData >= 13X There is a 0.31% of reference with a coverageData >= 14X There is a 0.3% of reference with a coverageData >= 15X There is a 0.29% of reference with a coverageData >= 16X There is a 0.29% of reference with a coverageData >= 17X There is a 0.28% of reference with a coverageData >= 18X There is a 0.27% of reference with a coverageData >= 19X There is a 0.27% of reference with a coverageData >= 20X There is a 0.26% of reference with a coverageData >= 21X There is a 0.26% of reference with a coverageData >= 22X There is a 0.25% of reference with a coverageData >= 23X There is a 0.25% of reference with a coverageData >= 24X There is a 0.24% of reference with a coverageData >= 25X There is a 0.24% of reference with a coverageData >= 26X There is a 0.23% of reference with a coverageData >= 27X There is a 0.23% of reference with a coverageData >= 28X There is a 0.23% of reference with a coverageData >= 29X There is a 0.22% of reference with a coverageData >= 30X There is a 0.22% of reference with a coverageData >= 31X There is a 0.22% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.21% of reference with a coverageData >= 34X There is a 0.21% of reference with a coverageData >= 35X There is a 0.2% of reference with a coverageData >= 36X There is a 0.2% of reference with a coverageData >= 37X There is a 0.2% of reference with a coverageData >= 38X There is a 0.2% of reference with a coverageData >= 39X There is a 0.19% of reference with a coverageData >= 40X There is a 0.19% of reference with a coverageData >= 41X There is a 0.19% of reference with a coverageData >= 42X There is a 0.19% of reference with a coverageData >= 43X There is a 0.18% of reference with a coverageData >= 44X There is a 0.18% of reference with a coverageData >= 45X There is a 0.18% of reference with a coverageData >= 46X There is a 0.18% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.17% of reference with a coverageData >= 50X There is a 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 148136672 0.5943281962775933 17.772722136492582 chr2 243199373 133606850 0.5493716877304614 16.388830973451135 chr3 198022430 97598095 0.4928638387075646 11.818887890203937 chr4 191154276 41365230 0.21639709487848444 8.54547975785765 chr5 180915260 55944345 0.30922955310679706 11.261223425868476 chr6 171115067 123235248 0.7201893448693212 20.947680407245812 chr7 159138663 131976282 0.8293162674113959 23.658768954896832 chr8 146364022 82133957 0.561162202826047 16.196260597866875 chr9 141213431 57699906 0.40860069464638954 14.105064410620797 chr10 135534747 42411102 0.3129168197731612 9.828347621994691 chr11 135006516 43162984 0.3197103760532566 9.86371651649755 chr12 133851895 70780636 0.528798161580006 13.356734072453866 chr13 115169878 52426061 0.45520636046866353 21.853127337754074 chr14 107349540 29435983 0.27420688528334636 8.910299086569744 chr15 102531392 26838972 0.2617634606969932 12.030672315673621 chr16 90354753 87309466 0.9662963275434996 35.94949587699317 chr17 81195210 62153281 0.7654796508316193 18.771696785652843 chr18 78077248 25396669 0.325276180328487 10.321547920371643 chr19 59128983 48214892 0.8154189291569585 21.654754704591795 chr20 63025520 50970256 0.8087240851007655 23.277403845794538 chr21 48129895 14949409 0.31060547711562636 12.983783067100145 chr22 51304566 12258694 0.23893962966181218 6.987831768250781 chrMT 16571 2268 0.1368656085933257 0.48331415583031345 chrX 155270560 127602431 0.8218069864628555 22.253700154494457 chrY 59373566 305157 0.005139610445496907 0.2563241313216653