BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472771.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 = 17,551,826 number of mapped reads = 17,358,556 (98.9%) number of supplementary alignments = 93,689 (0.53%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,712,622 number of mapped paired reads (second in pair) = 8,645,934 number of mapped paired reads (both in pair) = 17,246,714 number of mapped paired reads (singletons) = 111,842 number of mapped bases = 1,711,256,832 bp number of sequenced bases = 1,711,022,226 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,653,633 duplication rate = 47.61% >>>>>>> Insert size mean insert size = 34,696.5797 std insert size = 1,861,463.5874 median insert size = 248 >>>>>>> Mapping quality mean mapping quality = 55.032 >>>>>>> ACTG content number of A's = 473,639,565 bp (27.68%) number of C's = 384,817,176 bp (22.49%) number of T's = 470,488,597 bp (27.5%) number of G's = 381,746,632 bp (22.31%) number of N's = 330,256 bp (0.02%) GC percentage = 44.8% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 10,545,480 number of insertions = 103,964 mapped reads with insertion percentage = 0.59% number of deletions = 91,753 mapped reads with deletion percentage = 0.52% homopolymer indels = 46.24% >>>>>>> Coverage mean coverageData = 0.5528X std coverageData = 21.7467X There is a 4.62% of reference with a coverageData >= 1X There is a 2.07% of reference with a coverageData >= 2X There is a 0.97% of reference with a coverageData >= 3X There is a 0.67% of reference with a coverageData >= 4X There is a 0.49% of reference with a coverageData >= 5X There is a 0.43% of reference with a coverageData >= 6X There is a 0.38% of reference with a coverageData >= 7X There is a 0.35% of reference with a coverageData >= 8X There is a 0.33% of reference with a coverageData >= 9X There is a 0.31% of reference with a coverageData >= 10X There is a 0.3% of reference with a coverageData >= 11X There is a 0.29% of reference with a coverageData >= 12X There is a 0.28% of reference with a coverageData >= 13X There is a 0.27% of reference with a coverageData >= 14X There is a 0.26% of reference with a coverageData >= 15X There is a 0.25% of reference with a coverageData >= 16X There is a 0.25% of reference with a coverageData >= 17X There is a 0.24% of reference with a coverageData >= 18X There is a 0.23% of reference with a coverageData >= 19X There is a 0.23% of reference with a coverageData >= 20X There is a 0.22% of reference with a coverageData >= 21X There is a 0.22% of reference with a coverageData >= 22X There is a 0.21% of reference with a coverageData >= 23X There is a 0.21% of reference with a coverageData >= 24X There is a 0.21% of reference with a coverageData >= 25X There is a 0.2% of reference with a coverageData >= 26X There is a 0.2% of reference with a coverageData >= 27X There is a 0.2% of reference with a coverageData >= 28X There is a 0.19% of reference with a coverageData >= 29X There is a 0.19% of reference with a coverageData >= 30X There is a 0.19% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.18% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.17% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.16% of reference with a coverageData >= 40X There is a 0.16% of reference with a coverageData >= 41X There is a 0.16% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.15% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 171221471 0.6869450126665883 23.567318010693647 chr2 243199373 118458655 0.4870845411266747 18.592959290257323 chr3 198022430 193964825 0.97950936669144 25.40620735334508 chr4 191154276 56029519 0.29311151271342734 10.61935370563909 chr5 180915260 91202908 0.5041194866591132 22.98312188614928 chr6 171115067 98943713 0.578229110590244 24.272034266975712 chr7 159138663 71951920 0.4521334956798022 16.68248031529659 chr8 146364022 84770234 0.5791739858036971 25.140178829305725 chr9 141213431 109033316 0.7721171791371602 22.644489717641306 chr10 135534747 38494779 0.2840214767951719 14.42086419074868 chr11 135006516 72976541 0.5405408802638829 18.64508225337764 chr12 133851895 122495241 0.9151550749430929 29.24836244254556 chr13 115169878 52519386 0.45601668519610655 31.11387212560071 chr14 107349540 50380034 0.4693083361139694 16.346063294430945 chr15 102531392 31307903 0.3053494387357971 12.438291365008673 chr16 90354753 73018651 0.8081329268865358 30.3265913049823 chr17 81195210 45382035 0.5589250277202312 16.69623676039396 chr18 78077248 39258910 0.5028213853029246 22.255404034505716 chr19 59128983 46839525 0.7921584749732631 26.676025624607334 chr20 63025520 45328032 0.7192012378477798 26.38881598506298 chr21 48129895 5202261 0.10808793578294737 5.396163393749818 chr22 51304566 8257827 0.16095696043895977 6.872558133171744 chrMT 16571 3547 0.21404863918894454 0.5725725614119173 chrX 155270560 76493018 0.49264340902744214 25.70045394327527 chrY 59373566 7722581 0.13006766344470536 8.194373368682758