BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777307.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 361,068,554 number of mapped reads = 341,076,545 (94.46%) number of supplementary alignments = 10,671,708 (2.96%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 171,534,661 number of mapped paired reads (second in pair) = 169,541,884 number of mapped paired reads (both in pair) = 335,454,002 number of mapped paired reads (singletons) = 5,622,543 number of mapped bases = 32,454,778,393 bp number of sequenced bases = 32,419,983,156 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 149,756,008 duplication rate = 22.76% >>>>>>> Insert size mean insert size = 146,278.7586 std insert size = 3,742,194.0856 median insert size = 163 >>>>>>> Mapping quality mean mapping quality = 52.4709 >>>>>>> ACTG content number of A's = 9,359,101,404 bp (28.87%) number of C's = 6,894,107,575 bp (21.26%) number of T's = 9,156,958,530 bp (28.24%) number of G's = 7,008,532,191 bp (21.62%) number of N's = 1,283,456 bp (0%) GC percentage = 42.88% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 297,524,650 number of insertions = 11,788,842 mapped reads with insertion percentage = 3.17% number of deletions = 10,749,768 mapped reads with deletion percentage = 2.84% homopolymer indels = 28.89% >>>>>>> Coverage mean coverageData = 10.4838X std coverageData = 381.2508X There is a 61.45% of reference with a coverageData >= 1X There is a 52.45% of reference with a coverageData >= 2X There is a 45% of reference with a coverageData >= 3X There is a 39.7% of reference with a coverageData >= 4X There is a 35.38% of reference with a coverageData >= 5X There is a 31.86% of reference with a coverageData >= 6X There is a 28.89% of reference with a coverageData >= 7X There is a 26.37% of reference with a coverageData >= 8X There is a 24.18% of reference with a coverageData >= 9X There is a 22.27% of reference with a coverageData >= 10X There is a 20.59% of reference with a coverageData >= 11X There is a 19.1% of reference with a coverageData >= 12X There is a 17.78% of reference with a coverageData >= 13X There is a 16.59% of reference with a coverageData >= 14X There is a 15.51% of reference with a coverageData >= 15X There is a 14.54% of reference with a coverageData >= 16X There is a 13.66% of reference with a coverageData >= 17X There is a 12.85% of reference with a coverageData >= 18X There is a 12.12% of reference with a coverageData >= 19X There is a 11.44% of reference with a coverageData >= 20X There is a 10.82% of reference with a coverageData >= 21X There is a 10.25% of reference with a coverageData >= 22X There is a 9.72% of reference with a coverageData >= 23X There is a 9.23% of reference with a coverageData >= 24X There is a 8.77% of reference with a coverageData >= 25X There is a 8.35% of reference with a coverageData >= 26X There is a 7.95% of reference with a coverageData >= 27X There is a 7.58% of reference with a coverageData >= 28X There is a 7.24% of reference with a coverageData >= 29X There is a 6.91% of reference with a coverageData >= 30X There is a 6.61% of reference with a coverageData >= 31X There is a 6.32% of reference with a coverageData >= 32X There is a 6.05% of reference with a coverageData >= 33X There is a 5.8% of reference with a coverageData >= 34X There is a 5.56% of reference with a coverageData >= 35X There is a 5.33% of reference with a coverageData >= 36X There is a 5.12% of reference with a coverageData >= 37X There is a 4.92% of reference with a coverageData >= 38X There is a 4.73% of reference with a coverageData >= 39X There is a 4.55% of reference with a coverageData >= 40X There is a 4.38% of reference with a coverageData >= 41X There is a 4.21% of reference with a coverageData >= 42X There is a 4.06% of reference with a coverageData >= 43X There is a 3.91% of reference with a coverageData >= 44X There is a 3.77% of reference with a coverageData >= 45X There is a 3.64% of reference with a coverageData >= 46X There is a 3.51% of reference with a coverageData >= 47X There is a 3.39% of reference with a coverageData >= 48X There is a 3.28% of reference with a coverageData >= 49X There is a 3.17% of reference with a coverageData >= 50X There is a 3.06% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2498563007 10.024300027721896 173.48739098021653 chr2 243199373 2820389587 11.597026555656457 297.616779968481 chr3 198022430 1828357576 9.23308322193602 178.35141187933866 chr4 191154276 1960691645 10.257116325245061 284.6622506469906 chr5 180915260 1631374679 9.01734148352107 78.94111829659381 chr6 171115067 1622616775 9.482606081672516 182.7597050324386 chr7 159138663 1546559737 9.718315510794508 95.48496097926 chr8 146364022 1401223453 9.573551162730414 59.94909202536746 chr9 141213431 1349466594 9.556219861268012 162.07566522111438 chr10 135534747 2657159918 19.605008876432255 1467.0290029171892 chr11 135006516 1366700777 10.123220845133135 73.39111601128701 chr12 133851895 1246533911 9.312784932929041 40.22405523926898 chr13 115169878 887172979 7.7031685229361795 132.62196728655462 chr14 107349540 1190639407 11.091239021611084 478.1815338067175 chr15 102531392 860042009 8.388084782853626 125.78269582013144 chr16 90354753 1776311775 19.659306411916152 563.9107913606052 chr17 81195210 824987021 10.160538053907366 61.26543048810539 chr18 78077248 805408502 10.315533944024256 130.7260515637697 chr19 59128983 620936592 10.501391373499525 125.68113835386508 chr20 63025520 669651321 10.625082046129885 85.49692752910263 chr21 48129895 465097830 9.663387588940305 172.92253197152726 chr22 51304566 434816993 8.475210432537331 78.88672525483537 chrMT 16571 637353010 38461.95220566049 6148.661359225276 chrX 155270560 812578051 5.233304053260322 111.46012870355109 chrY 59373566 540145244 9.097402773483404 295.17465152618223