BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506327.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 6,798,316 number of mapped reads = 5,000,044 (73.55%) number of supplementary alignments = 71,895 (1.06%) number of secondary alignments = 0 number of mapped bases = 402,550,615 bp number of sequenced bases = 402,358,786 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 771,566 duplication rate = 10.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6561 >>>>>>> ACTG content number of A's = 112,861,589 bp (28.05%) number of C's = 75,344,344 bp (18.73%) number of T's = 110,712,833 bp (27.52%) number of G's = 103,347,210 bp (25.69%) number of N's = 92,810 bp (0.02%) GC percentage = 44.41% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 2,965,358 number of insertions = 36,520 mapped reads with insertion percentage = 0.71% number of deletions = 89,937 mapped reads with deletion percentage = 1.76% homopolymer indels = 42.31% >>>>>>> Coverage mean coverageData = 0.13X std coverageData = 0.9638X There is a 7.78% of reference with a coverageData >= 1X There is a 2.57% of reference with a coverageData >= 2X There is a 1.1% of reference with a coverageData >= 3X There is a 0.54% of reference with a coverageData >= 4X There is a 0.29% of reference with a coverageData >= 5X There is a 0.16% of reference with a coverageData >= 6X There is a 0.1% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% 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 29662395 0.11900630329823732 1.5592287817145252 chr2 243199373 33188967 0.13646814377272265 1.0390214236612356 chr3 198022430 25066644 0.12658487222886822 0.5604912862263617 chr4 191154276 24769525 0.12957871264151058 1.0972225344801025 chr5 180915260 29937660 0.16547890984983799 0.6435211269668719 chr6 171115067 13917690 0.08133526897429787 0.46659612794926353 chr7 159138663 21458308 0.1348403184711939 1.0111073217299895 chr8 146364022 24292744 0.1659748322576159 1.155111642954138 chr9 141213431 11157678 0.07901286670104347 0.7988613015822761 chr10 135534747 23804926 0.17563707113423838 1.5025369646044893 chr11 135006516 17762875 0.13157050138231846 0.8331471382473249 chr12 133851895 16363062 0.12224751842325429 0.5589427130348104 chr13 115169878 7579337 0.06581006363486813 0.39677674027831733 chr14 107349540 11687334 0.10887176600849896 0.5568164886847724 chr15 102531392 13850006 0.13508063949819388 0.5944966926016764 chr16 90354753 15998691 0.17706529505979612 0.9321841991295997 chr17 81195210 10885330 0.13406369661461556 0.6836819728075784 chr18 78077248 6692904 0.08572156641586548 1.1334469159994878 chr19 59128983 11204170 0.18948693908704636 1.2801792831866028 chr20 63025520 11802106 0.18725916105095206 0.7794783263390016 chr21 48129895 6938793 0.14416804773831315 0.9486499608190193 chr22 51304566 5215815 0.10166375834852594 0.5538387081217182 chrMT 16571 60384 3.6439563092148934 3.2796681387999214 chrX 155270560 27309491 0.17588325178965028 0.7157068646413437 chrY 59373566 1943780 0.03273813804614666 1.4837940851045872