BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506014.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 = 4,286,687 number of mapped reads = 2,993,893 (69.84%) number of supplementary alignments = 121 (0%) number of secondary alignments = 0 number of mapped bases = 139,300,583 bp number of sequenced bases = 139,272,087 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 189,608 duplication rate = 4.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7406 >>>>>>> ACTG content number of A's = 41,065,626 bp (29.49%) number of C's = 28,634,005 bp (20.56%) number of T's = 40,251,180 bp (28.9%) number of G's = 28,849,385 bp (20.71%) number of N's = 471,891 bp (0.34%) GC percentage = 41.27% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,128,828 number of insertions = 6,114 mapped reads with insertion percentage = 0.2% number of deletions = 20,627 mapped reads with deletion percentage = 0.69% homopolymer indels = 45.81% >>>>>>> Coverage mean coverageData = 0.045X std coverageData = 0.4494X There is a 3.39% of reference with a coverageData >= 1X There is a 0.73% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% 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 13916889 0.055834922072270386 0.8791369556756634 chr2 243199373 8402215 0.034548670485264776 0.3572355990416017 chr3 198022430 8575952 0.04330798283810577 0.26666213707946823 chr4 191154276 5794394 0.030312656987071532 0.22818183004009987 chr5 180915260 9798935 0.05416312034706194 0.2991170912107939 chr6 171115067 9354632 0.05466866339712797 0.3663851553515146 chr7 159138663 8754734 0.055013243387623534 0.6418149341459076 chr8 146364022 8238250 0.05628603182276584 0.48567684593607 chr9 141213431 6538400 0.046301544787195205 0.3553121022984879 chr10 135534747 4332209 0.03196382548306967 0.45388752824857115 chr11 135006516 7117066 0.0527164629594619 0.3646703331079464 chr12 133851895 3925673 0.02932848279809561 0.23322447506998592 chr13 115169878 4318347 0.03749545519185147 0.24545621796642364 chr14 107349540 4963408 0.04623595033569776 0.7185898475396768 chr15 102531392 4511595 0.044002084746884156 0.26593540878743305 chr16 90354753 4397504 0.04866931571380644 0.3236413924224192 chr17 81195210 2232362 0.02749376471838671 0.2357064174032855 chr18 78077248 4185691 0.053609612367485085 0.5357334557124762 chr19 59128983 3512319 0.059400970924867756 0.6480336812095076 chr20 63025520 3319479 0.05266880780991573 0.3080721452757804 chr21 48129895 2017048 0.04190842302897191 0.28383527567365746 chr22 51304566 969728 0.01890139758710755 0.17153678649937895 chrMT 16571 229946 13.87641059682578 8.728109186132826 chrX 155270560 9451118 0.060868705567880994 0.3499340339849794 chrY 59373566 442689 0.007455994810889412 0.13397115710754534