BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089664.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 21,269,964 number of mapped reads = 17,919,308 (84.25%) number of supplementary alignments = 709 (0%) number of secondary alignments = 0 number of mapped bases = 842,300,316 bp number of sequenced bases = 842,131,153 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,482,785 duplication rate = 5.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.322 >>>>>>> ACTG content number of A's = 246,155,336 bp (29.23%) number of C's = 175,493,676 bp (20.84%) number of T's = 239,948,720 bp (28.49%) number of G's = 180,516,901 bp (21.44%) number of N's = 16,520 bp (0%) GC percentage = 42.27% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 4,377,225 number of insertions = 34,705 mapped reads with insertion percentage = 0.19% number of deletions = 114,287 mapped reads with deletion percentage = 0.64% homopolymer indels = 45.54% >>>>>>> Coverage mean coverageData = 0.2721X std coverageData = 1.5616X There is a 15.77% of reference with a coverageData >= 1X There is a 5.61% of reference with a coverageData >= 2X There is a 2.39% of reference with a coverageData >= 3X There is a 1.17% of reference with a coverageData >= 4X There is a 0.64% of reference with a coverageData >= 5X There is a 0.38% of reference with a coverageData >= 6X There is a 0.24% of reference with a coverageData >= 7X There is a 0.16% of reference with a coverageData >= 8X There is a 0.11% of reference with a coverageData >= 9X There is a 0.08% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% 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 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% 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 68243058 0.2737929306904315 1.957505164439527 chr2 243199373 82301672 0.3384123527325048 2.554639188945612 chr3 198022430 76480855 0.38622319198890753 1.104456600015167 chr4 191154276 38587093 0.20186361407892336 0.7599436986878506 chr5 180915260 36108358 0.1995871326719482 0.7211277754862864 chr6 171115067 52059057 0.3042342086684862 1.101899795836115 chr7 159138663 56232941 0.3533581339689903 2.6190186844233825 chr8 146364022 66647996 0.45535777911323044 2.2966213050568505 chr9 141213431 29419693 0.2083349493859405 1.5818117843456856 chr10 135534747 33227703 0.24516003265199587 1.5426772535763216 chr11 135006516 42294064 0.3132742422595366 1.5370002479435427 chr12 133851895 29241294 0.21846006737521348 0.8019392221815492 chr13 115169878 23653106 0.20537580147475715 0.7164845050651765 chr14 107349540 27563090 0.2567602059589636 0.9953545772911416 chr15 102531392 20670330 0.20160001338907016 0.7130558281954763 chr16 90354753 16966270 0.18777396248319111 0.854571820346943 chr17 81195210 20121029 0.24781054202581654 0.96593627524308 chr18 78077248 40528805 0.5190859826411914 2.3439465119187526 chr19 59128983 14606826 0.24703326962346028 1.9157138468557684 chr20 63025520 18937335 0.30047090448440567 0.9671109156884216 chr21 48129895 13318593 0.2767218378515058 1.0295995731170395 chr22 51304566 6788231 0.13231241445449515 0.5659729715320875 chrMT 16571 566471 34.1844789089373 26.55477088173907 chrX 155270560 25775029 0.16600074734064205 1.1376936908374784 chrY 59373566 1961417 0.03303518943093295 0.5680497807276536