BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089700.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 = 22,696,728 number of mapped reads = 17,253,119 (76.02%) number of supplementary alignments = 728 (0%) number of secondary alignments = 0 number of mapped bases = 800,378,355 bp number of sequenced bases = 800,205,455 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,535,372 duplication rate = 6.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.5977 >>>>>>> ACTG content number of A's = 261,724,814 bp (32.71%) number of C's = 159,019,956 bp (19.87%) number of T's = 209,113,655 bp (26.13%) number of G's = 169,954,417 bp (21.24%) number of N's = 392,613 bp (0.05%) GC percentage = 41.11% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 4,709,619 number of insertions = 39,390 mapped reads with insertion percentage = 0.23% number of deletions = 115,099 mapped reads with deletion percentage = 0.67% homopolymer indels = 42.87% >>>>>>> Coverage mean coverageData = 0.2585X std coverageData = 1.4366X There is a 14.11% of reference with a coverageData >= 1X There is a 5.44% of reference with a coverageData >= 2X There is a 2.55% of reference with a coverageData >= 3X There is a 1.33% of reference with a coverageData >= 4X There is a 0.75% of reference with a coverageData >= 5X There is a 0.45% of reference with a coverageData >= 6X There is a 0.28% of reference with a coverageData >= 7X There is a 0.19% of reference with a coverageData >= 8X There is a 0.13% of reference with a coverageData >= 9X There is a 0.09% 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% 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 62026670 0.2488526197092203 1.6112900412477535 chr2 243199373 80845947 0.3324266259518687 1.9462964478619793 chr3 198022430 72205594 0.364633410467693 1.092210069697877 chr4 191154276 30282432 0.1584188051330853 0.6896350182830685 chr5 180915260 35151457 0.1942979105245185 0.7291583721182059 chr6 171115067 47079110 0.27513129513019446 1.0455531042543649 chr7 159138663 55604592 0.34940969687548523 2.0805955136647776 chr8 146364022 68615672 0.4688014927602905 3.435159918886684 chr9 141213431 29522077 0.2090599795709234 1.1775128402392743 chr10 135534747 28882642 0.21310138277677237 1.2785744703614457 chr11 135006516 40327644 0.29870887120737194 1.224194686029163 chr12 133851895 25227743 0.18847505296805847 0.7449397512823431 chr13 115169878 22517661 0.19551693021677075 0.7344460133006645 chr14 107349540 28595027 0.26637307435132 0.9609382479195253 chr15 102531392 19666473 0.1918092851016789 0.7203953034621651 chr16 90354753 15552695 0.17212924039535585 0.7789299526972354 chr17 81195210 18363735 0.22616771358803062 0.90079927778014 chr18 78077248 42142862 0.53975854784226 2.0172894348040034 chr19 59128983 12740055 0.21546210256990214 1.5000214886150252 chr20 63025520 18305843 0.2904512806875691 0.9572075712898073 chr21 48129895 12632808 0.2624732092185117 0.9870698037122996 chr22 51304566 6179029 0.12043818867895696 0.5617963849175683 chrMT 16571 196268 11.844064932713778 10.3274802494187 chrX 155270560 25857337 0.1665308413906667 0.9635048523162903 chrY 59373566 1856982 0.03127624168640974 0.5275797640666927