BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085086.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,580,416 number of mapped reads = 1,248,166 (78.98%) number of supplementary alignments = 6,564 (0.42%) number of secondary alignments = 0 number of mapped bases = 77,131,259 bp number of sequenced bases = 77,103,811 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 27,595 duplication rate = 1.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3781 >>>>>>> ACTG content number of A's = 22,916,746 bp (29.72%) number of C's = 14,853,233 bp (19.26%) number of T's = 22,452,434 bp (29.12%) number of G's = 16,879,698 bp (21.89%) number of N's = 1,700 bp (0%) GC percentage = 41.16% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 690,491 number of insertions = 6,132 mapped reads with insertion percentage = 0.49% number of deletions = 16,907 mapped reads with deletion percentage = 1.34% homopolymer indels = 45.76% >>>>>>> Coverage mean coverageData = 0.0249X std coverageData = 0.2193X There is a 2.29% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 5895330 0.02365221790159552 0.3574898650894252 chr2 243199373 6338295 0.0260621354480219 0.22564089296731793 chr3 198022430 5667347 0.02861972252335253 0.17923358822811794 chr4 191154276 5044704 0.026390746289138726 0.18005877029032663 chr5 180915260 4996660 0.027618786828706433 0.17675507181934746 chr6 171115067 4563803 0.026670959372619128 0.19536693516985265 chr7 159138663 4054613 0.025478491044002297 0.2029695511450381 chr8 146364022 4161000 0.028429117642039106 0.317386775200179 chr9 141213431 3133050 0.022186628975823127 0.19375949005446477 chr10 135534747 3807822 0.028094802877375792 0.23659254699248777 chr11 135006516 3588356 0.026579131928713723 0.21503696119034033 chr12 133851895 3397503 0.025382554352330985 0.17032471165280644 chr13 115169878 2607840 0.022643420704153216 0.15881003394545745 chr14 107349540 2372318 0.022099004802442562 0.1639758677999735 chr15 102531392 1989089 0.01939980489097427 0.1472068619751096 chr16 90354753 1967193 0.02177188177361295 0.16695813180845373 chr17 81195210 2057720 0.025342874290244462 0.18405472300425554 chr18 78077248 2068689 0.026495413875243144 0.3284086515100816 chr19 59128983 1410460 0.023853953314231704 0.24572454156297832 chr20 63025520 1393991 0.02211788177233603 0.1601079439654248 chr21 48129895 916067 0.019033222490927936 0.15555956785053177 chr22 51304566 739715 0.014418112415179577 0.12645381722431648 chrMT 16571 3956 0.23873031199082734 0.5372820024341584 chrX 155270560 4750255 0.03059340418428323 0.20038523558275187 chrY 59373566 205483 0.0034608499007790774 0.0818740901696077