BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472790.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 12,671,470 number of mapped reads = 12,557,856 (99.1%) number of supplementary alignments = 41,468 (0.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,298,321 number of mapped paired reads (second in pair) = 6,259,535 number of mapped paired reads (both in pair) = 12,493,168 number of mapped paired reads (singletons) = 64,688 number of mapped bases = 1,233,729,068 bp number of sequenced bases = 1,233,567,276 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,598,821 duplication rate = 46.23% >>>>>>> Insert size mean insert size = 22,245.1281 std insert size = 1,489,937.3555 median insert size = 227 >>>>>>> Mapping quality mean mapping quality = 55.1559 >>>>>>> ACTG content number of A's = 334,041,657 bp (27.08%) number of C's = 284,532,054 bp (23.07%) number of T's = 331,407,191 bp (26.87%) number of G's = 283,344,962 bp (22.97%) number of N's = 241,412 bp (0.02%) GC percentage = 46.04% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 7,347,231 number of insertions = 65,984 mapped reads with insertion percentage = 0.52% number of deletions = 68,116 mapped reads with deletion percentage = 0.54% homopolymer indels = 44.64% >>>>>>> Coverage mean coverageData = 0.3985X std coverageData = 14.4932X There is a 3.41% of reference with a coverageData >= 1X There is a 1.5% of reference with a coverageData >= 2X There is a 0.69% of reference with a coverageData >= 3X There is a 0.53% of reference with a coverageData >= 4X There is a 0.42% of reference with a coverageData >= 5X There is a 0.38% of reference with a coverageData >= 6X There is a 0.35% of reference with a coverageData >= 7X There is a 0.33% of reference with a coverageData >= 8X There is a 0.31% of reference with a coverageData >= 9X There is a 0.3% of reference with a coverageData >= 10X There is a 0.29% of reference with a coverageData >= 11X There is a 0.28% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.26% of reference with a coverageData >= 14X There is a 0.25% of reference with a coverageData >= 15X There is a 0.25% of reference with a coverageData >= 16X There is a 0.24% of reference with a coverageData >= 17X There is a 0.23% of reference with a coverageData >= 18X There is a 0.23% of reference with a coverageData >= 19X There is a 0.22% of reference with a coverageData >= 20X There is a 0.22% of reference with a coverageData >= 21X There is a 0.21% of reference with a coverageData >= 22X There is a 0.21% of reference with a coverageData >= 23X There is a 0.2% of reference with a coverageData >= 24X There is a 0.2% of reference with a coverageData >= 25X There is a 0.2% of reference with a coverageData >= 26X There is a 0.19% of reference with a coverageData >= 27X There is a 0.19% of reference with a coverageData >= 28X There is a 0.18% of reference with a coverageData >= 29X There is a 0.18% of reference with a coverageData >= 30X There is a 0.18% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.17% of reference with a coverageData >= 33X There is a 0.17% of reference with a coverageData >= 34X There is a 0.17% of reference with a coverageData >= 35X There is a 0.16% of reference with a coverageData >= 36X There is a 0.16% of reference with a coverageData >= 37X There is a 0.16% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.15% of reference with a coverageData >= 40X There is a 0.15% of reference with a coverageData >= 41X There is a 0.15% of reference with a coverageData >= 42X There is a 0.15% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.14% of reference with a coverageData >= 45X There is a 0.14% of reference with a coverageData >= 46X There is a 0.14% of reference with a coverageData >= 47X There is a 0.14% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 149849982 0.6012020407363399 25.332209016765006 chr2 243199373 64225498 0.26408578775406627 9.27052355709622 chr3 198022430 188866978 0.9537655810000918 24.969888186383802 chr4 191154276 50885143 0.2661993446591799 11.252919892798616 chr5 180915260 59204943 0.3272523445507029 11.716659785568824 chr6 171115067 78309489 0.45764227763765536 13.044107053271713 chr7 159138663 41681021 0.2619163703794596 8.185197811683842 chr8 146364022 50465550 0.34479477477053755 11.870721618679621 chr9 141213431 85783227 0.6074721532684806 16.20976560736513 chr10 135534747 24497582 0.18074761300878808 9.995164421461194 chr11 135006516 42369806 0.31383526703259274 10.55139042041683 chr12 133851895 59366427 0.4435232463462695 15.970104264862961 chr13 115169878 28309963 0.24581048006319847 10.667768501045039 chr14 107349540 27318471 0.254481491024554 8.354987027756971 chr15 102531392 23742030 0.23155864303490584 7.13739210339125 chr16 90354753 42223168 0.4673043376035791 12.257972235458663 chr17 81195210 52875342 0.6512125776877725 20.732178042426515 chr18 78077248 15333131 0.19638411179656332 7.527043449480776 chr19 59128983 35975308 0.6084208821924098 15.10035976013528 chr20 63025520 28104892 0.4459287602863094 13.73560638064829 chr21 48129895 3825883 0.07949078218433678 3.0074319425964284 chr22 51304566 11145674 0.21724526429090152 6.059938614953274 chrMT 16571 2893 0.17458210126123952 0.6368074631788593 chrX 155270560 67782338 0.4365433988258946 13.916980079727667 chrY 59373566 1584329 0.026684080252144533 1.0579030400716933