BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472464.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 = 14,170,982 number of mapped reads = 14,027,537 (98.99%) number of supplementary alignments = 52,190 (0.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,030,481 number of mapped paired reads (second in pair) = 6,997,056 number of mapped paired reads (both in pair) = 13,953,508 number of mapped paired reads (singletons) = 74,029 number of mapped bases = 1,375,745,129 bp number of sequenced bases = 1,375,581,413 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,337,531 duplication rate = 45.85% >>>>>>> Insert size mean insert size = 18,005.6207 std insert size = 1,314,410.7142 median insert size = 209 >>>>>>> Mapping quality mean mapping quality = 55.0792 >>>>>>> ACTG content number of A's = 375,517,617 bp (27.3%) number of C's = 313,228,299 bp (22.77%) number of T's = 375,440,761 bp (27.29%) number of G's = 311,222,068 bp (22.62%) number of N's = 172,668 bp (0.01%) GC percentage = 45.4% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 7,592,755 number of insertions = 80,202 mapped reads with insertion percentage = 0.57% number of deletions = 68,297 mapped reads with deletion percentage = 0.48% homopolymer indels = 46.55% >>>>>>> Coverage mean coverageData = 0.4444X std coverageData = 14.0128X There is a 4.1% of reference with a coverageData >= 1X There is a 1.79% of reference with a coverageData >= 2X There is a 0.77% of reference with a coverageData >= 3X There is a 0.59% of reference with a coverageData >= 4X There is a 0.45% of reference with a coverageData >= 5X There is a 0.42% of reference with a coverageData >= 6X There is a 0.38% of reference with a coverageData >= 7X There is a 0.36% of reference with a coverageData >= 8X There is a 0.35% of reference with a coverageData >= 9X There is a 0.33% of reference with a coverageData >= 10X There is a 0.32% of reference with a coverageData >= 11X There is a 0.31% of reference with a coverageData >= 12X There is a 0.3% of reference with a coverageData >= 13X There is a 0.29% of reference with a coverageData >= 14X There is a 0.29% of reference with a coverageData >= 15X There is a 0.28% of reference with a coverageData >= 16X There is a 0.27% of reference with a coverageData >= 17X There is a 0.27% of reference with a coverageData >= 18X There is a 0.26% of reference with a coverageData >= 19X There is a 0.25% of reference with a coverageData >= 20X There is a 0.25% of reference with a coverageData >= 21X There is a 0.24% of reference with a coverageData >= 22X There is a 0.24% of reference with a coverageData >= 23X There is a 0.23% of reference with a coverageData >= 24X There is a 0.23% of reference with a coverageData >= 25X There is a 0.23% of reference with a coverageData >= 26X There is a 0.22% of reference with a coverageData >= 27X There is a 0.22% of reference with a coverageData >= 28X There is a 0.21% of reference with a coverageData >= 29X There is a 0.21% of reference with a coverageData >= 30X There is a 0.21% of reference with a coverageData >= 31X There is a 0.2% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.19% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.17% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 192092788 0.7706812814721131 23.34696134026225 chr2 243199373 98252977 0.40400176936311427 13.466960333952565 chr3 198022430 134978733 0.6816335553502701 16.49161701712871 chr4 191154276 43595793 0.22806600988617173 7.4184438670861415 chr5 180915260 56092267 0.3100471845216374 9.370544616292872 chr6 171115067 99213985 0.5798085857629358 14.969693632955275 chr7 159138663 73538543 0.46210356184782075 12.849505621582558 chr8 146364022 68917954 0.4708667680640807 12.107721104040275 chr9 141213431 71361901 0.5053478305473649 13.935902506090047 chr10 135534747 33219261 0.24509774604146345 7.190714957786192 chr11 135006516 50693197 0.3754870394551919 11.796358711616632 chr12 133851895 58646125 0.4381419105048905 12.469046487303965 chr13 115169878 25657409 0.22277881548159667 7.233849134564176 chr14 107349540 30505845 0.28417303884115386 14.919446803209565 chr15 102531392 34700366 0.33843650537778713 9.932158487773487 chr16 90354753 63970404 0.7079915762704813 22.60498635286807 chr17 81195210 61099413 0.7525002152220556 19.411716218909163 chr18 78077248 27786013 0.35587848844262543 11.38549205716009 chr19 59128983 37259702 0.6301427846306776 17.326121287203282 chr20 63025520 25067686 0.3977386620530858 11.905637278454178 chr21 48129895 9401083 0.195327311642795 9.696700594128076 chr22 51304566 26979560 0.5258705433742485 15.53221568896485 chrMT 16571 1514 0.09136443183875445 0.3776107581646224 chrX 155270560 50801071 0.3271777405839201 10.402658143827768 chrY 59373566 1911539 0.03219511861558054 1.4042640828653263