BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082457.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 = 2,846,032 number of mapped reads = 2,608,939 (91.67%) number of supplementary alignments = 21,399 (0.75%) number of secondary alignments = 0 number of mapped bases = 183,457,120 bp number of sequenced bases = 183,387,958 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 86,860 duplication rate = 2.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6659 >>>>>>> ACTG content number of A's = 54,856,135 bp (29.91%) number of C's = 34,232,844 bp (18.67%) number of T's = 56,218,311 bp (30.66%) number of G's = 38,076,725 bp (20.76%) number of N's = 3,943 bp (0%) GC percentage = 39.43% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,543,500 number of insertions = 15,382 mapped reads with insertion percentage = 0.59% number of deletions = 41,681 mapped reads with deletion percentage = 1.58% homopolymer indels = 47.47% >>>>>>> Coverage mean coverageData = 0.0593X std coverageData = 0.5363X There is a 5.12% of reference with a coverageData >= 1X There is a 0.59% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 14308215 0.05740493220275668 0.9506062473188751 chr2 243199373 15804302 0.06498496194724976 0.5241081272181406 chr3 198022430 12675121 0.06400851156103882 0.28444837068387474 chr4 191154276 12569174 0.06575408232039759 0.3012909475241236 chr5 180915260 11673517 0.06452477806460329 0.285003856489612 chr6 171115067 11132225 0.06505695375147766 0.35799118841501104 chr7 159138663 10104410 0.06349437534233902 0.6257511083600619 chr8 146364022 9844007 0.0672570134756204 1.2292501805223237 chr9 141213431 7694225 0.05448649569317525 0.44132627902045324 chr10 135534747 8489934 0.0626402762975608 0.4829355749009947 chr11 135006516 8291930 0.061418739225890404 0.39611177392310054 chr12 133851895 8077930 0.06034976195144641 0.2790977752822437 chr13 115169878 6327145 0.054937498501127176 0.2590852944188863 chr14 107349540 5618552 0.05233885492196799 0.2809491761567521 chr15 102531392 4975795 0.04852947865956994 0.2445224539759969 chr16 90354753 4710805 0.05213677027040293 0.3059025848082838 chr17 81195210 4196676 0.051686250950025256 0.29259590322711765 chr18 78077248 5133572 0.0657499096279623 0.849996085983369 chr19 59128983 2971912 0.050261510501542025 0.718889770573746 chr20 63025520 3428001 0.054390681742887644 0.27059589570818793 chr21 48129895 2429867 0.050485607749611756 0.2710215225974107 chr22 51304566 1638006 0.031927099821875506 0.19527163035591777 chrMT 16571 4389 0.264860298111158 0.5347457897523304 chrX 155270560 10909670 0.07026232146003725 0.33286634502927337 chrY 59373566 447740 0.007541066339185354 0.17662211120989094