BamQC report ----------------------------------- >>>>>>> Input bam file = SRR053676.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 = 3,738,193 number of mapped reads = 2,794,940 (74.77%) number of supplementary alignments = 127 (0%) number of secondary alignments = 0 number of mapped bases = 130,263,609 bp number of sequenced bases = 130,238,708 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 653,426 duplication rate = 17.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.7232 >>>>>>> ACTG content number of A's = 40,032,194 bp (30.74%) number of C's = 27,175,318 bp (20.87%) number of T's = 34,889,892 bp (26.79%) number of G's = 28,100,295 bp (21.58%) number of N's = 41,009 bp (0.03%) GC percentage = 42.44% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 865,959 number of insertions = 6,078 mapped reads with insertion percentage = 0.22% number of deletions = 16,517 mapped reads with deletion percentage = 0.59% homopolymer indels = 41.13% >>>>>>> Coverage mean coverageData = 0.0421X std coverageData = 0.4919X There is a 1.98% of reference with a coverageData >= 1X There is a 0.76% of reference with a coverageData >= 2X There is a 0.42% of reference with a coverageData >= 3X There is a 0.27% of reference with a coverageData >= 4X There is a 0.18% of reference with a coverageData >= 5X There is a 0.13% of reference with a coverageData >= 6X There is a 0.09% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% 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% 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 9789493 0.03927570154378873 0.4790800991083087 chr2 243199373 14321240 0.05888682944918612 0.6427361939632898 chr3 198022430 8333870 0.04208548496248632 0.4627014317776128 chr4 191154276 6387948 0.03341776147346032 0.46260554843916746 chr5 180915260 6688682 0.03697135332862468 0.42216596291005637 chr6 171115067 7828314 0.04574882935352502 0.52118469211233 chr7 159138663 5944408 0.03735363794026597 0.5287645928019595 chr8 146364022 7777359 0.05313709539903187 0.5532780924048013 chr9 141213431 6595310 0.04670455177878937 0.5006463259360405 chr10 135534747 4628709 0.034151456378931376 0.4237528370840448 chr11 135006516 6413446 0.047504714513186906 0.5145159010291162 chr12 133851895 7017034 0.05242386743945612 0.5327737304189896 chr13 115169878 3537227 0.030713126222118598 0.3913072690551732 chr14 107349540 2630545 0.024504483205051462 0.3618122492110032 chr15 102531392 3192811 0.03113983861645027 0.3919645321526231 chr16 90354753 3519175 0.038948421451608636 0.4501702275212922 chr17 81195210 3334708 0.041070255252742126 0.4511802589690152 chr18 78077248 3830122 0.049055545605295924 0.5200470572029511 chr19 59128983 3018717 0.05105308508350296 0.5354269875382635 chr20 63025520 3058678 0.04853078562461682 0.524517061217855 chr21 48129895 1485383 0.030861962196260764 0.41846772110186553 chr22 51304566 1837647 0.035818390901113946 0.4396053736151432 chrMT 16571 21547 1.3002836280248626 5.317607832911648 chrX 155270560 8716943 0.05614034624464548 0.5531017098056662 chrY 59373566 354293 0.005967184116918293 0.18701160427521218