BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082944.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 = 6,189,904 number of mapped reads = 5,456,310 (88.15%) number of supplementary alignments = 39,317 (0.64%) number of secondary alignments = 0 number of mapped bases = 368,030,936 bp number of sequenced bases = 367,891,002 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 573,671 duplication rate = 6.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8083 >>>>>>> ACTG content number of A's = 103,727,268 bp (28.2%) number of C's = 64,889,739 bp (17.64%) number of T's = 120,411,530 bp (32.73%) number of G's = 78,759,620 bp (21.41%) number of N's = 102,845 bp (0.03%) GC percentage = 39.05% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 3,468,617 number of insertions = 32,757 mapped reads with insertion percentage = 0.6% number of deletions = 86,701 mapped reads with deletion percentage = 1.57% homopolymer indels = 48.66% >>>>>>> Coverage mean coverageData = 0.1189X std coverageData = 0.8446X There is a 7.06% of reference with a coverageData >= 1X There is a 1.95% of reference with a coverageData >= 2X There is a 0.94% of reference with a coverageData >= 3X There is a 0.59% of reference with a coverageData >= 4X There is a 0.39% of reference with a coverageData >= 5X There is a 0.26% of reference with a coverageData >= 6X There is a 0.18% of reference with a coverageData >= 7X There is a 0.12% of reference with a coverageData >= 8X There is a 0.08% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.04% 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 0.01% 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% 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 31984050 0.12832084378237116 1.0375983292148139 chr2 243199373 37098066 0.15254178307441607 1.23257901590159 chr3 198022430 27146559 0.137088303582579 0.6670067194647114 chr4 191154276 19726852 0.10319859127817785 0.5532494582008759 chr5 180915260 20131985 0.11127853449178361 0.6034111331592528 chr6 171115067 26081750 0.15242228786317222 0.8872746971468489 chr7 159138663 19519417 0.12265666075125942 0.9654014504133421 chr8 146364022 30644847 0.20937417940045402 1.3255472259443066 chr9 141213431 11764127 0.08330742279040015 0.8395745900437582 chr10 135534747 14381608 0.10611011802014136 0.71928917346308 chr11 135006516 14982459 0.11097582134480087 0.6813709594861973 chr12 133851895 15167871 0.11331831349866209 0.651096077138321 chr13 115169878 9532675 0.08277055741953639 0.49724948201246333 chr14 107349540 8844635 0.08239099114910041 0.5626753257946487 chr15 102531392 8313856 0.08108595658196077 0.5347076469014598 chr16 90354753 12156741 0.1345445656854377 0.6262989089191214 chr17 81195210 8003198 0.0985673662276383 0.6475730674990037 chr18 78077248 11237574 0.14392892024063142 1.5432294798616375 chr19 59128983 5274540 0.08920396956599101 0.79476913307052 chr20 63025520 6231323 0.09886983875737955 0.5484216714712234 chr21 48129895 5911763 0.12282933507334683 0.5351199853784955 chr22 51304566 3744874 0.07299299637385101 0.4045970811911994 chrMT 16571 391500 23.62561100718122 16.484582339813763 chrX 155270560 19043211 0.12264534242679359 0.7320794504002236 chrY 59373566 715455 0.012050059449014735 0.21107436648089753