BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080758.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 = 4,646,970 number of mapped reads = 3,529,754 (75.96%) number of supplementary alignments = 29,502 (0.63%) number of secondary alignments = 0 number of mapped bases = 225,786,459 bp number of sequenced bases = 225,705,320 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 449,886 duplication rate = 9.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9497 >>>>>>> ACTG content number of A's = 71,377,769 bp (31.62%) number of C's = 45,149,787 bp (20%) number of T's = 58,227,545 bp (25.8%) number of G's = 50,876,429 bp (22.54%) number of N's = 73,790 bp (0.03%) GC percentage = 42.54% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 1,557,814 number of insertions = 16,556 mapped reads with insertion percentage = 0.46% number of deletions = 43,144 mapped reads with deletion percentage = 1.21% homopolymer indels = 44.09% >>>>>>> Coverage mean coverageData = 0.0729X std coverageData = 0.5016X There is a 4.71% of reference with a coverageData >= 1X There is a 1.42% of reference with a coverageData >= 2X There is a 0.56% of reference with a coverageData >= 3X There is a 0.26% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 27929850 0.11205528751721745 0.7109910070552973 chr2 243199373 16471305 0.06772758003779887 0.4594569998199246 chr3 198022430 13945599 0.07042434031336753 0.39326878387055314 chr4 191154276 13492942 0.0705866605882256 0.4443697059699169 chr5 180915260 16873715 0.09326861095078436 0.4612757110511614 chr6 171115067 14841323 0.08673299937988511 0.5155013528936233 chr7 159138663 15119457 0.09500806852951882 0.5974884642779009 chr8 146364022 10610078 0.07249102515097597 0.8731020944311263 chr9 141213431 8265072 0.05852893695359615 0.3892781726807319 chr10 135534747 9788472 0.07222112570144097 0.5751170447435303 chr11 135006516 9126458 0.06760012975966286 0.4222780149106286 chr12 133851895 8934114 0.06674626459341498 0.38707506525272667 chr13 115169878 8888743 0.07717940796985129 0.41896754577126777 chr14 107349540 6040676 0.056271093476506745 0.3855009909505901 chr15 102531392 5631740 0.05492698275275537 0.3478054323801964 chr16 90354753 5705138 0.06314153722494266 0.40516532643446973 chr17 81195210 6359605 0.07832487901687797 0.42705398258095745 chr18 78077248 2823796 0.0361666948097351 0.4399233606207606 chr19 59128983 3830814 0.06478741567396822 0.6061621815242468 chr20 63025520 4010210 0.06362835245151488 0.39085314609823074 chr21 48129895 3375518 0.07013350018735756 0.452915661841586 chr22 51304566 1585278 0.030899355039861364 0.25602194733621536 chrMT 16571 33151 2.000543117494418 2.332248514752457 chrX 155270560 11481688 0.07394632955532587 0.4144241955732555 chrY 59373566 621717 0.010471276055745077 0.27566643382428235