BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081232.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 = 2,014,587 number of mapped reads = 1,773,130 (88.01%) number of supplementary alignments = 21,260 (1.06%) number of secondary alignments = 0 number of mapped bases = 116,441,512 bp number of sequenced bases = 116,397,843 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 75,388 duplication rate = 3.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4913 >>>>>>> ACTG content number of A's = 33,102,510 bp (28.44%) number of C's = 22,456,830 bp (19.29%) number of T's = 35,687,755 bp (30.66%) number of G's = 25,142,186 bp (21.6%) number of N's = 8,562 bp (0.01%) GC percentage = 40.89% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 994,091 number of insertions = 8,469 mapped reads with insertion percentage = 0.47% number of deletions = 26,582 mapped reads with deletion percentage = 1.48% homopolymer indels = 48.29% >>>>>>> Coverage mean coverageData = 0.0376X std coverageData = 0.2675X There is a 3.06% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% 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 12618807 0.0506269831921502 0.36309613432346033 chr2 243199373 7185189 0.029544438833730053 0.2947445763455557 chr3 198022430 7096870 0.03583871786645584 0.22691981383411675 chr4 191154276 5074430 0.026546254188946315 0.19398462194962646 chr5 180915260 6811131 0.03764818401720231 0.22981739716503702 chr6 171115067 9085313 0.05309475757619871 0.29838684823142464 chr7 159138663 8954503 0.05626855744037513 0.3697492817616497 chr8 146364022 6268274 0.042826603931395105 0.3135440881143184 chr9 141213431 2450886 0.017355898675105487 0.18064303712866722 chr10 135534747 3709321 0.02736804459449797 0.22871132434901403 chr11 135006516 6567587 0.048646444590867005 0.289651254008394 chr12 133851895 3690843 0.027574081039345763 0.1973564347527426 chr13 115169878 4056129 0.03521866194909054 0.2251986390650998 chr14 107349540 4162526 0.03877544328555111 0.24037927403185877 chr15 102531392 1814030 0.0176924351129457 0.1648790818793424 chr16 90354753 4141022 0.045830704666969764 0.2581632880719804 chr17 81195210 2285582 0.028149222103126526 0.20871325952701875 chr18 78077248 3376916 0.04325096089452333 0.3158979773573505 chr19 59128983 2921375 0.04940681966405544 0.32733336992208656 chr20 63025520 3341832 0.05302347366590549 0.2790130753649277 chr21 48129895 2075820 0.04312953518805723 0.252567042317357 chr22 51304566 850023 0.016568174458390313 0.15281730728800166 chrMT 16571 107510 6.487840202763865 4.731825631873322 chrX 155270560 7526477 0.048473303632060066 0.2693504148162489 chrY 59373566 269116 0.004532589469192401 0.08846472743923357