BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084784.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 = 1,617,170 number of mapped reads = 1,460,869 (90.33%) number of supplementary alignments = 12,117 (0.75%) number of secondary alignments = 0 number of mapped bases = 98,254,248 bp number of sequenced bases = 98,211,172 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 53,831 duplication rate = 2.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8162 >>>>>>> ACTG content number of A's = 27,147,555 bp (27.64%) number of C's = 18,173,694 bp (18.5%) number of T's = 31,151,581 bp (31.72%) number of G's = 21,700,182 bp (22.1%) number of N's = 38,160 bp (0.04%) GC percentage = 40.6% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 867,945 number of insertions = 7,594 mapped reads with insertion percentage = 0.52% number of deletions = 26,411 mapped reads with deletion percentage = 1.79% homopolymer indels = 46.87% >>>>>>> Coverage mean coverageData = 0.0317X std coverageData = 0.2895X There is a 2.85% of reference with a coverageData >= 1X There is a 0.24% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 7964926 0.03195549109584766 0.4777365765339196 chr2 243199373 8189958 0.03367590096541902 0.36041185689057653 chr3 198022430 6797356 0.034326192239939685 0.20062924057171536 chr4 191154276 6518299 0.03409967664024424 0.20813517128709894 chr5 180915260 6175651 0.03413560028048491 0.2011041708534916 chr6 171115067 5723315 0.03344717154568277 0.24343931396941235 chr7 159138663 5415848 0.03403225776755458 0.34535216869830265 chr8 146364022 5144641 0.03514962850638253 0.325449477549772 chr9 141213431 4200002 0.029742227564742055 0.2785419509814448 chr10 135534747 4524265 0.033380849561773264 0.2704850495446781 chr11 135006516 4527971 0.03353890711467586 0.26487585962121807 chr12 133851895 3997902 0.02986810160588313 0.19111216058631275 chr13 115169878 3196373 0.027753550281610962 0.1811072436608427 chr14 107349540 3094158 0.02882320688099828 0.19650036946432917 chr15 102531392 2767506 0.02699179193821927 0.18416677150089655 chr16 90354753 2688833 0.029758622659286114 0.20688704713221764 chr17 81195210 2534842 0.03121910762962495 0.22168996443755462 chr18 78077248 2759358 0.035341383958614934 0.5764893912021956 chr19 59128983 1832392 0.03098974321949694 0.36179110402057274 chr20 63025520 1972861 0.031302573941476404 0.20448093499209824 chr21 48129895 1295598 0.026918778858752965 0.1858051125250196 chr22 51304566 1003232 0.019554438877818398 0.14985746955023152 chrMT 16571 6098 0.36799227566230164 0.631480731303084 chrX 155270560 5693262 0.036666719048350185 0.2351895933481387 chrY 59373566 229601 0.003867057606073383 0.09223302481051794