BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708647.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 4,530,321 number of mapped reads = 4,395,064 (97.01%) number of supplementary alignments = 118 (0%) number of secondary alignments = 0 number of mapped bases = 219,219,921 bp number of sequenced bases = 219,198,650 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 22,555 duplication rate = 0.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9768 >>>>>>> ACTG content number of A's = 67,795,941 bp (30.93%) number of C's = 41,646,625 bp (19%) number of T's = 67,713,489 bp (30.89%) number of G's = 42,035,234 bp (19.18%) number of N's = 7,361 bp (0%) GC percentage = 38.18% >>>>>>> Mismatches and indels general error rate = 0.0017 number of mismatches = 353,276 number of insertions = 14,915 mapped reads with insertion percentage = 0.34% number of deletions = 12,380 mapped reads with deletion percentage = 0.28% homopolymer indels = 49.16% >>>>>>> Coverage mean coverageData = 0.0708X std coverageData = 0.2815X There is a 6.48% of reference with a coverageData >= 1X There is a 0.54% of reference with a coverageData >= 2X There is a 0.05% 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 20672497 0.08293859777384466 0.30629292502323063 chr2 243199373 18090149 0.0743840281200067 0.2868668980339083 chr3 198022430 21008418 0.1060911029119277 0.34478600127234665 chr4 191154276 14094248 0.07373231870575576 0.28614278876880583 chr5 180915260 11224222 0.062041322550679255 0.26071908421357165 chr6 171115067 15814323 0.09241923155720706 0.3201627892459477 chr7 159138663 11130166 0.06994004970369772 0.2784544770661624 chr8 146364022 11431493 0.07810316253812703 0.2945286995385316 chr9 141213431 10456682 0.07404877798061574 0.28683235922543937 chr10 135534747 6138602 0.04529172139156316 0.22223846664512883 chr11 135006516 8291275 0.06141388760820996 0.26345049140058846 chr12 133851895 12998406 0.09711036216558608 0.330584068917966 chr13 115169878 10025231 0.08704733541525501 0.3115207961140722 chr14 107349540 6433194 0.05992754137558484 0.2568147712453659 chr15 102531392 5451344 0.05316756062377462 0.24391931715022533 chr16 90354753 4442375 0.04916592489605943 0.23229364856686463 chr17 81195210 2814539 0.034663855170766845 0.19385962973472082 chr18 78077248 9601343 0.12297235425101048 0.36992155641855656 chr19 59128983 2011026 0.034010833570399815 0.19126655268299547 chr20 63025520 4222679 0.06699951067440618 0.27166057038264513 chr21 48129895 3529245 0.07332750258441245 0.28814184849576924 chr22 51304566 1515012 0.029529769338658862 0.17975029290035885 chrMT 16571 150 0.009051958240299317 0.1224935064367961 chrX 155270560 6066460 0.03907025259649994 0.20724007793580257 chrY 59373566 1756842 0.02958963253108294 0.18050968646766172