BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708642.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 = 5,326,904 number of mapped reads = 5,141,904 (96.53%) number of supplementary alignments = 124 (0%) number of secondary alignments = 0 number of mapped bases = 256,474,684 bp number of sequenced bases = 256,449,400 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 26,057 duplication rate = 0.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5807 >>>>>>> ACTG content number of A's = 79,289,926 bp (30.92%) number of C's = 48,748,243 bp (19.01%) number of T's = 79,077,820 bp (30.84%) number of G's = 49,324,567 bp (19.23%) number of N's = 8,844 bp (0%) GC percentage = 38.24% >>>>>>> Mismatches and indels general error rate = 0.0017 number of mismatches = 417,855 number of insertions = 17,337 mapped reads with insertion percentage = 0.34% number of deletions = 14,583 mapped reads with deletion percentage = 0.28% homopolymer indels = 49.04% >>>>>>> Coverage mean coverageData = 0.0828X std coverageData = 0.3015X There is a 7.61% of reference with a coverageData >= 1X There is a 0.61% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0% 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 21462073 0.08610639730361996 0.31028174089270544 chr2 243199373 25140630 0.10337456749939894 0.33495220836287715 chr3 198022430 19277089 0.09734800749591851 0.3246312661832331 chr4 191154276 18070385 0.09453298863165373 0.31889913459197095 chr5 180915260 19931637 0.1101711209988588 0.3457497036852852 chr6 171115067 13547796 0.079173600767722 0.29185833189549143 chr7 159138663 14352760 0.09019027638808301 0.3142692609549601 chr8 146364022 15091713 0.10311081093412423 0.33464235716186236 chr9 141213431 9488135 0.06719003237022121 0.27112901494581665 chr10 135534747 11457619 0.0845363956742399 0.3028510074662646 chr11 135006516 12175828 0.09018696549431733 0.3159159566056859 chr12 133851895 10991312 0.08211547546637274 0.2982947799339405 chr13 115169878 9001705 0.07816023734956114 0.2926729835291584 chr14 107349540 7187401 0.06695325382856787 0.2702673204410341 chr15 102531392 5799071 0.056558980492530525 0.24789053479639292 chr16 90354753 5158572 0.05709242545325756 0.25005771649664676 chr17 81195210 3747958 0.04615984120245517 0.22506452400843932 chr18 78077248 12096782 0.15493350892695398 0.41594810929479065 chr19 59128983 1918546 0.032446795169806995 0.18542238913740347 chr20 63025520 3580753 0.05681433489164389 0.2471285852405963 chr21 48129895 3503953 0.07280200798277245 0.2862790858547439 chr22 51304566 1309825 0.025530378719118296 0.1656510388998314 chrMT 16571 150 0.009051958240299317 0.09471019106894038 chrX 155270560 11225713 0.07229775560801739 0.2787049895679512 chrY 59373566 957278 0.016122966237197205 0.13137944639400786