BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818912.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 2,219,798 number of mapped reads = 2,112,015 (95.14%) number of supplementary alignments = 30,503 (1.37%) number of secondary alignments = 0 number of mapped bases = 195,928,604 bp number of sequenced bases = 195,803,582 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 552,248 duplication rate = 21.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.277 >>>>>>> ACTG content number of A's = 56,025,997 bp (28.61%) number of C's = 38,914,999 bp (19.87%) number of T's = 56,387,719 bp (28.8%) number of G's = 44,472,035 bp (22.71%) number of N's = 2,832 bp (0%) GC percentage = 42.59% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 1,193,889 number of insertions = 26,698 mapped reads with insertion percentage = 1.23% number of deletions = 64,465 mapped reads with deletion percentage = 2.98% homopolymer indels = 41.83% >>>>>>> Coverage mean coverageData = 0.0633X std coverageData = 0.7836X There is a 4.11% of reference with a coverageData >= 1X There is a 1.24% of reference with a coverageData >= 2X There is a 0.45% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% 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 17824109 0.07151079073941405 1.2357350874872237 chr2 243199373 14324234 0.05889914033618828 1.09068100424007 chr3 198022430 12129264 0.06125197029447624 0.35211882072801726 chr4 191154276 9450243 0.0494377797753266 0.43174397863986436 chr5 180915260 10256962 0.05669484155178507 0.3607099337615745 chr6 171115067 9375704 0.054791808602102816 0.3651359508212542 chr7 159138663 16890400 0.10613636989020073 1.768475428648062 chr8 146364022 18463565 0.12614824837213068 0.6585102024304833 chr9 141213431 6993861 0.04952688246771655 0.6202867240818656 chr10 135534747 8458023 0.0624048311389846 0.9343551299932871 chr11 135006516 8335118 0.0617386348967038 0.43998657916229145 chr12 133851895 7307946 0.05459725467465365 0.33477103374679723 chr13 115169878 6087360 0.05285548709185921 0.3210920297980391 chr14 107349540 6374190 0.05937789766029738 0.38393294463617356 chr15 102531392 5146743 0.05019675340016841 0.3144422614908005 chr16 90354753 4697377 0.051988156063024156 0.7997753516565732 chr17 81195210 5068799 0.06242731560149915 0.45853029135334294 chr18 78077248 3367871 0.043135114085988274 0.7189792102383533 chr19 59128983 4058737 0.06864209046179603 1.1355928049689539 chr20 63025520 7848986 0.12453663214520086 0.5469144307583047 chr21 48129895 2306726 0.047927093961040224 0.38368131472462086 chr22 51304566 2324599 0.045309787826681935 0.33293961655504456 chrMT 16571 437416 26.39647577092511 16.208574351118788 chrX 155270560 7718016 0.04970688583850023 0.3961516124031326 chrY 59373566 682355 0.011492572300609332 0.8892914302073434