BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1505989.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 7,672,424 number of mapped reads = 5,741,035 (74.83%) number of supplementary alignments = 228 (0%) number of secondary alignments = 0 number of mapped bases = 267,867,317 bp number of sequenced bases = 267,809,929 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 337,585 duplication rate = 4.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5131 >>>>>>> ACTG content number of A's = 81,358,200 bp (30.38%) number of C's = 53,316,495 bp (19.91%) number of T's = 79,229,097 bp (29.58%) number of G's = 53,904,999 bp (20.13%) number of N's = 1,138 bp (0%) GC percentage = 40.04% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 1,239,819 number of insertions = 11,720 mapped reads with insertion percentage = 0.2% number of deletions = 41,023 mapped reads with deletion percentage = 0.71% homopolymer indels = 48.2% >>>>>>> Coverage mean coverageData = 0.0865X std coverageData = 0.8046X There is a 6% of reference with a coverageData >= 1X There is a 1.72% of reference with a coverageData >= 2X There is a 0.52% of reference with a coverageData >= 3X There is a 0.16% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% 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% 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 28283323 0.11347343042326863 1.8042386578322773 chr2 243199373 15983420 0.06572146878026697 0.549327918038578 chr3 198022430 16582949 0.0837427810576812 0.394781579371439 chr4 191154276 14060170 0.07355404385513196 0.37837610368565733 chr5 180915260 18564926 0.10261669468899418 0.4448133565325133 chr6 171115067 17457450 0.10202169981910476 0.5629773790708145 chr7 159138663 16573185 0.10414304536415515 1.24242204102929 chr8 146364022 15503260 0.10592261532687315 1.2320807262831324 chr9 141213431 12851389 0.09100684622555485 0.5657587692406892 chr10 135534747 8444354 0.06230397877232176 0.688631416667466 chr11 135006516 13421280 0.09941209059864933 0.6562106553329783 chr12 133851895 7244147 0.05412061592404052 0.34985997822989373 chr13 115169878 7953275 0.06905690218756678 0.34840624770163264 chr14 107349540 9502706 0.08852116180469893 0.45840934437023517 chr15 102531392 9134884 0.08909353342242735 0.3971381111877305 chr16 90354753 8232619 0.09111439881862109 0.44694046615532823 chr17 81195210 4384063 0.05399410876577571 0.34815086581791593 chr18 78077248 7948821 0.10180713592774171 1.0276932456925985 chr19 59128983 5680808 0.09607484708471986 1.1614115677745702 chr20 63025520 6900125 0.10948144497657457 0.4511998854589457 chr21 48129895 3993151 0.08296612739337994 0.4308671209253022 chr22 51304566 1949212 0.03799295368759186 0.2510296650265463 chrMT 16571 106655 6.436244040794159 5.231450568899594 chrX 155270560 16424516 0.10577997528958484 0.5483167439354638 chrY 59373566 686629 0.011564557197052978 0.1964329212014564