BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081960.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 = 3,605,771 number of mapped reads = 3,328,757 (92.32%) number of supplementary alignments = 21,116 (0.59%) number of secondary alignments = 0 number of mapped bases = 232,449,752 bp number of sequenced bases = 232,358,302 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 149,404 duplication rate = 3.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.4024 >>>>>>> ACTG content number of A's = 67,876,731 bp (29.21%) number of C's = 43,121,566 bp (18.56%) number of T's = 73,591,530 bp (31.67%) number of G's = 47,738,028 bp (20.55%) number of N's = 30,447 bp (0.01%) GC percentage = 39.1% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 1,750,774 number of insertions = 16,497 mapped reads with insertion percentage = 0.49% number of deletions = 52,172 mapped reads with deletion percentage = 1.55% homopolymer indels = 48.02% >>>>>>> Coverage mean coverageData = 0.0751X std coverageData = 0.634X There is a 6.19% of reference with a coverageData >= 1X There is a 0.95% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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% 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 21913614 0.0879179915864683 1.3469872233547773 chr2 243199373 21435521 0.08813970503122967 0.7328230838095726 chr3 198022430 15326708 0.0773988482011861 0.32859272849809884 chr4 191154276 10580107 0.05534852382794722 0.29701668166558864 chr5 180915260 12860115 0.07108363882626595 0.3113454934203424 chr6 171115067 20215365 0.11813901227061437 0.5687684947879195 chr7 159138663 15185401 0.095422449288769 0.7320790194735001 chr8 146364022 13585402 0.09281927221158216 0.8815122253332484 chr9 141213431 10573691 0.07487737480155128 0.587554046316624 chr10 135534747 9961475 0.07349757328281285 0.7180909720555403 chr11 135006516 10230725 0.07577949052473883 0.41181658452766756 chr12 133851895 9938804 0.07425224723191255 0.32664833869280535 chr13 115169878 5560236 0.048278561170308786 0.2504209842943446 chr14 107349540 5819902 0.05421450338771829 0.29541053147362106 chr15 102531392 4866557 0.04746406837039723 0.25022855641671843 chr16 90354753 4594467 0.05084920103760341 0.34100895109482493 chr17 81195210 5665961 0.06978196127579447 0.3457653282860547 chr18 78077248 6706612 0.08589713612856846 0.8854890875597443 chr19 59128983 4367317 0.07386085094681909 0.9099061092810202 chr20 63025520 5857986 0.09294625415228625 0.3585340222417974 chr21 48129895 2540446 0.05278311951438913 0.3063904857202001 chr22 51304566 1830591 0.035680859282583154 0.21306100928718003 chrMT 16571 113694 6.861022267817271 4.202251545861986 chrX 155270560 12245844 0.07886777763923825 0.3841307967676503 chrY 59373566 473211 0.007970061963264932 0.1869088776412606