BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084845.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 = 2,935,829 number of mapped reads = 2,598,355 (88.5%) number of supplementary alignments = 22,262 (0.76%) number of secondary alignments = 0 number of mapped bases = 179,880,533 bp number of sequenced bases = 179,808,841 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 143,865 duplication rate = 4.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.0889 >>>>>>> ACTG content number of A's = 52,345,969 bp (29.11%) number of C's = 32,951,826 bp (18.33%) number of T's = 57,814,886 bp (32.15%) number of G's = 36,667,811 bp (20.39%) number of N's = 28,349 bp (0.02%) GC percentage = 38.72% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,519,823 number of insertions = 15,143 mapped reads with insertion percentage = 0.58% number of deletions = 39,917 mapped reads with deletion percentage = 1.52% homopolymer indels = 47.73% >>>>>>> Coverage mean coverageData = 0.0581X std coverageData = 0.5293X There is a 4.57% of reference with a coverageData >= 1X There is a 0.9% of reference with a coverageData >= 2X There is a 0.18% 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% 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 14636744 0.05872299912945854 0.9673924123499306 chr2 243199373 14121999 0.05806757980416339 0.46259879079956995 chr3 198022430 12561973 0.06343712174423877 0.3056308101346461 chr4 191154276 12972001 0.06786142204844008 0.34466335104975304 chr5 180915260 11991838 0.06628428138123893 0.3130458206151233 chr6 171115067 11438479 0.06684670847833639 0.330031057336074 chr7 159138663 10602734 0.06662575768906642 0.43671740226612915 chr8 146364022 8462905 0.05782093771651069 1.2165716637708006 chr9 141213431 7510277 0.053183871723929715 0.445082660010125 chr10 135534747 8914320 0.0657714733477165 0.49606047444865975 chr11 135006516 7828610 0.05798690486909536 0.3590797623608715 chr12 133851895 7968687 0.05953361362571669 0.30157889655584275 chr13 115169878 5810270 0.050449562862261606 0.2710176583276596 chr14 107349540 5476458 0.05101519764313848 0.30287405362666514 chr15 102531392 4917034 0.04795637613112675 0.26361272774524824 chr16 90354753 4367039 0.04833214474063141 0.3031123812190008 chr17 81195210 4130039 0.050865549827385136 0.3156328374266246 chr18 78077248 5173202 0.06625748387033313 0.8973478507240439 chr19 59128983 2782598 0.047059798068909794 0.6726241757448398 chr20 63025520 3214312 0.051000166281849 0.293490936922018 chr21 48129895 2340845 0.048635988090146465 0.2938674164310295 chr22 51304566 1460042 0.028458324742480036 0.20049763794600203 chrMT 16571 133702 8.068432804296663 4.943874157098881 chrX 155270560 10615246 0.06836612169106622 0.3512504789153781 chrY 59373566 449179 0.0075653027140057585 0.20485549215551407