BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081164.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 = 2,042,717 number of mapped reads = 1,835,983 (89.88%) number of supplementary alignments = 13,804 (0.68%) number of secondary alignments = 0 number of mapped bases = 123,816,831 bp number of sequenced bases = 123,770,648 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 64,503 duplication rate = 2.72% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3468 >>>>>>> ACTG content number of A's = 35,067,425 bp (28.33%) number of C's = 22,864,826 bp (18.47%) number of T's = 38,844,375 bp (31.38%) number of G's = 26,957,002 bp (21.78%) number of N's = 37,020 bp (0.03%) GC percentage = 40.25% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,033,025 number of insertions = 10,047 mapped reads with insertion percentage = 0.54% number of deletions = 28,349 mapped reads with deletion percentage = 1.53% homopolymer indels = 47.09% >>>>>>> Coverage mean coverageData = 0.04X std coverageData = 0.3357X There is a 3.54% of reference with a coverageData >= 1X There is a 0.34% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 9649784 0.038715185387642424 0.5342168823078024 chr2 243199373 10877309 0.04472589244709936 0.4059954282859956 chr3 198022430 8246558 0.04164456521415276 0.22345313958319243 chr4 191154276 8453034 0.04422100398109849 0.23825437260784454 chr5 180915260 7863829 0.04346691926374812 0.2294316664194708 chr6 171115067 7193910 0.04204135922174521 0.2756541966738154 chr7 159138663 6581084 0.04135440047023645 0.43961555086509907 chr8 146364022 6483177 0.04429488142926272 0.46601067176804933 chr9 141213431 5396280 0.03821364555613694 0.3440267945212874 chr10 135534747 5787593 0.04270191318540625 0.31187855564307465 chr11 135006516 5094036 0.0377317788128093 0.2775072315460091 chr12 133851895 5508429 0.04115316409976863 0.22704575659397044 chr13 115169878 4037408 0.03505611076535134 0.20483575459093242 chr14 107349540 3953798 0.03683106606698082 0.23020135844205009 chr15 102531392 3555845 0.03468054934824254 0.2057846732132189 chr16 90354753 3418209 0.03783098161974943 0.24141477661748392 chr17 81195210 2967230 0.036544397138698205 0.22754737469380593 chr18 78077248 3515135 0.045021246138183556 0.6199636115156673 chr19 59128983 2092640 0.035391104223794954 0.43681722115092514 chr20 63025520 2444400 0.03878428928472149 0.2266398789435441 chr21 48129895 1713436 0.035600243881687255 0.22152166389813613 chr22 51304566 1285335 0.025053033291422833 0.17188535518564102 chrMT 16571 3506 0.2115744372699294 0.5082783591612875 chrX 155270560 7400669 0.047663053446834996 0.26700478580538417 chrY 59373566 294197 0.004955016513577776 0.11174002786165985