BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472383.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 18,066,552 number of mapped reads = 17,925,621 (99.22%) number of supplementary alignments = 65,699 (0.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,984,729 number of mapped paired reads (second in pair) = 8,940,892 number of mapped paired reads (both in pair) = 17,850,846 number of mapped paired reads (singletons) = 74,775 number of mapped bases = 1,750,614,221 bp number of sequenced bases = 1,750,415,202 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,186,053 duplication rate = 47.71% >>>>>>> Insert size mean insert size = 16,017.9126 std insert size = 1,252,930.1811 median insert size = 207 >>>>>>> Mapping quality mean mapping quality = 54.8236 >>>>>>> ACTG content number of A's = 471,422,100 bp (26.93%) number of C's = 404,859,188 bp (23.13%) number of T's = 472,077,387 bp (26.97%) number of G's = 401,837,594 bp (22.96%) number of N's = 218,933 bp (0.01%) GC percentage = 46.09% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 8,904,221 number of insertions = 98,584 mapped reads with insertion percentage = 0.54% number of deletions = 80,769 mapped reads with deletion percentage = 0.44% homopolymer indels = 45.67% >>>>>>> Coverage mean coverageData = 0.5655X std coverageData = 16.8673X There is a 4.86% of reference with a coverageData >= 1X There is a 2.16% of reference with a coverageData >= 2X There is a 0.89% of reference with a coverageData >= 3X There is a 0.67% of reference with a coverageData >= 4X There is a 0.51% of reference with a coverageData >= 5X There is a 0.46% of reference with a coverageData >= 6X There is a 0.42% of reference with a coverageData >= 7X There is a 0.4% of reference with a coverageData >= 8X There is a 0.39% of reference with a coverageData >= 9X There is a 0.37% of reference with a coverageData >= 10X There is a 0.36% of reference with a coverageData >= 11X There is a 0.35% of reference with a coverageData >= 12X There is a 0.34% of reference with a coverageData >= 13X There is a 0.33% of reference with a coverageData >= 14X There is a 0.32% of reference with a coverageData >= 15X There is a 0.31% of reference with a coverageData >= 16X There is a 0.31% of reference with a coverageData >= 17X There is a 0.3% of reference with a coverageData >= 18X There is a 0.29% of reference with a coverageData >= 19X There is a 0.29% of reference with a coverageData >= 20X There is a 0.28% of reference with a coverageData >= 21X There is a 0.28% of reference with a coverageData >= 22X There is a 0.27% of reference with a coverageData >= 23X There is a 0.27% of reference with a coverageData >= 24X There is a 0.26% of reference with a coverageData >= 25X There is a 0.26% of reference with a coverageData >= 26X There is a 0.25% of reference with a coverageData >= 27X There is a 0.25% of reference with a coverageData >= 28X There is a 0.25% of reference with a coverageData >= 29X There is a 0.24% of reference with a coverageData >= 30X There is a 0.24% of reference with a coverageData >= 31X There is a 0.24% of reference with a coverageData >= 32X There is a 0.23% of reference with a coverageData >= 33X There is a 0.23% of reference with a coverageData >= 34X There is a 0.23% of reference with a coverageData >= 35X There is a 0.22% of reference with a coverageData >= 36X There is a 0.22% of reference with a coverageData >= 37X There is a 0.22% of reference with a coverageData >= 38X There is a 0.21% of reference with a coverageData >= 39X There is a 0.21% of reference with a coverageData >= 40X There is a 0.21% of reference with a coverageData >= 41X There is a 0.21% of reference with a coverageData >= 42X There is a 0.2% of reference with a coverageData >= 43X There is a 0.2% of reference with a coverageData >= 44X There is a 0.2% of reference with a coverageData >= 45X There is a 0.2% of reference with a coverageData >= 46X There is a 0.19% of reference with a coverageData >= 47X There is a 0.19% of reference with a coverageData >= 48X There is a 0.19% of reference with a coverageData >= 49X There is a 0.19% of reference with a coverageData >= 50X There is a 0.19% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 157714046 0.6327528708544321 18.82916452011932 chr2 243199373 137137736 0.56389017088461 16.395543742475876 chr3 198022430 129022311 0.6515540234507777 17.576691378560465 chr4 191154276 43297608 0.2265060918647721 8.652384651939716 chr5 180915260 61723179 0.341171767378827 12.285585128948185 chr6 171115067 160420642 0.9375015585272803 22.37714185937919 chr7 159138663 163728343 1.028840760086064 27.684267669739143 chr8 146364022 75218953 0.5139169583628961 14.365342209287011 chr9 141213431 57004275 0.4036745980628429 9.896647295802198 chr10 135534747 58322570 0.4303145229614071 14.533716318307201 chr11 135006516 53901772 0.3992531145681887 12.30723691235244 chr12 133851895 84284587 0.6296854220853578 14.082643853485898 chr13 115169878 74469378 0.6466046443150699 23.827859591860303 chr14 107349540 31258155 0.2911810800493416 9.662463233731508 chr15 102531392 47143608 0.45979682008023454 17.69805761238834 chr16 90354753 75644129 0.8371903689449519 19.491361506302383 chr17 81195210 70997223 0.8744016180264821 18.044291082074007 chr18 78077248 17094459 0.21894289870462647 6.972197408103079 chr19 59128983 48699663 0.8236174635372978 16.540627108673046 chr20 63025520 51057094 0.8101019079255515 22.06781322547441 chr21 48129895 17839892 0.3706613529906932 21.68046957939591 chr22 51304566 16282886 0.3173769367818061 9.009852704284636 chrMT 16571 8492 0.5124615291774788 0.8344383085058603 chrX 155270560 117978100 0.7598227249260903 18.11697788548636 chrY 59373566 365120 0.0061495379947365805 0.39897020424184787