BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124796.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 593,387 number of mapped reads = 592,179 (99.8%) number of supplementary alignments = 233,094 (39.28%) number of secondary alignments = 0 number of mapped bases = 87,486,861 bp number of sequenced bases = 87,465,282 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 818,204 duplication rate = 5.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.711 >>>>>>> ACTG content number of A's = 30,356,719 bp (34.71%) number of C's = 19,010,000 bp (21.73%) number of T's = 23,940,057 bp (27.37%) number of G's = 14,158,506 bp (16.19%) number of N's = 0 bp (0%) GC percentage = 37.92% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 630,058 number of insertions = 5,721 mapped reads with insertion percentage = 0.96% number of deletions = 20,725 mapped reads with deletion percentage = 3.46% homopolymer indels = 74.2% >>>>>>> Coverage mean coverageData = 0.0283X std coverageData = 89.7759X There is a 0.03% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 1140370 0.004575194217871176 3.8241053313301143 chr2 243199373 81891 3.3672372995797154E-4 0.14064163493460705 chr3 198022430 82620 4.1722546279227056E-4 0.18406611998348218 chr4 191154276 36833 1.9268729306374502E-4 0.01641484215008829 chr5 180915260 42216 2.333468166256401E-4 0.015406154166426466 chr6 171115067 85533 4.998566257172432E-4 0.28008139782932134 chr7 159138663 159245 0.0010006682034270956 0.4683266135619997 chr8 146364022 62444 4.266349007545037E-4 0.02280532164293441 chr9 141213431 32308 2.2878843585352727E-4 0.015298371852190702 chr10 135534747 85238306 0.6289037157386659 429.0226162859354 chr11 135006516 30150 2.2332255429804589E-4 0.01496262318276128 chr12 133851895 38795 2.8983526904867505E-4 0.01833285867525791 chr13 115169878 14898 1.2935674031017033E-4 0.0114802990854712 chr14 107349540 85694 7.982707704196963E-4 0.5646678940106648 chr15 102531392 53463 5.214305488020684E-4 0.15341381357777548 chr16 90354753 33854 3.746786845845287E-4 0.030079409837936444 chr17 81195210 26498 3.263493006545583E-4 0.040849562751615005 chr18 78077248 11601 1.4858361811113013E-4 0.012307272953896812 chr19 59128983 84183 0.0014237180436538204 0.4178877653032693 chr20 63025520 20137 3.195054955516432E-4 0.019358363443425914 chr21 48129895 8231 1.7101637142570122E-4 0.013075410311933086 chr22 51304566 7318 1.426383764751075E-4 0.011930035311660333 chrMT 16571 120 0.007241566592239454 0.08478871567331124 chrX 155270560 96107 6.18964728406982E-4 0.39124315997390596 chrY 59373566 14046 2.3656992406351338E-4 0.01639618767974648