BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083624.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 = 1,746,009 number of mapped reads = 1,611,649 (92.3%) number of supplementary alignments = 15,304 (0.88%) number of secondary alignments = 0 number of mapped bases = 108,543,070 bp number of sequenced bases = 108,502,391 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 65,421 duplication rate = 3.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2762 >>>>>>> ACTG content number of A's = 30,125,407 bp (27.76%) number of C's = 19,829,352 bp (18.28%) number of T's = 34,659,627 bp (31.94%) number of G's = 23,882,772 bp (22.01%) number of N's = 5,233 bp (0%) GC percentage = 40.29% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 772,038 number of insertions = 8,518 mapped reads with insertion percentage = 0.52% number of deletions = 25,309 mapped reads with deletion percentage = 1.56% homopolymer indels = 49.03% >>>>>>> Coverage mean coverageData = 0.0351X std coverageData = 0.3609X There is a 3.06% of reference with a coverageData >= 1X There is a 0.33% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% 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 10923764 0.04382642641439999 0.8102961378538287 chr2 243199373 9293150 0.038212063976003754 0.4009980348376876 chr3 198022430 9085746 0.0458824083716173 0.24048809811754607 chr4 191154276 4556386 0.02383617094707314 0.17383304788730633 chr5 180915260 5280779 0.029189240310629406 0.1904562429699466 chr6 171115067 7861251 0.04594131386454706 0.31434668013926476 chr7 159138663 8218092 0.05164107731632758 0.5084511615564054 chr8 146364022 7759867 0.053017585154909175 0.40711439045032993 chr9 141213431 4104860 0.029068481453439085 0.2531853492153833 chr10 135534747 4839781 0.035708783962241065 0.2692639191237147 chr11 135006516 3572039 0.026458271095596602 0.22105383383893862 chr12 133851895 3560418 0.026599683179681543 0.18226523199288489 chr13 115169878 3565056 0.03095476058418678 0.19584099144858183 chr14 107349540 2399041 0.022347939264574398 0.16892292706858517 chr15 102531392 2546184 0.024833214007276914 0.18043469424658473 chr16 90354753 3033695 0.033575378154152 0.21367906244307008 chr17 81195210 2247666 0.02768224874349115 0.1903537937809233 chr18 78077248 2992483 0.038327208971299806 0.44708340990319484 chr19 59128983 2835931 0.04796177536150081 0.5464734000422635 chr20 63025520 2310738 0.03666352931320519 0.2157163403485804 chr21 48129895 1700313 0.03532758590061333 0.21101324477814032 chr22 51304566 844189 0.01645446138263795 0.14097763907822708 chrMT 16571 3362 0.20288455735924205 0.49619286302859444 chrX 155270560 4792346 0.030864485836851495 0.20196495649494273 chrY 59373566 215933 0.003636854151559635 0.08427555577297115