BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084803.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 = 1,901,026 number of mapped reads = 1,727,659 (90.88%) number of supplementary alignments = 18,748 (0.99%) number of secondary alignments = 0 number of mapped bases = 116,110,258 bp number of sequenced bases = 116,065,640 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 77,677 duplication rate = 3.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8825 >>>>>>> ACTG content number of A's = 32,166,808 bp (27.71%) number of C's = 21,558,618 bp (18.57%) number of T's = 36,723,830 bp (31.64%) number of G's = 25,600,004 bp (22.06%) number of N's = 16,380 bp (0.01%) GC percentage = 40.63% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 875,956 number of insertions = 9,468 mapped reads with insertion percentage = 0.54% number of deletions = 26,814 mapped reads with deletion percentage = 1.54% homopolymer indels = 48.43% >>>>>>> Coverage mean coverageData = 0.0375X std coverageData = 0.271X There is a 3.11% of reference with a coverageData >= 1X There is a 0.49% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% 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 9770967 0.03920137474802921 0.3446160350272717 chr2 243199373 9490122 0.03902198382723626 0.39392177312748733 chr3 198022430 9185648 0.04638690677616672 0.25486267252041594 chr4 191154276 7077202 0.03702350869723678 0.2297651052867056 chr5 180915260 6369163 0.03520522812724587 0.22039748164499046 chr6 171115067 7286638 0.04258326357666681 0.25887443969287416 chr7 159138663 6192856 0.03891484246037683 0.2668623787845046 chr8 146364022 5760693 0.039358668348154574 0.281505685041714 chr9 141213431 7690615 0.05446093155260848 0.32174488502150456 chr10 135534747 4746441 0.035020104475496604 0.22934595291093082 chr11 135006516 4742402 0.035127208230453115 0.26313578282580563 chr12 133851895 4816537 0.03598407777491682 0.22337831255769675 chr13 115169878 3588709 0.03116013546528199 0.20837627833443387 chr14 107349540 2634509 0.024541409306458137 0.1853004027141002 chr15 102531392 2377900 0.023191921553157104 0.18454189168737686 chr16 90354753 1870797 0.0207050203546016 0.17530984446463418 chr17 81195210 2690315 0.03313391270248577 0.218885823343299 chr18 78077248 4871050 0.06238757288166714 0.4205481706102117 chr19 59128983 2365037 0.03999793130215008 0.281912027467415 chr20 63025520 2329900 0.03696756488482761 0.23013130594581338 chr21 48129895 1127285 0.02342172157242396 0.18185193487826184 chr22 51304566 1231136 0.02399661659743891 0.18106003674030063 chrMT 16571 23535 1.4202522479029631 1.520461390449027 chrX 155270560 7631221 0.0491478938441389 0.27059809380917466 chrY 59373566 239580 0.004035129033684789 0.08122825467483336