BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240249.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,274,593 number of mapped reads = 2,755,936 (84.16%) number of supplementary alignments = 31,520 (0.96%) number of secondary alignments = 0 number of mapped bases = 185,578,450 bp number of sequenced bases = 185,510,550 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 433,445 duplication rate = 10.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9597 >>>>>>> ACTG content number of A's = 53,435,544 bp (28.8%) number of C's = 34,485,909 bp (18.59%) number of T's = 58,777,890 bp (31.68%) number of G's = 38,793,017 bp (20.91%) number of N's = 18,190 bp (0.01%) GC percentage = 39.5% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 1,437,071 number of insertions = 13,618 mapped reads with insertion percentage = 0.49% number of deletions = 39,353 mapped reads with deletion percentage = 1.41% homopolymer indels = 48.05% >>>>>>> Coverage mean coverageData = 0.0599X std coverageData = 0.7795X There is a 2.31% of reference with a coverageData >= 1X There is a 1.34% of reference with a coverageData >= 2X There is a 0.85% of reference with a coverageData >= 3X There is a 0.53% of reference with a coverageData >= 4X There is a 0.33% of reference with a coverageData >= 5X There is a 0.2% of reference with a coverageData >= 6X There is a 0.12% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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 11881461 0.04766873178622893 0.9180129120790445 chr2 243199373 17468347 0.07182726988362753 0.7639869871137147 chr3 198022430 12053502 0.06086937727205954 0.5064095643332458 chr4 191154276 16018770 0.08380021799773917 0.6167310226824841 chr5 180915260 10403192 0.057503120521729345 0.49615307249552976 chr6 171115067 11028789 0.06445247162250184 0.5725880445601107 chr7 159138663 10961095 0.06887763660550547 0.7567656957708453 chr8 146364022 9159858 0.06258271585349028 2.0130944075252826 chr9 141213431 8131902 0.057585896344378176 0.7321849216804165 chr10 135534747 7908357 0.05834929547623681 0.5794131440773648 chr11 135006516 7612523 0.05638633767869397 0.5885855172111388 chr12 133851895 7807890 0.058332308257570804 0.5061820282749976 chr13 115169878 7108376 0.061720791264535335 0.5185189322087931 chr14 107349540 4916007 0.045794392784542906 0.49180850764173584 chr15 102531392 4323919 0.042171659973171925 0.41118198011970497 chr16 90354753 5739267 0.06351925946828718 0.5518597397469417 chr17 81195210 4352421 0.05360440597419478 0.49489820073051793 chr18 78077248 5564364 0.07126741967134907 1.4861298834990386 chr19 59128983 3088917 0.05224032011509482 0.6902132142458849 chr20 63025520 2831315 0.04492331043044151 0.46290692412675116 chr21 48129895 2390387 0.049665327547462966 0.4810320502938385 chr22 51304566 1479614 0.028839811255785695 0.322514637841387 chrMT 16571 47255 2.8516685776356283 3.5885045011582575 chrX 155270560 12794848 0.08240356703807857 0.6346105323693028 chrY 59373566 506074 0.008523557436317704 0.21641111643638458