BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524468.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,409,019 number of mapped reads = 1,300,832 (92.32%) number of supplementary alignments = 2,772 (0.2%) number of secondary alignments = 0 number of mapped bases = 75,668,208 bp number of sequenced bases = 75,644,587 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 52,835 duplication rate = 3.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3131 >>>>>>> ACTG content number of A's = 18,751,423 bp (24.79%) number of C's = 14,033,486 bp (18.55%) number of T's = 24,269,855 bp (32.08%) number of G's = 18,588,245 bp (24.57%) number of N's = 1,578 bp (0%) GC percentage = 43.13% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 354,004 number of insertions = 4,819 mapped reads with insertion percentage = 0.37% number of deletions = 13,899 mapped reads with deletion percentage = 1.06% homopolymer indels = 44.05% >>>>>>> Coverage mean coverageData = 0.0244X std coverageData = 0.2413X There is a 2.18% of reference with a coverageData >= 1X There is a 0.19% of reference with a coverageData >= 2X There is a 0.03% 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 7475800 0.029993104811562334 0.438661717770501 chr2 243199373 5991297 0.024635330782699017 0.2703891451869262 chr3 198022430 4148928 0.020951808338075643 0.15875584578377303 chr4 191154276 4304863 0.022520359419006666 0.18467664771443845 chr5 180915260 4210422 0.02327289582979346 0.1680639537556832 chr6 171115067 3178758 0.018576727670626455 0.18664970269000092 chr7 159138663 3802180 0.023892245468971923 0.3134980090096028 chr8 146364022 7039306 0.04809451054850078 0.27440132202134626 chr9 141213431 3247755 0.022998910068263975 0.21750539315651565 chr10 135534747 3977818 0.029349064266154568 0.2531713058772923 chr11 135006516 2584122 0.019140720585664177 0.21536717376006365 chr12 133851895 3448900 0.025766538456553044 0.17705014384102297 chr13 115169878 1672928 0.014525742573071059 0.13218763454554477 chr14 107349540 1796737 0.016737258492211516 0.14490093037739038 chr15 102531392 1993100 0.01943892461735036 0.1605452056252378 chr16 90354753 2345732 0.025961357007970573 0.1848621583290634 chr17 81195210 2608668 0.03212834845799401 0.20492306808013758 chr18 78077248 1787075 0.02288855006774829 0.3322584606133121 chr19 59128983 1512021 0.02557157122083429 0.2983338754206141 chr20 63025520 2153263 0.034164938266276895 0.20691568010166497 chr21 48129895 1018886 0.021169503901888837 0.16873983902171316 chr22 51304566 611156 0.011912312054252637 0.11899364705453545 chrMT 16571 4522 0.2728863677508901 0.5435590035889616 chrX 155270560 4505195 0.029015126885611798 0.20340622254371887 chrY 59373566 248776 0.0041900127743716795 0.11756695339741441