BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238609.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 = 3,829,772 number of mapped reads = 3,359,903 (87.73%) number of supplementary alignments = 31,814 (0.83%) number of secondary alignments = 0 number of mapped bases = 205,805,702 bp number of sequenced bases = 205,691,230 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,185,564 duplication rate = 20.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 37.5199 >>>>>>> ACTG content number of A's = 51,088,488 bp (24.84%) number of C's = 36,261,176 bp (17.63%) number of T's = 69,003,935 bp (33.55%) number of G's = 49,327,444 bp (23.98%) number of N's = 10,187 bp (0%) GC percentage = 41.61% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 1,307,420 number of insertions = 12,947 mapped reads with insertion percentage = 0.38% number of deletions = 68,171 mapped reads with deletion percentage = 2.01% homopolymer indels = 40.34% >>>>>>> Coverage mean coverageData = 0.0665X std coverageData = 1.0798X There is a 2.36% of reference with a coverageData >= 1X There is a 1.21% of reference with a coverageData >= 2X There is a 0.83% of reference with a coverageData >= 3X There is a 0.59% of reference with a coverageData >= 4X There is a 0.42% of reference with a coverageData >= 5X There is a 0.3% of reference with a coverageData >= 6X There is a 0.22% of reference with a coverageData >= 7X There is a 0.16% of reference with a coverageData >= 8X There is a 0.11% of reference with a coverageData >= 9X There is a 0.08% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% 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 4310493 0.01729381047359557 1.0849660816752662 chr2 243199373 4467206 0.01836849307995543 2.4538089638473872 chr3 198022430 18619738 0.09402842900170451 0.7344522689403817 chr4 191154276 23208978 0.1214149036352187 0.8412270426729499 chr5 180915260 24706841 0.1365658209263276 0.898673197736788 chr6 171115067 10947330 0.06397642353726805 0.896805564390341 chr7 159138663 2525347 0.01586884640346639 0.5385547139952562 chr8 146364022 2300720 0.01571916355236535 0.9518411686965899 chr9 141213431 9372510 0.0663712363167495 0.7807338068084962 chr10 135534747 2086202 0.015392377572372641 0.5183233894080602 chr11 135006516 27028813 0.20020376646116844 1.3016925781223851 chr12 133851895 18213795 0.1360742408615134 0.9157970435827814 chr13 115169878 1639981 0.014239669508028827 0.5182360651728549 chr14 107349540 2996156 0.02791028261509085 0.454758425186857 chr15 102531392 4960241 0.048377778778230185 0.6645897396893377 chr16 90354753 4743326 0.0524966959956163 0.633163806384899 chr17 81195210 2933511 0.03612911402039603 0.5483102969167902 chr18 78077248 8532738 0.10928584470600193 1.8328821977069698 chr19 59128983 8001902 0.13532960646388928 1.237069780361872 chr20 63025520 785555 0.012464078043306901 0.2263369749235363 chr21 48129895 690118 0.01433865583957746 0.2781160281899195 chr22 51304566 422921 0.008243340368574601 0.19055320938447107 chrMT 16571 44779 2.702250920282421 3.710934023067894 chrX 155270560 21676305 0.13960344446493914 0.9663419221523293 chrY 59373566 590196 0.009940383233845176 0.3770529129095897