BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238331.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 = 2,564,440 number of mapped reads = 2,291,365 (89.35%) number of supplementary alignments = 31,799 (1.24%) number of secondary alignments = 0 number of mapped bases = 152,730,196 bp number of sequenced bases = 152,661,853 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 153,014 duplication rate = 5.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0463 >>>>>>> ACTG content number of A's = 42,865,751 bp (28.08%) number of C's = 29,513,537 bp (19.33%) number of T's = 46,932,009 bp (30.74%) number of G's = 33,314,301 bp (21.82%) number of N's = 36,255 bp (0.02%) GC percentage = 41.15% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,296,140 number of insertions = 12,786 mapped reads with insertion percentage = 0.55% number of deletions = 39,405 mapped reads with deletion percentage = 1.7% homopolymer indels = 46.59% >>>>>>> Coverage mean coverageData = 0.0493X std coverageData = 0.4682X There is a 3.69% of reference with a coverageData >= 1X There is a 0.85% of reference with a coverageData >= 2X There is a 0.21% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 15246505 0.061169376183821025 0.6419000336788206 chr2 243199373 12266352 0.050437432665585036 0.5941929552222763 chr3 198022430 10228478 0.05165312838550663 0.28594010191572033 chr4 191154276 10361593 0.054205394808955254 0.37898347903616536 chr5 180915260 9313233 0.051478426971832004 0.2903464496772733 chr6 171115067 11114038 0.0649506685463297 0.3974225989243697 chr7 159138663 7677875 0.04824644655962706 0.5322730957474946 chr8 146364022 7278965 0.04973192797339226 0.9095888961581975 chr9 141213431 6077671 0.043038901873292776 0.4357118270472277 chr10 135534747 6360326 0.046927641367124844 0.505575916785612 chr11 135006516 5489555 0.04066140777975487 0.41518444296504053 chr12 133851895 8216099 0.06138201480076169 0.32513311012720997 chr13 115169878 2681699 0.023284725542558966 0.195840004311662 chr14 107349540 4030481 0.03754539609578206 0.2804968817310236 chr15 102531392 3688367 0.0359730510632295 0.24364995053083635 chr16 90354753 4353945 0.048187227073710225 0.30913328474191804 chr17 81195210 3518231 0.043330524054313056 0.2995459929547202 chr18 78077248 4464829 0.057184763991681674 0.8023664854887003 chr19 59128983 2463151 0.04165725292450912 0.4826626739964349 chr20 63025520 3708888 0.058847400227717284 0.3208749080217572 chr21 48129895 1931425 0.04012942475773114 0.3108794564535991 chr22 51304566 2061444 0.04018051726624098 0.2511897387444187 chrMT 16571 42078 2.5392553255687647 2.9226182745906866 chrX 155270560 9671061 0.06228522007005063 0.369461751223919 chrY 59373566 483907 0.008150209472006448 0.2625043783487761