BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716169.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 = 3,167,737 number of mapped reads = 2,957,128 (93.35%) number of supplementary alignments = 68,315 (2.16%) number of secondary alignments = 0 number of mapped bases = 224,836,767 bp number of sequenced bases = 224,754,653 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 117,865 duplication rate = 2.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2323 >>>>>>> ACTG content number of A's = 59,181,436 bp (26.33%) number of C's = 47,955,989 bp (21.34%) number of T's = 65,286,884 bp (29.05%) number of G's = 52,303,654 bp (23.27%) number of N's = 26,690 bp (0.01%) GC percentage = 44.61% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 1,715,487 number of insertions = 17,788 mapped reads with insertion percentage = 0.59% number of deletions = 46,908 mapped reads with deletion percentage = 1.56% homopolymer indels = 40.75% >>>>>>> Coverage mean coverageData = 0.0726X std coverageData = 0.5742X There is a 5.97% of reference with a coverageData >= 1X There is a 0.9% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.05% 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 18741585 0.07519172840897355 0.9759276865683503 chr2 243199373 21516190 0.08847140407718074 0.8742423498632489 chr3 198022430 16570384 0.08367932864978983 0.35165337656371787 chr4 191154276 9313678 0.048723356834560166 0.2809157150917393 chr5 180915260 14230145 0.078656410741692 0.3347895254290476 chr6 171115067 16132470 0.09427848922269363 0.4369311620416427 chr7 159138663 12607446 0.07922302325739661 0.8132785333992595 chr8 146364022 16256706 0.11107036946552343 0.6718357942884202 chr9 141213431 9730318 0.06890504629124124 0.5117634145825893 chr10 135534747 10513375 0.0775695918036428 0.5662278222708752 chr11 135006516 9160356 0.06785121393696286 0.44348875108772107 chr12 133851895 7667159 0.05728091484995412 0.28294795856177746 chr13 115169878 7917786 0.06874875737907789 0.306290804741262 chr14 107349540 5266482 0.04905919485076508 0.30665227374282644 chr15 102531392 5075607 0.04950295612879224 0.2613206759812462 chr16 90354753 6277714 0.06947851431789094 0.3650358971726933 chr17 81195210 6622116 0.08155796382569859 0.40868376341111473 chr18 78077248 6803780 0.08714164720559824 1.0527054957009956 chr19 59128983 4105799 0.06943801147400083 0.7568814356445721 chr20 63025520 4617185 0.07325897509453314 0.36144414163997335 chr21 48129895 4815079 0.10004341376601798 0.3931096982485748 chr22 51304566 3345732 0.0652131430173291 0.30694023308198887 chrMT 16571 67621 4.080683121115201 3.453572335507763 chrX 155270560 6994134 0.04504481725318695 0.32953463564251234 chrY 59373566 487920 0.00821779847280859 0.22906549572493035