BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230368.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 = 2,995,092 number of mapped reads = 2,843,418 (94.94%) number of supplementary alignments = 24,363 (0.81%) number of secondary alignments = 0 number of mapped bases = 204,708,725 bp number of sequenced bases = 204,621,025 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 161,308 duplication rate = 4.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.1534 >>>>>>> ACTG content number of A's = 61,257,969 bp (29.94%) number of C's = 41,520,900 bp (20.29%) number of T's = 60,166,538 bp (29.4%) number of G's = 41,580,371 bp (20.32%) number of N's = 95,247 bp (0.05%) GC percentage = 40.61% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,740,794 number of insertions = 18,406 mapped reads with insertion percentage = 0.64% number of deletions = 51,561 mapped reads with deletion percentage = 1.79% homopolymer indels = 46.98% >>>>>>> Coverage mean coverageData = 0.0661X std coverageData = 0.757X There is a 2.9% of reference with a coverageData >= 1X There is a 1.47% of reference with a coverageData >= 2X There is a 0.86% of reference with a coverageData >= 3X There is a 0.51% of reference with a coverageData >= 4X There is a 0.3% of reference with a coverageData >= 5X There is a 0.18% of reference with a coverageData >= 6X There is a 0.1% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% 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% 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 17089519 0.06856359647745873 1.448057932822164 chr2 243199373 19015311 0.0781881579933185 0.8048013823248602 chr3 198022430 13526008 0.0683054338844342 0.5013892164172083 chr4 191154276 13263602 0.0693868966865277 0.5528635319658298 chr5 180915260 12321294 0.06810533285030793 0.4975914044500604 chr6 171115067 12793311 0.07476437478179522 0.5837137544406212 chr7 159138663 12113274 0.07611773136487894 0.926623637874624 chr8 146364022 9699100 0.06626696825808737 0.774011932159183 chr9 141213431 8643881 0.06121146507657618 0.7238072545443189 chr10 135534747 9887081 0.07294868082795034 0.7329676819881321 chr11 135006516 9518497 0.070503982192978 0.7385498006022746 chr12 133851895 8133505 0.06076495965933094 0.4753862785037798 chr13 115169878 5777052 0.05016113675139953 0.4239002843917773 chr14 107349540 6245615 0.05818017478230461 0.48832255813699643 chr15 102531392 5494069 0.05358426227159776 0.43399595670958396 chr16 90354753 5611810 0.06210863085420642 0.5464393920368318 chr17 81195210 5025459 0.06189354027164903 0.5306456479541052 chr18 78077248 5566011 0.07128851416484351 1.3934491839250622 chr19 59128983 3610453 0.06106063079082554 0.8950871741031629 chr20 63025520 3971524 0.06301453760318043 0.49975712317007437 chr21 48129895 2798142 0.05813729699597309 0.5060770821380345 chr22 51304566 1988246 0.03875378265552427 0.35713009954732655 chrMT 16571 84373 5.091605817391829 4.604954142833029 chrX 155270560 11914475 0.07673363836647462 0.5743215051705901 chrY 59373566 617113 0.010393733130329413 0.32447955110905846