BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068174.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 = 5,632,856 number of mapped reads = 4,906,969 (87.11%) number of supplementary alignments = 28,541 (0.51%) number of secondary alignments = 0 number of mapped bases = 314,006,935 bp number of sequenced bases = 313,868,345 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 562,311 duplication rate = 9.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0463 >>>>>>> ACTG content number of A's = 80,223,470 bp (25.56%) number of C's = 56,670,318 bp (18.06%) number of T's = 101,934,907 bp (32.48%) number of G's = 75,004,201 bp (23.9%) number of N's = 35,449 bp (0.01%) GC percentage = 41.95% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 1,784,431 number of insertions = 19,142 mapped reads with insertion percentage = 0.39% number of deletions = 79,535 mapped reads with deletion percentage = 1.6% homopolymer indels = 44.19% >>>>>>> Coverage mean coverageData = 0.1014X std coverageData = 1.3279X There is a 7.61% of reference with a coverageData >= 1X There is a 1.66% of reference with a coverageData >= 2X There is a 0.41% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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% 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 33361815 0.13384847293921084 3.2814069786543305 chr2 243199373 28384622 0.11671338478327409 1.735483991752744 chr3 198022430 17793855 0.0898577752025364 0.39232373091300016 chr4 191154276 17835099 0.09330211896489304 0.42365261888400885 chr5 180915260 12964671 0.07166156685732315 0.3556011444083744 chr6 171115067 25816662 0.15087310809398216 0.7954087594418366 chr7 159138663 31610042 0.19863206969383676 2.363493001424268 chr8 146364022 11864555 0.08106196343798205 0.7404819888797239 chr9 141213431 11371332 0.0805258530967922 0.8459435760340122 chr10 135534747 18294679 0.13498146715100298 0.7648597226162147 chr11 135006516 11518467 0.08531785976907959 0.6392973337551647 chr12 133851895 8640129 0.06454991914757725 0.41641495569884185 chr13 115169878 7619823 0.06616159652439677 0.3822946527339955 chr14 107349540 7987099 0.07440273148818337 0.4971138175917117 chr15 102531392 5539318 0.05402558077042395 0.4142528240839928 chr16 90354753 7219067 0.07989692584296036 0.4442343622541968 chr17 81195210 9934973 0.12235910221797566 0.5267051590866729 chr18 78077248 6100359 0.0781323516935433 1.4548568307066756 chr19 59128983 7947037 0.13440171971163448 2.0553575580632453 chr20 63025520 3498618 0.05551113263325713 0.36696241934894747 chr21 48129895 4591517 0.09539844207015204 0.4266710377193245 chr22 51304566 3414920 0.06656171694347829 0.32362096933119344 chrMT 16571 152569 9.206988111761511 5.593045028446476 chrX 155270560 19823121 0.12766825211424496 0.6568446114703393 chrY 59373566 722586 0.012170163402346425 0.3200213617589184