BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238289.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 = 2,988,214 number of mapped reads = 2,678,255 (89.63%) number of supplementary alignments = 27,409 (0.92%) number of secondary alignments = 0 number of mapped bases = 177,427,981 bp number of sequenced bases = 177,350,297 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 110,932 duplication rate = 3.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3535 >>>>>>> ACTG content number of A's = 48,541,716 bp (27.37%) number of C's = 34,342,935 bp (19.36%) number of T's = 54,008,759 bp (30.45%) number of G's = 40,411,928 bp (22.79%) number of N's = 44,959 bp (0.03%) GC percentage = 42.15% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,443,568 number of insertions = 13,886 mapped reads with insertion percentage = 0.51% number of deletions = 46,903 mapped reads with deletion percentage = 1.73% homopolymer indels = 46.43% >>>>>>> Coverage mean coverageData = 0.0573X std coverageData = 0.4924X There is a 4.73% of reference with a coverageData >= 1X There is a 0.72% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% 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 12192673 0.04891732245674124 0.8675960949170554 chr2 243199373 11133458 0.04577913940592273 0.6402959588295055 chr3 198022430 11564188 0.0583983743659746 0.2795206424559709 chr4 191154276 9282361 0.04855952581463571 0.2717143492725245 chr5 180915260 13536160 0.07482044356015076 0.3238457281081579 chr6 171115067 9889959 0.057797125486325526 0.32573917563863186 chr7 159138663 5218368 0.032791327397289995 0.5794944751115072 chr8 146364022 5688766 0.03886724293487918 0.5756578415153365 chr9 141213431 6208957 0.04396860097535623 0.5070073409229878 chr10 135534747 10086901 0.07442298910994388 0.4399820188016382 chr11 135006516 4644867 0.03440476161906141 0.3521306604656894 chr12 133851895 8711175 0.0650806998287174 0.3115094981298847 chr13 115169878 4406240 0.03825861480898678 0.2251854073504193 chr14 107349540 6263594 0.058347655704905674 0.32599006136495506 chr15 102531392 5841406 0.05697187842724304 0.2814168246524509 chr16 90354753 6341676 0.07018641288300573 0.35504339631328774 chr17 81195210 6730430 0.08289195877441538 0.3793789483513426 chr18 78077248 7292115 0.09339615812278629 1.0277038060505184 chr19 59128983 5691695 0.09625896998769622 0.6221962638263611 chr20 63025520 5003249 0.07938449377331595 0.336956487714908 chr21 48129895 1717164 0.03567770093826301 0.26110528716286024 chr22 51304566 3766037 0.07340549377223073 0.319623459687261 chrMT 16571 47114 2.843159736889747 2.4393490326584986 chrX 155270560 15688996 0.10104295366745634 0.43958823096263516 chrY 59373566 480432 0.008091681742679898 0.15047475119668502