BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716784.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 = 2,047,661 number of mapped reads = 1,789,641 (87.4%) number of supplementary alignments = 44,451 (2.17%) number of secondary alignments = 0 number of mapped bases = 134,661,189 bp number of sequenced bases = 134,613,881 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 55,868 duplication rate = 2.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2281 >>>>>>> ACTG content number of A's = 34,738,091 bp (25.81%) number of C's = 28,670,013 bp (21.3%) number of T's = 40,419,848 bp (30.03%) number of G's = 30,768,989 bp (22.86%) number of N's = 16,940 bp (0.01%) GC percentage = 44.16% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 995,851 number of insertions = 12,204 mapped reads with insertion percentage = 0.67% number of deletions = 27,408 mapped reads with deletion percentage = 1.51% homopolymer indels = 39.41% >>>>>>> Coverage mean coverageData = 0.0435X std coverageData = 0.3361X There is a 3.74% of reference with a coverageData >= 1X There is a 0.44% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% 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 10595516 0.04250948686703573 0.3809856687629175 chr2 243199373 11440237 0.04704056946725763 0.4913551587087881 chr3 198022430 9006471 0.04548207493464251 0.24049546674629313 chr4 191154276 8562822 0.04479534635155114 0.260124278342722 chr5 180915260 8128665 0.04493078693306468 0.24119515637536473 chr6 171115067 7835141 0.04578872648309806 0.2699516378293159 chr7 159138663 7359107 0.046243363248565185 0.4118437103553685 chr8 146364022 6876484 0.046982065032347906 0.4285617365690616 chr9 141213431 5688612 0.04028378858665363 0.36096637901899953 chr10 135534747 6476090 0.0477817692019597 0.34415754773812085 chr11 135006516 6009557 0.04451308853863024 0.3483303142028602 chr12 133851895 6176972 0.0461478113552296 0.24650940919182995 chr13 115169878 4290155 0.03725066896398032 0.21746587850204188 chr14 107349540 4036777 0.03760404562516057 0.24932489003669925 chr15 102531392 3923450 0.03826584154831332 0.22065535794049196 chr16 90354753 3999531 0.04426475494875184 0.2667306695116756 chr17 81195210 3693190 0.045485318653649645 0.2707620993354389 chr18 78077248 3629001 0.046479622335049514 0.6440732355331045 chr19 59128983 2712116 0.045867793802575635 0.3595043482558359 chr20 63025520 2850012 0.045219968038343834 0.24862272193836646 chr21 48129895 1805091 0.03750456966506991 0.24149478211252823 chr22 51304566 1581370 0.03082318248243246 0.19914572725515212 chrMT 16571 5487 0.33112063243014905 0.72049160033289 chrX 155270560 7637641 0.049189241025471925 0.3073375012211509 chrY 59373566 341694 0.005754985307771476 0.1611524711341471