BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068178.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 = 2,983,442 number of mapped reads = 2,694,407 (90.31%) number of supplementary alignments = 16,704 (0.56%) number of secondary alignments = 0 number of mapped bases = 167,868,394 bp number of sequenced bases = 167,788,133 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 821,892 duplication rate = 20.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0419 >>>>>>> ACTG content number of A's = 41,707,050 bp (24.86%) number of C's = 29,664,237 bp (17.68%) number of T's = 55,375,788 bp (33%) number of G's = 41,023,513 bp (24.45%) number of N's = 17,545 bp (0.01%) GC percentage = 42.13% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 1,086,294 number of insertions = 10,968 mapped reads with insertion percentage = 0.4% number of deletions = 45,315 mapped reads with deletion percentage = 1.66% homopolymer indels = 45.49% >>>>>>> Coverage mean coverageData = 0.0542X std coverageData = 0.6905X There is a 2.21% of reference with a coverageData >= 1X There is a 1.12% of reference with a coverageData >= 2X There is a 0.69% of reference with a coverageData >= 3X There is a 0.45% of reference with a coverageData >= 4X There is a 0.29% of reference with a coverageData >= 5X There is a 0.19% of reference with a coverageData >= 6X There is a 0.13% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% 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 0.01% of reference with a coverageData >= 15X There is a 0.01% 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 12163646 0.04880086537477473 0.978447044410881 chr2 243199373 20569750 0.08457978220198784 1.3603951455111694 chr3 198022430 10518340 0.05311691205890161 0.5032764443105527 chr4 191154276 8485048 0.0443884812704896 0.4614465052160028 chr5 180915260 14080939 0.07783168208143415 0.5690868360655048 chr6 171115067 8554926 0.049995164949443054 0.5955448784696044 chr7 159138663 9065525 0.0569662006020498 0.6131635631583365 chr8 146364022 7342363 0.050165080869395626 0.5972318169189403 chr9 141213431 6198470 0.04389433750108373 0.49467208893648645 chr10 135534747 6621045 0.04885127354094666 0.5325415409201989 chr11 135006516 6946613 0.051453909083914146 0.5314551589171856 chr12 133851895 6514104 0.04866650561801908 0.47825146351366304 chr13 115169878 7020384 0.06095677204763558 0.5110927974305871 chr14 107349540 4676613 0.04356435062507021 0.46838569695436666 chr15 102531392 4251227 0.04146268686179546 0.46383488630024794 chr16 90354753 5125986 0.056731780341428194 0.5268413973693141 chr17 81195210 4796255 0.0590706643901777 0.5274191636705431 chr18 78077248 7473423 0.09571831988750423 0.9759799981012862 chr19 59128983 3017233 0.051027987408476146 0.8661246949455843 chr20 63025520 2858444 0.04535375511380152 0.4811812897650601 chr21 48129895 2162671 0.04493404774724732 0.4637608933123567 chr22 51304566 1764200 0.03438680292120588 0.40699108746285323 chrMT 16571 422111 25.472874298473236 16.06205082808619 chrX 155270560 6102873 0.0393047658229609 0.41456615364510274 chrY 59373566 1136205 0.019136546388337193 0.30876731547909575