BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063572.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 = 2,701,558 number of mapped reads = 2,107,719 (78.02%) number of supplementary alignments = 14,912 (0.55%) number of secondary alignments = 0 number of mapped bases = 139,348,571 bp number of sequenced bases = 139,280,966 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 265,555 duplication rate = 9.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.1028 >>>>>>> ACTG content number of A's = 38,499,867 bp (27.64%) number of C's = 25,333,745 bp (18.19%) number of T's = 44,775,412 bp (32.15%) number of G's = 30,668,190 bp (22.02%) number of N's = 3,752 bp (0%) GC percentage = 40.21% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 1,063,289 number of insertions = 9,873 mapped reads with insertion percentage = 0.46% number of deletions = 38,805 mapped reads with deletion percentage = 1.82% homopolymer indels = 47.89% >>>>>>> Coverage mean coverageData = 0.045X std coverageData = 0.469X There is a 2.37% of reference with a coverageData >= 1X There is a 1.05% of reference with a coverageData >= 2X There is a 0.49% of reference with a coverageData >= 3X There is a 0.24% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% 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% 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 11663782 0.046795397954093765 0.6471253059570938 chr2 243199373 17602339 0.07237822525142777 0.5198628830276772 chr3 198022430 9058455 0.04574459065066518 0.3647537183711318 chr4 191154276 7352848 0.03846551672221028 0.33860012648128107 chr5 180915260 7585988 0.0419311671110552 0.346352604419634 chr6 171115067 5923875 0.034619248344741026 0.34045704626299284 chr7 159138663 5412908 0.034013783312984096 0.38193601838432695 chr8 146364022 7411235 0.05063563366685837 0.5097776520466936 chr9 141213431 5034805 0.0356538677967537 0.37284687334480165 chr10 135534747 5021415 0.03704891263050058 0.3895243129237473 chr11 135006516 11478257 0.08502002229284993 0.7514749996009343 chr12 133851895 5820255 0.04348279865593237 0.3559752046551841 chr13 115169878 4146798 0.036005925090933935 0.3227285905272514 chr14 107349540 3139955 0.029249822588899774 0.3022629124478865 chr15 102531392 4021524 0.039222368111417036 0.33073088279588414 chr16 90354753 3418805 0.037837577841643814 0.3436941517521997 chr17 81195210 2853959 0.035149351790579764 0.3686894488291171 chr18 78077248 3161480 0.04049169355969104 0.5988409978237355 chr19 59128983 2079315 0.03516574942613168 0.4495626810363064 chr20 63025520 2373713 0.03766272773314683 0.3374278491419039 chr21 48129895 1764462 0.03666041656646041 0.3388430335826647 chr22 51304566 1415007 0.027580527627891833 0.272918323408932 chrMT 16571 981750 59.24506668275904 36.89535248861301 chrX 155270560 10290715 0.06627602167468193 0.4602077610769045 chrY 59373566 334926 0.005640995186309005 0.12632730586529217