BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524904.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 = 1,208,112 number of mapped reads = 1,106,732 (91.61%) number of supplementary alignments = 4,199 (0.35%) number of secondary alignments = 0 number of mapped bases = 64,099,032 bp number of sequenced bases = 64,078,484 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 53,756 duplication rate = 3.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6562 >>>>>>> ACTG content number of A's = 16,168,276 bp (25.23%) number of C's = 12,464,541 bp (19.45%) number of T's = 20,205,845 bp (31.53%) number of G's = 15,239,279 bp (23.78%) number of N's = 543 bp (0%) GC percentage = 43.23% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 330,567 number of insertions = 4,214 mapped reads with insertion percentage = 0.38% number of deletions = 12,237 mapped reads with deletion percentage = 1.1% homopolymer indels = 42.5% >>>>>>> Coverage mean coverageData = 0.0207X std coverageData = 0.2139X There is a 1.84% of reference with a coverageData >= 1X There is a 0.17% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 6576850 0.026386493937762344 0.36571424006705666 chr2 243199373 5638181 0.023183369802520008 0.2667077808935445 chr3 198022430 4037398 0.020388589312836936 0.15811296932739424 chr4 191154276 2821630 0.014761009060555884 0.15900802093780025 chr5 180915260 3959495 0.021885909458383996 0.16282913871779778 chr6 171115067 4062830 0.02374326277182827 0.17697439308948357 chr7 159138663 3949464 0.024817752804671987 0.2591973541192966 chr8 146364022 5515426 0.037682935496265606 0.28915678132413064 chr9 141213431 2401114 0.01700343928333559 0.17256495787711412 chr10 135534747 2817505 0.020788064037925272 0.229695523729039 chr11 135006516 3250991 0.024080252541292157 0.19158688571950602 chr12 133851895 2181304 0.016296399838044876 0.14415215549549584 chr13 115169878 1543357 0.013400700137930162 0.1273355483442905 chr14 107349540 1141097 0.010629733485583636 0.11796629859824172 chr15 102531392 1637763 0.01597328357738477 0.13886255020299487 chr16 90354753 1937132 0.0214391820649435 0.16816585179884977 chr17 81195210 1428180 0.017589461250238775 0.1506540374980159 chr18 78077248 1713338 0.02194413921966102 0.26629228841032637 chr19 59128983 1331671 0.022521459569159172 0.27637664572361803 chr20 63025520 1202373 0.019077557789289164 0.15673699472435193 chr21 48129895 610008 0.012674201761711718 0.1450918413045738 chr22 51304566 1245681 0.024280119629118392 0.17395775491889862 chrMT 16571 1641 0.09902842314887454 0.3365110058949774 chrX 155270560 2900549 0.01868061144366324 0.16106946553913037 chrY 59373566 194054 0.003268356830714867 0.1268124338320096