BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716307.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 = 1,911,015 number of mapped reads = 1,783,506 (93.33%) number of supplementary alignments = 32,784 (1.72%) number of secondary alignments = 0 number of mapped bases = 141,601,487 bp number of sequenced bases = 141,534,053 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 77,541 duplication rate = 3.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5926 >>>>>>> ACTG content number of A's = 35,318,471 bp (24.95%) number of C's = 26,753,272 bp (18.9%) number of T's = 44,357,624 bp (31.34%) number of G's = 35,094,522 bp (24.8%) number of N's = 10,164 bp (0.01%) GC percentage = 43.7% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 928,491 number of insertions = 12,361 mapped reads with insertion percentage = 0.68% number of deletions = 34,903 mapped reads with deletion percentage = 1.92% homopolymer indels = 42.27% >>>>>>> Coverage mean coverageData = 0.0457X std coverageData = 0.4141X There is a 3.88% of reference with a coverageData >= 1X There is a 0.48% of reference with a coverageData >= 2X There is a 0.09% 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 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 13638728 0.05471893287680114 0.8342185415873627 chr2 243199373 11611962 0.047746677373218395 0.44295349699182257 chr3 198022430 8911850 0.04500424522615948 0.23815368577817012 chr4 191154276 8885692 0.04648440090348803 0.31845544776212575 chr5 180915260 8159495 0.04510119820738173 0.2409968927007173 chr6 171115067 7705216 0.04502944208881384 0.26522481607696424 chr7 159138663 7367264 0.04629462043425613 0.4959000816694173 chr8 146364022 6942646 0.047434102350644616 0.4520427020903884 chr9 141213431 5647417 0.039992067043537805 0.33638619889985716 chr10 135534747 6555047 0.04836432830025499 0.4068440439386249 chr11 135006516 8025078 0.059442153147630294 0.47966392093433885 chr12 133851895 6167725 0.04607872753687947 0.2439576374159872 chr13 115169878 4913001 0.042658732346664466 0.23474850035160671 chr14 107349540 4055792 0.0377811772644764 0.24016928569124932 chr15 102531392 3968764 0.03870779399932461 0.22144626104021284 chr16 90354753 3204909 0.035470286770636184 0.23988690956971168 chr17 81195210 4632199 0.05705015111113082 0.3326543740451202 chr18 78077248 3703141 0.04742919473801126 0.5951137029680259 chr19 59128983 2815331 0.047613384454794364 0.6072721615607934 chr20 63025520 2960722 0.046976558067271794 0.259737120267703 chr21 48129895 1884070 0.03914552483440905 0.2660391026123422 chr22 51304566 1696726 0.03307163732756262 0.20810092923834322 chrMT 16571 115608 6.976525254963491 4.430660581128057 chrX 155270560 7595732 0.048919331520411856 0.2974547065576801 chrY 59373566 437372 0.0073664431743917826 0.2522876474672072