BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063536.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 = 5,899,874 number of mapped reads = 5,484,544 (92.96%) number of supplementary alignments = 54,299 (0.92%) number of secondary alignments = 0 number of mapped bases = 356,751,255 bp number of sequenced bases = 356,623,104 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,594,924 duplication rate = 18.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4755 >>>>>>> ACTG content number of A's = 91,600,228 bp (25.69%) number of C's = 65,641,547 bp (18.41%) number of T's = 114,494,544 bp (32.11%) number of G's = 84,846,127 bp (23.79%) number of N's = 40,658 bp (0.01%) GC percentage = 42.2% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 1,813,339 number of insertions = 24,358 mapped reads with insertion percentage = 0.44% number of deletions = 72,969 mapped reads with deletion percentage = 1.32% homopolymer indels = 44.29% >>>>>>> Coverage mean coverageData = 0.1152X std coverageData = 1.2006X There is a 4.78% of reference with a coverageData >= 1X There is a 2.55% of reference with a coverageData >= 2X There is a 1.51% of reference with a coverageData >= 3X There is a 0.92% of reference with a coverageData >= 4X There is a 0.57% of reference with a coverageData >= 5X There is a 0.35% of reference with a coverageData >= 6X There is a 0.22% of reference with a coverageData >= 7X There is a 0.14% of reference with a coverageData >= 8X There is a 0.09% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% 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 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% 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 38969555 0.1563468722511227 1.9544794638260248 chr2 243199373 34779374 0.14300766309952617 2.32995341421376 chr3 198022430 22227954 0.11224967797839872 0.6692287825012831 chr4 191154276 18170917 0.0950589093806094 0.6881028272997716 chr5 180915260 12189703 0.06737797021655331 0.5199522998282627 chr6 171115067 26939830 0.157436925177372 0.9898702917020539 chr7 159138663 24488417 0.15388100250660017 1.326495450464238 chr8 146364022 11970041 0.08178267334031036 1.4211496008019247 chr9 141213431 12101166 0.08569415751962008 0.8582387216410958 chr10 135534747 20123805 0.1484770912657549 0.9637197310843179 chr11 135006516 17599350 0.13035926354843494 0.9235208290489139 chr12 133851895 13844664 0.10343270821828858 0.666321759326492 chr13 115169878 7263912 0.0630712832742603 0.5532878033419327 chr14 107349540 8237291 0.07673336094407111 0.6088961361592141 chr15 102531392 6393362 0.06235516630848043 0.5272814702484324 chr16 90354753 8387736 0.09283115410652498 0.6462287649202397 chr17 81195210 10299723 0.12685136229095287 0.755582941448918 chr18 78077248 9508261 0.12178017596111994 1.6245977556239755 chr19 59128983 7163607 0.1211522105834291 1.3091661968677841 chr20 63025520 5576000 0.08847209828653536 0.6383312436472044 chr21 48129895 6346619 0.13186438491087504 0.7701966474711519 chr22 51304566 4224316 0.08233801256597707 0.5686730440970083 chrMT 16571 900305 54.33015509021785 38.96749932735005 chrX 155270560 27829294 0.17923097591713458 0.9944766774135587 chrY 59373566 1216053 0.02048138728942102 0.5213647243624917