BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237282.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 = 3,056,714 number of mapped reads = 236,770 (7.75%) number of supplementary alignments = 2,427 (0.08%) number of secondary alignments = 0 number of mapped bases = 12,214,081 bp number of sequenced bases = 12,203,626 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 32,362 duplication rate = 7.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 29.9763 >>>>>>> ACTG content number of A's = 3,498,555 bp (28.67%) number of C's = 2,120,434 bp (17.38%) number of T's = 3,977,776 bp (32.6%) number of G's = 2,606,747 bp (21.36%) number of N's = 114 bp (0%) GC percentage = 38.74% >>>>>>> Mismatches and indels general error rate = 0.0197 number of mismatches = 231,999 number of insertions = 4,490 mapped reads with insertion percentage = 1.83% number of deletions = 5,763 mapped reads with deletion percentage = 2.35% homopolymer indels = 38.5% >>>>>>> Coverage mean coverageData = 0.0039X std coverageData = 0.1623X There is a 0.31% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 978281 0.003924888917327913 0.16514929316242713 chr2 243199373 993392 0.004084681583451286 0.1932385784088434 chr3 198022430 952579 0.004810460107978677 0.14521294534482915 chr4 191154276 794940 0.004158630487554461 0.1419040499193464 chr5 180915260 795303 0.004395997330462892 0.19210773913579243 chr6 171115067 769733 0.004498335614128006 0.1256545817268665 chr7 159138663 655772 0.004120758511085392 0.20648062136123416 chr8 146364022 608194 0.00415535178447064 0.11195132377393333 chr9 141213431 481291 0.003408252292942305 0.10965904623456728 chr10 135534747 571676 0.004217929443583939 0.1200970954392585 chr11 135006516 533477 0.003951490756194316 0.1433914248738613 chr12 133851895 507973 0.003795037791583003 0.16508298660781298 chr13 115169878 406441 0.003529056443039733 0.10408354802636366 chr14 107349540 367831 0.0034264795172853093 0.123081809530983 chr15 102531392 336135 0.0032783618113757787 0.194800950064172 chr16 90354753 310466 0.0034360782326525756 0.0803426864761821 chr17 81195210 295723 0.00364212371641135 0.13824414738283142 chr18 78077248 317733 0.004069469764098243 0.16843486097634275 chr19 59128983 200016 0.0033827065823202134 0.09491623784787993 chr20 63025520 267201 0.004239568352629221 0.26230569612782134 chr21 48129895 145141 0.0030156101524842303 0.12512139834606956 chr22 51304566 120343 0.002345658669054914 0.16399866256965495 chrMT 16571 11814 0.7129322310059742 0.9934261165881393 chrX 155270560 755960 0.004868662803818058 0.2708225361864282 chrY 59373566 36666 6.175475463272663E-4 0.036417071342277556