BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234105.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 = 4,848,640 number of mapped reads = 4,582,614 (94.51%) number of supplementary alignments = 34,566 (0.71%) number of secondary alignments = 0 number of mapped bases = 295,600,836 bp number of sequenced bases = 295,489,486 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 547,189 duplication rate = 9.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9636 >>>>>>> ACTG content number of A's = 76,374,336 bp (25.85%) number of C's = 53,566,417 bp (18.13%) number of T's = 95,945,209 bp (32.47%) number of G's = 69,574,687 bp (23.55%) number of N's = 28,837 bp (0.01%) GC percentage = 41.67% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 1,578,569 number of insertions = 18,617 mapped reads with insertion percentage = 0.4% number of deletions = 64,080 mapped reads with deletion percentage = 1.39% homopolymer indels = 44.49% >>>>>>> Coverage mean coverageData = 0.0955X std coverageData = 0.9456X There is a 7.14% of reference with a coverageData >= 1X There is a 1.62% of reference with a coverageData >= 2X There is a 0.41% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 26029994 0.10443301563529504 1.850051109506146 chr2 243199373 22493084 0.09248824831468624 1.7572614989602267 chr3 198022430 33499903 0.16917226498028531 0.5308177403711491 chr4 191154276 10729354 0.05612929108632652 0.371803760384659 chr5 180915260 15382923 0.08502833315442822 0.38096369672721864 chr6 171115067 20960167 0.12249165060374256 0.7155589628863424 chr7 159138663 18077727 0.11359732863911268 1.1866013898776082 chr8 146364022 14175684 0.09685224419427337 0.95142934919394 chr9 141213431 12271929 0.08690341218322215 0.6211851145568539 chr10 135534747 13976143 0.10311852354732326 0.7125106048335663 chr11 135006516 12369440 0.09162105923835558 0.6423397217870545 chr12 133851895 9755090 0.07287973024214561 0.36720727632290295 chr13 115169878 12721132 0.11045537445129533 0.48275388423414217 chr14 107349540 11373574 0.1059489775177425 0.4613267523695172 chr15 102531392 5502096 0.05366255048990264 0.33341978578495424 chr16 90354753 9013454 0.09975627956174038 0.49680699528123845 chr17 81195210 7081323 0.08721355607061057 0.4574245980590102 chr18 78077248 5209694 0.06672486714695681 1.4982212646502457 chr19 59128983 7230972 0.122291499584899 1.0583018186163957 chr20 63025520 6726708 0.10672990877346192 0.46547963846376916 chr21 48129895 5434699 0.11291732508454465 0.46056879819446545 chr22 51304566 2400864 0.04679630269165516 0.26810517164781666 chrMT 16571 255613 15.425321344517531 9.055175076227606 chrX 155270560 12135722 0.07815855111232935 0.4623831816891295 chrY 59373566 793547 0.013365324898962612 0.250454599129589