BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708566.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 4,049,430 number of mapped reads = 3,349,297 (82.71%) number of supplementary alignments = 85 (0%) number of secondary alignments = 0 number of mapped bases = 167,031,186 bp number of sequenced bases = 167,016,324 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,990 duplication rate = 0.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1837 >>>>>>> ACTG content number of A's = 51,685,028 bp (30.95%) number of C's = 31,750,210 bp (19.01%) number of T's = 51,512,880 bp (30.84%) number of G's = 32,060,492 bp (19.2%) number of N's = 7,714 bp (0%) GC percentage = 38.21% >>>>>>> Mismatches and indels general error rate = 0.0016 number of mismatches = 259,322 number of insertions = 11,006 mapped reads with insertion percentage = 0.33% number of deletions = 8,786 mapped reads with deletion percentage = 0.26% homopolymer indels = 47.56% >>>>>>> Coverage mean coverageData = 0.054X std coverageData = 0.2403X There is a 5.08% of reference with a coverageData >= 1X There is a 0.29% of reference with a coverageData >= 2X There is a 0.02% 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 14506955 0.05820228227234788 0.2506745411146303 chr2 243199373 16505039 0.06786628927698757 0.26879687007567793 chr3 198022430 14600694 0.07373252615877908 0.2805319345017612 chr4 191154276 12370700 0.06471579008779275 0.26255331110633406 chr5 180915260 11597788 0.06410618982610974 0.2605044847570637 chr6 171115067 9092240 0.05313523910784548 0.23677138889989902 chr7 159138663 8799311 0.055293357592177336 0.24313502298935474 chr8 146364022 7391221 0.05049889241223502 0.23094887625489366 chr9 141213431 6396331 0.04529548609296236 0.2206116216200858 chr10 135534747 7740874 0.057113575458254996 0.24661134217661282 chr11 135006516 8307492 0.0615340077363377 0.2568003180913365 chr12 133851895 7453256 0.055682857534441334 0.24325995224106495 chr13 115169878 7310936 0.06347958447954595 0.26134757329391595 chr14 107349540 4543972 0.04232875147858109 0.21265503277175643 chr15 102531392 4108523 0.04007087897528983 0.20734233454464465 chr16 90354753 3296937 0.03648880540905247 0.19694651721260326 chr17 81195210 2770048 0.034115904127842024 0.19058041498126826 chr18 78077248 4449723 0.05699128893477393 0.24580798027228654 chr19 59128983 1436013 0.02428611024816713 0.16030104017679675 chr20 63025520 2804066 0.044490961756444056 0.21888943250029136 chr21 48129895 1281589 0.02662771236047783 0.16823732352562304 chr22 51304566 821210 0.016006567524613696 0.12996386522814066 chrMT 16571 146 0.00881057268722467 0.0934502353991032 chrX 155270560 9220895 0.059385984052611133 0.2519071999381009 chrY 59373566 225227 0.003793388458426095 0.06387957783528685