BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080726.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,161,006 number of mapped reads = 1,909,568 (88.36%) number of supplementary alignments = 25,029 (1.16%) number of secondary alignments = 0 number of mapped bases = 126,345,305 bp number of sequenced bases = 126,304,000 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 95,544 duplication rate = 3.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.7912 >>>>>>> ACTG content number of A's = 34,617,894 bp (27.41%) number of C's = 24,502,129 bp (19.4%) number of T's = 37,664,511 bp (29.82%) number of G's = 29,517,490 bp (23.37%) number of N's = 1,976 bp (0%) GC percentage = 42.77% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,084,689 number of insertions = 10,694 mapped reads with insertion percentage = 0.55% number of deletions = 24,069 mapped reads with deletion percentage = 1.25% homopolymer indels = 43.94% >>>>>>> Coverage mean coverageData = 0.0408X std coverageData = 0.6655X There is a 3.54% of reference with a coverageData >= 1X There is a 0.33% of reference with a coverageData >= 2X There is a 0.05% 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 14943081 0.05995203117267259 1.0941787512237753 chr2 243199373 8539962 0.035115065859976535 0.5574188272128943 chr3 198022430 7490421 0.037826124040594794 0.21375015631265132 chr4 191154276 5247016 0.027449116545004728 0.20452112470698658 chr5 180915260 5671210 0.03134732802528654 0.1983799703160129 chr6 171115067 7370746 0.0430747924728335 0.4169925721535302 chr7 159138663 8530464 0.05360396926295655 2.060790952768845 chr8 146364022 14044866 0.09595845897156338 0.7062687069990469 chr9 141213431 4066028 0.028793493446101454 0.40147799644851123 chr10 135534747 6093493 0.04495889898993946 0.43828264099976594 chr11 135006516 5348299 0.03961511753995637 0.39656915591735237 chr12 133851895 4113006 0.030728037133878457 0.20918923083230265 chr13 115169878 2472705 0.02147006702568531 0.15966572913815516 chr14 107349540 2500770 0.023295581890709547 0.214170638138164 chr15 102531392 2327666 0.02270198379828882 0.18722498363381507 chr16 90354753 3365965 0.037252771860269485 0.24082054682031148 chr17 81195210 2308849 0.028435778415992766 0.23938374283612512 chr18 78077248 3838884 0.04916776779837322 0.7429685213304273 chr19 59128983 2649887 0.044815365757263234 0.6463293587033225 chr20 63025520 3282642 0.05208433028398655 0.27673787742565764 chr21 48129895 1828842 0.03799804674412857 0.23511598872068026 chr22 51304566 1373126 0.026764206523060736 0.17652582605414238 chrMT 16571 69368 4.186108261420554 3.4267391269015457 chrX 155270560 8525521 0.05490751756160343 0.33717273776106604 chrY 59373566 342488 0.00576835826232839 0.12831912614274632