BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549041.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 11,045,929 number of mapped reads = 9,300,884 (84.2%) number of secondary alignments = 0 number of mapped bases = 368,336,071 bp number of sequenced bases = 368,302,750 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 692,179 duplication rate = 6.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.0706 >>>>>>> ACTG content number of A's = 104,816,073 bp (28.46%) number of C's = 77,027,837 bp (20.91%) number of T's = 107,640,559 bp (29.23%) number of G's = 78,817,948 bp (21.4%) number of N's = 333 bp (0%) GC percentage = 42.31% >>>>>>> Mismatches and indels general error rate = 0.0026 number of mismatches = 932,764 number of insertions = 10,238 mapped reads with insertion percentage = 0.11% number of deletions = 25,540 mapped reads with deletion percentage = 0.27% homopolymer indels = 41.93% >>>>>>> Coverage mean coverageData = 0.119X std coverageData = 0.845X There is a 7.37% of reference with a coverageData >= 1X There is a 2.47% of reference with a coverageData >= 2X There is a 0.98% of reference with a coverageData >= 3X There is a 0.44% of reference with a coverageData >= 4X There is a 0.21% of reference with a coverageData >= 5X There is a 0.11% of reference with a coverageData >= 6X There is a 0.07% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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% 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 30031308 0.12048639188746495 1.072956873758593 chr2 243199373 32070667 0.13186985889145364 0.7773062961454759 chr3 198022430 25304321 0.12778512514971158 0.5444115567457153 chr4 191154276 25091874 0.13126504164625646 0.5942612528097662 chr5 180915260 23717915 0.13109958220218682 0.5580430060310669 chr6 171115067 21802393 0.12741363681317439 0.5838608075947662 chr7 159138663 20437930 0.1284284385372774 1.0336792239614008 chr8 146364022 19235492 0.13142226987995725 2.189520715748903 chr9 141213431 15624449 0.11064421343887608 0.7321555759449662 chr10 135534747 17372957 0.12818083469031008 0.7059431744038915 chr11 135006516 17235458 0.12766389734848058 0.6547307067402055 chr12 133851895 16934643 0.12651776801516332 0.5502204142895818 chr13 115169878 12227611 0.10617021752857983 0.5013589414186358 chr14 107349540 11068229 0.10310457781188442 0.5482969291037842 chr15 102531392 10302399 0.10048043627458018 0.4822305397177058 chr16 90354753 10219192 0.11310076847866542 0.5636780674655884 chr17 81195210 9484817 0.11681498206606031 0.5471285889558773 chr18 78077248 9711496 0.12438317498075752 1.1964345570426982 chr19 59128983 6965396 0.11780003048589556 0.9771448943998056 chr20 63025520 7625685 0.12099360703410302 0.5554653068255349 chr21 48129895 4900400 0.10181613735080867 0.6115968259790932 chr22 51304566 4163482 0.08115227015076981 0.6212716977944044 chrMT 16571 24207 1.460805020819504 4.365513038548726 chrX 155270560 13488027 0.08686789691490776 0.5168017508190166 chrY 59373566 3295723 0.055508254296196394 0.5200804636140464