BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080549.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 = 3,041,220 number of mapped reads = 2,502,643 (82.29%) number of supplementary alignments = 23,367 (0.77%) number of secondary alignments = 0 number of mapped bases = 166,371,584 bp number of sequenced bases = 166,306,206 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 139,000 duplication rate = 4.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.4924 >>>>>>> ACTG content number of A's = 45,580,635 bp (27.41%) number of C's = 29,851,424 bp (17.95%) number of T's = 53,955,414 bp (32.44%) number of G's = 36,780,399 bp (22.12%) number of N's = 138,334 bp (0.08%) GC percentage = 40.07% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 1,473,619 number of insertions = 13,603 mapped reads with insertion percentage = 0.54% number of deletions = 39,703 mapped reads with deletion percentage = 1.57% homopolymer indels = 48.97% >>>>>>> Coverage mean coverageData = 0.0537X std coverageData = 0.3372X There is a 4.22% of reference with a coverageData >= 1X There is a 0.84% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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 14530121 0.05829522486926923 0.3729116203295907 chr2 243199373 13947163 0.05734867992443385 0.35221916426499866 chr3 198022430 11844744 0.05981516336305943 0.30040915418370195 chr4 191154276 10655248 0.055741614694509896 0.29735327410961143 chr5 180915260 10991234 0.060753493099476516 0.30138750878039255 chr6 171115067 9739124 0.05691564261842588 0.3290544604675435 chr7 159138663 8341698 0.05241779617062637 0.3561638505291787 chr8 146364022 8207569 0.05607641063594167 0.4507583063914779 chr9 141213431 7258245 0.051399112312482516 0.3400688153921898 chr10 135534747 7093013 0.052333539236252086 0.3288376849218699 chr11 135006516 7325355 0.05425926997479144 0.31278107749387374 chr12 133851895 7033703 0.05254840060351779 0.28378644237162426 chr13 115169878 5875060 0.05101212315254862 0.2827802911194071 chr14 107349540 4430227 0.041269175443136505 0.26227121865231756 chr15 102531392 4874176 0.04753837731960179 0.27146473041252056 chr16 90354753 4996948 0.05530365403134908 0.30237132036813424 chr17 81195210 4421751 0.05445827407799056 0.29069605358616796 chr18 78077248 4365855 0.05591712197643032 0.5325490232527605 chr19 59128983 3023112 0.05112741411432698 0.3515212919091954 chr20 63025520 3670276 0.05823475950694258 0.29865572875369795 chr21 48129895 1780539 0.03699445012294334 0.2399992663921717 chr22 51304566 2108099 0.04108989051773677 0.24985740594824687 chrMT 16571 335734 20.26033431899101 23.782343767531415 chrX 155270560 9219827 0.05937910573646414 0.31212844211901497 chrY 59373566 302763 0.005099289471681725 0.10440304434913864