BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3212676.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 = 2,771,178 number of mapped reads = 2,524,094 (91.08%) number of supplementary alignments = 18,684 (0.67%) number of secondary alignments = 0 number of mapped bases = 170,779,241 bp number of sequenced bases = 170,715,559 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 129,805 duplication rate = 4.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.367 >>>>>>> ACTG content number of A's = 47,023,821 bp (27.55%) number of C's = 32,818,086 bp (19.22%) number of T's = 52,706,331 bp (30.87%) number of G's = 38,165,468 bp (22.36%) number of N's = 1,853 bp (0%) GC percentage = 41.58% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,468,200 number of insertions = 12,155 mapped reads with insertion percentage = 0.48% number of deletions = 36,080 mapped reads with deletion percentage = 1.42% homopolymer indels = 47.37% >>>>>>> Coverage mean coverageData = 0.0552X std coverageData = 0.4393X There is a 4.44% of reference with a coverageData >= 1X There is a 0.76% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.04% 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 0.01% 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 12977726 0.05206697559240986 0.7904187415857782 chr2 243199373 12711361 0.05226724412648876 0.4998200912310057 chr3 198022430 10599210 0.05352530013897921 0.275551434650302 chr4 191154276 12400271 0.06487048712423257 0.32714039754304824 chr5 180915260 9848015 0.05443440757844308 0.2798222647445392 chr6 171115067 10105829 0.059058674242870736 0.3812855171564369 chr7 159138663 9868465 0.06201173752477737 0.5667682671600068 chr8 146364022 8400695 0.05739590156930779 0.42993262323622866 chr9 141213431 7129473 0.05048721604958384 0.42221804815522046 chr10 135534747 8661271 0.06390443182809792 0.4320393347497926 chr11 135006516 7193661 0.05328380594607745 0.39881214894673706 chr12 133851895 7117854 0.05317708800461884 0.28142635466415655 chr13 115169878 5885528 0.05110301497410634 0.26864180133020055 chr14 107349540 6083036 0.056665692279631565 0.3054946176338148 chr15 102531392 5173192 0.05045471342084188 0.2693137209368674 chr16 90354753 5437346 0.06017775290692234 0.3385663142794769 chr17 81195210 4584248 0.05645958671699969 0.3330727572399077 chr18 78077248 5506826 0.07053048283669014 0.7936903867061107 chr19 59128983 3155213 0.05336152999621184 0.5636166240320882 chr20 63025520 4152219 0.06588155083845401 0.31433819621701586 chr21 48129895 2314222 0.04808283915848975 0.297509719357058 chr22 51304566 1981736 0.03862689336461788 0.23418151330930204 chrMT 16571 65360 3.944239937239756 3.0496160600402304 chrX 155270560 8986496 0.057876367548362034 0.32805092580305717 chrY 59373566 439988 0.007410503185879049 0.18252344232175272