BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082945.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 = 1,789,066 number of mapped reads = 1,645,521 (91.98%) number of supplementary alignments = 15,624 (0.87%) number of secondary alignments = 0 number of mapped bases = 110,395,593 bp number of sequenced bases = 110,353,268 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 76,643 duplication rate = 3.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7682 >>>>>>> ACTG content number of A's = 30,629,785 bp (27.76%) number of C's = 20,184,159 bp (18.29%) number of T's = 35,310,744 bp (32%) number of G's = 24,222,754 bp (21.95%) number of N's = 5,826 bp (0.01%) GC percentage = 40.24% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 784,178 number of insertions = 9,311 mapped reads with insertion percentage = 0.56% number of deletions = 25,618 mapped reads with deletion percentage = 1.54% homopolymer indels = 48.4% >>>>>>> Coverage mean coverageData = 0.0357X std coverageData = 0.3288X There is a 3.02% of reference with a coverageData >= 1X There is a 0.4% of reference with a coverageData >= 2X There is a 0.07% 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% 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 10225040 0.04102312748099432 0.6287873766628003 chr2 243199373 11716602 0.048176941640388195 0.43918676476323965 chr3 198022430 8377122 0.042303904663729255 0.23398434840087146 chr4 191154276 5929350 0.031018662642942917 0.20860180488467747 chr5 180915260 6199377 0.034266744552117936 0.21305481589169573 chr6 171115067 7562988 0.044198258707399504 0.3243648476112567 chr7 159138663 5434611 0.03415016123391711 0.27674264589239145 chr8 146364022 9544093 0.06520791701119008 0.4048840405377561 chr9 141213431 3497265 0.02476580998871134 0.2777469520017999 chr10 135534747 3867359 0.02853407768562847 0.24052603040921258 chr11 135006516 4262894 0.03157546854997725 0.25607824811021224 chr12 133851895 3606998 0.026947679747081652 0.19101865840664875 chr13 115169878 2386100 0.020718090888313695 0.16680526266164702 chr14 107349540 2320952 0.02162051183451741 0.18735644413369026 chr15 102531392 2147592 0.020945702170901963 0.17303663736681663 chr16 90354753 3845757 0.0425628632950831 0.24921870893846196 chr17 81195210 2752355 0.0338979971848093 0.23448389311259366 chr18 78077248 3954526 0.05064889069860659 0.6076012556783483 chr19 59128983 1693083 0.0286337243446247 0.396063482025622 chr20 63025520 2242224 0.0355764458587569 0.22447944782431903 chr21 48129895 2480183 0.051531028688095 0.26691898347700954 chr22 51304566 1376065 0.026821491872672697 0.18535225163029448 chrMT 16571 56581 3.4144589946291712 2.7399349687993273 chrX 155270560 4708610 0.03032519493714713 0.21785711247282533 chrY 59373566 207866 0.003500985606961859 0.08344724306490049