BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472395.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 14,376,156 number of mapped reads = 14,235,618 (99.02%) number of supplementary alignments = 52,806 (0.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,138,610 number of mapped paired reads (second in pair) = 7,097,008 number of mapped paired reads (both in pair) = 14,161,568 number of mapped paired reads (singletons) = 74,050 number of mapped bases = 1,394,445,347 bp number of sequenced bases = 1,394,250,806 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,398,542 duplication rate = 46.63% >>>>>>> Insert size mean insert size = 18,594.3397 std insert size = 1,326,194.228 median insert size = 212 >>>>>>> Mapping quality mean mapping quality = 54.8574 >>>>>>> ACTG content number of A's = 369,246,203 bp (26.48%) number of C's = 328,519,848 bp (23.56%) number of T's = 370,458,194 bp (26.57%) number of G's = 325,854,317 bp (23.37%) number of N's = 172,244 bp (0.01%) GC percentage = 46.93% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 7,612,322 number of insertions = 77,024 mapped reads with insertion percentage = 0.54% number of deletions = 70,562 mapped reads with deletion percentage = 0.48% homopolymer indels = 45.26% >>>>>>> Coverage mean coverageData = 0.4504X std coverageData = 13.3862X There is a 4.01% of reference with a coverageData >= 1X There is a 1.76% of reference with a coverageData >= 2X There is a 0.77% of reference with a coverageData >= 3X There is a 0.6% of reference with a coverageData >= 4X There is a 0.47% of reference with a coverageData >= 5X There is a 0.43% of reference with a coverageData >= 6X There is a 0.4% of reference with a coverageData >= 7X There is a 0.38% of reference with a coverageData >= 8X There is a 0.36% of reference with a coverageData >= 9X There is a 0.35% of reference with a coverageData >= 10X There is a 0.34% of reference with a coverageData >= 11X There is a 0.33% of reference with a coverageData >= 12X There is a 0.32% of reference with a coverageData >= 13X There is a 0.31% of reference with a coverageData >= 14X There is a 0.3% of reference with a coverageData >= 15X There is a 0.29% of reference with a coverageData >= 16X There is a 0.29% of reference with a coverageData >= 17X There is a 0.28% of reference with a coverageData >= 18X There is a 0.27% of reference with a coverageData >= 19X There is a 0.27% of reference with a coverageData >= 20X There is a 0.26% of reference with a coverageData >= 21X There is a 0.26% of reference with a coverageData >= 22X There is a 0.25% of reference with a coverageData >= 23X There is a 0.25% of reference with a coverageData >= 24X There is a 0.24% of reference with a coverageData >= 25X There is a 0.24% of reference with a coverageData >= 26X There is a 0.23% of reference with a coverageData >= 27X There is a 0.23% of reference with a coverageData >= 28X There is a 0.23% of reference with a coverageData >= 29X There is a 0.22% of reference with a coverageData >= 30X There is a 0.22% of reference with a coverageData >= 31X There is a 0.22% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.21% of reference with a coverageData >= 34X There is a 0.21% of reference with a coverageData >= 35X There is a 0.2% of reference with a coverageData >= 36X There is a 0.2% of reference with a coverageData >= 37X There is a 0.2% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.19% of reference with a coverageData >= 40X There is a 0.19% of reference with a coverageData >= 41X There is a 0.19% of reference with a coverageData >= 42X There is a 0.18% of reference with a coverageData >= 43X There is a 0.18% of reference with a coverageData >= 44X There is a 0.18% of reference with a coverageData >= 45X There is a 0.18% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.17% of reference with a coverageData >= 50X There is a 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 127630857 0.5120583310402264 14.768997603650625 chr2 243199373 108896982 0.4477683501264619 14.470027275420792 chr3 198022430 89197395 0.45044086672403727 11.38810730988672 chr4 191154276 31016045 0.16225661098996289 5.880302095496397 chr5 180915260 54992166 0.30396643157686093 9.736545244566564 chr6 171115067 110443500 0.6454341042919383 17.780345060215794 chr7 159138663 111923593 0.7033086170894876 17.192800479114986 chr8 146364022 66490918 0.45428457821417345 12.258959217167092 chr9 141213431 41236634 0.2920163734283887 7.0848031994852 chr10 135534747 40050825 0.29550226703119903 8.770066087366057 chr11 135006516 49536270 0.3669176234427085 12.139101640855888 chr12 133851895 65859488 0.4920325408915578 11.27613616493752 chr13 115169878 47225064 0.410047008993098 13.220761751319902 chr14 107349540 21482429 0.20011663766793972 5.50554830010168 chr15 102531392 31870231 0.3108338858795558 10.099423164622017 chr16 90354753 69437390 0.7684973694742987 17.935938911092908 chr17 81195210 61422996 0.7564854626276599 19.616034140699746 chr18 78077248 17081145 0.21877237527634172 7.849892070744501 chr19 59128983 50831283 0.859667804535045 21.065258314381975 chr20 63025520 64554775 1.0242640600188622 25.152389947418495 chr21 48129895 12596347 0.2617156551037562 11.604812955202416 chr22 51304566 11545971 0.22504763026355198 5.630287016122897 chrMT 16571 7184 0.4335284533220687 0.8416065550215767 chrX 155270560 108830314 0.7009075899513726 17.784229286135457 chrY 59373566 285545 0.004809295099438697 0.33766317331734746