BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472660.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 = 16,247,194 number of mapped reads = 16,117,328 (99.2%) number of supplementary alignments = 101,899 (0.63%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,082,573 number of mapped paired reads (second in pair) = 8,034,755 number of mapped paired reads (both in pair) = 16,026,060 number of mapped paired reads (singletons) = 91,268 number of mapped bases = 1,589,964,827 bp number of sequenced bases = 1,589,766,808 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,856,422 duplication rate = 49% >>>>>>> Insert size mean insert size = 23,425.5509 std insert size = 1,498,571.6921 median insert size = 234 >>>>>>> Mapping quality mean mapping quality = 54.7433 >>>>>>> ACTG content number of A's = 438,247,835 bp (27.57%) number of C's = 358,651,567 bp (22.56%) number of T's = 439,488,697 bp (27.64%) number of G's = 353,082,384 bp (22.21%) number of N's = 296,325 bp (0.02%) GC percentage = 44.77% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 9,971,345 number of insertions = 107,716 mapped reads with insertion percentage = 0.66% number of deletions = 82,339 mapped reads with deletion percentage = 0.5% homopolymer indels = 46.45% >>>>>>> Coverage mean coverageData = 0.5136X std coverageData = 22.1963X There is a 3.28% of reference with a coverageData >= 1X There is a 1.45% of reference with a coverageData >= 2X There is a 0.73% of reference with a coverageData >= 3X There is a 0.57% of reference with a coverageData >= 4X There is a 0.46% of reference with a coverageData >= 5X There is a 0.42% of reference with a coverageData >= 6X There is a 0.38% of reference with a coverageData >= 7X There is a 0.36% of reference with a coverageData >= 8X There is a 0.35% of reference with a coverageData >= 9X There is a 0.33% of reference with a coverageData >= 10X There is a 0.32% of reference with a coverageData >= 11X There is a 0.31% of reference with a coverageData >= 12X There is a 0.3% of reference with a coverageData >= 13X There is a 0.29% of reference with a coverageData >= 14X There is a 0.28% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.27% of reference with a coverageData >= 17X There is a 0.26% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.25% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.24% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.23% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.22% of reference with a coverageData >= 26X There is a 0.22% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.21% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.2% of reference with a coverageData >= 31X There is a 0.2% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 196455530 0.7881847162980589 30.91897593492293 chr2 243199373 119777473 0.49250732648887213 18.526690308043055 chr3 198022430 205486773 1.0376944318883472 40.47183624642959 chr4 191154276 60436003 0.3161634898504703 18.553568541192345 chr5 180915260 59211384 0.3272879468542344 13.01056953979274 chr6 171115067 89542388 0.5232875723328326 13.940009154326804 chr7 159138663 69005093 0.4336161414149873 13.819600004679186 chr8 146364022 72597448 0.4960061018274013 16.321380568283757 chr9 141213431 102492863 0.725801096072795 19.043593786728064 chr10 135534747 31552383 0.23279921716310872 12.838063327781484 chr11 135006516 26254915 0.19447146536245702 7.177175303601014 chr12 133851895 55177908 0.412231055824798 14.81038226020728 chr13 115169878 36931528 0.3206700279738075 11.681458281323119 chr14 107349540 24309368 0.2264506023966195 10.207831978695351 chr15 102531392 16368057 0.1596394692466479 6.16173911718618 chr16 90354753 111118892 1.2298068259895525 46.74837823103631 chr17 81195210 62569843 0.7706100273649148 23.21543903799782 chr18 78077248 17870754 0.22888555190879678 20.974409073143928 chr19 59128983 40129248 0.6786730629207677 19.709414382414344 chr20 63025520 74093804 1.1756159092380356 44.29431989378333 chr21 48129895 11710070 0.24330138264378096 18.0198602834236 chr22 51304566 34393684 0.6703825152716427 36.576385473895336 chrMT 16571 6795 0.4100537082855591 0.8163987092500375 chrX 155270560 71667912 0.4615679366391156 14.488233182802924 chrY 59373566 804711 0.013553354703337172 0.8098216205245905