BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777283.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 33,149,956 number of mapped reads = 32,785,527 (98.9%) number of supplementary alignments = 1,233,876 (3.72%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 16,394,309 number of mapped paired reads (second in pair) = 16,391,218 number of mapped paired reads (both in pair) = 32,626,874 number of mapped paired reads (singletons) = 158,653 number of mapped bases = 3,240,769,881 bp number of sequenced bases = 3,237,612,797 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,930,096 duplication rate = 36.21% >>>>>>> Insert size mean insert size = 276,712.8948 std insert size = 5,257,267.7362 median insert size = 226 >>>>>>> Mapping quality mean mapping quality = 53.3314 >>>>>>> ACTG content number of A's = 853,339,638 bp (26.36%) number of C's = 766,217,292 bp (23.67%) number of T's = 851,064,366 bp (26.29%) number of G's = 766,872,074 bp (23.69%) number of N's = 119,427 bp (0%) GC percentage = 47.35% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 16,032,830 number of insertions = 1,097,550 mapped reads with insertion percentage = 3.04% number of deletions = 850,141 mapped reads with deletion percentage = 2.36% homopolymer indels = 30.45% >>>>>>> Coverage mean coverageData = 1.0469X std coverageData = 38.5688X There is a 12.23% of reference with a coverageData >= 1X There is a 6.45% of reference with a coverageData >= 2X There is a 4.02% of reference with a coverageData >= 3X There is a 3.08% of reference with a coverageData >= 4X There is a 2.52% of reference with a coverageData >= 5X There is a 2.19% of reference with a coverageData >= 6X There is a 1.96% of reference with a coverageData >= 7X There is a 1.8% of reference with a coverageData >= 8X There is a 1.66% of reference with a coverageData >= 9X There is a 1.55% of reference with a coverageData >= 10X There is a 1.46% of reference with a coverageData >= 11X There is a 1.38% of reference with a coverageData >= 12X There is a 1.31% of reference with a coverageData >= 13X There is a 1.24% of reference with a coverageData >= 14X There is a 1.19% of reference with a coverageData >= 15X There is a 1.14% of reference with a coverageData >= 16X There is a 1.09% of reference with a coverageData >= 17X There is a 1.05% of reference with a coverageData >= 18X There is a 1% of reference with a coverageData >= 19X There is a 0.97% of reference with a coverageData >= 20X There is a 0.93% of reference with a coverageData >= 21X There is a 0.9% of reference with a coverageData >= 22X There is a 0.87% of reference with a coverageData >= 23X There is a 0.84% of reference with a coverageData >= 24X There is a 0.81% of reference with a coverageData >= 25X There is a 0.79% of reference with a coverageData >= 26X There is a 0.76% of reference with a coverageData >= 27X There is a 0.74% of reference with a coverageData >= 28X There is a 0.72% of reference with a coverageData >= 29X There is a 0.7% of reference with a coverageData >= 30X There is a 0.68% of reference with a coverageData >= 31X There is a 0.66% of reference with a coverageData >= 32X There is a 0.64% of reference with a coverageData >= 33X There is a 0.62% of reference with a coverageData >= 34X There is a 0.61% of reference with a coverageData >= 35X There is a 0.59% of reference with a coverageData >= 36X There is a 0.58% of reference with a coverageData >= 37X There is a 0.56% of reference with a coverageData >= 38X There is a 0.55% of reference with a coverageData >= 39X There is a 0.53% of reference with a coverageData >= 40X There is a 0.52% of reference with a coverageData >= 41X There is a 0.51% of reference with a coverageData >= 42X There is a 0.5% of reference with a coverageData >= 43X There is a 0.48% of reference with a coverageData >= 44X There is a 0.47% of reference with a coverageData >= 45X There is a 0.46% of reference with a coverageData >= 46X There is a 0.45% of reference with a coverageData >= 47X There is a 0.44% of reference with a coverageData >= 48X There is a 0.43% of reference with a coverageData >= 49X There is a 0.42% of reference with a coverageData >= 50X There is a 0.41% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 345583952 1.3864918394726888 17.78906011326561 chr2 243199373 307612228 1.2648561721415292 88.67591402426065 chr3 198022430 167141140 0.8440515551697856 11.521500349904795 chr4 191154276 117025970 0.612206917097685 22.665161042725522 chr5 180915260 148141091 0.818842429322988 19.622535685621873 chr6 171115067 158968065 0.9290126684168613 22.503612728308934 chr7 159138663 173630857 1.0910664556733143 30.028508073117877 chr8 146364022 99786161 0.6817670055555046 11.508437320370389 chr9 141213431 115633434 0.8188557786688152 19.230449602863484 chr10 135534747 144797419 1.068341677724901 81.75202467442654 chr11 135006516 229848743 1.7025011074280296 33.23016679994025 chr12 133851895 184285658 1.3767878146215262 15.687974346675112 chr13 115169878 73803173 0.6408201022840364 10.292790879191736 chr14 107349540 63995980 0.5961458241926327 19.668409261573572 chr15 102531392 148435653 1.4477093317917697 13.839301133567101 chr16 90354753 138113000 1.5285637491588295 63.59938554856793 chr17 81195210 174237734 2.145911489113705 24.381242636473935 chr18 78077248 42439420 0.5435568118384501 11.631954825338557 chr19 59128983 147341440 2.491864945487055 27.135428907234992 chr20 63025520 97106495 1.5407488109578469 17.805332582825887 chr21 48129895 18011569 0.374228304466486 5.7078628448181545 chr22 51304566 47153565 0.9190910025435163 15.416378309710959 chrMT 16571 664956 40.12769295757649 12.531612177852027 chrX 155270560 80154626 0.5162255227262657 11.424203132753535 chrY 59373566 16857552 0.28392352246452573 85.50879906902797