BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472685.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 = 16,254,314 number of mapped reads = 16,123,868 (99.2%) number of supplementary alignments = 102,804 (0.63%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,082,246 number of mapped paired reads (second in pair) = 8,041,622 number of mapped paired reads (both in pair) = 16,039,030 number of mapped paired reads (singletons) = 84,838 number of mapped bases = 1,585,512,248 bp number of sequenced bases = 1,585,288,349 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,277,280 duplication rate = 47.47% >>>>>>> Insert size mean insert size = 22,704.2747 std insert size = 1,447,854.0466 median insert size = 206 >>>>>>> Mapping quality mean mapping quality = 54.7368 >>>>>>> ACTG content number of A's = 437,868,576 bp (27.62%) number of C's = 356,356,568 bp (22.48%) number of T's = 438,664,576 bp (27.67%) number of G's = 352,098,069 bp (22.21%) number of N's = 300,560 bp (0.02%) GC percentage = 44.69% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 9,534,493 number of insertions = 96,063 mapped reads with insertion percentage = 0.59% number of deletions = 91,628 mapped reads with deletion percentage = 0.56% homopolymer indels = 46.9% >>>>>>> Coverage mean coverageData = 0.5122X std coverageData = 30.4207X There is a 3.42% of reference with a coverageData >= 1X There is a 1.61% of reference with a coverageData >= 2X There is a 0.76% of reference with a coverageData >= 3X There is a 0.58% of reference with a coverageData >= 4X There is a 0.44% of reference with a coverageData >= 5X There is a 0.39% of reference with a coverageData >= 6X There is a 0.35% of reference with a coverageData >= 7X There is a 0.32% of reference with a coverageData >= 8X There is a 0.31% of reference with a coverageData >= 9X There is a 0.29% of reference with a coverageData >= 10X There is a 0.28% of reference with a coverageData >= 11X There is a 0.27% of reference with a coverageData >= 12X There is a 0.26% of reference with a coverageData >= 13X There is a 0.25% of reference with a coverageData >= 14X There is a 0.24% of reference with a coverageData >= 15X There is a 0.24% of reference with a coverageData >= 16X There is a 0.23% of reference with a coverageData >= 17X There is a 0.22% of reference with a coverageData >= 18X There is a 0.22% of reference with a coverageData >= 19X There is a 0.21% of reference with a coverageData >= 20X There is a 0.21% of reference with a coverageData >= 21X There is a 0.2% of reference with a coverageData >= 22X There is a 0.2% of reference with a coverageData >= 23X There is a 0.19% of reference with a coverageData >= 24X There is a 0.19% of reference with a coverageData >= 25X There is a 0.19% of reference with a coverageData >= 26X There is a 0.18% of reference with a coverageData >= 27X There is a 0.18% of reference with a coverageData >= 28X There is a 0.18% of reference with a coverageData >= 29X There is a 0.17% of reference with a coverageData >= 30X There is a 0.17% of reference with a coverageData >= 31X There is a 0.17% of reference with a coverageData >= 32X There is a 0.16% of reference with a coverageData >= 33X There is a 0.16% of reference with a coverageData >= 34X There is a 0.16% of reference with a coverageData >= 35X There is a 0.16% of reference with a coverageData >= 36X There is a 0.15% of reference with a coverageData >= 37X There is a 0.15% of reference with a coverageData >= 38X There is a 0.15% of reference with a coverageData >= 39X There is a 0.15% of reference with a coverageData >= 40X There is a 0.15% of reference with a coverageData >= 41X There is a 0.14% of reference with a coverageData >= 42X There is a 0.14% of reference with a coverageData >= 43X There is a 0.14% of reference with a coverageData >= 44X There is a 0.14% of reference with a coverageData >= 45X There is a 0.14% of reference with a coverageData >= 46X There is a 0.14% of reference with a coverageData >= 47X There is a 0.13% of reference with a coverageData >= 48X There is a 0.13% of reference with a coverageData >= 49X There is a 0.13% of reference with a coverageData >= 50X There is a 0.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 166333236 0.6673332862027253 56.24121794670079 chr2 243199373 122596655 0.5040993876246548 25.824157657638256 chr3 198022430 142761361 0.7209353051570976 21.18153243967406 chr4 191154276 44695334 0.2338181229071747 21.007804242911423 chr5 180915260 63572662 0.3513946916362943 27.844210261040367 chr6 171115067 124239221 0.7260565839009373 38.37650416072624 chr7 159138663 113224773 0.7114850085173834 34.33710219658341 chr8 146364022 88492540 0.6046058231441603 28.445087789445314 chr9 141213431 103190532 0.7307416247113209 37.725048049681874 chr10 135534747 40107983 0.2959239891450124 24.769099629164078 chr11 135006516 24489948 0.18139826673254794 10.320735679473966 chr12 133851895 59170160 0.4420569465975809 18.230946025187972 chr13 115169878 40168826 0.34877892290551876 13.21358495793881 chr14 107349540 42449511 0.39543263063819367 18.456037933706185 chr15 102531392 20328426 0.1982653858829889 11.879061718540273 chr16 90354753 109760112 1.2147685468190035 60.3139877855773 chr17 81195210 39081510 0.48132777783319974 20.171464184967064 chr18 78077248 5445323 0.06974276296213719 2.5637697347177606 chr19 59128983 31784389 0.5375433059621539 16.244413051292813 chr20 63025520 69192371 1.0978468880542358 40.12261537926709 chr21 48129895 18927653 0.39326188016824054 35.81102628096143 chr22 51304566 14410529 0.28088199791028345 12.067735995591171 chrMT 16571 3247 0.1959447227083459 0.5961256990734167 chrX 155270560 100220683 0.6454583727913392 22.67587971595412 chrY 59373566 865263 0.014573202492166294 0.5021326864636616