BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504660.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP013494//SRP013494.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 = 96,067,140 number of mapped reads = 95,571,781 (99.48%) number of supplementary alignments = 1,027,529 (1.07%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 47,884,135 number of mapped paired reads (second in pair) = 47,687,646 number of mapped paired reads (both in pair) = 95,337,496 number of mapped paired reads (singletons) = 234,285 number of mapped bases = 8,876,027,988 bp number of sequenced bases = 8,868,768,199 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 48,416,666 duplication rate = 25.84% >>>>>>> Insert size mean insert size = 23,475.6255 std insert size = 1,446,841.1448 median insert size = 144 >>>>>>> Mapping quality mean mapping quality = 53.1054 >>>>>>> ACTG content number of A's = 2,625,397,144 bp (29.6%) number of C's = 1,800,993,314 bp (20.31%) number of T's = 2,661,783,266 bp (30.01%) number of G's = 1,775,636,193 bp (20.02%) number of N's = 4,958,282 bp (0.06%) GC percentage = 40.33% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 86,479,602 number of insertions = 2,748,606 mapped reads with insertion percentage = 2.81% number of deletions = 2,965,258 mapped reads with deletion percentage = 3.02% homopolymer indels = 37.56% >>>>>>> Coverage mean coverageData = 2.8672X std coverageData = 417.8452X There is a 31.09% of reference with a coverageData >= 1X There is a 22.55% of reference with a coverageData >= 2X There is a 15.89% of reference with a coverageData >= 3X There is a 12.55% of reference with a coverageData >= 4X There is a 10.14% of reference with a coverageData >= 5X There is a 8.49% of reference with a coverageData >= 6X There is a 7.22% of reference with a coverageData >= 7X There is a 6.25% of reference with a coverageData >= 8X There is a 5.48% of reference with a coverageData >= 9X There is a 4.85% of reference with a coverageData >= 10X There is a 4.33% of reference with a coverageData >= 11X There is a 3.9% of reference with a coverageData >= 12X There is a 3.53% of reference with a coverageData >= 13X There is a 3.22% of reference with a coverageData >= 14X There is a 2.95% of reference with a coverageData >= 15X There is a 2.71% of reference with a coverageData >= 16X There is a 2.5% of reference with a coverageData >= 17X There is a 2.32% of reference with a coverageData >= 18X There is a 2.15% of reference with a coverageData >= 19X There is a 2.01% of reference with a coverageData >= 20X There is a 1.88% of reference with a coverageData >= 21X There is a 1.76% of reference with a coverageData >= 22X There is a 1.65% of reference with a coverageData >= 23X There is a 1.56% of reference with a coverageData >= 24X There is a 1.47% of reference with a coverageData >= 25X There is a 1.39% of reference with a coverageData >= 26X There is a 1.31% of reference with a coverageData >= 27X There is a 1.25% of reference with a coverageData >= 28X There is a 1.18% of reference with a coverageData >= 29X There is a 1.13% of reference with a coverageData >= 30X There is a 1.07% of reference with a coverageData >= 31X There is a 1.02% of reference with a coverageData >= 32X There is a 0.98% of reference with a coverageData >= 33X There is a 0.93% of reference with a coverageData >= 34X There is a 0.89% of reference with a coverageData >= 35X There is a 0.86% of reference with a coverageData >= 36X There is a 0.82% of reference with a coverageData >= 37X There is a 0.79% of reference with a coverageData >= 38X There is a 0.76% of reference with a coverageData >= 39X There is a 0.73% of reference with a coverageData >= 40X There is a 0.7% of reference with a coverageData >= 41X There is a 0.67% of reference with a coverageData >= 42X There is a 0.65% of reference with a coverageData >= 43X There is a 0.63% of reference with a coverageData >= 44X There is a 0.61% of reference with a coverageData >= 45X There is a 0.58% of reference with a coverageData >= 46X There is a 0.57% of reference with a coverageData >= 47X There is a 0.55% of reference with a coverageData >= 48X There is a 0.53% of reference with a coverageData >= 49X There is a 0.51% of reference with a coverageData >= 50X There is a 0.5% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 490927620 1.9696144307700643 14.50697213165792 chr2 243199373 577455746 2.3744129718623905 10.78428523226854 chr3 198022430 558497747 2.8203761917273713 51.83331741070014 chr4 191154276 567212477 2.9673020602479223 29.422713830676983 chr5 180915260 492433086 2.7218991145357223 18.74228518097467 chr6 171115067 490863431 2.8686160699104306 27.88176497696994 chr7 159138663 319551075 2.008004019739691 8.53026820807284 chr8 146364022 386151031 2.6382920182392913 19.123407115562056 chr9 141213431 2228787583 15.78311331448352 1953.6752695591597 chr10 135534747 338926305 2.500659886132373 38.93231726399763 chr11 135006516 320436864 2.3734918394605486 13.379948450102068 chr12 133851895 297104342 2.2196498749606794 10.5187671251513 chr13 115169878 219807477 1.908550055076033 8.157110591734181 chr14 107349540 250967101 2.3378498035482966 31.589811942855043 chr15 102531392 186266710 1.8166798125592598 8.887309550325043 chr16 90354753 158655446 1.7559169908859138 15.714791112841988 chr17 81195210 106590354 1.3127665289614991 5.775540258960694 chr18 78077248 160693442 2.0581340418145886 8.872116363511084 chr19 59128983 75481838 1.2765624262470403 7.204598446065051 chr20 63025520 96910194 1.537634183740174 6.398773215356577 chr21 48129895 63447243 1.3182501852538844 5.911303372383266 chr22 51304566 50247365 0.9793936274599808 5.080346404724242 chrMT 16571 1968 0.11876169211272705 0.5048787122022982 chrX 155270560 431931177 2.7817969935833298 13.554283293357797 chrY 59373566 6680366 0.11251414476267098 1.288997251262256