BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504603.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 443,087,182 number of mapped reads = 381,054,852 (86%) number of supplementary alignments = 2,068,903 (0.47%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 190,902,481 number of mapped paired reads (second in pair) = 190,152,371 number of mapped paired reads (both in pair) = 378,641,932 number of mapped paired reads (singletons) = 2,412,920 number of mapped bases = 37,837,510,029 bp number of sequenced bases = 37,827,642,290 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 95,968,764 duplication rate = 22.45% >>>>>>> Insert size mean insert size = 29,830.4161 std insert size = 1,680,382.5911 median insert size = 213 >>>>>>> Mapping quality mean mapping quality = 53.961 >>>>>>> ACTG content number of A's = 9,975,242,268 bp (26.37%) number of C's = 8,834,050,722 bp (23.35%) number of T's = 9,988,088,690 bp (26.4%) number of G's = 8,997,755,411 bp (23.79%) number of N's = 32,505,199 bp (0.09%) GC percentage = 47.14% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 247,554,208 number of insertions = 2,857,357 mapped reads with insertion percentage = 0.73% number of deletions = 3,836,708 mapped reads with deletion percentage = 0.98% homopolymer indels = 40.36% >>>>>>> Coverage mean coverageData = 12.2226X std coverageData = 25.3704X There is a 78.78% of reference with a coverageData >= 1X There is a 70.34% of reference with a coverageData >= 2X There is a 63.18% of reference with a coverageData >= 3X There is a 57.19% of reference with a coverageData >= 4X There is a 52.02% of reference with a coverageData >= 5X There is a 47.53% of reference with a coverageData >= 6X There is a 43.6% of reference with a coverageData >= 7X There is a 40.12% of reference with a coverageData >= 8X There is a 37.04% of reference with a coverageData >= 9X There is a 34.28% of reference with a coverageData >= 10X There is a 31.81% of reference with a coverageData >= 11X There is a 29.59% of reference with a coverageData >= 12X There is a 27.58% of reference with a coverageData >= 13X There is a 25.76% of reference with a coverageData >= 14X There is a 24.1% of reference with a coverageData >= 15X There is a 22.58% of reference with a coverageData >= 16X There is a 21.2% of reference with a coverageData >= 17X There is a 19.93% of reference with a coverageData >= 18X There is a 18.77% of reference with a coverageData >= 19X There is a 17.69% of reference with a coverageData >= 20X There is a 16.7% of reference with a coverageData >= 21X There is a 15.79% of reference with a coverageData >= 22X There is a 14.94% of reference with a coverageData >= 23X There is a 14.15% of reference with a coverageData >= 24X There is a 13.42% of reference with a coverageData >= 25X There is a 12.74% of reference with a coverageData >= 26X There is a 12.1% of reference with a coverageData >= 27X There is a 11.51% of reference with a coverageData >= 28X There is a 10.96% of reference with a coverageData >= 29X There is a 10.44% of reference with a coverageData >= 30X There is a 9.95% of reference with a coverageData >= 31X There is a 9.5% of reference with a coverageData >= 32X There is a 9.07% of reference with a coverageData >= 33X There is a 8.67% of reference with a coverageData >= 34X There is a 8.29% of reference with a coverageData >= 35X There is a 7.93% of reference with a coverageData >= 36X There is a 7.6% of reference with a coverageData >= 37X There is a 7.28% of reference with a coverageData >= 38X There is a 6.98% of reference with a coverageData >= 39X There is a 6.7% of reference with a coverageData >= 40X There is a 6.43% of reference with a coverageData >= 41X There is a 6.18% of reference with a coverageData >= 42X There is a 5.94% of reference with a coverageData >= 43X There is a 5.71% of reference with a coverageData >= 44X There is a 5.5% of reference with a coverageData >= 45X There is a 5.29% of reference with a coverageData >= 46X There is a 5.1% of reference with a coverageData >= 47X There is a 4.91% of reference with a coverageData >= 48X There is a 4.74% of reference with a coverageData >= 49X There is a 4.57% of reference with a coverageData >= 50X There is a 4.41% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3889175550 15.603473862558602 26.4003591540028 chr2 243199373 2595502177 10.672322650272623 19.393710007226165 chr3 198022430 2799280218 14.136177492620407 23.46533928456313 chr4 191154276 1581892958 8.275477750756671 13.19172140836601 chr5 180915260 1538665962 8.504898713353423 14.34198757883182 chr6 171115067 1933609343 11.300053098188016 18.49738396241286 chr7 159138663 3077585008 19.339015107849686 28.860300851485096 chr8 146364022 2884749513 19.709416792331655 48.57332724192125 chr9 141213431 1487371437 10.53279016356454 20.60955758476607 chr10 135534747 1780322405 13.135542319638521 24.900815086810326 chr11 135006516 1930123703 14.296522569325468 24.305819554582644 chr12 133851895 1290822649 9.64366361044048 16.3678531268175 chr13 115169878 858662080 7.455613350567238 14.017714971437233 chr14 107349540 1263481820 11.769792585976614 20.552003309560902 chr15 102531392 843500820 8.226756738072961 15.376449554554842 chr16 90354753 1105034645 12.22995590503136 21.045063982647754 chr17 81195210 1374048783 16.922781319242848 52.25647789570115 chr18 78077248 494243960 6.330191863319773 29.304967623691063 chr19 59128983 1116549117 18.883279575432574 32.90806981597019 chr20 63025520 1704728083 27.048219245156567 40.44593042144044 chr21 48129895 358238556 7.44316097095163 18.98143691677805 chr22 51304566 778659577 15.177198399846127 28.25690847207567 chrMT 16571 276215 16.66857763562851 13.156996080491401 chrX 155270560 1113009632 7.168194872228193 12.698663766951395 chrY 59373566 37975818 0.639608171757782 15.114826775536383