BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472726.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 = 17,630,146 number of mapped reads = 17,481,087 (99.15%) number of supplementary alignments = 58,107 (0.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,766,122 number of mapped paired reads (second in pair) = 8,714,965 number of mapped paired reads (both in pair) = 17,392,572 number of mapped paired reads (singletons) = 88,515 number of mapped bases = 1,719,446,028 bp number of sequenced bases = 1,719,218,985 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,179,862 duplication rate = 47.29% >>>>>>> Insert size mean insert size = 20,000.5161 std insert size = 1,394,444.2048 median insert size = 228 >>>>>>> Mapping quality mean mapping quality = 55.1428 >>>>>>> ACTG content number of A's = 466,710,310 bp (27.15%) number of C's = 395,689,926 bp (23.02%) number of T's = 463,215,825 bp (26.94%) number of G's = 393,267,636 bp (22.87%) number of N's = 335,288 bp (0.02%) GC percentage = 45.89% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 9,934,421 number of insertions = 96,271 mapped reads with insertion percentage = 0.55% number of deletions = 91,695 mapped reads with deletion percentage = 0.51% homopolymer indels = 45.5% >>>>>>> Coverage mean coverageData = 0.5554X std coverageData = 19.3301X There is a 5.01% of reference with a coverageData >= 1X There is a 2.26% of reference with a coverageData >= 2X There is a 1% of reference with a coverageData >= 3X There is a 0.71% of reference with a coverageData >= 4X There is a 0.52% of reference with a coverageData >= 5X There is a 0.45% of reference with a coverageData >= 6X There is a 0.41% of reference with a coverageData >= 7X There is a 0.38% of reference with a coverageData >= 8X There is a 0.36% of reference with a coverageData >= 9X There is a 0.35% of reference with a coverageData >= 10X There is a 0.33% of reference with a coverageData >= 11X There is a 0.32% of reference with a coverageData >= 12X There is a 0.31% of reference with a coverageData >= 13X There is a 0.3% of reference with a coverageData >= 14X There is a 0.29% of reference with a coverageData >= 15X There is a 0.29% of reference with a coverageData >= 16X There is a 0.28% of reference with a coverageData >= 17X There is a 0.27% of reference with a coverageData >= 18X There is a 0.27% of reference with a coverageData >= 19X There is a 0.26% of reference with a coverageData >= 20X There is a 0.26% of reference with a coverageData >= 21X There is a 0.25% of reference with a coverageData >= 22X There is a 0.25% of reference with a coverageData >= 23X There is a 0.24% of reference with a coverageData >= 24X There is a 0.24% of reference with a coverageData >= 25X There is a 0.23% of reference with a coverageData >= 26X There is a 0.23% of reference with a coverageData >= 27X There is a 0.22% of reference with a coverageData >= 28X There is a 0.22% of reference with a coverageData >= 29X There is a 0.22% of reference with a coverageData >= 30X There is a 0.21% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.2% of reference with a coverageData >= 36X There is a 0.2% of reference with a coverageData >= 37X There is a 0.19% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.19% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.18% of reference with a coverageData >= 42X There is a 0.18% of reference with a coverageData >= 43X There is a 0.18% of reference with a coverageData >= 44X There is a 0.18% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.17% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 194355630 0.7797598626644946 27.874924700045064 chr2 243199373 130134798 0.5350951213184254 19.265691032346673 chr3 198022430 180284340 0.910423834310083 21.009498162312404 chr4 191154276 68322775 0.3574221640744254 12.608914925406756 chr5 180915260 79227202 0.4379243740964692 13.353055098305298 chr6 171115067 96292641 0.5627361908463618 15.439626134641989 chr7 159138663 84855355 0.533216462928308 19.09114869641046 chr8 146364022 74728480 0.5105659094282063 15.357815867493104 chr9 141213431 87490899 0.6195649973266353 17.271773789808 chr10 135534747 49180894 0.3628655757183802 13.989105299329355 chr11 135006516 89846638 0.6654985304561152 28.998470999900825 chr12 133851895 130803824 0.9772280325205706 34.69923048840815 chr13 115169878 31121378 0.27022150705065434 9.56817973017397 chr14 107349540 41016154 0.3820803889797758 15.454164947428126 chr15 102531392 36814172 0.35905268895598336 10.165095105421292 chr16 90354753 60835209 0.6732928482467325 18.538564599714686 chr17 81195210 66302332 0.8165793524026849 22.68447830357055 chr18 78077248 31880678 0.4083222554155597 18.469656612528638 chr19 59128983 39626984 0.6701786837767868 21.861452698910487 chr20 63025520 36999835 0.5870611618912466 17.59444786001423 chr21 48129895 9336439 0.19398419630875988 7.728316199069722 chr22 51304566 13594082 0.26496826812646657 6.689702778079616 chrMT 16571 978 0.059018767726751555 0.26935707578329926 chrX 155270560 84127756 0.5418139536561213 17.330492698680718 chrY 59373566 2266555 0.038174479868701164 1.4050838885044774