BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695920.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 107,485,596 number of mapped reads = 106,822,713 (99.38%) number of supplementary alignments = 1,366,222 (1.27%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 53,574,694 number of mapped paired reads (second in pair) = 53,248,019 number of mapped paired reads (both in pair) = 106,367,176 number of mapped paired reads (singletons) = 455,537 number of mapped bases = 10,599,403,282 bp number of sequenced bases = 10,597,036,284 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,154,707 duplication rate = 4.3% >>>>>>> Insert size mean insert size = 82,187.4694 std insert size = 2,744,202.2206 median insert size = 325 >>>>>>> Mapping quality mean mapping quality = 53.8479 >>>>>>> ACTG content number of A's = 3,148,774,636 bp (29.71%) number of C's = 2,120,689,643 bp (20.01%) number of T's = 3,129,351,899 bp (29.53%) number of G's = 2,186,382,417 bp (20.63%) number of N's = 11,837,689 bp (0.11%) GC percentage = 40.64% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 67,659,735 number of insertions = 1,056,940 mapped reads with insertion percentage = 0.97% number of deletions = 1,026,761 mapped reads with deletion percentage = 0.94% homopolymer indels = 45.76% >>>>>>> Coverage mean coverageData = 3.4239X std coverageData = 4.546X There is a 81.01% of reference with a coverageData >= 1X There is a 66.1% of reference with a coverageData >= 2X There is a 51.23% of reference with a coverageData >= 3X There is a 38.39% of reference with a coverageData >= 4X There is a 28.18% of reference with a coverageData >= 5X There is a 20.43% of reference with a coverageData >= 6X There is a 14.74% of reference with a coverageData >= 7X There is a 10.62% of reference with a coverageData >= 8X There is a 7.66% of reference with a coverageData >= 9X There is a 5.55% of reference with a coverageData >= 10X There is a 4.04% of reference with a coverageData >= 11X There is a 2.96% of reference with a coverageData >= 12X There is a 2.18% of reference with a coverageData >= 13X There is a 1.62% of reference with a coverageData >= 14X There is a 1.21% of reference with a coverageData >= 15X There is a 0.92% of reference with a coverageData >= 16X There is a 0.7% of reference with a coverageData >= 17X There is a 0.54% of reference with a coverageData >= 18X There is a 0.42% of reference with a coverageData >= 19X There is a 0.33% of reference with a coverageData >= 20X There is a 0.27% of reference with a coverageData >= 21X There is a 0.22% of reference with a coverageData >= 22X There is a 0.18% of reference with a coverageData >= 23X There is a 0.15% of reference with a coverageData >= 24X There is a 0.12% of reference with a coverageData >= 25X There is a 0.11% of reference with a coverageData >= 26X There is a 0.09% of reference with a coverageData >= 27X There is a 0.08% of reference with a coverageData >= 28X There is a 0.07% of reference with a coverageData >= 29X There is a 0.06% of reference with a coverageData >= 30X There is a 0.06% of reference with a coverageData >= 31X There is a 0.05% of reference with a coverageData >= 32X There is a 0.05% of reference with a coverageData >= 33X There is a 0.04% of reference with a coverageData >= 34X There is a 0.04% of reference with a coverageData >= 35X There is a 0.04% of reference with a coverageData >= 36X There is a 0.03% of reference with a coverageData >= 37X There is a 0.03% of reference with a coverageData >= 38X There is a 0.03% of reference with a coverageData >= 39X There is a 0.03% of reference with a coverageData >= 40X There is a 0.03% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 872707329 3.501324592487174 4.683626320817512 chr2 243199373 942788765 3.8766085346774313 5.242484063673038 chr3 198022430 764870725 3.8625458994720954 3.5090246601904695 chr4 191154276 775326714 4.056026002787403 4.481545702264979 chr5 180915260 664732652 3.674276299301673 3.3464874387687527 chr6 171115067 699385938 4.087225924997008 4.152223458406641 chr7 159138663 532913338 3.3487358003001444 3.4651997613443206 chr8 146364022 485454361 3.316760187144898 3.264121710744148 chr9 141213431 447717019 3.170498838740063 4.101767100545122 chr10 135534747 503677975 3.716227654890594 5.063865867587583 chr11 135006516 537902873 3.9842734183289346 3.9681822954271277 chr12 133851895 518674222 3.8749860209300735 3.739681026912539 chr13 115169878 370456591 3.2166100844528116 3.527675147488567 chr14 107349540 319232448 2.973766333791463 3.4473610971837436 chr15 102531392 330851686 3.2268330659160465 3.7153770010604537 chr16 90354753 260370198 2.881643625322068 5.165274521461852 chr17 81195210 240708072 2.964560002985398 4.030766647633396 chr18 78077248 295119201 3.7798361053914196 4.8866022323642815 chr19 59128983 143643747 2.4293288961185078 3.4985649386242406 chr20 63025520 185694971 2.946345718369321 3.5567801998064237 chr21 48129895 143399582 2.979428523581861 6.065070035413373 chr22 51304566 104625782 2.039307417589304 3.150333501519961 chrMT 16571 12589625 759.7383984068554 205.32830203560545 chrX 155270560 379265835 2.4426126562562795 2.6712963366628055 chrY 59373566 67293633 1.1333938237767291 4.814313019329922