BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504623.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 = 567,503,902 number of mapped reads = 523,133,602 (92.18%) number of supplementary alignments = 5,365,427 (0.95%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 263,269,010 number of mapped paired reads (second in pair) = 259,864,592 number of mapped paired reads (both in pair) = 511,472,592 number of mapped paired reads (singletons) = 11,661,010 number of mapped bases = 50,141,658,800 bp number of sequenced bases = 50,098,115,883 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 201,871,577 duplication rate = 28.28% >>>>>>> Insert size mean insert size = 106,229.2848 std insert size = 3,053,174.8962 median insert size = 328 >>>>>>> Mapping quality mean mapping quality = 52.2148 >>>>>>> ACTG content number of A's = 13,450,718,536 bp (26.85%) number of C's = 11,542,081,110 bp (23.04%) number of T's = 13,527,336,167 bp (27%) number of G's = 11,563,220,475 bp (23.08%) number of N's = 14,759,595 bp (0.03%) GC percentage = 46.12% >>>>>>> Mismatches and indels general error rate = 0.0155 number of mismatches = 717,207,089 number of insertions = 14,701,450 mapped reads with insertion percentage = 2.61% number of deletions = 13,240,702 mapped reads with deletion percentage = 2.36% homopolymer indels = 34.42% >>>>>>> Coverage mean coverageData = 16.1972X std coverageData = 395.6454X There is a 87.54% of reference with a coverageData >= 1X There is a 82.8% of reference with a coverageData >= 2X There is a 77.71% of reference with a coverageData >= 3X There is a 72.75% of reference with a coverageData >= 4X There is a 67.99% of reference with a coverageData >= 5X There is a 63.54% of reference with a coverageData >= 6X There is a 59.38% of reference with a coverageData >= 7X There is a 55.53% of reference with a coverageData >= 8X There is a 51.95% of reference with a coverageData >= 9X There is a 48.62% of reference with a coverageData >= 10X There is a 45.53% of reference with a coverageData >= 11X There is a 42.66% of reference with a coverageData >= 12X There is a 39.97% of reference with a coverageData >= 13X There is a 37.47% of reference with a coverageData >= 14X There is a 35.12% of reference with a coverageData >= 15X There is a 32.92% of reference with a coverageData >= 16X There is a 30.86% of reference with a coverageData >= 17X There is a 28.93% of reference with a coverageData >= 18X There is a 27.12% of reference with a coverageData >= 19X There is a 25.42% of reference with a coverageData >= 20X There is a 23.82% of reference with a coverageData >= 21X There is a 22.32% of reference with a coverageData >= 22X There is a 20.91% of reference with a coverageData >= 23X There is a 19.59% of reference with a coverageData >= 24X There is a 18.35% of reference with a coverageData >= 25X There is a 17.19% of reference with a coverageData >= 26X There is a 16.1% of reference with a coverageData >= 27X There is a 15.08% of reference with a coverageData >= 28X There is a 14.13% of reference with a coverageData >= 29X There is a 13.23% of reference with a coverageData >= 30X There is a 12.4% of reference with a coverageData >= 31X There is a 11.61% of reference with a coverageData >= 32X There is a 10.88% of reference with a coverageData >= 33X There is a 10.2% of reference with a coverageData >= 34X There is a 9.56% of reference with a coverageData >= 35X There is a 8.96% of reference with a coverageData >= 36X There is a 8.41% of reference with a coverageData >= 37X There is a 7.89% of reference with a coverageData >= 38X There is a 7.4% of reference with a coverageData >= 39X There is a 6.95% of reference with a coverageData >= 40X There is a 6.52% of reference with a coverageData >= 41X There is a 6.13% of reference with a coverageData >= 42X There is a 5.76% of reference with a coverageData >= 43X There is a 5.41% of reference with a coverageData >= 44X There is a 5.09% of reference with a coverageData >= 45X There is a 4.79% of reference with a coverageData >= 46X There is a 4.51% of reference with a coverageData >= 47X There is a 4.25% of reference with a coverageData >= 48X There is a 4% of reference with a coverageData >= 49X There is a 3.78% of reference with a coverageData >= 50X There is a 3.56% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3863243104 15.499432212046525 117.38118692527036 chr2 243199373 3948126762 16.234115710487462 381.3299471487344 chr3 198022430 2679026118 13.528902347072501 35.46046243041262 chr4 191154276 3792864673 19.841903369192746 1115.9897755046331 chr5 180915260 2607179756 14.411054965733681 50.1792493172192 chr6 171115067 2147962629 12.552738146664781 49.92133566956585 chr7 159138663 2465443943 15.492425891500671 56.52908279887913 chr8 146364022 2356310616 16.098974213758623 302.44145124300326 chr9 141213431 1830970311 12.965978505259885 136.203238753553 chr10 135534747 3305440123 24.38813806912555 861.0922974821049 chr11 135006516 2150341427 15.92768623849237 47.98252607167641 chr12 133851895 2003195859 14.965763906443012 28.571411161292595 chr13 115169878 1118631853 9.71288562969564 21.729218733244124 chr14 107349540 1337879950 12.46283821989363 46.245727035245174 chr15 102531392 1459999915 14.239540559441542 24.244896894489457 chr16 90354753 2247082531 24.869555351448973 302.02358016467537 chr17 81195210 1715955784 21.13370707459221 111.90310686594589 chr18 78077248 1138928124 14.58719605486095 448.70578159514264 chr19 59128983 1669222839 28.230197008461992 64.78608404542904 chr20 63025520 1281241380 20.328929931875216 272.52152354455086 chr21 48129895 834522142 17.338956214219873 364.3659185445862 chr22 51304566 924205647 18.014101259525322 46.008669852489795 chrMT 16571 18889210 1139.8956007482952 531.9233898631973 chrX 155270560 2453651617 15.80242653211272 32.651646862257266 chrY 59373566 791342487 13.328195362225674 937.3606197461264