BamQC report ----------------------------------- >>>>>>> Input bam file = SRR26104297.sorted.bam outfile = /mainsd2/zhouyj/SRP461548/SRP461548.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 = 2,583,457,124 number of mapped reads = 2,348,905,187 (90.92%) number of supplementary alignments = 18,559 (0%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,180,306,461 number of mapped paired reads (second in pair) = 1,168,598,726 number of mapped paired reads (both in pair) = 2,329,301,380 number of mapped paired reads (singletons) = 19,603,807 number of mapped bases = 115,715,546,169 bp number of sequenced bases = 115,700,758,759 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,791,778,132 duplication rate = 50.24% >>>>>>> Insert size mean insert size = 7,707.9988 std insert size = 945,679.6905 median insert size = 143 >>>>>>> Mapping quality mean mapping quality = 52.8037 >>>>>>> ACTG content number of A's = 28,304,189,664 bp (24.46%) number of C's = 29,582,491,039 bp (25.57%) number of T's = 28,382,098,454 bp (24.53%) number of G's = 29,421,299,631 bp (25.43%) number of N's = 10,679,971 bp (0.01%) GC percentage = 51% >>>>>>> Mismatches and indels general error rate = 0.0029 number of mismatches = 321,913,022 number of insertions = 7,035,685 mapped reads with insertion percentage = 0.3% number of deletions = 8,404,302 mapped reads with deletion percentage = 0.36% homopolymer indels = 45.63% >>>>>>> Coverage mean coverageData = 37.3795X std coverageData = 1,289.8869X There is a 88.87% of reference with a coverageData >= 1X There is a 85.52% of reference with a coverageData >= 2X There is a 81.81% of reference with a coverageData >= 3X There is a 77.9% of reference with a coverageData >= 4X There is a 73.86% of reference with a coverageData >= 5X There is a 69.8% of reference with a coverageData >= 6X There is a 65.78% of reference with a coverageData >= 7X There is a 61.87% of reference with a coverageData >= 8X There is a 58.09% of reference with a coverageData >= 9X There is a 54.49% of reference with a coverageData >= 10X There is a 51.07% of reference with a coverageData >= 11X There is a 47.85% of reference with a coverageData >= 12X There is a 44.83% of reference with a coverageData >= 13X There is a 42.01% of reference with a coverageData >= 14X There is a 39.37% of reference with a coverageData >= 15X There is a 36.92% of reference with a coverageData >= 16X There is a 34.65% of reference with a coverageData >= 17X There is a 32.54% of reference with a coverageData >= 18X There is a 30.58% of reference with a coverageData >= 19X There is a 28.78% of reference with a coverageData >= 20X There is a 27.1% of reference with a coverageData >= 21X There is a 25.56% of reference with a coverageData >= 22X There is a 24.13% of reference with a coverageData >= 23X There is a 22.81% of reference with a coverageData >= 24X There is a 21.59% of reference with a coverageData >= 25X There is a 20.46% of reference with a coverageData >= 26X There is a 19.41% of reference with a coverageData >= 27X There is a 18.45% of reference with a coverageData >= 28X There is a 17.55% of reference with a coverageData >= 29X There is a 16.72% of reference with a coverageData >= 30X There is a 15.95% of reference with a coverageData >= 31X There is a 15.24% of reference with a coverageData >= 32X There is a 14.58% of reference with a coverageData >= 33X There is a 13.96% of reference with a coverageData >= 34X There is a 13.38% of reference with a coverageData >= 35X There is a 12.85% of reference with a coverageData >= 36X There is a 12.35% of reference with a coverageData >= 37X There is a 11.88% of reference with a coverageData >= 38X There is a 11.45% of reference with a coverageData >= 39X There is a 11.04% of reference with a coverageData >= 40X There is a 10.66% of reference with a coverageData >= 41X There is a 10.3% of reference with a coverageData >= 42X There is a 9.97% of reference with a coverageData >= 43X There is a 9.65% of reference with a coverageData >= 44X There is a 9.35% of reference with a coverageData >= 45X There is a 9.07% of reference with a coverageData >= 46X There is a 8.81% of reference with a coverageData >= 47X There is a 8.56% of reference with a coverageData >= 48X There is a 8.33% of reference with a coverageData >= 49X There is a 8.11% of reference with a coverageData >= 50X There is a 7.9% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 10597214669 42.51630197142016 850.7470182081679 chr2 243199373 8267995734 33.99678063314744 298.9645387424252 chr3 198022430 6641823942 33.54076577082707 192.2718513548866 chr4 191154276 4818490699 25.20733932731905 148.60687838959075 chr5 180915260 5751323482 31.790151267505017 261.5558610410685 chr6 171115067 6130699121 35.82793279682379 195.7363893963677 chr7 159138663 5478334897 34.42491468587995 236.64536390130888 chr8 146364022 4461829187 30.484466920429394 178.08133349574103 chr9 141213431 4492547430 31.813881995403115 194.46458572779306 chr10 135534747 4813353744 35.51379886369656 190.74492331844178 chr11 135006516 5400290675 40.00022247074356 285.8296730385361 chr12 133851895 5234537826 39.10693850094539 221.8466537884062 chr13 115169878 2525762560 21.9307565820292 303.8189154364978 chr14 107349540 3479612304 32.41385388330495 206.17335583223877 chr15 102531392 4062792457 39.624863934354856 232.53773217179958 chr16 90354753 3960561434 43.83345980703417 249.4056662339464 chr17 81195210 4929863585 60.71618738346757 371.8113957878276 chr18 78077248 2141301875 27.4254271231486 162.61626880877512 chr19 59128983 4674718720 79.05968414846573 403.0119778201599 chr20 63025520 2630628308 41.739097241879165 218.80238581273034 chr21 48129895 1197387874 24.878256518116235 184.17961152156133 chr22 51304566 2137150101 41.65613838347254 237.365479535914 chrMT 16571 8639735157 521376.81232273247 137505.27136685548 chrX 155270560 3126781491 20.13763260079696 111.71496842621816 chrY 59373566 120808897 2.034725301828763 82.2599157375641