BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094139.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 508,872 number of mapped reads = 485,095 (95.33%) number of supplementary alignments = 7,617 (1.5%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 243,411 number of mapped paired reads (second in pair) = 241,684 number of mapped paired reads (both in pair) = 482,520 number of mapped paired reads (singletons) = 2,575 number of mapped bases = 69,750,906 bp number of sequenced bases = 69,065,588 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 483,597 duplication rate = 44.57% >>>>>>> Insert size mean insert size = 98,119.25 std insert size = 3,680,838.0773 median insert size = 217 >>>>>>> Mapping quality mean mapping quality = 20.4039 >>>>>>> ACTG content number of A's = 19,183,961 bp (27.78%) number of C's = 14,976,663 bp (21.68%) number of T's = 19,407,057 bp (28.1%) number of G's = 15,497,104 bp (22.44%) number of N's = 803 bp (0%) GC percentage = 44.12% >>>>>>> Mismatches and indels general error rate = 0.0245 number of mismatches = 1,656,991 number of insertions = 24,677 mapped reads with insertion percentage = 5.03% number of deletions = 90,139 mapped reads with deletion percentage = 18.08% homopolymer indels = 40.91% >>>>>>> Coverage mean coverageData = 0.0225X std coverageData = 28.6451X There is a 0.01% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 179158 7.187865742569203E-4 0.5393871981963481 chr2 243199373 1859175 0.007644653754925594 7.617574756879076 chr3 198022430 342413 0.0017291627014172082 0.9199556537074342 chr4 191154276 2431838 0.012721860326054124 7.986324663877499 chr5 180915260 4645329 0.02567682239740307 24.173075512920654 chr6 171115067 209464 0.0012241119597025316 0.8574305692526312 chr7 159138663 422433 0.002654496349513757 2.3412098694852506 chr8 146364022 603681 0.004124517704221055 2.8883379288418523 chr9 141213431 107618 7.620946480650272E-4 0.512544379134931 chr10 135534747 42054 3.1028205630545796E-4 0.12314863737280461 chr11 135006516 241771 0.0017908098598737265 1.2355809379935627 chr12 133851895 584045 0.004363367436822616 2.649412186986612 chr13 115169878 157911 0.0013711137212457584 0.7614592896891909 chr14 107349540 126134 0.0011749840753858842 0.41664910676044126 chr15 102531392 15965 1.5570840977171166E-4 0.0903361926121332 chr16 90354753 27663 3.061598762823246E-4 0.10516532535234921 chr17 81195210 391753 0.004824828952348297 3.221406446434801 chr18 78077248 19016 2.4355366623577716E-4 0.07026479145570183 chr19 59128983 15991 2.704426693758626E-4 0.12772709383935982 chr20 63025520 14068 2.2321116906294465E-4 0.07804490233736915 chr21 48129895 13230 2.7488113157113684E-4 0.10290437233754443 chr22 51304566 4288 8.357930559241062E-5 0.017198129498137642 chrMT 16571 46602932 2812.3186289300584 11539.738282257564 chrX 155270560 10623346 0.06841828869555182 20.61418370053397 chrY 59373566 69630 0.0011727441130957167 0.5555460905917012