plink1.9目前采用的是major与minor allele的概念,软件会自动计算频率,对原始数据进行操作时会自动改变allele的排序,如果你使用plink1.9 的—frq选项计算频率,你会发现输出的文件中是MAF ,minor allele frequency,不会高于0.5。 PLINK1.9中,A1为minor,A2为major allele,所以这里MAF是指A1(minor allele)的频率。 CHR SN...
1. 频率主导的major与minor allelemajor和minor allele的区分基于特定群体的频率。在一个二态SNP（单核苷酸多态性）环境中，频率最高的那个allele被称为major allele，频率较低的则是minor allele。在多态性更高的SNP中，minor allele通常是指频率第二高的。例如，在PLINK 1.9中，MAF（minor allele fr...
ALLELE FREQUENCY EFFECT OF THE APOLIPOPRPTEIN E POLYMORPHISM ON THE LIPID LEVELS IN IRANIAN POPULATION: TEHRAN LIPID GLUCOSE STUDYMost diseases involve many genes in complex interactions, in addition to environmental influences. The genetic susceptibility to a particular disease due to the presence of...
wheremiis the minor allele frequency and βithe magnitude of the association between the i-th SNP on trait Y47. TheF statisticwas calculated as previously described by Noyce et al.35: $$F = \frac{{R^{2} \left( {n - 1 - k} \right)}}{{\left( {1 - R^{2} } \right)~ \ti...
The allele frequency of D256N is 0.005. We investigated the effects of D256N and Y483D, which is located on the common exon of UGT1, on propofol glucuronidation by an in vitro expression study. The Km of wild-type, D256N and Y483D for propofol glucuronidation were 111.2, 43.6 and...
We considered variable heritability (0.1, 0.3 and 0.5), different standard errors, (SE: 0.0, 0.05, 0.1 and 0.15) associated with the estimated QTL effects and different initial allele frequency. Given an estimate of QTL effect and its standard error, we sampled a true QTL effect according to...
For both the breeds, the same tendency of minor allele frequency was found for all SNPs and protein genes, except onLEPA1457GandLEPC963T. This study indicated significant (P<0·05) associations between the studied SNPs and several compositional parameters. Protein content was influenced byLEPA1457...
To test the first hypothesis, we use high quality resequencing data in groups of temperate and tropical inbred maize lines to identify regions that show high divergence in allele frequency between the two groups. We then use SNP data from hybrids grown as part of the Maize G × E projec...
which can be configured, for example: reporting only one VariationFeatureOverlapAllele per input variant; removing intergenic VariationFeatureOverlapAlleles (i.e., those produced from variants that don’t overlap a genomic feature); filtering based on allele frequency of a co-located known variant. ...
9.3% of Illumina SNPs and 6.7% of Affymetrix SNPs which have high minor allele frequency (≥40%) appear to be under balancing selection. Pedigree structure errors in 15 of 143 pedigrees were detected using microsatellite markers from the autosomes and/or selected SNPs from chromosomes 1 to 18 ...