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Allele frequency, or gene frequency, is the relative frequency of an allele (variant of a gene) at a particular locus in a population, expressed as a fraction or percentage. [1] Specifically, it is the fraction of all chromosomes in the population that carry that allele over the total population or sample size.
Once an allele becomes fixed, genetic drift comes to a halt, and the allele frequency cannot change unless a new allele is introduced in the population via mutation or gene flow. Thus even while genetic drift is a random, directionless process, it acts to eliminate genetic variation over time.
The allele frequency spectrum can be written as the vector = (,,,,), where is the number of observed sites with derived allele frequency .In this example, the observed allele frequency spectrum is (,,,,), due to four instances of a single observed derived allele at a particular SNP loci, two instances of two derived alleles, and so on.
Mutation will have a very subtle effect on allele frequencies through the introduction of new allele into a population. Mutation rates are of the order 10 −4 to 10 −8, and the change in allele frequency will be, at most, the same order. Recurrent mutation will maintain alleles in the population, even if there is strong selection against them.
[4] [11] This direct method is only suitable for some types of organisms, more often indirect methods are used that infer gene flow by comparing allele frequencies among population samples. [1] [4] The more genetically differentiated two populations are, the lower the estimate of gene flow, because gene flow has a homogenizing effect. Isolation ...
For example, if a population includes allele A with frequency equal to 20%, and allele a with frequency equal to 80%, there is an 80% chance that after an infinite number of generations a will be fixed at the locus (assuming genetic drift is the only operating evolutionary force).
1. Introduce the reference of a SNP of interest, as an example: rs429358, in a database (dbSNP or other). 2. Find MAF/MinorAlleleCount link. MAF/MinorAlleleCount: C=0.1506/754 (1000 Genomes, where number of genomes sampled = N = 2504); [4] where C is the minor allele for that particular locus; 0.1506 is the frequency of the C allele (MAF), i.e. 15% within the 1000 Genomes database; and 754 is ...
For instance, in the classic mutation–selection balance model, [29] the force of mutation pressure pushes the frequency of an allele upward, and selection against its deleterious effects pushes the frequency downward, so that a balance is reached at equilibrium, given (in the simplest case) by f = u/s.