5.3 Allele frequency, fixation, and loss
The Wright-Fisher model describes the behavior of a single allele, which can be at any variable site in a population (a SNP, insertion/deletion, version of a gene, etc.).
The allele of interest begins the simulation at some initial allele frequency (AF). This allele frequency is the proportion of individuals in the population who carry that allele, and is always between 0 and 1.
An allele becomes fixed in a population if it reaches an allele frequency of 1, and is lost if it reaches a frequency of 0. At either of these points, it is no longer considered a variable site because either everyone or no one in the population carries it.
