The Site Frequency Spectrum (SFS) (Neutral coalescence, Infinite Sites Model)
The expected
SFS for n = 10 haploid individuals
under the standard neutral coalescence model, with
an infinite sites mutation model. There are n-1
= 9 classes, because a SNP variant
could occur in 1/10, 2/10, 3/10, ..., or 9/10
individuals. [A base that occurs in 10/10
individuals would be invariant]. About 33% of SNP
sites will be singletons [allele
frequency = 1, a unique allele in one
individual, as 0 0 0 0 0 0 0 0 0 1]. About 3% of
all sites will have different alleles in
all ten individuals [allele frequency = 9,
as 0 1 2 3 4 5 6 7 8 9].
Figure © 2013 [corrected] by Sinauer; Text material © 2017 by Steven M. Carr