Site frequency spectrum (${\xi }_i$)

The counts or proportions of segregating variants at different sample frequencies. Unfolded spectra use an inferred ancestral state; folded spectra use minor-allele counts.

The unfolded site frequency spectrum counts segregating sites according to the number of sampled copies carrying the derived allele. In a sample of five haploid sequences, a mutation carried by one sequence contributes to the singleton class, while one carried by four contributes to class four. Assigning ancestral and derived states is essential: reversing them exchanges classes $i$ and $n-i$. A folded site frequency spectrum removes this directional distinction. ^[ref]