Table 2 . Illustration of the outcomes of allelic dropout using two distinct alleles at locus ℓ, A_ℓk and A_ℓh.

True genotype	Genotype frequency	Dropout state	Conditional probability	Observed genotype	Conditional probability
giℓ	ℙ(giℓ|Φ, ρ)	ziℓ	ℙ(ziℓ|giℓ, Γ)	wiℓ	ℙ(wiℓ|giℓ, Γ)
AℓkAℓk	$\left(1-\rho \right){\phi }_{\ell k}^2+\rho {\phi }_{\ell k}$	AℓkAℓk	(1 − γiℓ)2	AℓkAℓk	$1-{\gamma }_{i\ell }^2$
		AℓkX	2γiℓ(1 − γiℓ)
		XX	${\gamma }_{i\ell }^2$	XX	${\gamma }_{i\ell }^2$
AℓkAℓh	2(1 − ρ)φℓkφℓh	AℓhAℓk	(1 − γiℓ)2	AℓkAℓh	(1 − γiℓ)2
		AℓhX	γiℓ(1 − γiℓ)	AℓhAℓh	γiℓ(1 − γiℓ)
		AℓkX	γiℓ(1 − γiℓ)	AℓkAℓk	γiℓ(1 − γiℓ)
		XX	${\gamma }_{i\ell }^2$	XX	${\gamma }_{i\ell }^2$

Genotype frequencies are calculated from allele frequencies using Equation 5, where ρ is the inbreeding coefficient, a parameter used to model the total deviation from Hardy–Weinberg equilibrium. Dropout is assumed to happen independently to each copy at locus ℓ of individual i, with probability γ_iℓ specified by Equation 1. $h\ne k$.