Table 3.

Misclassification Matrix for the Allele-Independent Model^ab

Observed Genotype Z	True Genotype X
	0	1	2
0	$1-2\text{ϵ}(1-\text{ϵ})-{\text{ϵ}}^2$	$\text{ϵ}(1-\text{ϵ})$	${\text{ϵ}}^2$
1	$2\text{ϵ}(1-\text{ϵ})$	$1-2\text{ϵ}(1-\text{ϵ})$	$2\text{ϵ}(1-\text{ϵ})$
2	${\text{ϵ}}^2$	$\text{ϵ}(1-\text{ϵ})$	$1-2\text{ϵ}(1-\text{ϵ})-{\text{ϵ}}^2$

^aGenotype can be coded as 0 (major-allele homozygous), 1 (heterozygous), or 2 (minor-allele homozygous).

^bϵ = Prob(allele A is misclassified into allele a) = Prob(allele a is misclassified into allele A).