Table 1 . Notation used in the article.

Notation	Meaning	Type
i	Index of an individual	Basic notation
ℓ	Index of a locus	Basic notation
k, h	Index of an allele	Basic notation
N	No. individuals	Basic notation
L	No. loci	Basic notation
Kℓ	No. distinct alleles at locus ℓ	Basic notation
Aℓk, Aℓh	Allele k (h) at locus ℓ	Basic notation
X	Missing data (dropout)	Basic notation
γiℓ	Dropout probability at locus ℓ of individual i	Basic notation
wiℓ	Observed genotype at locus ℓ of individual i	Observed data point
W	Observed genotypes, W = {wiℓ}	Observed data set
giℓ	True genotype at locus ℓ of individual i	Latent variable
siℓ	IBD state at locus ℓ of individual i	Latent variable
ziℓ	Dropout state at locus ℓ of individual i	Latent variable
G	True genotypes, G = {giℓ}	Latent variable set
S	IBD states, S = {siℓ}	Latent variable set
Z	Dropout states, Z = {ziℓ}	Latent variable set
ρ	Inreeding coefficient	Parameter
φℓk	Frequency of allele Aℓk	Parameter
γi⋅	Sample-specific dropout rate for individual i	Parameter
γ⋅ℓ	Locus-specific dropout rate for locus ℓ	Parameter
Φ	Allele frequencies, Φ = {φℓk}	Parameter set
Γ	Dropout rates, Γ = {γi⋅, γ⋅ℓ}	Parameter set
Ψ	Model parameters, Ψ = {ρ, Φ, Γ}	Parameter set
nℓk	No. independent copies of allele Aℓk	Summary statistic
diℓ	No. dropouts at locus ℓ for individual i	Summary statistic
di⋅	No. sample-specific dropouts for individual i	Summary statistic
d⋅ℓ	No. locus-specific dropouts at locus ℓ	Summary statistic
s	No. genotypes having two alleles IBD	Summary statistic

i ε {1, 2, …, N}, ℓ ε {1, 2, … , L}, and k, h ε {1, 2, … , K_ℓ}.