Table 1:

P(L), Genotype prior probabilities for a reference allele “A”.

L	Zygosity	Number of SNPs	Number of indels	Number of transversions	Prior probability P(L)
AA	Hom.	–	–	0	1
GG	Hom.	1	0	2	θ/2 * ε * ε
CC, TT	Hom.	1	0	0	θ/2
AG	Het.	1	0	1	θ * ε
AC, AT	Het.	1	0	0	θ
CG, GT	Het.	2	0	1	θ * θ/2 * ε
CT	Het.	2	0	0	θ * θ/2
AX	Het.	0	1	0	ω
GX	Het.	1	1	1	ω * θ/2 * ε
CX, TX	Het.	1	1	0	ω * θ/2
XX	Hom.	0	1	0	ω/2
XY	Het.	0	2	0	ω * ω/2

Hom.: homozygous; Het.: heterozygous.