Table 1.

Conditional Probability P(b_ij|e_ijg_i) of Read b_ij Given True Genotype g_i, and Read Error e_ij

True Genotype gi	Base Calling Error Event eij	Pr(bij = A)	Pr(bij = B)	Pr(bij = E)b
gi = AAa	eij = 0	1	0	0
	eij = 1	0	1/3	2/3
gi = ABa	eij = 0	1/2	1/2	0
	eij = 1	1/6	1/6	2/3
gi = BBa	eij = 0	0	1	0
	eij = 1	1/3	0	2/3

^aAA, AB, BB: A allele homozygote, heterozygote, and B allele homozygote

^bE: alleles other than A or B; assumes four possible alleles (bases)