. 2010 Jun 30;11:58. doi: 10.1186/1471-2156-11-58

Table 5.

HMM with phased genotype emissions.

Phased genotype	NO	LL	LR	RL	RR
(AA, AA)	p⁴	p³	p³	p³	p³
(AA, AB)	p³q	p²q	0	p²q	0
(AA, BA)	p³q	0	p²q	0	p²q
(AA, BB)	p²q²	0	0	0	0
(AB, AA)	p³q	p²q	p²q	0	0
(AB, AB)	p²q²	pq²	0	0	p²q
(AB, BA)	p²q²	0	pq²	p²q	0
(AB, BB)	pq³	0	0	pq²	pq²
(BA, AA)	p³q	0	0	p²q	p²q
(BA, AB)	p²q²	0	p²q	pq²	0
(BA, BA)	p²q²	p²q	0	0	pq²
(BA, BB)	pq³	pq²	pq²	0	0
(BB, AA)	p²q²	0	0	0	0
(BB, AB)	pq³	0	pq²	0	pq²
(BB, BA)	pq³	pq²	0	pq²	0
(BB, BB)	q⁴	q³	q³	q³	q³

The matrix displays emission probabilities for hidden states NO, LL, LR, RL, RR for the HMM with genotype emission, with p the minor allele frequency, and q = 1 - p.