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Table 5 HMM with phased genotype emissions.

From: Improved IBD detection using incomplete haplotype information

Phased genotype NO LL LR RL RR
(AA, AA) p 4 p 3 p 3 p 3 p 3
(AA, AB) p 3 q p 2 q 0 p 2 q 0
(AA, BA) p 3 q 0 p 2 q 0 p 2 q
(AA, BB) p 2 q 2 0 0 0 0
(AB, AA) p 3 q p 2 q p 2 q 0 0
(AB, AB) p 2 q 2 pq 2 0 0 p 2 q
(AB, BA) p 2 q 2 0 pq 2 p 2 q 0
(AB, BB) pq 3 0 0 pq 2 pq 2
(BA, AA) p 3 q 0 0 p 2 q p 2 q
(BA, AB) p 2 q 2 0 p 2 q pq 2 0
(BA, BA) p 2 q 2 p 2 q 0 0 pq 2
(BA, BB) pq 3 pq 2 pq 2 0 0
(BB, AA) p 2 q 2 0 0 0 0
(BB, AB) pq 3 0 pq 2 0 pq 2
(BB, BA) pq 3 pq 2 0 pq 2 0
(BB, BB) q 4 q 3 q 3 q 3 q 3
  1. 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.