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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.