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Table 2 HMM with phased genotype transitions.

From: Improved IBD detection using incomplete haplotype information

A NO LL LR RL RR B NO LL LR RL RR
NO ϵ/4 ϵ/4 ϵ/4 ϵ/4 NO ϵ/4 ϵ/4 ϵ/4 ϵ/4
LL ϵ 0 0 0 LL ϵ 0 0
LR ϵ 0 0 0 LR ϵ 0 0
RL ϵ 0 0 0 RL ϵ 0 0
RR ϵ 0 0 0 RR ϵ 0 0
C NO LL LR RL RR D NO LL LR RL RR
NO ϵ/4 ϵ/4 ϵ/4 ϵ/4 NO ϵ/4 ϵ/4 ϵ/4 ϵ/4
LL ϵ 0 0 LL ϵ
LR ϵ 0 0 LR ϵ
RL ϵ 0 0 RL ϵ
RR ϵ 0 0 RR ϵ
  1. The matrices show the transition probabilites among the five hidden states when the next genotype is respcectively homozygous for both samples (A), homozygous for the first sample and heterozygous for the second sample (B), heterozygous for the first sample and homozygous for the second sample (C), and heterozygous for both samples (D), with = 1 - ϵ, = 1 - λ, and = 1 - μ.