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Table 1 HMM with genotype/haplotype emissions.

From: Improved IBD detection using incomplete haplotype information

A NO IBD IBD lev G
{AA, AA} p 4 p 3 log2(p)
{AA, AB} 4p3q 2p2q 1 + log2(p)
{AA, BB} 2p2q2 0 γ
{AB, AB} 4p2q2 pq 2 + log2(pq)
{AB, BB} 4pq3 2pq2 1 + log2(q)
{BB, BB} q 4 q 3 log2(q)
B NO IBD IBD lev H
{A, A} p 2 p log2(p)
{A, B} 2pq 0 γ
{B, B} q 2 q log2(q)
  1. Second and third column display emission probabilities for hidden states NO IBD and IBD for the HMM with genotype (A) and haplotype (B), with p the minor allele frequency, and q = 1 - p. The last column shows the log-evidence.