TABLE 8.

Posterior probability distribution of diplotype configuration for each subject: four-locus data

Subject (i)	Quantitative phenotype	Diplotype configuration	True or falsea	Posterior distributionb	Posterior distributionc
1	157.1	GCCT  GCCT	True	1.0000	1.0000
2	170.3	CCTC  CTCC	True	0.9993	0.9999
CCCC  CTTC	False	0.0007	0.0001
3	173.4	CCTC  GCCT	True	1.0000	1.0000
4	158.2	CTCT  GCCT	True	1.0000	1.0000
5	170.6	CTCT  GCCT	True	1.0000	1.0000
6	162.4	CTCC  CTCC	True	1.0000	1.0000
7	161.6	CTCC  GCCT	True	0.9975	0.9975
CTCT  GCCC	False	0.0025	0.0025
8	149.4	CTCC  CTCC	True	1.0000	1.0000
9	164.3	CCTC  GCCT	True	1.0000	1.0000
10	165.1	CTCC  GCCT	True	0.9975	0.9975
		CTCT  GCCC	False	0.0025	0.0025

Simulations were started by assigning diplotype configurations to N = 1000 number of subjects according to the haplotype frequencies employed from the four-locus data for the SAA1 gene. Depending on whether the subject possessed the phenotype-associated haplotype CCTC, a quantitative phenotype was drawn from N(μ₁, σ²) or N(μ₂, σ²), where μ₁ = 165, μ₂ = 160, and σ = 5. After removing the phase information, QTLHAPLO was used to determine the posterior probability distribution of the diplotype configuration (diplotype distribution) for each subject either by using only genotype data or by using both genotype and phenotype data.

^aPossible diplotype configurations for each subject were compared with the diplotype configuration before the phase information was removed. “True” means that the diplotype configuration before the removal of the phase information was the same as the estimated diplotype configuration, while “False” means that they were different.

^bPosterior probability distribution of the diplotype configuration given only the observed genotype data [P(d_i = a_k|G_obs)].

^cPosterior probability distribution of the diplotype configuration given the observed genotype and phenotype data [P(d_i = a_k|G_obs, Ψ_obs)].