BMC Bioinformatics

Table 1 Assumed and estimated haplotype frequencies

From: NullHap – a versatile application to estimate haplotype frequencies from unphased genotypes in the presence of null alleles

haplotype	frequency h_i
	assumed	Arlequin	PHASE	Haplo-IHP	NullHap
A ₀ B ₁ C ₀	0.2	0.068	0.068	0.294	0.20
A ₀ B ₁ C ₁	0.2	0.172	0.172	0.294	0.20
A ₀ B ₂ C ₀	0.1	0.034	0.034	0.147	0.10
A ₀ B ₂ C ₁	0.02	0.038	0.038	0.029	0.02
A ₀ B ₃ C ₀	0.02	0.007	0.007	0.0	0.02
A ₀ B ₃ C ₁	0.02	0.017	0.017	0.0	0.02
A ₀ B ₄ C ₀	0.02	0.007	0.007	0.0	0.02
A ₀ B ₄ C ₁	0.02	0.017	0.017	0.0	0.02
A ₁ B ₁ C ₀	0.1	0.089	0.089	0.147	0.10
A ₁ B ₁ C ₁	0.02	0.125	0.125	0.029	0.02
A ₁ B ₂ C ₀	0.02	0.028	0.028	0.029	0.02
A ₁ B ₂ C ₁	0.02	0.042	0.042	0.029	0.02
A ₁ B ₃ C ₀	0.02	0.015	0.015	0.0	0.02
A ₁ B ₃ C ₁	0.02	0.035	0.035	0.0	0.02
A ₁ B ₄ C ₀	0.02	0.015	0.015	0.0	0.02
A ₁ B ₄ C ₁	0.02	0.035	0.035	0.0	0.02
A ₂ B ₁ C ₀	0.02	0.028	0.029	0.0	0.02
A ₂ B ₁ C ₁	0.02	0.078	0.078	0.0	0.02
A ₂ B ₂ C ₀	0.02	0.019	0.019	0.0	0.02
A ₂ B ₂ C ₁	0.02	0.039	0.039	0.0	0.02
A ₂ B ₃ C ₀	0.02	0.013	0.013	0.0	0.02
A ₂ B ₃ C ₁	0.02	0.033	0.033	0.0	0.02
A ₂ B ₄ C ₀	0.02	0.013	0.013	0.0	0.02
A ₂ B ₄ C ₁	0.02	0.033	0.033	0.0	0.02
error	-	79%	79%	82%	0%

The assumed and estimated haplotype frequencies for a polymorphism with 3 loci: A(multiallelic with null variant), B(multiallelic), C(biallelic with null variant).

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ISSN: 1471-2105

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