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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%
  1. 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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