Table 1.

Reference sample to estimate allele frequencies at loci that are untyped in a study sample

Sample haplotype	Reference haplotypes
10?00	11100
	11100
	00000
	00000
	00000
	10100
	10000
	10000
	10000
	11100

Question mark denotes location of untyped locus in the study sample. Bold 0 or 1 denote alleles in the reference sample at the untyped locus. Underlined reference haplotypes are those with the same allelic states at those loci observed in the sample haplotype. Restricting computations to these haplotypes gives an allele frequency estimate (1/4) that is quite different from the alíele frequency in the reference population (4/10).