Table 1.

Summary of Haplotype Phasing

	Number of Trios	Total Sites	All Missing Sites	Sites of Mendelian Errors	Unphaseable Sites	Inconsistent Sites	Phased Sites
Family 1	5	189,280	1,016	21	3,282	3	187,363 (98.98%)
Family 2	4	189,280	1,087	2	3,246	2	186,505 (98.53%)
Family 3	3	189,280	940	6	789	3	187,582 (99.10%)
Family 4	4	189,280	858	39	1,691	11	187,540 (99.08%)

For a given family, phased haplotypes were generated for 189,280 contiguous sites (chr4: 3,066,408–3,255,687; hg19 assembly) in complete trios from Figure 1. Missing sites were those not called in any trio member. Unphaseable sites were (1) variants heterozygous in all three trio members and (2) variants that could not be phased because of missing genotypes. Inconsistent sites had different phased allele calls within a family.