Table 1. Numbers of shared rare variants remaining after filtering.

	II.1	II.2
% Captured regions, coverage >10x; Q>30	92	91
Average coverage of captured region (x)	51	43
Total number of SNPs	91 412	82 221
Total number of indels	6851	5937
Rare homozygous variants	0
Rare compound heterozygous variants	11 (0)
Rare X-linked variants	4 (2)
Rare de novo variants	0
Rare inherited variants (maternal)	56 (5)
Rare inherited variants (paternal)	49 (5)

Abbreviation: SNP, single-nucleotide polymorphism.

Provides the numbers of rare variants (MAF <1%) remaining after filtering against population databases (1000 genomes and the Exome Variant Server), with the number predicted functionally damaging by all four prediction algorithms within brackets, and listed by potential mechanisms of inheritance.