Results of missing data, genotype discordance, uncertainty coefficients and frequencies of exome chip data ascertained by three calling methods and compared to exome sequence genotypes.

A total of 185,119 variants were used for these analyses, excluding duplicated variants, short insertion/deletions, XY chromosome SNPs, Y chromosome SNPs, mitochondrial SNPs, sites not identified in the exome sequencing dataset, and failing SNPs as identified by the CHARGE best practices guidelines. Genotype classes are represented as AA = common variant homozygote, AB = heterozygote, BB = rare variant homozygote, and XX = missing data. Dataset I: exome chip genotypes called with Illumina cluster file. Dataset Z: zCall assigned genotypes to missing data in Dataset I. Dataset C: exome chip genotypes called with the CHARGE cluster file.