Genotypic discrepancies arising from imputation

BMC Proceedings

Table 2 Discrepancies by process type

Discrepancy		High call rate SNPs (98% call rate) 235,549 SNPs		Full comparison SNPs 451,279 SNPs
Type	Subjects	Genotypes (N)	% Discrepant	Genotypes (N)	% Discrepant
Imputation	463	205,962	25.16	1,864,804	28.82
Sequencing	463	107,780,325	0.03	197,178,315	0.06
Inference	495	116,463,033	0.10	222,926,764	0.20
Inference Families with sequence	349	82,103,861	0.07	157,186,202	0.18
Inference Families without sequence	146	34,359,172	0.18	65,740,562	0.26

Discrepancies between genome-wide association study (GWAS) data and GENO data sets, divided by analytical process. "Imputation" fills in missing genotypes in sequence data. "Inference" infers phased sequence data on unsequenced individuals based on GWAS data. SNP, single-nucleotide polymorphism.

ISSN: 1753-6561