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.