Table 1 Concordance rate and proportion of non-missing genotypes (using a posterior probability threshold of 0.9) for chromosome 12 markers in the studied reference panels
Reference Panel | IMPUTE Version | Concordance rate (%) | Proportion of non-missing genotypes (%) |
|---|---|---|---|
HapMap phase II combined | Version 2 (Single-step) | 99.09 | 85.5 |
HapMap phase II combined + MXL | Version 2 (Single-step) | 99.37 | 85.9 |
HapMap phase II combined | Version 2 (Two-steps: Phasing & Imputation) | 98.40 | 90.1 |
1,000 Genomes Phase I (June 2011 release) | Version 2 (Two-steps: Phasing & Imputation) | 98.44 | 94.7 |