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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

From: Evaluation of the imputation performance of the program IMPUTE in an admixed sample from Mexico City using several model designs

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