We then imputed into these 7,278 phased haplotypes with the MCTFR sequences and again separately with the 1000 Genomes as the haplotype reference panels, using minimac with 200 states and 5 rounds (Howie et al., 2012). Imputation accuracy statistics for both reference panels are provided in Table 2. While it may appear that the MTFS sequences perform better than 1000 Genomes because higher minimac RSQ values were obtained, a direct comparison using the summaries in Table 2 is not entirely appropriate. The 1,325 sequenced individuals are included in these estimates and bias them upward—that is, for 1,325 individuals we used their own sequences to conduct imputation into their array genotypes.
