Fig. 3: The accuracy of imputation varies extensively by parental birthplace.

a Shows the imputation accuracy (r²) in iPSYCH samples grouped by parental birthplace as ascertained from the Danish civil registers at different minor allele frequency bins within the 10,000 SNPs common to both genotyping arrays, masked prior to phasing. (Both parents were born in Africa: Red, Asia: Blue, Denmark: Dark Green, Scandinavia non-Danish: Light Green, Europe non-Danish or Scandinavian: Gray, Middle East: Yellow). b Shows the imputation accuracy (r²) in admixed samples where at least one parent was born in Denmark (Non-Danish parent born in Africa: Maroon, Asia: Blue, Australia: Fluorescent Green, Europe non-Danish or Scandinavian: Brown, Greenland: Black, Middle East: Orange, North America: Cyan, South America: Pink, Scandinavia non-Danish: Lavender, Unknown: Purple). All imputations were performed using a separate protocol, haplotype estimation was performed using BEAGLE5 phase-states = 560, imputations were performed using BEAGLE5.1 with the HRCv1.1 as the reference.