Markers typed in a specific chromosome were selected and sorted by their chromosomal position. The association statistics of a marker under a log-additive model of inheritance were collected and using a minus-log transformation plotted (Y-axis) with their position in the sorted vector. Markers in different specific chromosomes were plotted in grey and black, respectively. The bias was determined as the algebraic difference between minus log transformed association statistics derived from direct genotyping and imputation ((-log10 (P-value- empiric) - (log10 (P-value - imputed)). All the analyses were conducted on the R statistical environment; the complete set of developed programs can be obtained upon request.
