Fig. 2

Genotype correlation (R) between loci within 200Kb of each other in the original data plotted against the corresponding R in a single simulated data set. Red crosses represent the SNP pairs with an observed R that differs from that based on the original data by at least 0.1 and where the MAF is at least 0.02 in both SNPs in the original data (0.1% of the correlations shown are in this category). The red triangles represent the SNPs pairs with a correlation coefficient differing from the original data by at least 0.1 and where the MAF is less than 0.02 in either SNP in the original data (0.3% of the correlations shown are in this category)