Figure 3

Representation of haplotype frequencies and LD in MIDAS. For SNPs the expected (under no LD) haplotype frequencies for each allele combination are plotted with an unfilled, black rectangle divided into four quadrants by two lines. The estimated haplotype frequencies are represented by solid red or blue rectangles. Where a coloured rectangle exceeds the size of the black rectangle it is coloured red, indicating an excess of that haplotype (D' ≥ 0). The opposite situation is indicated by a blue rectangle (D'<0). For multi-allelic markers the principle is the same, but a separate plot is shown for each combination of alleles, i.e. locus 1 allele i/allele not-i, locus 2 allele j/allele not-j.