Figure 6

LD between a complex microsatellite and SNPs. (a) Previous work [22] indicated SNP alleles in LD with two size ranges of the CSH1.01 microsatellite. The lower size range has dinucleotide spacing, the upper has tetranucleotide spacing. This suggested two major lineages. (b) Plotting interallelic LD between a SNP (GH1V004) and the CSH1.01 microsatellite demonstrates clear LD with the two lineages. The common SNP alleles associate with the lower size range and the rare SNP alleles associate with the upper size range. Results are boxed in red where the haplotype frequency is significantly higher than expected (D' ≥ 0) and blue where it is significantly lower (D'<0). (c) SNP haplotypes (four SNPs, including GH1V004) confirm these findings and demonstrate the ability of MIDAS to handle haplotype data as a multi-allelic marker.