Characteristics of outbred mouse colonies.

For each colony listed in column one, we report the number of animals we used (No.); the number of markers analysed (genome-wide marker sets were used for six populations); the sex ratio (Male to Female); the supplier's breeding scheme (where available); the number of groups of animals used in that scheme and the size of the colony. Some colonies have been culled since the sampling date and these are indicated by a * in the column headed Status 12/09. We provide four genetic measures for each colony: the mean minor allele frequency (Mean MAF), heterozygosity (Het) and an inbreeding coefficient. The LD decay radius, a measure of the colony's suitability for high-resolution mapping, is the average physical separation between SNPs beyond which the squared correlation coefficient drops below 0.5. Colonies where we found evidence for population structure are show in the column Struct. The multi-dimensional scaling of IBS pairwise distance matrices on which this is based is shown in Figure S1.