English: Pairwise similarity between strains gives some insight on the similarity of the unmodeled factor. In this toy example, we consider 10 SNPs where the even numbered SNPs are the causal SNPs with an effect on the trait. (a) Since B6 and C3H share alleles at 9 out of 10 SNPs, these strains have a similar value for the unmodeled factor. (b) When we consider other strains, the unmodeled factors may be larger. For example, B6 and CAST, which share few SNPs, will have different values for their unmodeled factor.
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