Fig 3. Schematic of allele effects when divergent SNP effects are observed between groups, depending on the biological hypothesis: (a) local genomic difference between groups (LD or mutation) and (b) allele effects interacting with the genetic background.

The denomination of the allelic states on the x-axis include the SNP allele (0/1), its ancestry (D/F) and the genetic background in which it is observed (D/A/F), as presented in Table 2.