Information content and allele frequency difference

by Ketil Malde; July 17, 2014

ESI scores and allele frequency difference

Just a quick note on the relationship between ESI scores and allele frequencies. Allele frequency differences is of course related to – perhaps even the definition of – diversification, but the information we gain from observing an allele also depends on the specific allele frequencies involved. The graph below shows how this is related.

Each line represents a fixed allele difference, from 0.05 at the bottom, to 0.95 at the top, and the x-axis is the average allele frequency between populations. We see that for small differences, the actual frequencies matter little, but for moderate to large allele differences, allele frequencies near the extremes have a large effect.

Note that this is information per allele, and thus not ESI (which is the expected information from observing the site, in other words a weighted average over all alleles).

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