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The Shannon entropy is used as a measure of probabilistic uncertainty. Having the epialleles composition, the Shannon entropy estimates how heterogeneous is the population of the epialleles species at one locus, with values ranging from 0 (when all the reads carry the same epiallele) to n_CpX (when all possible epiallele states are found with equal frequency).
Given n_CpX sites in the region, the Shannon entropy is calculated as:
where e is the maximum number of distinct epiallele species that can be observed in one locus () and pk represents the frequency of the k-th epiallele.
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