Nucleotide diversity - π


Nucleotide diversity (π) measures the mean nucleotide differences per site between two randomly chosen sequences from a population. In simpler terms, it is the probability of two alleles being different at a given nucleotide.

The formula that represents π is the following:



where:

n is the number of sequences or individuals in the population,

dij is the number of nucleotide differences between sequences i and j,

L is the alignment length,

(n 2) is the number of possible pairs of sequences.


Nucleotide diversity values of 0.01-0.05 are considered high (found in Drosophila, for example), while 0.001 is considered low (found in humans).

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