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ksamuk / pixy

Software for painlessly estimating average nucleotide diversity within and between populations
https://pixy.readthedocs.io/
MIT License
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heterozygous sites increase nucleotide diversity? #61

Closed caixu0518 closed 2 years ago

caixu0518 commented 2 years ago

Hi Kieran,

I wonder if pixy will consider heterozygous sites when calculating π value? I found there is a high level of nucleotide diversity in the regions with higher heterozygoousity?

Best, Xu

ksamuk commented 2 years ago

Hi Xu!

Good observation. Pixy definitely considers heterozygous sites in its calculations. It is also generally expected that regions with high heterozygosity will also have high nucleotide diversity.

Hope that helps and all the best,

Kieran