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I am interested in 20 different SNPs that all are either As or Gs, and they all occur on the same chromosome. How can I assess the co-occurrence of these SNPs? In other words, I want to know, if SNP1 is "G", does that make SNP2 to be more likely to be a "G" as well?

I know this is broad and I'm not looking for a script or anything so specific, just a point in the right direction. I'm working with a non-model organism, so any organism-specific application won't be useful without being able to learn the methodology.

Googling thus far has only brought up GWAS and similar methods of correlating a genotype and a phenotype, but not within a genotype.

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    $\begingroup$ Okay, just found the term "linkage disequilibirum" which should be helpful... $\endgroup$
    – CephBirk
    Apr 13, 2020 at 18:54
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    $\begingroup$ I agree with @CephBirk that you are just looking for linkage disequilibrium. To calculate this in a simple way, it is just the Pearson correlation coefficient squared. $\endgroup$
    – Phoenix Mu
    Apr 13, 2020 at 22:48

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I found the LDheatmap package in R very helpful at calculating linkage disequilibrium. You can make plots such as this:

enter image description here

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