What is the difference between chromosome X and autosomes using --assoc？

[chrchang]

What is the difference between chromosome X and autosomes using --assoc？

[chrchang]

--assoc is based on allele counts. Males have only 1 allele per variant on chrX, while females have 2.

[Jingjiao-ma]

so we calculate the number of allele1 in the case cohort like this：
female het_mut * 1 + female hom_mut * 2 + male mut * 1 is it right?

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