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

[Jingjiao-ma]

hello,

My shell is

plink --vcf GWAS.23chr.vcf \
                  --a2-allele GWAS.23chr.vcf.ref \
		  --keep-allele-order \
		  --double-id \
		  --set-missing-var-ids @:# \
		  --allow-no-sex \
		  --update-sex pheno.gender.txt 3 \
		  --pheno pheno.gender.txt --mpheno 4 \
		  --recode \
		  --make-bed \
		  --out vcf2plink && \
plink --file vcf2plink --maf 0.05 --geno 0.1 --hwe 0.000005 --mind 0.2 --make-bed --recode --out plink.filter &&\
plink --bfile plink.filter --assoc --out plink_asso --allow-no-sex

The pheno.gender.txt file contains gender information, how dose PLINK consider male and female samples for chromosome X results?

thank you
best

[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?

thank you
best