I have run PLINK --assoc for a list of snps and the associated genotypes and qt measurements.

The SNP I have added as control (control= it is known that it is highly associated with the analyzed quantitative trait ) is returned as having a p-value of 0. When doing a separate linear regression analysis in R the p-value is 1.212e-308 .

The genotypes have been used for already published studies.

**The p-value is normally very low for that association, but why is it returned as 0 by plink?**

Plink returned the 3 expected most significant SNPs (out of 700) as having a p-value of 0.

That must be the case ... I have looked in the documentation, forums, examples but I couldn't find anything similar to what I have or any information about the thresholds...