I'm new to GWAS data analysis. When I do QQ plot for my association analysis result produced by snptest software. The observed p-value is deviated from expected p-value. But the inflation factor lambda is quite small, it's only 1.03. How to explain this phenomenon. Followings are my codes.
chisq = qchisq(gwas$PVAL,1,lower.tail=FALSE); lambda <- median(chisq) / qchisq(0.5,1)