deflated QQ plot but lambda >1

Question

[putty]

Dear All,

What might be the reason for a deflated QQ-plot but lambda showing > 1 value. GWAS (case-control using glm-logistic regression adjusting for PC1-PC3 and three covariates) was done in plink2.0, and QQ plot using QQman package

TIA

Answer 1

[chrchang523]

1.03 is barely different from 1, and most of the points are at the bottom left of the plot where parts of the curve are probably slightly on top of the diagonal.