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deflated QQ plot but lambda >1

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 packageenter image description here

TIA

package plink deflation gwas qq-plot qqman
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updated by chrchang523 chrchang523 • written by putty • putty

1 answer

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.

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written by chrchang523 chrchang523

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