Figure 4.

The mixed model dramatically reduces inflation of p-values. Quantile-Quantile plot showing strong p-values inflation for a marginal GWAS that does not consider population structure (red line). Accounting for population structure with the mixed model dramatically reduces inflation (blue line). The grey line indicates the expected p-value distribution under the null hypothesis of no causative markers in the data. Note, that after correction for population structure, only the most significant markers deviate from the null expectation.