Fig. 2

Comparison between E-GWAS and BSLMM, MLMM, mrMLM, BLINK, and FarmCPU using simulated phenotypes. Three levels of heritability were used in the simulations: 0.2 (left), 0.6 (middle), and 0.8 (right). Four gradients of QTN numbers were set for each level of heritability: 20 (a), 100 (b), 500 (c), and 1000 (d). The number of true QTN (crimson) and the number of false QTN (dark cyan) were recorded. For the E-GWAS-U, the permutation test was not used and for the E-GWAS-P, it was used. As the heritability increased, more true QTN were detected by the different methods and the E-GWAS retained a large number of true QTN. After the permutation test, compared with the single methods, E-GWAS resulted in a smaller number of false positives in each simulated scenario