Additional file 2 of E-GWAS: an ensemble-like GWAS strategy that provides effective control over false positive rates without decreasing true positives

Additional file 2: Figure S2. Comparison between E-GWAS strategy and BSLMM, MLMM, mrMLM, BLINK, or FarmCPU under different numbers of QTN with a heritability of 0.2 and 0.8. The comparisons were conducted between different simulated scenarios. The numbers of true and false positives among 100 replicates were recorded. Phenotypes were simulated based on the real genotypes of 4555 individuals and 41,078 SNPs with different numbers of QTN (m = 20, 100, 500 and 1000) and different levels of heritability (h2 = 0.2, 0.8). Line charts a, b illustrate the numbers of true QTN detected and the rate of false positive variants, respectively. BSLMM, MLMM, mrMLM, BLINK, FarmCPU, and E-GWAS are represented by different colors, as shown in the legend