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Figure S1: PeRC W detection proportion (counts per replicate) for each causal gene for Scenario 1. In the 3 plots on the left, we have permuted the genotypes for gene 9 to break any genotype to phenotype correlation. The 3 plots on the right correspond to the original analysis in Figure 2.

Figure S2: PeRC W detection proportion (counts per replicate) for each causal gene for Scenario 2. In the 3 plots on the left, we have permuted the genotypes for gene 9 to break any genotype to phenotype correlation. The 3 plots on the right correspond to the original analysis in Figure 3.

Figure S3: Power versus false positive rates after removing gene 9 for Scenario 1. The p-value threshold or penalty parameter rate was varied to obtain points for the curves, which are an average over all replicates at each point.

Figure S4: Power versus false positive rates after removing gene 9 for Scenario 2. The p-value threshold or penalty parameter rate was varied to obtain points for the curves, which are an average over all replicates at each point.

Figure S5: Average power over all replicates for each causal gene at 3 different false positive rates for Scenario 1 for PeRC B over a variety of penalty parameter ratios.

Figure S6: Average power over all replicates for each causal gene at 3 different false positive rates for Scenario 2 for PeRC B over a variety of penalty parameter ratios.

Figure S7: Average power over all replicates for each causal gene at 3 different false positive rates for Scenario 1 for PeRC W over a variety of penalty parameter ratios.

Figure S8: Average power over all replicates for each causal gene at 3 different false positive rates for Scenario 2 for PeRC W over a variety of penalty parameter ratios.

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