Methods S1 Generation of near-isogenic lines (NILs) and double-introgression lines (DILs).

Notes S1 Formal demonstration that an inflated signature of antagonistic epistasis can result when the main effect of a near-isogenic line (NIL) is a false positive.

Fig. S1 The probability density function of U, the random variable for antagonistic epistasis between near-isogenic lines (NILs) conditional on one of them being a false positive.

Table S1 Sample sizes for all genotypes in the study

Table S2 Significant differences in trait means between double-introgression lines (DILs) and the parental Solanum lycopersicum (SL) genotype

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