Summary of overlapping rare allele QTL and GWAS associations.

Comparisons include QTL between populations, which are overlapping QTL for the same trait mapped in both maize and teosinte; QTL within populations, which are overlapping QTL for the same trait and population, but identified as the contrast between different specific parental alleles and the rest of the population alleles; GWAS hits within QTL, which are GWAS SNPs that are encompassed by a QTL for the same trait and population; and QTL containing GWAS SNPs, which are QTL that encompass a GWAS SNP for the same trait and population. Each comparison is quantified by the mean number of overlaps per comparison (Mean.overlaps), the number of comparisons with zero overlaps (N.zero), the empirical permutation-based p-value for mean overlaps (Means.overlaps.pval), the empirical permutation-based p-value for the number of comparisons with zero overlaps (N.zero.overlaps.pval), and the total number of QTL or GWAS associations that represent the ‘denominator’ of these comparisons (N.QTL.or.hits). In addition, a Boolean variable (Clustered) indicates whether the observed mean number of overlaps is greater than the mean number obtained from the permutation test; this is not a significance test, if the empirical p-value indicates that the observed number of overlaps is significantly different than the random distribution, the variable Clustered indicates evidence of clustering (True) or overdispersion (False).
(CSV)