The design of this trait enrichment analysis tool aims at allowing evaluation of all reported QTL/associations of selected traits throughout a genome, to determine if a trait or traits are over-represented in one or more regions of the genome. The setup of the analysis is based on an underlining assumption, that the selected traits are related. For example the traits may belong to a given trait type, or are from a given trait ontology path.

In this implementation we used Chi-squared analysis of the frequencies of reported QTL/associations classified by traits and their chromosome locations. The contingency p-values (p) are estimated to indicate the degree of over-representations (enrichments) of QTL/associations. The false discovery rates (FDR) is also estimated with Benjamini–Hochberg procedure. The size of Chi-squares in each contingency class are graphically indicated with bars of varying lengthes drawn with transformed Chi-square values.

In addition, some available trait correlation data are appended when available, to provide additional support information for users to evaluate the results.