The basic linear model is
Trait = Mean + Slope x Marker + Error
The marker value will be in the range [-1, 1] inclusive. Two hypotheses are compared. The null hypothesis is that the Slope is zero. The alternate is that the Slope is non-zero. A p-value for the likelihood ratio of these to hypotheses is calculated for each marker-trait combination. LRmapqtl outputs a table with parameter estimates, F statistics, Likelihood ratios and p-values.