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The levels of each factor can be represented by a single character, word or numerical number. NOTE: the design matrix of the mean in the model (which is a vector of all ones) is always a linear combination of the design matrix of a discrete covariate so that not all the effects of the levels (or classes, e. male and female) of a discrete covariate are estimable.

GCTA will always constrain the effect of the first level to be zero and the effect of any other level represents its difference in effect compared to the first level.