- Allele_Y and Allele_X denote the response allele and explanatory allele in an LMM Y∼X, respectively. An association is denoted by a filled circle in the column LMM when it is significant, otherwise, an unfilled circle is drawn. Directionality is shown in this table for comparing the value of \(\hat {\lambda }\), which denotes an REML estimate of parameter λ for evaluating structural random effects in an LMM. sd: score of APDs. pIBD: an estimate of the probability that APDs used for calculating the sd are in IBD