The BOLT-LMM software package computes statistics for association between phenotype and genotypes using a linear mixed model (LMM) [1]. By default, BOLT-LMM assumes a Bayesian mixture-of-normals prior for the random effect attributed to SNPs other than the one being tested. This model generalizes the standard "infinitesimal" mixed model used by existing mixed model association methods (e.g., EMMAX [2], FaST-LMM [3-6], GEMMA [7], GRAMMAR-Gamma [8], GCTA-LOCO [9]), providing an opportunity for increased power to detect associations while controlling false positives. Additionally, BOLT-LMM applies algorithmic advances to compute association statistics much faster than existing methods, both when using the Bayesian mixture model and when specialized to standard mixed model association.