The Knockout Mouse Project at The Jackson Laboratory has characterized over 300 mouse knockout lines in 28 assays including 10 behavioral and 18 metabolic/physiology assays. This public dataset represents one of the largest using a classical rapid test battery approach. Here we present a comprehensive analysis of this data. We have statistically modeled the environmental and genetic contributions to phenotype variation using multiple statistical approaches. By modeling environmental variables captured in individual test metadata fields, we are able to increase the sensitivity and precision with which mutants can be detected. By modeling across behavioral, metabolic and physiological phenotypes we provide rich phenotypic resource for the mouse genetics community.