We selected 198 samples for genotyping with the Mouse Diversity array including 36 wild caught mice, 62 wild-derived laboratory strains and 100 classical strains. Wild caught mice, including representatives from M. m. domesticus, M. m. musculus and M. m. castaneus, were used as references to infer the phylogenetic origin of laboratory strains (http://msub.csbio.unc.edu/). Our laboratory samples include strains derived from different stocks and by different laboratories as well as 13 sets of classical substrains that are thought to be closely related to each other. We used 549,599 SNPs that passed quality control filtering and performed additional steps to improve the quality of the genotype calls. Our genotype data include SNPs, deletions larger than 100kb, and VINOs (Variable INtensity Oligonucleotides). The latter represent previously unknown genetic variants that substantially alter the performance of SNP detection probes. There are six possible calls: homozygous for either allele (A or B), heterozygous (H), VINO (V), deletion (D) and no call (N). There are 117,203 probes with VINOs in at least one of the 198 strains. In analyses based on SNPs, we treated VINOs as no calls. In analyses based on VINOs we treated data as binary for presence and absence of VINOs.