MGI contains information about mouse genes, DNA segments, cytogenetic markers and QTLs. Each record may include the marker symbol, name, other names or symbols and synonyms, nomenclature history, alleles, STSs, chromosomal assignment, centimorgan location, cytogenetic band, EC number (for enzymes), phenotypic classifications, human disease data, Gene Ontology (GO) terms, MGI accession IDs and supporting references. See Using the Marker Summary Report and Using the Marker Detail Report for more information about the content of the display of a marker record as it appears in the query results.

MGI contains a variety of maps and mapping data. Users can create graphical displays of genome features on the mouse genome using Mouse Genome Browser, build a Mouse Linkage Map with Orthologs, or view Cytogenetic Maps or Physical Maps. A variety of types of Genetic Mapping Data are available and searchable, including data from genetic linkage crosses, cytogenetic localization, recombinant inbred and recombinant congenic strains, and radiation hybrid mapping.