The NCBI Map Viewer presents a graphical view of several types of maps for the mouse, including genetic, radiation hybrid, sequence, fingerprint clone, and YAC maps. Extensive documentation is provided to describe the resource features and methods used, tutorials, and statistics.

The sequence maps include the reference assembly as well as several alternate assemblies. The reference assembly represents the C57BL/6J genome and includes contigs assembled from finished (phase 3) high throughput genomic sequence (HTGs), single fragment HTGS phase 2 and WGS contigs. A hand-curated tiling path was used to guide the assembly of the reference genome. The alternate assemblies include a mixed-strain WGS assembly from Celera, the MGSCv3 assembly, and several BAC-based partial assemblies from other strains (129 substrain, A/J, B6/CBAF1J, Balb/c, C3H, and NOD).

By default, the sequence maps show the data and annotations from the reference assembly. To see the data from another assembly, select the name of the desired assembly and choose from the available maps in the Maps & Options dialog box, which is available from the display of any chromosome or chromosome region.

The Map Viewer Help document provides information on how to search a genome and control the display. A separate document describes all of the available mouse maps, and includes links to documents describing the genome build process for HTGs and WGS data.

There are some important changes in the data and display of mouse genomic sequence data as of the newest mouse build, released on May 8, 2006.