mm9

mm9 is the mouse reference genome assembly used in genomics and bioinformatics. It is also known as NCBI37 and is the UCSC Genome Browser’s designation for the corresponding mouse genome build. The assembly provides a standardized coordinate system for Mus musculus and was widely used for mapping sequencing reads, variant discovery, and functional annotation before newer releases became common.

The mm9 assembly was produced by the Mouse Genome Sequencing Consortium and related projects, with the goal of delivering a high-quality reference for the mouse genome. It comprises the assembled autosomes 1 through 19, the X and Y sex chromosomes, the mitochondrial genome, and a set of unplaced scaffolds. As with many large eukaryotic genomes, the assembly contains gaps and regions with limited accuracy, particularly in complex or repeat-rich areas and on the Y chromosome.

In practice, mm9 served as a primary reference for alignment, annotation, and comparative studies for many years. A variety of gene models, transcripts, regulatory elements, and other annotations were mapped to mm9 from resources such as Ensembl and RefSeq, and the assembly is supported by multiple genome browsers and analysis tools. LiftOver and other utilities exist to translate coordinates between mm9 and newer assemblies.

mm9 has largely been superseded by more recent mouse genome builds (notably mm10, also known as GRCm38) that offer improved continuity and accuracy. Nonetheless, mm9 remains in use for legacy datasets and for studies that require compatibility with older analyses.