mm10

mm10 is the reference genome assembly for the house mouse (Mus musculus), also known as GRCm38. It was produced by the Genome Reference Consortium and distributed through major repositories such as the UCSC Genome Browser, Ensembl, and NCBI. As the standard coordinate system for mouse genomics, mm10 provides the primary chromosomal sequences used for alignment, annotation, and comparative analyses.

The assembly covers the mouse genome with the typical karyotype of 19 autosomes plus the X and Y sex chromosomes, along with the mitochondrial genome. In addition to the main chromosome sequences, mm10 includes unplaced scaffolds and, for some regions, alternative haplotypes or patch sequences that reflect historical variation and assembly updates. The project accompanying mm10 ships with a variety of annotation tracks and gene models, enabling researchers to map transcripts, genes, regulatory elements, and variants to the reference coordinates.

usage and impact: mm10 serves as a reference framework for read alignment, variant calling, gene annotation, and comparative studies in mouse genetics and model organism research. It supports common bioinformatic workflows with compatibility to tools such as BWA, Bowtie, and GATK, and it enables cross-study liftover to other assemblies where needed. While mm10 remains widely used, newer assemblies have since been released, and some contemporary projects prefer the latest reference (mm39) for improved accuracy. Researchers should consider assembly choice in the context of their specific analyses and available annotation resources.