GRCm38mm10

GRCm38mm10 refers to the mouse reference genome assembly produced by the Genome Reference Consortium and commonly known as mm10. It represents GRCm38, the 38th release of the reference genome for the house mouse (Mus musculus). The designation mm10 is the naming convention used by many public resources, including UCSC, Ensembl, and NCBI, to denote this assembly.

Purpose and significance: GRCm38/mm10 provides a standardized coordinate system for aligning sequencing reads, calling variants, and annotating genomic features in mouse research. It superseded the earlier GRCm37 (mm9) assembly and incorporated improvements in sequence contiguity, accuracy, and the correction of misassemblies. The assembly serves as a reference point for gene models, regulatory elements, and comparative analyses across studies.

Content and scope: The assembly covers the majority of the mouse genome, roughly around 2.7 gigabases in length, and is organized into the autosomes (1–19) plus sex chromosomes X and Y, with mitochondrial DNA typically represented as a separate contig in datasets. It is paired with major annotation sets from sources such as RefSeq and Ensembl, and is used in a wide range of genomic and transcriptomic analyses.

Availability and usage: GRCm38/mm10 is distributed by the Genome Reference Consortium and is mirrored by major genome browsers and databases. It provides the foundation for high-throughput experiments, including RNA-Seq, ChIP-Seq, and whole-genome sequencing, and serves as the baseline for coordinate-based analyses and data integration.

Updates and legacy: Since its release, researchers have issued patch builds and, later, newer assemblies (such as GRCm39/mm39). Users may convert coordinates between mm10 and newer assemblies using liftOver or equivalent tools when integrating legacy data.