Mus musculus (Jun 2020) mouse (GRCm39/mm39) genome assembly

The files listed below are formatted for visualization in the Integrated Genome Browser, available from BioViz.org.

Annotation (bed) and alignment (psl) files (if available) were downloaded from the UCSC Genome Bioinformatics Table Browser. Each file is named for its corresponding table in the UCSC Genome database. See the annots.xml meta-data file in this directory for details.

Files with extension .gz were compressed and indexed using bgzip and tabix tools from htslib.org.

The file named M_musculus_Jun_2020.2bit contains sequence data and is from the UCSC Genome Bioinformatics Web site. To convert a .2bit to fasta, use twoBitToFa. The file genome.txt lists sequences and their sizes and was made from M_musculus_Dec_2011.2bit sequence file using twoBitInfo.

Both twoBitInfo and twoBitToFa are available from http://hgdownload.cse.ucsc.edu/admin/exe/.

	Name	Last modified	Size	Description
	Parent Directory		-
	M_musculus_Jun_2020_all_est.psl.gz	2023-07-24 18:36	204M	PSL (alignments) blat output file
	M_musculus_Jun_2020_all_est.psl.gz.tbi	2023-07-24 18:36	1.0M	Tabix index file
	M_musculus_Jun_2020_all_mrna.psl.gz	2023-07-24 18:36	41M	PSL (alignments) blat output file
	M_musculus_Jun_2020_all_mrna.psl.gz.tbi	2023-07-24 18:36	1.1M	Tabix index file
	M_musculus_Jun_2020_ncbiRefSeq.bed.gz	2023-07-24 18:36	5.8M	Annotation or junction file
	M_musculus_Jun_2020_ncbiRefSeq.bed.gz.tbi	2023-07-24 18:36	142K	Tabix index file
	M_musculus_Jun_2020_refGene.bed.gz	2023-07-24 18:36	2.6M	Data from UCSC refGene table
	M_musculus_Jun_2020_refGene.bed.gz.tbi	2023-07-24 18:36	104K	Tabix index file
	annots.xml	2025-03-11 10:01	1.6K	Annotation and data file list
	genome.txt	2023-07-24 18:36	1.4K	Chromosome lengths and assembly information