Mouse (c57bl6j)
Mus_musculus_wgs - Genome Reference Consortium
The c57bl6j viewer represents a whole genome shotgun assembly of the C57BL/6J strain of mouse, assembled by the Broad Institute using ALLPATHS-LG. The assembly is also known as MmusALLPATHS2 (GCA_000185105.2)
Technical Notes
The 01 versions of WGS projects AEKQ00000000 and AEKR00000000 are assembled from the same sequence reads using different methodologies. The AEKQ00000000 contigs were assembled with ALLPATHS-LG v. 34731, and the AEKR00000000 contigs were assembled with SOAPdenovo v. 1.05. They are reported in Gnerre et al. 2011, PNAS.
This 02 version of AEKQ00000000 was de novo assembled using the ALLPATHS-LG assembler from Illumina sequence data, in support of the paper by Williams et al. 2012 Genome Res. The 01 version, AEKQ01000000 can be still retrieved in Entrez Assembly by a search for its accession prefix plus version, AEKQ01, or its assembly name, MmusALLPATHS1.
Example region
More information and statistics (N50, Coverage, BUSCO)
Retrieve a live status of the current tiling path using the tool Chromoview
Display your data in gEVAL
Punchlist OverviewPunchlists
The Mouse Punchlists are automated lists created to facilitate identification of and navigation to common issues or regions of interest.
Examples include:
- Gap Locations
- Overlap Issues
- Clone Spanning Locations
If you would like to recommend a punchlist to be added to a specific organism or in general please contact us
The Genome Reference Consortium
The Mouse gEVAL is maintained and improved by the Genome Reference Consortium (GRC)
Jira Ticketing System: Jira is the ticketing tracking system used by the GRC for genome issues. This can be a gap, path, variation, gene or other issues submitted by external users
Comparative genomics
gEVAL provides intra-species alignments. This is available for intermediate builds, major reference releases, and WGS/NGS assemblies.