Strain Variation Table
Short sequence variations between the 18 mouse strains represented in Ensembl are displayed in the Strain Table. The data comes from the Mouse Genome Project.
This view shows all the observed alleles for the different mouse strains in a given genomic location.
The table columns are as follows:
- ID - The identifier of this particular genetic variant in an external database. Frequently, this will be an rs identifier, a reference SNP from NCBI dbSNP.
- Chr:bp - Chromosome name and base pair co-ordinates
- Class - For example, Single Nucleotide Polymorphism (SNP) and Insertion-Deletion (InDel)
- Conseq. type - Consequence type based on SO (Sequence Ontology) terms.
- Alleles - Possible nucleotides at the position listed in the Chr:bp column. These are reported for the forward strand of the genome sequence
- Reference - The reference allele, from the C57BL/6NJ mouse reference genome
- Strain - Displays the observed allele at a genomic location for one of the 18 different mouse strains represented in Ensembl. A vertical bar represents the presence of the reference allele at that location for the corresponding strain. A dot signifies a lack of resequencing coverage at that position.
You can order the table by the columns by clicking on the up/down arrows by the column titles. Filters above the table allow you to filter the data by variant class or variant consequence.