Below are some user hints. For resource documentation click here.
Video tutorial sessions 12, 13 and 10 demonstrate some SNP retrievals.
Standard retrievals use Sanger1 (SNPs, 56+ million locations, 19 inbred strains) except for queries on rs numbers and other exact locations in which case the 5 larger inbred strain SNP data sets are searched. For indels and SVs see below.
Navigation: Retrievals are specified using a step-by-step web interface. For best results proceed forward through the steps to the end where a result is produced. At this point you can click on "Refine your query" if necessary to go around again and make adjustments, or to begin a new query. Try to avoid using your browser's Reload or Back buttons. These policies are in place to curtail automated request activity.
Your results will be a viewable HTML list or the result can be downloaded as a CSV or text file. Haplotype strain grouping views (Hap View) and strain % polymorphic number grid (Matrix) viewing options are also available from the result list page.
File downloads: [More info]
Genomic region: Enter gene or marker symbols, GRCm38 chr locations, or rs numbers. Use spaces or returns to separate items. Upper/lower case doesn't matter.
• Gene and marker symbols must use current MGI nomenclature. Find genes
• Recognized symbols include genes, Mit markers, miRNA and QTLs.
• For best results lists of genes should be cleaned using MGI batch query.
• Coordinates may be bp or Mbp and may include embedded commas
• For an exact location use rs number or coordinates e.g. 1:4834655
• For an entire chromosome use e.g. 3:all For entire genome use: all.
(these cannot be used with the 5 largest data sets however)
• Don't mix exact locations (such as rs numbers) with genes or ranges
• See also the SNP retrieval examples page
For Chr Y and MT coverage use Perlegen2 or CGD-MDA.
Additional flank can be specified and will apply to each genomic region given. For genes, "upstream" is the region adjacent to the 5' end. For other entities such as Mit markers, rs numbers and basepair specifications, "upstream" will refer to the adjacent region with lower basepair coordinates.
Retrieving indels or SVs: Use the Choose Data Sets selection, then see Sanger2, Sanger3, and Amgen1 data sets. The majority of data in this resource are SNPs. [More info on MPD representation of indels and SVs]
Variation effect filter allows locations to be retrieved based on annotated variation status such as coding, UTR, splice, noncoding transcript, intronic, or intergenic. Also useful for significantly paring down results where appropriate.
Query size limitations
• Up to 100 gene symbols, rs numbers, or chromosome locations can be entered into the region box for standard (Sanger1) retrievals.
• Up to 50 Mbp can be retrieved from Sanger1 if specific variation effects (non-intronic) are selected.
• Up to 10 Mbp can be retrieved from Sanger1 if no constraints are specified.
• Up to one entire chromosome can be retrieved from the other large data sets.
• Limits may vary depending on the situation.... and will be indicated when exceeded.
Caution . . . . . . Usage caveats
These data sets may include mixtures of high-, medium-, and low-confidence calls, and some data may be considered preliminary by the provider. Selective filtering can amplify underlying error rates. Independent validation is strongly recommended for findings of particular interest. For Sanger data the "S" linkouts can be used to see Sanger's quality/confidence scores for each of their SNP and indel calls.
Automated usage is prohibited. All usage of this resource must be by live interactive users via our web page interface. Usage judged to be violating this policy is subject to blockage. Consider file downloads (above) as an alternative.
The URL for our genotype variation resource is http://phenome.jax.org/SNP
Also at JAX