Frequently Asked Questions
How to get flanking sequences with dbSNP redesign?
With dbSNP redesign, the flanking sequences upstream and downstream of a SNP site are not shown directly on the RefSNP page. Instead of going back to the ‘classic’ site, a user can get the flanking sequences with a few steps.
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Mouse over the marker near the lock icon and right click to bring up the pop-up menu options.
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Select “Marker Detail” from pop-up menu.
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Copy the flanking sequences in the marker detail box.
An example screenshot is shown below. A user can select “Reveal in Sequence View” in Step 2, if longer flanking sequences are needed.
How can a variant like rs2084511460 have a frequency of 0 and still be considered and reported as an SNP?
The frequency of 0 for the rs2084511460 variant in dbSNP indicates that the ALFA project has examined this variant, but no alternate allele was found within its dataset. This could mean either: - the alternate allele is extremely rare and wasn't detected in over 5,000 samples; or - it might not be a genuine variant despite its having been reported in a dbGaP study.
Note: Although the ALFA frequency for a variant may be listed as 0, an alternate allele has been observed somewhere (by virtue of its presence in dbSNP), and frequency information outside the scope of ALFA may still be found on the variant page in dbSNP.