Wednesday, May 09, 2007

Searching SMGF for mtDNA sequences

Adapted from a GENEALOGY-DNA mailing list post by Ann Turner

Assuming that you don't have any mtDNA results from other places.

Use the Search by Surname option for the rarest surname in your maternal line (born before 1900), leaving the section for "Values" clear.

On the data entry screen, enter "Other" for DNA Testing Company, {your rarest surname} for the surname, and clear the "Values" section.

If your {rarest} surname is rare enough, when you click on Search, the results show where you differ from the CRS, e.g. if for location 16209, the faint font below shows the CRS value.    You can see the differences from the CRS.

If your {rarest} surname is not quite so rare, you may see several results.    Look for the result on which the matrilineal names (listed beneath the result) match yours.    Click on the 'Pedigree' symbol to the left of that result to determine that it is, indeed, yours.

Print out that screen, then click on Search Again.    This time fill in some non-CRS values.    In theory, there could be 3 other possible substitutions for a T (C or G or A), but in practice, the vast majority of substitutions will be C.    You can search the GENEALOGY-DNA mailing list archives using the keywords 'transitions transversions' for more background on why this is so, but the substitutions will generally be back and forth between these pairs:

C <-> T
G <-> A

On the other hand, if an item showing is 315.1, for example, with no CRS value below it.    That means that you have an insertion compared to the CRS (practically everybody does have this, as the CRS has the rare version there).    This insertion is in a stretch of C's, so you have 315.1C.

When you have entered those non-CRS values in HVR1 and HVR2, then search again.    This time you should be a perfect match, with all pink squares and the bases from your query in a bold font.

Now you can go back and Search by Differences instead of Search by Surname.    If you allow up to two differences, you may have many more matches.    Some of those show purple squares, where *they* differ from the CRS but you don't (faint font).

Since ALL of you should have tested with SMGF, if any of you would like me to do this search for you, drop me an email containing your matrilineal surnames similar to our yAncestry listings but including 'place of birth' for each that you know.


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