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Tuesday, January 10, 2012

James Lick's Response to my Inquiry, re the Accuracy of my mtDNA Classification by 'Family Tree DNA'

['James Lick' quote]:

"The answer will be a bit confusing, so bear with me and read the whole thing and then hopefully it will make sense.

"Yes, if analyzing only based on HVR1 results, X is the best choice, and W1e only comes up as 9th place choice, not at all a good match.

"However, because it is often very difficult to make accurate haplogroup determinations based on only HVR1 results, FTDNA also does an additional test of 22 coding region SNPs. The results of this panel are not reported to the customer, but are used to make the haplogroup determination. Presumably what happened is that your original result was prior to when they did the 22-snp panel and your new result was after they did, and they gave you a free upgrade.

"The pre-release version of mthap includes a new feature to derive the results of the 22-SNP panel. Using this form:

http://vps1.jameslick.com/dna/mthap-new/advanced.php

"Load your data file on the first line as usual, then on the 4th line down where it says "FTDNA Haplogroup" enter "W" and then press the upload button. (You don't need to bother with any of the other settings in this case.)

"With that you will have an extra line listing "Derived Markers" showing the assumed results of the 22-SNP panel. And this will give your best match as W1e. This is mostly based on you presumably having marker 8994A which would put you in W instead of X, and presumably not having 6371T which would be required for X. However, X does remain your 2nd best match.

"What really confuses things is that you have the HVR1 markers for both X and W1e, so that your extra markers for W1e are what would match X and the extra markers for X would match W1e. This is what makes your HVR1 matches so problematic.

"But in the end, if you take the 22-SNP panel into account that gives a two-marker advantage to W1e, so it is most likely that it is the correct match, but without more markers there's still a small chance that X is correct. The good news is that three of the markers for W are in HVR2, so an upgrade to the HVR2 should be able to answer X vs. W."
[quote]

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Thanks for all your help, James, and for explaining the problem (and its solution) so clearly.  For now, I'll just assume that I'm a W1e, and maybe sometime later on test the HVR2 markers for a better clarification. Using the mthap analytic tool was lots of fun, and provided me with valuable info, imho!

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