mthap Advanced Options Frequently Asked Questions
Q. Why would I want to use the advanced options version?
A. The basic version of mthap makes a lot of assumptions about the data your are uploading. Usually these are good assumptions, but sometimes they are not. The advanced options screen does require some additional knowledge, so if any of it is confusing, read this FAQ. If you still aren't sure, stick to the basic version.
Q. Do I have to fill out all of these? What happens if I leave one out?
A. No, it's not necessary to fill out or change any of these options. You should only set the options you are interested in changing. Anything you don't enter will use the defaults, which in most cases is the same setting used automatically by the basic version.
Q. Why would I want to change the version of PhyloTree used?
A. Haplogroup assignments can change over time, and various testing services use different references when reporting a haplogroup determination. This option lets you see what haplogroup you would have had in an older version of PhyloTree.
Q. What's the "Include Modifications" option?
A. The modifications mostly include some anchors from GenBank which usually help improve the matching. In addition there are sometimes changes made to reflect new knowledge about the phylogenetic tree which aren't yet official but improve matching. If you would prefer to use just the generic PhyloTree, you can deselect this option.
Q. What does the identifier field do?
A. This is used in the report page title so that you can easily distinguish different reports if you run several samples at once, and will also usually show at the top of printouts depending on your browser. This is based on the filename used if you don't set it manually.
Q. Why would I enter the FTDNA/Genographic Haplogroup? Isn't this "cheating?"
A. Determining accurate haplogroup matches with only HVR results can be challenging in many cases. In order to make a more accurate haplogroup determination, Family Tree DNA also performs a test panel of 22 SNPs in the mtDNA coding region. These SNPs cover major branch points in the phylogenetic tree and helps ensure that at least the major haplogroup (the first letter) can be determined. However, FTDNA does not report the results of these SNPs to the customer. Previously, some mthap users would get a result completely different from FTDNA's result due to the ambiguity of their HVR results. Now, the FTDNA haplogroup can be entered to derive the results of the 22-SNP panel, and these additional SNPs should result in a more accurate determination. The haplogroup entered here is used ONLY to derive the 22 SNP panel results; it has no other effect on how the haplogroup matching is done so that the results aren't biased.
The Genographic Project also uses the same 22-SNP panel, but also partially report the results of the SNPs. You can either use the predicted haplogroup to derive the results of the full panel, or enter the SNP results you received in the next option.
Q. What are Genographic SNPs?
A. Results from participants in The Genographic Project include a list SNPs in addition to HVR1 results. These SNPs are from the same 22 SNP panel used by FTDNA, and some of these are reported to the customer. By including these SNP results, mthap can more accurately determine the best haplogroup match. See the previous question for more details.
Q. What is the difference between the old and new 22-SNP panels?
A. The original 22-SNP panel had markers 8994 and 13298, which were replaced with markers 1243 and 3970 respectively in a newer version of the panel. The old and new markers are usually indicative of equivalent haplogroups, but not always. For example, the 13928 marker was designed to detect haplogroup R9, but also occurs in L2c.
Q. Why would I want to change the minimum number of matches?
A. By default, mthap displays at least three matches. It often will display more if some matches are equally ranked. For more ambiguous results, or cases where there are many possible subclade matches, it might be desirable to see more than the top three. This can also help when you want to see why some close matches didn't show up in the top three. This can be set to a maximum of 99, though for practical purposes more than 10 is rarely useful.
Q. Why would I set the regions sequenced and the ranges of each?
A. Different testing services sequence different areas of the mtDNA sequence. By default mthap uses the ranges used by Family Tree DNA. If you have results from a different service, the tested ranges may be different. In some cases this can affect the haplogroup match as it may assume that a marker is not present instead of not sequenced (or the reverse) or may incorrectly detect that the coding region was fully sequenced. You can check with your testing service to find out which positions were fully sequenced, or you can consult this chart for some common values. This can also be used to mask out certain ranges to see what the match would be based on a smaller range of markers tested. You must select at least one range for these options to take effect.
Q. What if I have HVR3 results?
A. Some testing service split what is usually called HVR2 into two regions called HVR2 and HVR3. Since these are adjacent regions, just include them in the HVR2 range if applicable.
Need more help?
There is a discussion about mthap on eng.molgen.org. You can also email your questions to me at email@example.com. So that I can best help you, please include a copy of the complete mthap report and/or your mtDNA data file in your email.