The Trouble with Matches

Update: Ancestry no longer provides Y and mitochondrial DNA testing, but I’m leaving this article for historical context.

While working on a client’s mitochondrial DNA report, I came across the worst case I’ve seen in a long time of mismatches being shown as matches at  This has been a pervasive problem for a long time.

10 Point Question – If you match another person exactly on every location, HVR1&HVR2, must you have the exact same haplogroup?

Answer:  Most of the time.

You didn’t think this was going to be easy did you?

Because Family Tree DNA is the only company to test to the full sequence level, their clients are going to have far more advanced, detailed and accurate haplogroup assignments than people who test at companies who only offer the HVR1+HVR2 regions.

Therefore, like in this case, we see a client whose haplogroup is H1.  The “1” part of H1 is determined by location 3010A, a position found in the coding region that can only be read by full sequence testing.  So, at Ancestry, and in other data bases outside of Family Tree DNA, we would expect to see matches to both haplogroup H and H1 (assuming the data base allows outside results to be input), and possibly some other H haplogroups as well, if the HVR1+HVR2 region mutations match those of our H1 person.

OK – next 10 point question.  Will someone who is haplogroup H match someone who is haplogroup M or N or some other haplogroup?

Answer: No, not an exact match, but they may share some common mutations.

Then why does Ancestry show them as matches when a simple comparison would eliminate them?

The answer is two-fold.  Part of the issue could be how Ancestry assigns haplogroups.  We really don’t know how they do it, and they aren’t as forthcoming about these things as Family Tree DNA is.  Secondly, and probably the biggest issue is that Ancestry allows people to enter their own data from other labs into their data base, including their haplogroup, apparently without any verification process.  So, in essence, Ancestry has muddied their own waters.

My client’s 251 matches at ancestry were all shown with “0” differences which means they are exact matches.  That’s exciting to see, except it isn’t real.

I clicked on the “download matches” button, which dumps everything into a spreadsheet, a wonderfully handy feature.  As we talk about this, keep in mind that my client had a total of 5 mutations in the HVR1+HVR2 regions, so based on “0” differences, everyone on that list should share all of those mutations with no additional mutations.

Here’s what I found after sorting the spreadsheet.

Exact matches = 32, hardly the 251 displayed on the match page.

Of the 251 “exact” matches shown, the haplogroup breakdown is shown below:

A – 10 (Native American)

B- 7 (Native American)

C – 3 (Native American)

D – 2 (Native American)

H – 154, over half with no matching markers at all to client

HV – 10

I – 5

J – 5

K – 4

L – 12 (African)

M – 4

N – 5

R – 6

T – 7

U – 11

V – 3

W – 1

X – 1

Z – 1

But even this isn’t the worst part.  Of the 251 matches shown with “0” differences, 32 are actually exact matches.  Of those exact matches, we find 4 different haplogroups, including 3 in haplogroup M, a generally Asian haplogroup which is rare as hen’s teeth here in the US.  Hmmm….anyone spot a problem?

Of the remaining 219, 162 have no mutations whatsoever that match the clients, so they not only shouldn’t be shown with “0” differences, they shouldn’t be shown at all.  So this means that the balance of the matches that do share at least one marker but aren’t exact matches, 57 in number, are shown incorrectly, with “0” differences.

So let’s give Ancestry a report card on this.  32 out of 251 correct equals 13% correct.

Last 10 point question – What letter grade do you get for 13% right, which is 87% wrong?

In my book, and in any school I ever attended, that was a big fat F!

And no, this is not just a recently introduced software bug.  It’s been like this forever.

So now that we know how well Ancestry does on basic things like mitochondrial DNA matches, which are exceedingly easy, anyone feel good about how they’ll do with autosomal DNA?  Comparatively speaking, that’s the tough stuff.



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38 thoughts on “The Trouble with Matches

  1. That is very scary and just reaffirms my disgust for Ancestry’s DNA tests. This type of inaccurate reporting reflects badly on the genealogy DNA testing field. I am so glad I did the full sequence mtDNA at FTDNA. I wonder how badly they are going to screw up the autosomal testing…

    • Wish I’d known this before my mother spent a bunch of money on both her & my tests. I’ve never liked Ancestry. I don’t like how they’ve hijacked so many genealogy websites & are trying to get a monopoly. If there isn’t one already, we need to file a class action lawsuit against them.

  2. The matches are not the only problem with the Ancestry tests. Ancestry only sequence HVR1 and HVR2. They do not check any SNPs in the coding region. Their mtDNA haplogroups are therefore predicted rather than confirmed. Consequently I’ve come across people who have been given incorrect haplogroup predictions from Ancestry. These people only find out the mistake when they get tested elsewhere. Family Tree DNA tests 22 mtDNA coding region SNPs to confirm the haplogroup as can be seen from their FAQs here:

    • Debbie, Ancestry does test HVR2, but not the same HVR2 tested by FTDNA. FTDNA’s version of HVR2 includes the “classic” HVR2 and HVR3. Ancestry does not test the classic HVR3 – as far as I have seen. Relative Genetics, before being bought by Ancestry, had just started selling an HVR3 test; apparently Ancestry did not continue it. Here are two HVR1/HVR2 sequences from FTDNA:

      K1c1: 16224C, 16311C, 16519C, 73G, 146C, 152C, 263G, 315.1C, 498-
      K2a2a1: 16224C, 16311C, 16519C, 73G, 146C, 152C, 263G, 315.1C, 512C

      See the difference? One has 498-; the other 512C. Since both mutations are above position 400, they are in the classic HVR3, so Ancestry does not test for them. So, for Ancestry these would be exact matches. In reality, the two don’t have a common ancestor since the founding of K, maybe 16,000 or more years ago.

      • Bill, I see that I’ve misunderstood the ISOGG chart:

        The problem seems to be that HVR2 has a different meaning depending on whether you test at FTDNA or with a Sorenson lab. Ancestry only test bases 1-390 in HVR2 whereas FTDNA test bases 1-574. Presumably Sorenson call bases 391-574 HVR3, hence my confusion. This means that the Ancestry mtDNA test is even worse value for money than I’d realised!

  3. Wow, interesting stuff. I know what would be said of less professional websites or people, like myself, who might publish data like Ancestry. And how would they correct it, even if they wanted to.( client input).
    And to think that I have stopped posting on blogs, because someone might assume I am some sort of authority.
    They should have disclaimers across each page.
    Thanks for your efforts and info!
    And, you are right in shamelessly supporting FTDNA. They always respond to my queries, and are supportive in all ways.

  4. When Ancestry tries to tie faulty test results to their questionable ancestry charts on file, the resulting mess will grow. ISOGG needs to make a statement saying that ISOGG does not provide education support to DNA testing done by Ancestry.

  5. I can say that I tested my mtDNA with Ancestry and have found that their test is unreliable and when I asked where 16140C and 16260T came from they did not have an answer. The said my haplogroup is K but the new RSRS says that my haplogroup is H2h2a. To me that is a huge difference. I do not know much about DNA but I do know that I will retest with Family Tree because of the comments that I have read here. I tested three years ago and do not have a match at all. I guess the old saying is true> You do get what you pay for!

  6. I had concern about their matching capabilities when members had to manually input data.
    After 40 years as a database analyst, this demonstrates the adage of “Garbage in Garbage Out”!

  7. You focus on mtDNA, but’s presentation of Y-chromosome DNA matches is horrendous.

    For each match, no matter how few markers comprise the match, they show a predicted TMRCA. What they DON”T show is how meaningless that predicted TMRCA is, (especially when comparing few markers, as when a person tested at ancestry matches a person tested at FTDNA whose results were entered manually). The problem is that they don’t even HINT about the possible error in any TMRCA prediction. In reality, the actual Most Recent Common Ancestor could be several hundred years previous to their predicted TMRCA. (I should mention what I feel is the main problem, namely that they do not test enough markers to be as informative as is often required to understand real situations. But that for now is a fundamental limitation, not one they could easily fix by changing their presentation.)

    To their credit, the aspects of their autosomal testing presentation that are enabled so far seem FAR more customer-friendly than 23andMe or FTDNA’s equivalents. These are 1) finding matches to predicted relatives using imputed phasing, which should allow accurate matching of shorter DNA segments (more distant relatives), 2) enabling contact with predicted relatives who are ancestry subscribers, 3) allowing easy comparison of matches’ family trees with highlighting of shared ancestors. AS far as the latter, 23andMe is working on something, we’ll have to wait & see how it compares. A major hole in’s autosomal presentation is their failure to report specific matching segments -this information is vital for understanding one’s matches, and for reconstructing the DNA passed down from specific ancestors. And ALL of these features require a very expensive subscription; people tend to forget about the recurring major expense of the yearly subscription.

  8. Ancestry dot com has never verified anything and never corrects anything, but it is always repeated. While it is a large outfit, this is making it less and less useful as a genealogical tool. Soon, we will all be back to having no reliable sources. That’s my rant for the day! Thanks for the clear explanations of DNA matching, by the way!

  9. If possible, could you also do a report on the problems with Y-DNA matching at similar to what you have done for mtDNA.

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  12. Thank you for this article..I just had dna testing done using my brothers dna..and I called them to dispute the results because the ethncity and family origin my family is derived from on paper didn’t match the test…when I called to ask if they ever had issues with mixed up test results I was told no…I asked then how did the dna results show my family ancestry to come from scandinavian and eastern europe when my family came from portugal…I was told because the vikings migrated..yet portugal was never mentioned in the results…I will redo the test using the test and company mentioned and if your test shows differen results I will not be surprised..thank you

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  19. My son and I do not show up as matches in I called up and Ancestry told me that it was possible for a son to have NONE of his mothers DNA.
    I think they need help there.

  20. Warning! Don’t not buy ancestryDNA it is a waste of time and money. Invest in getting a DNA test done elsewhere. Trust me you won’t regret it but with ancestry you will…BIG TIME!

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  22. There seems to be mostly criticism here of another site that does similar testing. I was very excited and interested in using your company for DNA testing. However, I am turned off by the endless negativity towards another company. True or not, this seems petty takes the focus away from DNA testing on the whole and I don’t think it’s necessary to get more sales this way. The testing should speak for itself either way. A decade or more from now, we may come up with even more sophisticated testing methods and be critical of what we are doing today. Let the customer decide. I would rather do my own research and comparisons independent of the this site’s opinion of their competitors.

  23. The following scenario has been recommended to me: Ancestry does not allow uploads of raw data. So it was suggested that I start with an autosomal test at Ancestry. It’s cheaper and it allows the results for the person/family member being tested to be attached to my Ancestry/FTM tree and see their Circles. Then, it was recommended that, from there, I upload the raw data to FamilyTreeDNA and Gedmatch. If I do this, and then upgrade the data to a Y-DNA or mtDNA test at FamilyTreeDNA, will I get accurate results? What are your thoughts on this plan of action? Or is it better, from the standpoint of accuracy, to start with FamilyTreeDNA from the beginning?

    • That’s fine. When you upload your raw data to Family Tree DNA, just your results are going, not your actual DNA sample. So when you do the Y and mtDNA at FTDNA, you’ll be sent a swab kit.

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  25. My parents are still living (ages 96 & 93) are computer savvy and want to have their DNA done.

    My father has had his Y done to 37 markers. My mother has had nothing done. I would like to give them DNA tests for Christmas, but I need to know which test would be best for genealogy. I have had the complete sequencing done from My father is very “hot” about Ancestry. I told him that it was not as reliable, but at 96, he knows “everything.” He said that there would be more matches at Ancestry. I said that there would be more “mistakes” at Ancestry. He was very upset that his DNA did not match the work (40 years worth) on our Smith family which he had been told all his life was true. He even spent major holidays with the Smith family members. He now just says that “James” was adopted. All the usual genealogy work (census, land records, posted Banns, marriage licenses, cemeteries etc) point to “James” as his grandfather. But no, I said that maybe “James ” was adopted into the family, because he was family. In other words, maybe a Smith girl had a child out-of-wedlock. Oh boy, you would have thought I said a “bad word” in front of my father. Frankly, I don’t care, I just want to know the truth. Which test would be the best to give my dad? I was thinking the Autosomal (darn, I just can’t spell it correctly!). What do you think?

    And for my mom? Her Family Tree has been well documented do to a relative’s fine work in the 1920’s-1980’s. There are paintings, and much documentation and then there are several connections to people that just zoom up the line. However, there seems to be a glitch at one level. Our Canadian cousins are asking for her DNA tests results and are willing to work together. They’re OK with mine, but they say that her DNA would be better. Is that true? Her mother, my grandmother bear the family name in question. I found the “cousin” in Canada as my 4th closest match from my FamilytreeDNA “peoplefinder.” Turns out that my mother had been corresponding with her for years!

    Another quick question, my test came back with Native American? No family lore regarding Native American Ancestry. I know my father’s family came to Jamestown and then south to the Carolinas and to the Lunnenburg, VA area. What is the best way to find out who this person or persons could be? I know I am a White Bolling.

    Thanks all.

    • This is easy. Test both your parents at Ancestry and then transfer their autosomal results to Family Tree DNA for $39. That way they will be in both data bases and you’ll have the best of both worlds. And your Dad will be happy. Your Dad already has his Y at FTDNA and your mtDNA will be the same as your Moms. By testing both parents, you’ll be able to see where your Native comes from. Have a great Christmas with your parents.

  26. If someone has done a mtdna test already and since have lost their mom.Would it have been wise to have tested my mom before even I inherited her mtdna?If needed be could my sister be tested to get similar mtdna results as me?

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