Counting the SNPs - 23andMe V FT-DNA

Comparing 23andMe V4 kit raw file to FT-DNA raw file.

Both tests were taken by myself this year (2016).  I am here comparing the quality of two separate atDNA tests from the same person, by two different DNA for Ancestry companies.  As will be seen, the quality varies considerably, at least in terms of the number of SNPs that are tokenized once forwarded to  This is NOT a test of how well both companies ascertain our DNA ancestry from these files.  Both use their own reference populations and analysis programs.  I've reviewed that elsewhere.  This test simply weighs how many SNPs are registered from the autosomes and X chromosome of one person.

Using the GEDmatch DNA file diagnostic utility, I received the following SNP counts:

Kit M551698 (23andMe V4)

Token File data:
Chr Token SNP Count
1 40974
2 42110
3 34199
4 31020
5 30421
6 36383
7 26352
8 27900
9 23644
10 27888
11 25363
12 25395
13 19880
14 15957
15 15529
16 16551
17 13745
18 16775
19 9006
20 13530
21 7324
22 7386
X 15359

Processed in batch 5355
Number of SNPs utilized by GEDmatch template = 523997
Number of regular SNPs = 517780
Heterozygosity index = 0.302721 (fraction of total SNPs that are heterozygous)
No-calls = 4911 = 0.93956084952678 percent.
Kit M551698 has approximately 19959 total matches with other kits. Of these matches there are 4982 >= 7cM and 14977 < 7cM.

Kit T444495 (FT-DNA file):

Chr Token SNP Count
1 57931
2 59602
3 47094
4 41772
5 39314
6 47546
7 36567
8 36753
9 30643
10 36889
11 35941
12 35850
13 26763
14 22650
15 20899
16 21935
17 18379
18 22586
19 12773
20 19587
21 10001
22 9750
X 19176

Processed in batch 5914
Number of SNPs utilized by GEDmatch template = 709242
Number of regular SNPs = 694324
Heterozygosity index = 0.281384 (fraction of total SNPs that are heterozygous)

No-calls = 16077 = 2.263088030563 percent.

Kit T444495 has approximately 48755 total matches with other kits. Of these matches there are 9351 >= 7cM and 39404 < 7cM.


If the quality of a raw atDNA file is merely down to the number of SNPs that are tested, then FT-DNA clearly wins hands down, when compared with the 23andMe file, following tokenization for GEDmatch use.  The FT-DNA file utilises 709,209 SNPs compared with 23andMe's 523,997 SNPs

I thought that it might be interesting to compare how these files, of the same person, might compare on the same GEDmatch heritage admixture program.

On Eurogenes K13 Oracle, my 23andMe kit gets as top ten closest GD's:

1 South_Dutch 3.89
2 Southeast_English 4.35
3 West_German 5.22
4 Southwest_English 6.24
5 Orcadian 6.97
6 French 7.63
7 North_Dutch 7.76
8 Danish 7.95
9 North_German 8.17
10 Irish 8.22

On the same, using my FT-DNA kit (with many more SNPs tested as demonstrated above:

1 Southeast_English 3.75
2 South_Dutch 4.03
3 West_German 5.42
4 Southwest_English 5.68
5 Orcadian 6.33
6 North_Dutch 7.15
7 Danish 7.36
8 Irish 7.59
9 West_Scottish 7.62
10 North_German 7.7

Based on the numbers of SNPs tokenized, I will in future regard the FT-DNA (Family Tree DNA) file as superior in quality, over the 23andMe file, despite my disappointment in the FT-DNA My Origins ancestry analysis.

The Southern European DNA enigma. Option 3. Autosomal DNA Analysis does not work

Here I'm considering the third option to my enigma.  My known ancestry is 100% English.  However, autosomal DNA tests for Ancestry, by commercial companies, and by third party analysis, suggest that I have a mixture of European ancestries, including varying percentages of Southern European.  I'm trying to best explain this phenomena.  In previous posts, I considered 1) that my paper record is incomplete, or biologically incorrect.  2) that something ancient is picked up in analysis of present day English testers - that maybe reflect shared algorithms with ancient admixture, perhaps prehistoric, or Roman.

Now in this post, I consider the third option.  That commercial DNA companies exaggerate their claims to be able to differentiate to any successful degree, between different regions of Europe in my ancestry.  If this is indeed the case, it has significant repercussions for testers for example, in the USA, Canada, Australia, etc.  If they have a poor paper trail, and poorly known ancestry, maybe it's all too easy for them to regard such DNA tests for ancestry, as indisputable and accurate truths.

Commercial DNA companies for Ancestry, are under pressure to supply to market demands.  Their markets have been dominated particularly by USA customers.  Some of them seasoned genealogists with good quality paper trails.  Others, attracted by the easy option to know their ancestry before the, as 23andMe puts it, the Age of Migration before the past few centuries.  Instead of spending a lifetime chasing documents, they can simply send a DNA sample to a company, and know their roots.  People trust the science of DNA testing for ancestry.  That is the demand that commercial companies can cater for.

But what if their abilities to accurately detect ancestry from Autosomal DNA is exaggerated?

Lack of agreement between analysis.

As one evidence.  Test autosomal DNA with three different companies, and you will receive three different results.  That is well known in genetic genealogy circles.  Some apologists excuse it away by pointing to the different companies claims, to be focusing on different periods.  23andMe say that they zoom in on 500 years ago, by rejecting short chains.  Is it really, really possible yet, to be able to zoom in on one particular period?  I'm not convinced.  Is it even possible to securely locate all ancestry from the past 500 years?  I'd expect genetic recombination to wash away an awful lot of ancestral DNA long before that.  The truth is that beyond our great great grandparent's generation, there is less and less chance of us carrying any surviving DNA from any one particular ancestor! Especially from the autosomal DNA passed down on your father's side.  You might have a Balkan g.g.g.g grandfather, but chances are, there will be no evidence of their existence remaining in your autosomes.  His DNA, and all that belonged to his Balkan ancestry, will be lucky to survive the following 250 years, never mind 500 years.  My Y-DNA has strong evidence that I had an Asian ancestor on my paternal line, arrive in Southern England between 1,800 and 500 years ago.  However, nothing remains in my autosomal DNA analysis that suggests Asia.  Washed away.

Getting back to those three companies giving three different ancestries. My South European percentages have varied from 2% (with a hint at Iberia), to 19% (with a hint at Balkans), to FT-DNA's claim of 32%!  Eurogenes K13 hints at Iberia in it's admixture programs on GEDmatch.

Population References

One more thing.  Autosomal DNA tests for ancestry do not use ancient DNA references.  Not yet anyway.  They instead use present-day references, often from their own customer client bases, based on what ancestry they claim.  This is not necessarily the DNA that existed in past populations.  Populations and genes shuffle, genetic drift forms.  I recently read a report that FT-DNA Y data for NW Europe heavily biases to Irish ancestry.  Therefore, references from Americans of Irish and / or British descent, will bias to the West.  The quality of a reference is critical.

Is it all Bunk?

Am I saying that autosomal DNA testing for Ancestry is all a waste of time?  Actually no, not yet.  The tests DO find me to be pretty much 100% European.  That is a success.  Some tests even find me with a degree of confidence, to be NW European.  That is awesome.  However, beyond such regional level, should we be trusting such tests to be providing concrete results, infallible "truths" with a high degree of accuracy?  Shouldn't we be cautious, and regard such speculations as just that - speculations, to be assessed by other forms of evidence?  Some of my ancestors might have lived in Southern Europe.  Maybe Option 1 was correct - one of my Norfolk ancestors brought a Portuguese wife home from the Peninsular Wars.  Perhaps.  Maybe Option 2 was correct - the patterns that DNA companies pick up as Southern European, are ancient, related to Neolithic, Iron Age, or Roman admixture from the South, or sharing ancient ancestry with Southern Europeans.  Maybe.

I'm not at all disenchanted with DNA testing for ancestry though.  I've commissioned five so far this year, including three autosomal DNA tests.  This leads me to my most recent commission.  Perhaps this one will convince me more.  It's a very new test.  I'll post on that next.