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.

A new test - LivingDNA test for Ancestry

You might think that following my recent posts, that I've lost all faith in DNA testing for Ancestry.  Not at all.  I just object when people take the analysis results of autosomal DNA tests for ancestry, as infallible truths.  They are clearly not.

So far this year, I have commissioned two 23andMe tests, and three FT-DNA tests, a FullGenomes analysis, and a YFull analysis.  I have also used free analysis at WeGene and, and have run three raw files on GEDmatch calculators.  You'd might also think that I've done enough testing for one year!  I thought that as well.  Then a new service just entered the market.

Living DNA Ancestry attracted my commission on two particular points.  1) it has an incredible British reference, that promises to break ancestry composition into 30 British regions - in addition to global analysis.  If it works, then this is a must for people with significant British ancestry.  2) it uses the latest cutting edge test chip.  The latest Illumina chip based on Global Screen Array (GSA).  In addition, it uses a European based lab (Denmark), it tests Y-DNA, mtDNA, and autosomes.  It tests more SNPs on all three counts, than other current chips used by competitors offering autosomal plus tests.  Raw files for the test results will be available for download.

The British Reference

Living DNA will be using a British reference broken down into an incredible 30 regions, across England, Scotland, Wales, Orkney, and Northern Ireland.  The reference uses the much heralded POBI (Peopling of the British Isles 2015) data set.  This project collected 4,500 blood samples from people that could claim four grandparents in the same area, from across the regions of Britain.

A little about the POBI project below:

The British reference does not include the Republic of Ireland.  However, LivingDNA are confident that they have collected a good global reference, and I understand, that they are seeking a similar quality Irish data-set for the future.  

In comparison, other providers of DNA tests for ancestry, only reference to Britain, or the British Isles & Ireland, as a single reference point.  And as can be seen by my previous posts, with limited success.

They also hope to provide imports for formats of raw file from other test companies in the future.  LivingDNA do not themselves currently offer relative matching, or health information.  Their service is for now, primarily for ancestry.

The Chip

They will be using a custom version of the latest Illumina chip technology, the Global Screen Array (GSA).  It is encoded with:

650,000 autosomal DNA SNPs

20,000 Y-DNA SNPs

4,000 MT-DNA SNPs.

In comparison for example, the 23andMe V4 chip scans for:

577,000 atDNA SNPs

2,329 Y-DNA SNPs

3,100 MT-DNA SNPs.

I hope that LivingDNA will also use up-to-date haplogroup nomenclature and information.  23andMe with their V4 chip still use very dated 2009 nomenclature.

So, let's see if this new service is any improvement to my results, compared with the hit and miss of 23andMe, and Family Tree DNA (FT-DNA).  Will they be able to identify and locate my English roots successfully?  What will the improved chip make of my haplogroups?

FTDNA (Family Tree DNA) My Origins Autosome Test for Ancestry

I know I should have smiled!  Me, myself sitting outside of the archaeology museum earlier this year, at Sofia, Bulgaria.South-West Europe.

FT-DNA Family Finder My Origins

I haven't posted much coherent lately, because, well, my Life changed, and consequently I've been pretty busy, in a very good way.  However, my exploration into genetic genealogy hasn't ceased at all.  Indeed, I took advantage of the Family Tree DNA (FTDNA) Summer sale, and bought the USD $79 Family Finder test.

No need to send a fresh sample, this was the third test from the sample that I sent to FT-DNA's US lab earlier this year.  FTDNA Family Finder is an autosomal DNA test only, without haplogroup results - but I've tested my Y-DNA to death already, and I know my mtDNA haplotype.  The services supplied include relationship matching, raw file download, and an Ancestry analysis named My Origins.  Hey, for that price, in GBP £, that is el cheapo good value.  And it's a good test, with about 690,000 SNPs tested, against 23andMe's current 577,382.  Smoking.

My prime interests was in 1) comparing the raw data with 23andMe on GEDmatch, and 2) seeing what FTDNA My Origins has to say about my autosomal DNA for ancestry.

So what did I find.

The former, comparing raw data files, I've done.  But briefly, the calculators DO vary for the two files, but not by very much - except maybe, that on Eurogenes K13, the nearest GD on my FT-DNA file is closer to correct - putting SE English closer this time than South Dutch.

The latter?

Family Tree DNA reported My Origins as:

100% European.

Broken into:

36% British Isles
32% Southern Europe
26% Scandinavia
6% Eastern Europe

This is a pretty bizarre result.  36% almost hits dead on my 23andMe Ancestry Composition (spec) result for British Isles (32% before phasing, 37% after phasing with one parent).  Perhaps they are using a similarly biased reference?  I'll blog on that soon as well.

26% Scandinavian is massive.  23andMe AC spec reported 7% before phasing, and 2% after phasing with one parent.

That's pretty much my first report for Eastern European, except for's claim of some Balkans (hence my excuse for the above photograph).

but .... 32% Southern Europe, really?  Let's go there next, off to Southern Europe now: