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 GEDmatch.com. 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.
Conclusion
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.