we're seeking an active SNPedian for a magazine interview - email email@example.com if interested
FamilyTreeDNA has several types of tests. There is an the STR test which cannot be used with SNPedia/Promethease, and also a SNP test which can be used. The SNP test uses an Affymetrix Axiom CEU microarray chip with 3,269 SNPs removed (563,800 SNPs reported) for autosomal and X (but not Y or mitochondrial) ancestry testing for $99. Other sources have cited 548011 snps. This platform tests 5497 of the 57301 snps in SNPedia. There seems to also be full sequencing of the mitochondrial also returned in fasta, which Promethease cannot help with.
FTDNA switched to use Illumina OmniExpress-12 BeadChip for Family Finder on February 1st, 2011. Near the end of 2013, as supplies of the 12 sample chips ran out, they moved to Illumina Human OmniExpress-24 BeadChip, which tests nearly identical list of SNP's. According to FTDNA's chief scients Dr. Mittelman, there are about 3,000 or 0.3% SNP's difference between the two OmniExpress versions. Unlike 23andMe, FTDNA is using the stock chip without custom health-implicated SNP's, making the two companies' SNP-lists so different FTDNA doesn't accept autosomal raw data transfer from 23andMe's v4 chip.
Family Finder test build 36 raw data file done in March 2014 with the 24 sample chip contained 693,733 autosomal SNP's and 17,691 X-chromosome SNP's for 711,424 total including no-calls and SNP's otherwise not recognized by Promethease. Some 11,062 of these have annotations in SNPedia. FTDNA does not report Y-chromosome and mitochondrial SNP's, and suppresses some other SNP's on the chip. Build 37 files have 27 fewer SNP's listed, likely because they are no longer mapped on it.
Example Promethease reports for this company
|Platform||Raw data available||Summary|
FTDNA Family Finder
|23andMe v2 & v3, FTDNA Family Finder, Ancestry.com|