Based on http://www.yourgeneticgenealogist.com/2013/03/ancestrydna-raw-data-and-rootstech.html AncestryDNA chip is identified as "Illumina OmniExpress Plus", where the "Plus" means there's room for 50,000 custom chosen SNP's. This isn't backed up by the rest of the article which talks about the difference in SNP counts being due to "poorly performing probes", not different custom SNP's which would be the obvious explanation. In general, it's very unlikely for genealogy-only companies to be using the Plus edition, because they have no need for specific extra SNP's that would justify the additional cost. It's much more likely both FTDNA and AncestryDNA are currently using the same Human OmniExpress-24 chip, but FTDNA does some filtering for their results while AncestryDNA gives as returned by the Illumina tools.
[PMID 16252274] Multiple hypothesis testing strategies for genetic case-control association studies.