The difference between FTDNA and Ancestry is mostly nomenclature.

Take the marker that the geneticists call 464.  It's a multicopy maker.
Most men have 4 copies of it.  The geneticists call it 464a, 464b, 464c, and
464d.  Since there's 4 copies of it, it gets counted 4 times.  Some men have
an extra rare copy or two of that maker.  (The geneticists call it 464e and
464f).  If FTDNA finds it, they report it to the testee.  Because it's rare,
they don't label it in their count.  Ancestry counts it and reports it back
as a 0 or null.

>From Max Blankfeld, Vice President, Family Tree DNA:
A "37-marker test could also be called a “41-marker test” as we do test and
report markers 464e, 464f, 464g, and DYS19b.  Though we test them, it is
very rare that individuals have results for these markers. Therefore, by our
conservative counting method, our competitor's “33-marker test” is actually
a “29-marker test.” We mention this to make sure that you understand the
difference
between these tests and are able to compare “apples to apples.”

Different companies will test a couple of different markers than the
competition.

Family Tree DNA is the oldest and largest DNA testing company.  Its sole
focus is DNA only.  They have things set up in projects (I think Ancestry
may have that feature finally) and FTDNA makes it easy for admins to manage
the projects.  FTDNA has live help in Texas too.

The Azores Project, housed at FTDNA, has 178 members with 164 kits
returned.  Portugal has 183 members, but I don't know how many kits
returned.  Madeira has 59 members and Cape Verde has 47.  If you are in the
Azores (or Madeira or Cape Verde) you can also join the Portugal project, if
you like.  You can have your DNA compared against only those members in the
project or against the entire FTDNA database (249,503 members).  You can
have your DNA uploaded to a public database (YSearch.org or MitoSearch.org)
to compare against other companies (Ancestry.com, Oxford Ancestors, etc).

A comparison chart of the various companies for Y-DNA can be found here:
http://www.isogg.org/ydnachart.htm
A comparison chart of the various companies for mitochondrial (mt) DNA can
be found here: http://www.isogg.org/mtdnachart.htm

Cheri Mello
Family Tree DNA Adminstrator
Azores DNA

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