1/10/2021 Genetic Genealogy using GEDmatch - An Absolute Beginners Guide

Genetic Genealogy using GEDmatch

An Absolute Beginners Guide

by Jared Smith

Please contact me if you have any corrections or clarifications.

Overview
This document WILL:

Provide a basic introduction to chromosome inheritance and how analyzing

chromosomes is useful for genealogy research.
Show you how to use the basic GEDmatch.com tools - One-to-many
Matches, One-to-one Compare, and People who match one or both of two
kits. While this guide is specific to GEDmatch tools, the concepts are
applicable to similar tools provided by the DNA major testing services.
Help you understand what DNA matches mean - and what they don't mean.
Explain half matches and chromosome pair analysis, and why your matches
don't always match each other.
Teach you strategies for analyzing DNA matches and building your genetic
genealogy.

This document WILL NOT:

Explore the advanced GEDmatch tools.

Go into depth on X-DNA, Y-DNA, or Mitochondrial DNA analysis.

Getting Started
This guide assumes you have uploaded your DNA data to GEDmatch.com
and that it has been fully batch processed. This means your DNA data is in the
GEDmatch database so it can be used to compare to others. If you haven't
uploaded yet, please follow the instructions at GEDmatch to upload your file(s),
then wait a day or two until the analysis has completed.

Chromosome Basics
Chromosomes are tiny structures found within
your cells. They contain the DNA information
and instructions that define who you are - what
you look like, how your body works, and even
what genetic diseases you might have.

Humans have 46 chromosomes. But

chromosomes come in pairs, so we typically
think of them as 23 pairs of chromosomes. The
first 22 chromosome pairs (called autosomes)
are numbered 1 through 22. We'll primarily focus on these autosomal
chromosomes. The 23rd pair are called the sex chromosomes - men have an X
and a Y sex chromosome and women have two X chromosomes.

Chromosome Inheritance
One autosomal chromosome from each pair comes from your mother and the
other comes from your father. This means you get half of your DNA from your
mother and half from your father. Each chromosome they pass on to you is a
combination of their own pair of chromosomes which they got from their parents
(your grandparents).

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The image above depicts how one pair of chromosomes may be passed from your
parents to you. The colors don't mean anything special - they simply depict the
individual chromosomes and chromosome sections.

You'll notice that the chromosome passed to you from each parent may not be an
exact 50/50 combination of their own chromosomes. This means that you might
have a bigger portion of one of their chromosomes than the other - you might be
more related to one of your grandparents than another on that chromosome. In
fact, you might have an exact copy of one of your parent's chromosomes, and thus
you'll get no portion of their other chromosome.

If you add in another generation, things get a bit more complex. This depicts just
one chromosome pair. Remember that you have 22 pairs that will be various
combinations of your grandparent's chromosome pairs. In this example, one of the
mother's chromosomes (the one she got from her father) was passed on directly to
the child. This child will not match his maternal grandmother on this chromosome.
I'm not sure how often this non-recombination occurs, but of my 44 autosomes, 6
were not recombined from my parents to me. While lop-sided chromosomes or
non-recombination may occur on a particular chromosome, across all 46
chromosomes, things tend to average out - you'll get around 25% of your DNA
from each of your grandparents.

For each generation you go into the past, you will get less and less of that
ancestor's DNA. The chromosome segments they pass on will become smaller or
lost due to recombination. This is why autosomal DNA analysis is usually only
useful to at most 6 or 7 generations back - you have so little DNA from very distant
ancestors that it becomes difficult to analyze it reliably.

Some Definitions
cM
Centimorgan (abbreviated cM) is a measure of genetic linkage. Think of it as a
measure of DNA information within a chromosome. Each chromosome contains

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different amounts of information. Chromosome 1 contains 281.5cM of information.
Chromosome 2 has 263.7cM. Chromosome 21 has only 70.2cM.

SNP
SNPs, or single-nucleotide polymorphisms, are tiny pieces of a chromosome that
contain distinct blocks of information. There are thousands of them per
chromosome. SNPs are compared between two people to see if they match. The
amount of information in matching SNPs is measured in cM.

The cM values for SNP matches are sometimes referred to as "chromosome

length" or "match length". However, information is more densely packed in certain
areas or SNPs within chromosomes, so there's not a direct correlation between
number of SNPs and cM amount. When you view GEDmatch's graphical depiction
of chromosome matches, a bigger matching block does not always mean a higher
cM value.

Segment
A "segment" refers to a section or block of contiguous SNPs. A "matching
segment" is a section that is the same between two people.

Start and End Location

Individual markers (called base pairs - the things that SNPs are made of) within a
chromosome are numbered. There are millions of these markers per chromosome.
A segment of a chromosome can be identified by these location numbers.

IBS and IBD

Sometimes SNPs marker values match between two people simply by chance.
This is called IBS or Identical By State. And sometimes they match because they
were passed down from a common ancestor. This is called IBD or Identical By
Descent.

MRCA
This is Most Recent Common Ancestor - the ancestor from which you and a DNA
match received your common DNA segments.

Putting This All Together

Using the terms above, you can begin to speak the language of genetic genealogy.
For example, you may have a match with another person on a segment of
Chromosome 3 from marker start location 36,495 to end location 5,168,135 for a
total of 15.8cM of information in 2,114 matching SNPs.

GEDmatch can show these types of matches in a table and with a graphical
representation of the chromosome:

The blue bars indicate two segments that match on Chromosome 3 between two
people. The table indicates Start and End Locations and the cM and number of
matching SNPs in each segment. You'll notice that the start location for the first
segment is 36,495 instead of 0 even though it appears at the beginning of the
chromosome - this is because not all markers in a chromosome, especially those
near the ends, are tested. We'll discuss the other colors in this graphic later.

The larger the segment (more SNPs and higher cM) of matching markers/base
pairs, the more likely it is IBD (you share a common ancestor) rather than IBS (just
matching by chance). Matching segments smaller than 7cM or 700 SNPs have
a high likelihood of being IBS, so they should be considered questionable.
Matches smaller than 3cM or 300SNPs should be highly suspect and rarely
used alone for genetic genealogy.

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Determining Relatedness
If you add up the total of all cM values for the segments someone shares with you,
you can get a rough calculation of how closely you are related to them. There is a
total of around 6800cM in all 44 autosomal chromosomes. The following are
expected cM matching values for various relationships:

Identical twin - 6800cM (all chromosomes are identical. As noted below, this
will be presented as 3400cM at GEDmatch.
Parents - 3400cM (50% of the chromosomes are a match)
Full siblings - 2500cM (37.5% match)
Grandparents and aunts/uncles - 1700cM (25% match)
Great-grandparents and first cousins - 850cM (12.5% match)
Second cousins and first cousins twice removed - 212.5cM (3.125% match)

The cM match amount or overlap decreases as your relationship gets more

distant. You might share only 13cM (.195%) with your fourth cousin (someone with
whom you share a 3rd great-grandparent). Of course with the variability of many
generations of recombination (or non-recombination) of chromosomes, you could
share much more than that, or you could share 0cM and not be identified as a
cousin match at all.

You can get a full table of expected cM match values for various relationships at
http://isogg.org/wiki/CentiMorgan.

IMPORTANT!

There is much variability in DNA tests. Each company tests

slightly different things in different ways. DNA inheritance is highly
variable. For all of these reasons, keep in mind that the cM match
values and predicted relationships are VERY ROUGH
ESTIMATES ONLY!.

This is especially true for more distant cousins. Additionally, if you

are related to someone on multiple lines - or if you or your match
are related to your common ancestor on multiple lines (e.g., your
grandparents were cousins) - then the total cM will suggest a
closer relationship than is actually the case.

One-to-many Matches
The One-to-many Matches report will provide a list of people you share
chromosome segments with. To view the report, click the 'One-to-many' matches
link on the home page and select your kit # (found on the homepage) on the next
page. We'll be comparing Autosomal chromosomes, not X, so make sure
Autosomal is selected. Keep threshold at 7 cM and select Display Results.

The large table will list your matches in order of Total cM overlap. Most everyone
on the list (especially those near the top) will be related to you... somehow. The
report also displays the largest cM segment amount you share. The Gen column
provides a rough estimate of the number of generations between you and the Most
Recent Common Ancestor (MRCA) you and that match both share - 1 for parent-
child, 2 for 2 generations (grandparent-grandchild), etc.

In the screenshot above, the top two results are my grandmothers. Notice their
Gen values are 1.4 and 1.5 - I got a bit more than 25% of my DNA from each of
them. The next several results are all known cousins of mine - generally in the 3rd
cousin range. Gen of around 3 suggests common great-grandparents (probably
around 2nd cousins), Gen of 4 suggests common great-great-grandparents
(around 3rd cousins), etc.
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Kit Nbr provides an identifier for each person you match. The beginning letter
indicates the testing system they used - T = Family Tree DNA, A = Ancestry.com,
and M = 23andMe.

Clicking the "L" in the List column will run a One-to-many Matches report for that
person. This can be handy to see who that person matches.

Clicking the "A" in the Details column will run a 'One-to-one' compare report
between the person whose matches list you are viewing and the person listed in
that row.

The other columns are either self-explanatory or are not relevant to this discussion.
Names that begin with a * in the Name column are alias names and may not be
the actual match's name.

You should regularly monitor your matches list for new DNA cousins. Newly added
kits show with a green background. I recommend keeping a spreadsheet or
document with information and notes about your cousins - especially ones with
whom you have identified your relationship and common ancestor.

IMPORTANT!

GEDmatch uses a batch process to generate your One-to-many

matches list. It can sometimes display people you aren't
actually related to. Be sure to do a One-to-one compare with a
listed match to ensure you actually share matching DNA
segments.

X-DNA
We will not explore X Chromosome analysis in depth here, but keep the following
in mind:

X-DNA is different. The cM match amounts are not very helpful in

determining how closely related you are.
The X Chromosome is not passed from father to son, so the lines between
you and a strong (over perhaps 4cM) X-DNA match and your common
ancestor will not have any father-son relationships. You'll notice in the
screenshot above that I (being male), as expected, have 0cM X-DNA match
with my paternal grandmother and 69.7cM match with my maternal
grandmother.
If you are a male, any X-DNA matches will be related to you on your mother's
line. If your X-DNA match is male, you will be related to him via his mother.

You can read more about X Chromosome matching at

http://smithplanet.com/stuff/x-chromosome.htm.

One-to-one Compare
The One-to-one compare utility allows you to look for chromosome segment
matches between two people. You can run this utility by selecting 'One-to-one'
compare on the homepage and entering the kit #s for the people you want to
compare, or by clicking the "A" link on the One-to-many report. The default settings
will generally suffice for most matches, though I prefer to enable the Show graphic
bar for each Chromosome? option to give a more visual presentation of the
segment overlaps.

Full and Half Matches

Remember, our chromosomes come in pairs. However, when the DNA testing
tools do chromosome comparisons, they can't distinguish between the two pairs of
a chromosome - they instead treat them essentially as one combined chromosome
- as if the chromosomes have been laid on top of each other.
This means that when you match someone on a
chromosome segment, you can't be sure which of your
chromosomes they match. It could be the chromosome you
got from your father or the one you got from your mother.

Think of this like looking through a double-pane window.

When you see a streak on the window, it's difficult to tell

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whether it's on the inside pane or the outside pane without analyzing it very closely
or from another angle. The same applies to DNA matches - you must analyze
them closely or compare them with someone else in order to know what they
mean.

IMPORTANT!

If you match two different people on the same, large (7cM+)

chromosome segment, those two people are related to you,
but they may not share a common ancestor or be related to
each other. You must always do a One-to-one compare
between your matches to make sure they also match each
other on the same segment(s).

A half match indicates that an SNP of one of your chromosome pairs matches the
corresponding SNP in one (or the other) of someone else's chromosome pairs.
Half matches are depicted in yellow in the chromosome graphic bar.

When the SPNs for both of your chromosome pairs are identical to both pairs from
someone else, this is called a full match. Full matches display in green in the
chromosome graphic bar. Full matches on large segments are not common -
typically only in twins and full siblings, or when someone's parents are related (as
is common in endogamous cultures or regions). The small green lines in the
graphic below indicate SNPs that match on both chromosomes simply by chance
(IBS).

The red lines below indicate there is not a match on these SNPs. The yellow lines
interspersed with the red lines are IBS matches - the SNPs match, but only by
chance. The blue bars indicate large segments (>7cM by default) that are half or
full matches. Because DNA tests report only the total amount of DNA where either
(half match) or both (full match) of the pairs are the same, identical twins will show
as sharing 3400cM of DNA, rather than the actual 6800cM.

Chromosome Match Analysis

The graphic above shows the Chromosome 3 segment overlaps between me and
3 separate matches. At first glance, you might assume that all three of them are
related - they each share notable overlaps in the same areas of my Chromosome
3. All four of us must have received the matching segments from a common
ancestor, right? WRONG!

In this case, Match #1 is my paternal grandmother and Match #2 is my

maternal grandmother. They do not share any DNA with each other and are
not related (except for sharing me as a grandson)! They appear to be matches
because we're actually comparing both of their Chromosome 3s to both of my
Chromosome 3s. My paternal grandmother matches these sections of one of my
chromosomes and my maternal grandmother matches these sections on my other
chromosome. The fact they match in similar areas is simply coincidental. A One-to-
one compare between my grandmothers proves there is no match and my
grandmothers are not closely related (at least on this chromosome):
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As before, the small half and full match lines are IBS only because these segments
are so small.

Let's now analyze Match #3. The process of determining if a match is related to
another match is called triangulation. We know all three matches are related to
me, but we want to triangulate to see if Match #3 is related to one or both of my
grandparents.

I only have two Chromosome 3s - and the area in which Match #3 matches me is
the same area in which I match my grandmothers - so we can be assured that
Match #3 is thus related to one of my grandmothers. But which one? We can
determine this by doing a One-to-one compare between Match #3 and both of my
grandmothers. Comparing Match #1 (my paternal grandmother) and Match #3
shows no matching segments. We therefore know that the match is with my
maternal grandmother (Match #2)! This is what we see when we One-to-one
compare them:

This is definitely a match! They match each other, and both of them match me on
the same segement. In this case, Match #3 is my maternal grandmother's first
cousin (my first cousin twice removed).

You can see that my grandmother and her cousin share much more of
Chromosome 3 than I share with her cousin. This is to be expected - Match #3 is
more closely related to my grandmother than to me. This also indicates that the
portion of Chromosome #3 that they share, but that I don't share with my maternal
grandmother was not passed on from my grandmother to me via my mother. So, if
I match a cousin in the area of Chromosome #3 I didn't get from my grandmother,
then I know I match them on either my maternal grandfather's line or one of my
paternal lines. Eliminating lines for possible MRCAs can be very valuable.

Building Your Chromosome Map

You can use this type of logic and analysis to slowly build a mapping or
spreadsheet of all 23 of your chromosome pairs. As you establish your relationship
to cousins, you can begin to identify whether a match is on your mother's or
father's side, and then which two of your four grandparents a particular
chromosome pair segment maps to. If you have identified a common ancestor with
a cousin for that segment, then matches on that chromosome which also
triangulates as a match to another known descendant of that ancestor will also
share that common ancestor (or perhaps an ancestor or descendant of that
ancestor). If you don't have known cousins with which to triangulate, you have to
be careful in making assumptions - the match could be on either of your
chromosomes and on any of your family lines.

The more cousins you identify common ancestors with, the easier it becomes to
identify common ancestors with additional cousins. Start at the top of your matches
list and start contacting matches (be sure to One-to-one compare first!) and slowly
build a list or spreadsheet of your cousins, the chromosome segments you share,
and your common ancestors.

People who match both kits, or 1 of 2 kits

This very valuable GEDmatch tool allows you to more easily identify cousins who
are related to each other. It is often called the "In Common With" (ICW) tool. This
tool shows you those who are (and are not) related to two different people. If you
have identified a cousin, run this tool on your kit # and their kit # to find people who
are related to both of you.

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You can now analyze these common matches to verify (or refute) your relationship
via triangulation. The Gen columns provide estimates of the distance to the MRCA
for the two people you're comparing and the common match. Differences in these
values may suggest that one of you is more closely related to the MRCA than the
other (i.e., you are probably cousins once or twice removed). As before,
GEDmatch can't differentiate between your chromosomes, so make sure you
do One-to-one between everyone involved before assuming that matching
segments mean you share a common ancestor.

Why Testing Relatives Is Helpful

Each child gets an entirely different combination of their parent's chromosomes
(unless they are identical twins). This means that you can match with someone
that a sibling (or other relative) does not.

In this example, you can see how the children match different segments of their
grandparent's chromosomes. A match with a distant cousin in the dark blue section
for Child #1 would not be present at all for Child #2. And Child #1 wouldn't match
any relatives on the maternal grandmother's line on this chromosome due to lack
of recombination.

IMPORTANT!

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If you don't match someone, this does not always mean you
are not related. It's possible that matching segments from an
ancestor simply weren't passed down to each of you. A match to
one of your known relatives may still be your cousin, even if you
don't match them - especially if their segments align on your
chromosome map to your ancestor. Testing additional relatives
can be helpful in finding additional cousins and unknown
ancestors. They will establish a family baseline with which to
triangulate to determine genetic ancestry lines.

Testing older relatives (especially parents and grandparents) will

get you an extra generation (or 2 or 3) further back in time -
enough to discover cousin connections that would otherwise be
impossible!

Useful Notes and Tips

Start and/or End Locations do not have to be identical to indicate a match.
Variability will result in these being off by quite a bit (perhaps several hundred
thousand) with actual matches.
Because of recombination of chromosomes at each generation, multiple
matches that have matchings segments with the same (or very similar) Start
and/or End Locations are more likely to be related. In the example above, the
matching segments for Match #2 and Match #3 start very near the same
location, thus suggesting (though not guaranteeing) they match each other.
The locations where chromosomes are split across ancestors due to
recombination are called cross-over points.
The Chromosome Browser tool at GEDmatch allows you to compare multiple
people to you at one time to analyze segment matches and overlaps.
Multiple large (>7cM) matching segments increase the likelihood of a
common ancestor, but single very large (>15cm) segments are even more
likely to indicate this.

Strategies If You Were Adopted or Don't Know Your

Parent(s)
If you were adopted and don't have any known DNA relatives or genealogy
information, then you will need to establish possible relationships with matches. A
match with Gen = 4 means you probably share the same great-great-grandfather.
Collect surname lists and family trees for matches. Continue to connect with
additional cousins to find common surnames. Triangulate with multiple cousins to
add credibility to your possible relationships - if two of your matches both share the
same great-great-grandfather, that person or someone on his line is probably your
ancestor. As you weave together possible relationships, you may discover
intersections such as two different possible great-great-grandfathers who had
grandchildren who married each other - they are probably your grandparents!

This is essential genealogy research in reverse - instead of trying to expand your

lines and find new distant ancestors, you want to discover multiple possible
ancestors and try to find where they or their descendants intersect.

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