Do you want to hit a home run with your DNA test, but find yourself a mite bewildered?
Yep, those matches can be somewhat confusing – especially if you don’t understand what’s going on. Do you have a nagging feeling that you might be missing something?
I’m going to explain chromosome matching, and its big sister, triangulation, step by step to remove any confusion, to help you sort through your matches and avoid imposters.
This article is one of the most challenging I’ve ever written – in part because it’s a concept that I’m so familiar with but can be, and is, misinterpreted so easily. I see mistakes and confusion daily, which means that resulting conclusions stand a good chance of being wrong.
I’ve tried to simplify these concepts by giving you easy-to-use memory tools.
There are three key phrases to remember, as memory-joggers when you work through your matches using a chromosome browser: double-sided, two faces and imposter. While these are “cute,” they are also quite useful.
When you’re having a confusing moment, think back to these memory-jogging key words and walk yourself through your matches using these steps.
These three concepts are the foundation of understanding your matches, accurately, as they pertain to your genealogy. Please feel free to share, link or forward this article to your friends and especially your family members (including distant cousins) who work with genetic genealogy.
Now, it’s time to enjoy your double-sided, two-faced chromosomes and avoid those imposters:)
Are you ready? Grab a nice cup of coffee or tea and learn how to hit home runs!
Double-Sided – Yes, Really
Your chromosomes really are double sided, and two-faced too – and that’s a good thing!
However, it’s initially confusing because when we view our matches in a chromosome browser, it looks like we only have one “bar” or chromosome and our matches from both our maternal and paternal sides are both shown on our one single bar.
How can this be? We all have two copies of chromosome 1, one from each parent.
This is my chromosome 1, with my match showing in blue when compared to my chromosome, in gray, as the background.
However, I don’t know if this blue person matches me on my mother’s or father’s chromosome 1, both of which I inherited. It could be either. Or neither – meaning the dreaded imposter – especially that small blue piece at left.
What you’re seeing above is in essence both “sides” of my chromosome number 1, blended together, in one bar. That’s what I mean by double-sided.
There’s no way to tell which side or match is maternal and which is paternal without additional information – and misunderstanding leads to misinterpreting results.
Let’s straighten this out and talk about what matches do and don’t mean – and why they can be perplexing. Oh, and how to discover those imposters!
Your Three Matches
Let’s say you have three matches.
At Family Tree DNA, the example chromosome browser I’m using, or at any vendor with a chromosome browser, you select your matches which are viewed against your chromosomes. Your chromosomes are always the background, meaning in this case, the grey background.
- This is NOT three copies each of your chromosomes 1, 2, 3 and 4.
- This is NOT displaying your maternal and paternal copies of each chromosome pictured.
- We CANNOT tell anything from this image alone relative to maternal and paternal side matches.
- This IS showing three individual people matching you on your chromosome 1 and the same three people matching you in the same order on every chromosome in the picture.
Let’s look at what this means and why we want to utilize a chromosome browser.
I selected three matches that I know are not all related through the same parent so I can demonstrate how confusing matches can be sorted out. Throughout this article, I’ve tried to explain each concept in at least two ways.
Please note that I’m using only chromsomes 1-4 as examples, not because they are any more, or less, important than the other chromosomes, but because showing all 22 would not add any benefit to the discussion. The X chromosome has a separate inheritance path and I wrote about that here.
Let’s start with a basic question.
Why Would I Want to Use a Chromosome Browser?
Genealogists view matches on chromosome browsers because:
- We want to see where our matches match us on our chromosomes
- We’d like to identify our common ancestor with our match
- We want to assign a matching segment to a specific ancestor or ancestral line, which confirmed those ancestors as ours
- When multiple people match us on the same location on the chromosome browser, that’s a hint telling us that we need to scrutinize those matches more closely to determine if those people match us on our maternal or paternal side which is the first step in assigning that segment to an ancestor
Once we accurately assign a segment to an ancestor, when anyone else matches us (and those other people) on that same segment, we know which ancestral line they match through – which is a great head start in terms of identifying our common ancestor with our new match.
That’s a genetic genealogy home run!
There are four bases in a genetic genealogy home run.
- Determine whether you actually match someone on the same segment
- Which is the first step in determining that you match a group of people on the same segment
- And that you descend from a common ancestor
- The fourth step, or the home run, is to determine which ancestor you have in common, assigning that segment to that ancestor
If you can’t see segment information, you can’t use a chromosome browser and you can’t confirm the match on that segment, nor can you assign that segment to a particular ancestor, or ancestral couple.
The entire purpose of genealogy is to identify and confirm ancestors. Genetic genealogy confirms the paper trail and breaks down even more brick walls.
But before you can do that, you have to understand what matches mean and how to use them.
The first step is to understand that our chromosomes are double-sided and you can’ t see both of your chromosomes at once!
Double Sided – You Can’t See Both of Your Chromosomes at Once
The confusing part of the chromosome browser is that it can only “see” your two chromosomes blended as one. They are both there, but you just can’t see them separately.
Here’s the important concept:
You have 2 copies of chromosomes 1 through 22 – one copy that you received from your mother and one from your father, but you can’t “see” them separately.
When your DNA is sequenced, your DNA from your parents’ chromosomes emerges as if it has been through a blender. Your mother’s chromosome 1 and your father’s chromosome 1 are blended together. That means that without additional information, the vendor can’t tell which matches are from your father’s side and which are from your mother’s side – and neither can you.
All the vendor can tell is that someone matches you on the blended version of your parents. This isn’t a negative reflection on the vendors, it’s just how the science works.
Applying this to chromosome 1, above, means that each segment from each person, the blue person, the red person and the teal person might match you on either one of your chromosomes – the paternal chromosome or the maternal chromosome – but because the DNA of your mother and father are blended – there’s no way without additional information to sort your chromosome 1 into a maternal and paternal “side.”
Hence, you’re viewing “one” copy of your combined chromosomes above, but it’s actually “two-sided” with both maternal and paternal matches displayed in the chromosome browser.
Let’s explain this another way.
The example above shows one of my parents matching me. Don’t be deceived by the color blue which is selected randomly. It could be either parent. We don’t know.
You can see that I match my parent on the entire length of chromosome 1, but there is no way for me to tell if I’m looking at my mother’s match or my father’s match, because both of my parents (and my children) will match me on exactly the same locations (all of them) on my chromosome 1.
In fact, here is a combination of my children and my parents matching me on my chromosome 1.
To sort out who is matching on paternal and maternal chromosomes, or the double sides, I need more information. Let’s look at how inheritance works.
Stay with me!
Let’s take a look at how inheritance works visually, using an example segment on chromosome 1.
In the example above:
- The first column shows addresses 1-10 on chromosome 1. In this illustration, we are only looking at positions, chromosome locations or addresses 1-10, but real chromosomes have tens of thousands of addresses. Think of your chromosome as a street with the same house numbers on both sides. One side is Mom’s and one side is Dad’s, but you can’t tell which is which by looking at the house numbers because the house numbers are identical on both sides of the street.
- The DNA pieces, or nucleotides (T, A, C or G,) that you received from your Mom are shown in the column labeled Mom #1, meaning we’re looking at your mother’s pink chromosome #1 at addresses 1-10. In our example she has all As that live on her side of the street at addresses 1-10.
- The DNA pieces that you received from your Dad are shown in the blue column and are all Cs living on his side of the street in locations 1-10.
In other words, the values that live in the Mom and Dad locations on your chromosome streets are different. Two different faces.
However, all that the laboratory equipment can see is that there are two values at address 1, A and C, in no particular order. The lab can’t tell which nucleotide came from which parent or which side of the street they live on.
The DNA sequencer knows that it found two values at each address, meaning that there are two DNA strands, but the output is jumbled, as shown in the First and Second read columns. The machine knows that you have an A and C at the first address, and a C and A at the second address, but it can’t put the sequence of all As together and the sequence of all Cs together. What the sequencer sees is entirely unordered.
This happens because your maternal and paternal DNA is mixed together during the extraction process.
Looking at the portion of chromosome 1 where the blue and teal people both match you – your actual blended values are shown overlayed on that segment, above. We don’t know why the blue and the teal people are matching you. They could be matching because they have all As (maternal), all Cs (paternal) or some combination of As and Cs (a false positive match that is identical by chance.)
There are only two ways to reassemble your nucleotides (T, A, C, and G) in order and then to identify the sides as maternal and paternal – phasing and matching.
As you read this next section, it does NOT mean that you must have a parent for a chromosome browser to be useful – but it does mean you need to understand these concepts.
There are two types of phasing.
- Parental Phasing is when your DNA is compared against that of one or both parents and sorted based on that comparison.
Parental phasing requires that at least one parent’s DNA is available, has been sequenced and is available for matching.
In our example, Dad’s first 10 locations (that you inherited) on chromosome 1 are shown, at left, with your two values shown as the first and second reads. One of your read values came from your father and the other one came from your mother. In this case, the Cs came from your father. (I’m using A and C as examples, but the values could just as easily be T or G or any combination.)
When parental phasing occurs, the DNA of one of your parents is compared to yours. In this case, your Dad gave you a C in locations 1-10.
Now, the vendor can look at your DNA and assign your DNA to one parent or the other. There can be some complicating factors, like if both your parents have the same nucleotides, but let’s keep our example simple.
In our example above, you can see that I’ve colored portions of the first and second strands blue to represent that the C value at that address can be assigned through parental phasing to your father.
Conversely, because your mother’s DNA is NOT available in our example, we can’t compare your DNA to hers, but all is not lost. Because we know which nucleotides came from your father, the remaining nucleotides had to come from your mother. Hence, the As remain after the Cs are assigned to your father and belong to your mother. These remaining nucleotides can logically be recombined into your mother’s DNA – because we’ve subtracted Dad’s DNA.
I’ve reassembled Mom, in pink, at right.
- A second type of phasing uses something referred to as statistical or academic phasing.
Statistical phasing is less successful because it uses statistical calculations based on reference populations. In other words, it uses a “most likely” scenario.
By studying reference populations, we know scientifically that, generally, for our example addresses 1-10, we either see all As or all Cs grouped together.
Based on this knowledge, the Cs can then logically be grouped together on one “side” and As grouped together on the other “side,” but we still have no way to know which side is maternal or paternal for you. We only know that normally, in a specific population, we see all As or all Cs. After assigning strings or groups of nucleotides together, the algorithm then attempts to see which groups are found together, thereby assigning genetic “sides.” Assigning the wrong groups to the wrong side sometimes happens using statistical phasing and is called strand swap.
Once the DNA is assigned to physical “sides” without a parent or matching, we still can’t identify which side is paternal and which is maternal for you.
Statistical or academic phasing isn’t always accurate, in part because of the differences found in various reference populations and resulting admixture. Sometimes segments don’t match well with any population. As more people test and more reference populations become available, statistical/academic phasing improves. 23andMe uses academic phasing for ethnicity, resulting in a strand swap error for me. Ancestry uses academic phasing before matching.
By comparison to statistical or academic phasing, parental phasing with either or both parents is highly accurate which is why we test our parents and grandparents whenever possible. Even if the vendor doesn’t use our parents’ results, we certainly can!
If someone matches you and your parent too, you know that match is from that parent’s side of your tree.
The second methodology to sort your DNA into maternal and paternal sides is matching, either with or without your parents.
Matching to multiple known relatives on specific segments assigns those segments of your DNA to the common ancestor of those individuals.
In other words, when I match my first cousin, and our genealogy indicates that we share grandparents – assuming we match on the appropriate amount of DNA for the expected relationship – that match goes a long way to confirming our common ancestor(s).
The closer the relationship, the more comfortable we can be with the confirmation. For example, if you match someone at a parental level, they must be either your biological mother, father or child.
While parent, sibling and close relationships are relatively obvious, more distant relationships are not and can occur though unknown or multiple ancestors. In those cases, we need multiple matches through different children of that ancestor to reasonably confirm ancestral descent.
Ok, but how do we do that? Let’s start with some basics that can be confusing.
What are we really seeing when we look at a chromosome browser?
The Grey/Opaque Background is Your Chromosome
It’s important to realize that you will see as many images of your chromosome(s) as people you have selected to match against.
This means that if you’ve selected 3 people to match against your chromosomes, then you’ll see three images of your chromosome 1, three images of your chromosome 2, three images of your chromosome 3, three images of your chromosome 4, and so forth.
Remember, chromosomes are double-sided, so you don’t know whether these are maternal or paternal matches (or imposters.)
In the illustration below, I’ve selected three people to match against my chromosomes in the chromosome browser. One person is shown as a blue match, one as a red match, and one as a teal match. Where these three people match me on each chromosome is shown by the colored segments on the three separate images.
My chromosome 1 is shown above. These images are simply three people matching to my chromosome 1, stacked on top of each other, like cordwood.
The first image is for the blue person. The second image is for the red person. The third image is for the teal person.
If I selected another person, they would be assigned a different color (by the system) and a fourth stacked image would occur.
These stacked images of your chromosomes are NOT inherently maternal or paternal.
In other words, the blue person could match me maternally and the red person paternally, or any combination of maternal and paternal. Colors are not relevant – in other words colors are system assigned randomly.
Notice that portions of the blue and teal matches overlap at some of the same locations/addresses, which is immediately visible when using a chromosome browser. These areas of common matching are of particular interest.
Let’s look closer at how chromosome browser matching works.
What about those colorful bars?
Chromosome Browser Matching
When you look at your chromosome browser matches, you may see colored bars on several chromosomes. In the display for each chromosome, the same color will always be shown in the same order. Most people, unless very close relatives, won’t match you on every chromosome.
Below, we’re looking at three individuals matching on my chromosomes 1, 2, 3 and 4.
The blue person will be shown in location A on every chromosome at the top. You can see that the blue person does not match me on chromosome 2 but does match me on chromosomes 1, 3 and 4.
The red person will always be shown in the second position, B, on each chromosome. The red person does not match me on chromosomes 2 or 4.
The aqua person will always be shown in position C on each chromosome. The aqua person matches me on at least a small segment of chromosomes 1-4.
When you close the browser and select different people to match, the colors will change and the stacking order perhaps, but each person selected will always be consistently displayed in the same position on all of your chromosomes each time you view.
The Same Address – Stacked Matches
In the example above, we can see that several locations show stacked segments in the same location on the browser.
This means that on chromosome 1, the blue and green person both match me on at least part of the same addresses – the areas that overlap fully. Remember, we don’t know if that means the maternal side or the paternal side of the street. Each match could match on the same or different sides.
Said another way, blue could be maternal and teal could be paternal (or vice versa,) or both could be maternal or paternal. One or the other or both could be imposters, although with large segments that’s very unlikely.
On chromosome 4, blue and teal both match me on two common locations, but the teal person extends beyond the length of the matching blue segments.
Chromosome 3 is different because all three people match me at the same address. Even though the red and teal matching segments are longer, the shared portion of the segment between all three people, the length of the blue segment, is significant.
The fact that the stacked matches are in the same places on the chromosomes, directly above/below each other, DOES NOT mean the matches also match each other.
The only way to know whether these matches are both on one side of my tree is whether or not they match each other. Do they look the same or different? One face or two? We can’t tell from this view alone.
We need to evaluate!
Two Faces – Matching Can be Deceptive!
What do these matches mean? Let’s ask and answer a few questions.
- Does a stacked match mean that one of these people match on my mother’s side and one on my father’s side?
They might, but stacked matches don’t MEAN that.
If one match is maternal, and one is paternal, they still appear at the same location on your chromosome browser because Mom and Dad each have a side of the street, meaning a chromosome that you inherited.
Remember in our example that even though they have the same street address, Dad has blue Cs and Mom has pink As living at that location. In other words, their faces look different. So unless Mom and Dad have the same DNA on that entire segment of addresses, 1-10, Mom and Dad won’t match each other.
Therefore, my maternal and paternal matches won’t match each other either on that segment either, unless:
- They are related to me through both of my parents and on that specific location.
- My mother and father are related to each other and their DNA is the same on that segment.
- There is significant endogamy that causes my parents to share DNA segments from their more distant ancestors, even though they are not related in the past few generations.
- The segments are small (segments less than 7cM are false matches roughly 50% of the time) and therefore the match is simply identical by chance. I wrote about that here. The chart showing valid cM match percentages is shown here, but to summarize, 7-8 cMs are valid roughly 46% of the time, 8-9 cM roughly 66%, 9-10 cM roughly 91%, 10-11 cM roughly 95, but 100 is not reached until about 20 cM and I have seen a few exceptions above that, especially when imputation is involved.
In this inheritance example, we see that pink Match #1 is from Mom’s side and matches the DNA I inherited from pink Mom. Blue Match #2 is from Dad’s side and matches the DNA I inherited from blue Dad. But as you can see, Match #1 and Match #2 do not match each other.
Therefore, the address is only half the story (double-sided.)
What lives at the address is the other half. Mom and Dad have two separate faces!
Looking at our example of what our DNA in parental order really looks like on chromosome 1, we see that the blue person actually matches on my maternal side with all As, and the teal person on the paternal side with all Cs.
- Does a stacked match on the chromosome browser mean that two people match each other?
Sometimes it happens, but not necessarily, as shown in our example above. The blue and teal person would not match each other. Remember, addresses (the street is double-sided) but the nucleotides that live at that address tell the real story. Think two different looking faces, Mom’s and Dad’s, peering out those windows.
If stacked matches match each other too – then they match me on the same parental side. If they don’t match each other, don’t be deceived just because they live at the same address. Remember – Mom’s and Dad’s two faces look different.
For example, if both the blue and teal person match me maternally, with all As, they would also match each other. The addresses match and the values that live at the address match too. They look exactly the same – so they both match me on either my maternal or paternal side – but it’s up to me to figure out which is which using genealogy.
When my matches do match each other on this segment, plus match me of course, it’s called triangulation.
Triangulation – Think of 3
If my two matches match each other on this segment, in addition to me, it’s called triangulation which is genealogically significant, assuming:
- That the triangulated people are not closely related. Triangulation with two siblings, for example, isn’t terribly significant because the common ancestor is only their parents. Same situation with a child and a parent.
- The triangulated segments are not small. Triangulation, like matching, on small segments can happen by chance.
- Enough people triangulate on the same segment that descends from a common ancestor to confirm the validity of the common ancestor’s identity, also confirming that the match is identical by descent, not identical by chance.
The key to determining whether my two matches both match me on my maternal side (above) or paternal side is whether they also match each other.
If so, assuming all three of the conditions above are true, we triangulate.
Next, let’s look at a three-person match on the same segment and how to determine if they triangulate.
Three Way Matching and Identifying Imposters
Chromosome 3 in our example is slightly different, because all three people match me on at least a portion of that segment, meaning at the same address. The red and teal segments line up directly under the blue segment – so the portion that I can potentially match identically to all 3 people is the length of the blue segment. It’s easy to get excited, but don’t get excited quite yet.
Given that three people match me on the same street address/location, one of the following three situations must be true:
- Situation 1- All three people match each other in addition to me, on that same segment, which means that all three of them match me on either the maternal or paternal side. This confirms that we are related on the same side, but not how or which side.
In order to determine which side, maternal or paternal, I need to look at their and my genealogy. The blue arrows in these examples mean that I’ve determined these matches to all be on my father’s side utilizing a combination of genealogy plus DNA matching. If your parent is alive, this part is easy. If not, you’ll need to utilize common matching and/or triangulation with known relatives.
- Situation 2 – Of these three people, Cheryl, the blue bar on top, matches me but does not match the other two. Charlene and David, the red and teal, match each other, plus me, but not Cheryl.
This means that at least either my maternal or paternal side is represented, given that Charlene and David also match each other. Until I can look at the identity of who matches, or their genealogy, I can’t tell which person or people descend from which side.
In this case, I’ve determined that Cheryl, my first cousin, with the pink arrow matches me on Mom’s side and Charlene and David, with the blue arrows, match me on Dad’s side. So both my maternal and paternal sides are represented – my maternal side with the pink arrow as well as my father’s side with the blue arrows.
If Cheryl was a more distant match, I would need additional triangulated matches to family members to confirm her match as legitimate and not a false positive or identical by chance.
- Situation 3 – Of the three people, all three match me at the same addresses, but none of the three people match each other. How is this even possible?
This situation seems very counter-intuitive since I have only 2 chromosomes, one from Mom and one from Dad – 2 sidesof the street. It is confusing until you realize that one match (Cheryl and me, pink arrow) would be maternal, one would be paternal (Charlene and me, blue arrow) and the third (David and me, red arrows) would have DNA that bounces back and forth between my maternal and paternal sides, meaning the match with David is identical by chance (IBC.)
This means the third person, David, would match me, but not the people that are actually maternal and paternal matches. Let’s take a look at how this works
The addresses are the same, but the values that live at the addresses are not in this third scenario.
Maternal pink Match #1 is Cheryl, paternal blue Match #2 is Charlene.
In this example, Match #3, David, matches me because he has pink and blue at the same addresses that Mom and Dad have pink and blue, but he doesn’t have all pink (Mom) nor all blue (Dad), so he does NOT match either Cheryl or Charlene. This means that he is not a valid genealogical match – but is instead what is known as a false positive – identical by chance, not by descent. In essence, a wily genetic imposter waiting to fool unwary genealogists!
In his case, David is literally “two-faced” with parts of both values that live in the maternal house and the paternal house at those addresses. He is a “two-faced imposter” because he has elements of both but isn’t either maternal or paternal.
This is the perfect example of why matching and triangulating to known and confirmed family members is critical.
All three people, Cheryl, Charlene and David match me (double sided chromosomes), but none of them match each other (two legitimate faces – one from each parent’s side plus one imposter that doesn’t match either the legitimate maternal or paternal relatives on that segment.)
Remember Three Things
- Double-Sided – Mom and Dad both have the same addresses on both sides of each chromosome street.
- Two Legitimate Faces – The DNA values, nucleotides, will have a unique pattern for both your Mom and Dad (unless they are endogamous or related) and therefore, there are two legitimate matching patterns on each chromsome – one for Mom and one for Dad. Two legitimate and different faces peering out of the houses on Mom’s side and Dad’s side of the street.
- Two-Faced Imposters – those identical by chance matches which zig-zag back and forth between Mom and Dad’s DNA at any given address (segment), don’t match confirmed maternal and paternal relatives on the same segment, and are confusing imposters.
Are you ready to hit your home run?
Now that we understand how matching and triangulation works and why, let’s put this to work at the vendors. Join me for my article in a few days, Triangulation in Action at Family Tree DNA, MyHeritage, 23andMe and GedMatch.
We will step through how triangulation works at each vendor. You’ll have matches at each vendor that you don’ t have elsewhere. If you haven’t transferred your DNA file yet, you still have time with the step by step instructions below:
- Ancestry Step by Step Guide: How to Upload-Download DNA Files
- 23andMe Step by Step Guide: How to Upload-Download DNA Files
- MyHeritage Step by Step Guide: How to Upload-Download DNA Files
- Family Tree DNA Step by Step Guide: How to Upload-Download DNA Files
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