Are you ready to create some segments? We’ll, let’s use visual pH and create some segments today.
Howdy, I’m Andy Lee with Family History Fanatics where we help you understand your DNA, climb your family tree and write the story of your ancestors along the way. This is a segment of DNA. Be sure to subscribe to our channel and click on that bell if you wanna be notified about upcoming episodes. This is the second video in a series about visual phasing, and there’ll be a total of four videos. Now, in the first video, we went through the basic setup process and we’re just looking at one chromosome. So remember that, and if you want to go back and review that video, then there’ll be a link in the description below that, you can review the first step of setting up your visual phasing. This is where we left off. We have our comparison with other people. We have gone through and we’ve identified each one of the recombination points, which is where they change from one color to a next.
And we have assigned those recombination points to a specific person, and that’s what those letters along the bottom are. So we are now ready to create our segments. The first principle of creating segments is that every chromosome pair has a maternal chromosome and a paternal chromosome. Those chromosomes are separate from each other and they don’t intermix. So for instance, you’re not going to have a segment of your paternal grandmother right next to a segment of your maternal grandmother. That just can’t happen cuz they’re on separate chromosomes. So while we are looking at one graph for each pair of people from this, we’re actually going to create segments for six different chromosomes, two chromosomes for each person. So step one is let’s draw a table that has those two chromosomes for each person. How do we do this? And again, depending on what you’re using, that’s going to depend on how you will draw it.
If you’re using Excel, then you can just use a little table on there. If you’re using Word or PowerPoint, you can create a table that has that. If you’re doing it by hand, you can actually just draw it out. I’m gonna draw it out for you just to show what it might be. And I’ll try to keep the lines as straight as possible. But we’re gonna start and end right along with these other chromosomes. So here I’ve drawn one bar and I’m gonna divide it in half. So that’s going to be one for the maternal and one for the paternal. So I’ve done that for A, and I can do that same thing for B. And drawing on the computer is not as easy as drawing on paper. So my lines aren’t totally straight, but that’s the beauty of this is I’ll straighten this up here in just a second.
And C. So each one of these bars represents a chromosome pair and I have them divided out into two chromosomes. So you can see that the pink lines go through and they identify different segments along that. And the black bars there are representing the different chromosomes for person A, person B, and person C. Let me clean that up just a bit. So that looks a lot better. And again, if you’re using a spreadsheet or a Word document or even a PowerPoint file, then you’re just creating a table on here that then overlaps where these different segments are. Now I said that on principle number one, that each chromosome pair is made up of a maternal and a paternal chromosome. And that leads us to principle number two is that each chromosome, not chromosome pair, but each chromosome is made up of grandmother and grandfather segments.
Okay? So on your paternal chromosome, it represents your paternal grandfather and your paternal grandmother. And on your maternal chromosome, it represents your maternal grandfather and your maternal grandmother. Now, because the paternal and the maternal chromosomes are not related to each other, they don’t interact with each other For this, your grandparents segments have to say separate. And I mentioned that already once, and I’m just gonna mention it again so that you don’t get confused. Now, at this point, we still don’t know which one of these bars represents the maternal side and the paternal side. And we certainly don’t know which of these segments is the grandparents for the maternal or the paternal side, but those are principles we need to keep in mind as we’re going forward because we’re eventually in the next video actually going to assign those segments to different people. Now, principle number three as we are creating segments is that segments can only switch between grandmother and grandfather at a recombination point for that person.
Remember, we assign people to each one of these recombination points. And so as we’re creating the segments, it can only go from a grandmother to grandfather at one of those recombination points. So for instance, if I’m just looking at right here with the C, it’s all the way at the end. Well that means C, it’s gonna have a big long segment that goes all the way to the beginning of the chromosome no matter what because there’s no other place where a C shows up. So step two is you want to pick a location and assign the segments. Now union may be wondering, well, what segments should I assign and where should I start? And honestly, it doesn’t really matter. You can actually pick anywhere to start. Now there’s some places that’s probably more advantageous. Usually I like to pick the place where I’m going to see the most solved right away.
So looking at this, I can see that recombination point C at the end of the chromosome, there’s only one of those. And so if I pick something to the left of that, then that entire segment’s gonna be the same. And I’m just gonna use colors to actually represent this. And I’ll use four different colors. So in this case, I’ve got a maroon and I’ve got a blue, so a maroon in a blue. And you can see I filled in everything all the way across. Now again, if you wanted to start with B or with A, that’s fine, but let me just show you real quick what that B or that A might have looked like. If I had started with A, then I might fill in this area right here and you can see that a stops right there. So I get a couple of those segments and then I’d be able to change the color down below to the teal.
And you can see that it’s not near as much information as what I’m seeing with the C by choosing the C. And so that’s why I say usually you wanna take a look at it and choose what’s gonna give you the most to start out with. But in the end you’re going to be able to get the different parts of it regardless of where you start for the most part. Now that leads us to step number three. We’re going to use the full match regions and the no match regions. That would be the green and the red. And we wanna assign our other segments based on those greens and those reds. Let’s look at one principle before we start coloring is that those segments, they’re always going to be extended to the next recombination point. So once you’ve colored one of those segments, you can extend it to the right or the left until you hit the next recombination point for that person.
And let’s go through this as we are drawing these out. So I’m gonna start with from the far left going to the right and I have a maroon and a teal, and so I’m gonna start and just color it in the maroon. And these first little bits are all the same. So I’m gonna color this in maroon and I’m gonna color this in maroon and B and C happen to be the same in the next section as well. So I’m gonna color that maroon there. Now I’ll go in and color my teal, and that’s gonna be right below that. So there’s my teal and there is my teal. So you can see A and C right there. We’ve called that a green. And then B and C, well that’s a green right there. So next on A and C is this segment right here. And so I can color this teal and I can color it actually goes, extends out to there. You can see that’s between A and a, so it extends out. And I can go and get the maroon colored in that same area because A and C are the same colors. So you can see A and C, A and C down here. Now B and C, it’s just yellow there. So I don’t know which one is different, but one of those two colors is different. But then I get to this next part, and this is where B and C is the same, and it goes all the way down to right here.
Where where the next B is. So that’s gonna be all colored. And let me go and get my teal and color the bottom one as well.
And a C. They’re yellow in this area, so I don’t know what color they are. Next is this little skinny bit and it’s just A and B that are different. And so I’m not going to worry about it because I really need to see what C is. I don’t know what B is right there. And I don’t know what A is right there. But let get to the next one. I can see B and C. This is a red region, this is a no match region. And so I need to change the colors for B, and I’m gonna use orange and purple. So let me change this to orange. And in this area it’s going to be orange range, so it’s a separate color. And in the bottom one I’m gonna make that one the purple. But I haven’t filled in that little skinny area in between there because I don’t know what it is.
But, you can see that there’s a B and a B there. So one of these is changing to orange and the other is changing to purple at each of those locations. I just don’t know which one yet. I’m gonna try to solve that. And then I go to this next last one. And this is A and C are the same except I don’t know what C is right here. Now I want to go and I wanna look and C, what I can extend out. So starting again for per and A, I can see that hey, there’s an A right there. So I can’t change that. In this next segment there is an A, and then there is another A at the end of it. So I can’t change that. I go to the B, there’s a B right there, go to the next segment. There’s a B there, there’s a B there. The next segment, there’s a B there. Ah look, there’s a C there. So I can actually extend this segment out. I can draw this purple all the way to the end,
And I can draw this orange all the way to the end, but that tells me nothing about A and C yet. So this is where I’ve gotten just with the initial coloring, and this looks like it’s about half done. Now, depending on the chromosome, you may get more than this done just in our initial look. Or you may get less of this done in our initial look. Let me clean that up just a bit so we can start to see how some of these segments are. Now again, we don’t know which one is the maternal and which one is the paternal. And we don’t know within those, which one is the grandmother and the grandfather yet all we know is that they’re separate segments. Step number four is a difficult one for some people to understand and it’s because it’s not really that intuitive. But up till now, like I mentioned, we don’t know which one is a paternal, which one is the maternal.
So, maroon and orange could be paternal and teal and purple could be maternal or it could be the other way around. And at this point it doesn’t really matter because we haven’t assigned anything else because they’re symmetrical. But what we’re going to do is we’re going to choose one segment and one recombination point and we’re going to switch it. And that’s going to lock in what the rest of our solution is going to be. Now we can only do this once. So whenever you’re doing a chromosome, make sure you understand that you’ve either done this or you haven’t done it. That’s why I like to get this as complete as possible with just the greens and the reds. And then do your switch. And again, you can only switch it once. So let’s just take a look at this in general and think about where we might want to switch it. Again, as with the beginning, we want to get as much information as possible. And so usually I look for where is the biggest gap that I’m going to be able to fill up. Looking at this, I can see that hey, at this recombination point A, there’s no other a’s over here. So if I switch one of these colors, I can fill in everything in this area right here. So let me do that. I’m going to go and change this top one to orange and I’m gonna be able to fill in all of this orange.
Now again, I said just change one segment, not both of the chromosomes. So this bottom one is going to be teal. So now I have an orange and teal all throughout here.
So let’s take a look at how that matches up. So with A and C, A and B, they have to have at least one of those colors the same cuz it’s a yellow, well, A and B have that blue in this segment, the same A and C also have to have one of those colors because it’s yellow. And again they have the blue, whereas B and C, they have to have both colors. So they’re still both maroon and blue. So this is all matching up and you can actually go through the whole thing and see that. Now, once I’ve done that, I’m ready to start filling in some other things. So for instance, now I can go back to this little skinny sliver where A and B are red. They’re opposite colors. So if they are opposite colors, then I know that the red has to be the maroon in here for B. And I know that this has to be the purple. So I’m gonna change this to my purple. And you can see that because I have those two Bs right together, one of those chromosomes switched the blue to the purple, and then shortly the other chromosome happened to switch. And this is just by chance. Again, these two aren’t related to each other, but those two recombination points happen to be pretty close together.
Now the other thing I wanna do is come down here to this last part, A and C. They are the same. So it’s gonna be orange and blue on this last part. So let me go over to my orange and I’m gonna put this orange right in here. And now I’m going to go and put the teal right in here.
So that allows me to solve that end of it. Now if I go back to this other end, remember I can only switch once, so I can’t do a switch on this other side. So these are gonna remain unsolved because at this point of a, I don’t know whether it’s the maroon that switches or whether it is the teal that switches. And likewise on the B person, I don’t know which one switches at either one of these points, but let me clean that up for you. So that is now what our segments look like. We’ve gone through and we’ve painted everything that we can with different colors. And again, these four colors represent our four grandparents, but we don’t know which color corresponds with which grandparent. And we don’t know which chromosome of the pair corresponds with the paternal or the maternal side yet we just know where the segments are.
And segmenting now is mostly complete. Like I said, there was a few little areas that we weren’t able to solve. And you may find that as you’re going through a set of chromosomes, you’ll be able to solve all of the high number chromosomes. So in other words, a shorter chromosome, cause there’s not as many recombination points in them. But once you get into the longer chromosomes, there’s gonna be some areas and in some cases some big areas where you’re not gonna be able to solve it. And again, it’s because you can only do that switch once. Don’t do that switch twice, it doesn’t work. You can only do that switch once. And what we’re gonna see in the next video is some ways you can actually use some other people to help solve these other areas. That completes video two in our four part series about visual phasing. In the first video we talked about getting started and setting up your visual phasing. In the second video here, we have gone through creating our segments. So if you have any questions about creating segments, then put it in the comments below and I’ll try to answer it for you. And if you like this video, give it a thumbs up and share it with all your friends.