Category: DNA General

This should be the final Blog for the visual phasing of my childrens’ autosomal DNA. I will be looking at Chromosomes 19-22 and the X Chromosome sometimes called Chromosome 23.

Chromosome 19

There appears to be a discrepancy at position 46 between the crossover line and where my mother matches JJ. However, as these are smaller chromosomes, any difference will be exagerrated in the view.

I’m not seeing any easy cousin matches on the maternal side.

I had said that the the shorter chromosomes can be easier to solve. There is the other problem that they are so short, that there may not be any identifiable matches on them. I can put in a G3 and G4 on the right hand side of the Chromosome:

I checked Heather at MyHeritage and she has a match with Richard who has all Polish ancestors:

Now that I have this, the G3 and G4’s are not useful:

Heather and Richard have a shared match with Krystyna:

I am showing some progress:

JJ and Richard have a shared match at MyHeritage with Patricia here:

That leaves a small area to fill in on the left side of Chromosome 19:

From a comparison between JJ and Heather, it appears that the first crossover should be at about 5.2M. I’m having trouble figuring out the left hand side of Chromosome 19, so I will leave it as is for now.

Downloading Heather and JJ’s MyHeritage Segment Data

While working on Chromosome 19, I downloaded Heather and JJ’s segment data from MyHeritage. I waited a little while and got an email with the information I was looking for. Heather did have these matches at MyHeritage which appear to go through position 5.2:

However, it is difficult to tell for sure if these are real matches, maternal, paternal or if they in fact clearly straddly position 5.2M.

Chromosome 20

On the paternal side, all but one segment is Rathfelder DNA:

I am having trouble finding DNA matches on Heather and JJ’s maternal side on this Chromosome also.

Now it’s time to get creative. I put a Poland filter on Heather’s matches at MyHeritage. I see a match there with Grzegorz:

Unfortunately, it is rather a small match. Heather and JJ have several small matches in this area. I’ll take a chance and give that segment to Jarek:

JJ clearly has matches that go through position 18:

That is about as far as I can get. However, that is built upon small matches on the left side of Chromosome 20.

Chromosome 21

Here, Heather and JJ have all Rathfelder and no Hartley on their paternal side.

Heather and Jarek-side Richard have this match:

I’ll say that Heather’s match goes through position 41.2.

Heather has a match on the Cavanaugh side with Martha:

That should finish Chromosome 21:

JJ’s match with Martha further confirms the visual phasing:

This Chromosome is further shortened by some unusable area at the beginning of the Chromosome.

 

Chromosome 22

There are no obvious matches on the maternal side yet:

JJ and Nicholas match:

He is probably on the Jarek side, but I can’t be certain.

Heather’s match with David:

I didn’t see any Polish ancestors on David’s tree. Also, this is a paternal match as my siblings show up as common matches with Heather and David.

I’ll leave Chromosome 22 like this and hope that I get more or find more matches:

I did find this match at MyHeritage between Heather and Krzysztof after filtering for matches from Poland:

Here is another match that Heather has at MyHeritage with Rafal from Poland:

I see now that I should have extended the segments to here anyway:

Now, I’m doing better than I thought I could. I see that MyHeritage shows that JJ matches Rafal, but not on Chromosome 22:

This suggests to me that JJ should have the crossover at 43.9 M:

Heather and JJ’s X Chromosome

Here we have a different situation. JJ has no paternal side to his X Chromosome as these are not passed down from father to son. Heather’s paternal side of her X Chromosome is just from my mom, so her paternal grandmother. That leaves Heather and JJ’s maternal side DNA to fill in: Jarek and Cavanaugh.

Another complication is that MyHeritage does not report the X Chromosome and Heather and JJ did not test at 23andMe. That means any matches will have to be from Gedmatch or FTDNA.

This is what I have for Heather at DNAPainter:

I am not sure why there is a gap in the paternal side as Heather should match her grandmother the whole way.

Here is Heather’s match with Martha on the Cavanaugh side:

The blue portion in the comparison betweeen Heather and JJ on the top row indicates that JJ should match the same on his maternal side. JJ also has a small match with Peter on the Jarek side here:

JJ’s match list shows that he has no X Match with Peter:

So perhaps 6.4cM is below FTDNA’s X Chromosome match threshold. Heather, on the other hand shows no X match with Peter on the FTDNA Chromosome Browser.

Assuming that is a valid match, I get this:

JJ’s Interesting X Match with Ellen at Gedmatch

If this match is correct, then it suggests that my mapping above in incorrect. I would assume that JJ’s match is with either on the Jarek or Cavanaugh side, but not both. Here is JJ’s ancestry where the match can be:

From the right-hand column, there are two Polish lines, two English lines and three French Canadian lines. I have sent an email to Ellen to see if she has family history information.

So how do I interpret the new information? I need to disregard the small DNA match with Peter for now. One interesting thing is that JJ matches Martha on the Cavanaugh side where he doesn’t match Ellen:

JJ’s match with Martha is from about position 9-33 where I have the red arrow pointing to the black region. I take it to mean that both Martha and Ellen match JJ on his Cavanaugh side, but down different branches of the Cavanaugh line. For example, JJ’s match with Martha may be on the Morrow side and JJ’s match with Ellen may be on the Cavanaugh/Warren side.

Here is my guess on how the the X Chromosome should look:

I now have JJ as mostly Cavanaugh due to the match with Ellen.

Heather and Ellen

Here is how Heather matches Ellen at Gedmatch:

Heather has a smaller match with Ellen, but it is still significant. In the area I have mapped as Jarek for Heather, she does not match Ellen, so that is consistant with the visual phasing that I have done above. That means that Ellen should match JJ and Heather on the Cavanaugh line. That would likely mean a French Canadian or English connection.

One Last Step: Heather and JJ’s X Chromosome Segments

I already downloaded Heather and JJ’s autosomal segments at Gedmatch. However, this did not include their X Chromosome segments. I picked the Segement Option at Tier 1 for Heather. The minimum I could pick was 1,000 matches so I picked that. I don’t need a lot for the X Chromosome. I picked the csv download option and then saved the file as an Excel file. I formatted the positions with commas:

Next, I would like to see if Heather has matches that go through the next crossover on the X Chromosome which is at 143.7. However, my download was for all of Heather’s X Chromosome matches: paternal and maternal. I really want the maternal side. For that I have to choose Heather’s phased maternal kit to get the segments. When I try to do this, I get no segments. I assume that when Heather’s phased maternal kit was created, it didn’t include the X Chromosme.

JJ’s matches will already be phased, so I will try him next. JJ has one match that goes through 143.7, but I am not convinced that this match will help me:

One problem is that the SNP count is quite low.

Heather has matches that go through 143.7, but they are mostly on the paternal side:

TX is a match where I can’t tell if it is paternal or maternal. All the other matches are close paternal matches. That means that I will leave the X Chromosome visually phased as is for now:

Summary and Conclusions

• I was able to visually phase my two childrens’ 23 chromosomes.
• Some were fully phased and some were partially phased
• Because I had tested my mother, Heather and JJ were already phased on the paternal side
• There are more DNA cousin matches on the maternal Jarek side than the maternal Cavanaugh side. This is offset by Martha who is a fairly close Cavanaugh relative to my two children
• I am interested in DNA matches on the Cavanaugh side due to some confusion in the genealogy. For example, Cavanaugh going back should actually be Warren the way I understand it
• Visually phasing the X Chromosome is a little different than the others. I found a large Cavanaugh side X Chromosome match to Heather and JJ and wrote to the match. I hope that she writes back so we can find the connection.
• Some chromosomes may need updating and filling in as new maternal matches are identified
• Using the Fox Spreadsheet is a handy way to do visual phasing and keeps all the information in one need spreadsheet

 

 

In Part Three of this series, I will be looking at Chromosomes 13-18 for my children and visually phasing them to the extent that I can.

Chromosome 13

Here, Heather gets a full dose of her Rathfelder Grandmother’s DNA:

I didn’t see any of the Jarek-matching DNA on the Fox Spreadsheet. I don’t have to open JJ’s FTDNA account each time for his Cavanaugh side match Martha as I aready downloaded JJ’s segments:

Here is where Heather matches Martha:

That takes care of the right half of Chromosome 13:

Heather has this maternal match with Pavel that JJ does not:

It is small, but likely to be real as it is a phased match. This appears to be the correct solution for Heather and JJ’s Chromosome 13:

Chromosome 14

Here is what Heather and JJ’s paternal side looks like:

Heather has a small DNA match with Robert that JJ doesn’t have on the Jarek side:

That is enough to map the left side of Chromosome 14:

The maternal side DNA can move over two lines as those are taken up by paternal crossovers.

Heather matches Peter, a Jarek-side matche, here:

Here is JJ’s match with Peter at FTDNA:

This indicates to me that JJ has a crossover to Jarek at about position 70:

Next, I need to get the position number for the right side of the green FIR.

This is at about 96.6.

JJ has a maternal match with Ashley that goes to about 98:

Heather’s matches do not go that far, so I would give the crossover to Heather:

Other than to JJ, Heather’s furthest out math is at 91.

Chromosome 15

Let’s see how Chromosome 15 shakes out for Heather and JJ:

This shows that Chromosome 15 only has two crossovers and one of those is on the paternal side. It also shows that JJ got a full dose of Rathfelder DNA on his paternal side. Heather and JJ’s match with Jarek-side match Robert shows where the other crossover is:

Here is the finished, simple Chromosome 15:

This tells me that if I was looking for Cavanaugh matches on this Chromosome, I should look at Heather’s match list and not JJ’s.

A Further Check on Chromosome 15

I show that Heather has a match with Jarek-side LeeAnne here:

---

I had assumed that LeeAnne was on the Jarek side, so something seems wrong. Perhaps LeeAnne is on the Cavanaugh side. When I check on LeeAnne’s tree at Ancestry, I assumed that the Dziura in her family was the Dziuria in my children’s family:

That could mean that LeeAnne could match on the Cavanaugh side? Very confusing. However, LeeAnne’s shared matches at AncestryDNA are clearly on the Jarek side. The only explanation that I can think of is that Heather and JJ have a crossover at nearly the same poine where (going from right to left) JJ goes from Jarek to Cavanaugh and Heather goes from Cavanaugh to Jarek.

Checking Martha on the Cavanaugh Side

I see that JJ matches Martha here:

This confirms that at some point on the left side of Chromosome 15, JJ needs to have Cavanaugh DNA and Heather has to have Jarek DNA, but I can’t figure out where that is.

One More Check

When I check on Heather compared to JJ at Gedmatch with a lower match limit of 3 cM, I get this:

These are just two small matches at the beginning of the Chromosome. These two small matches may or may not be important. I’m tempted to think that Heather and JJ had maternal crossovers at about the same point:

I don’t know where that point was, but it must have been after position 54.3. Here are Heather’s maternal matches:

The crossover is likely between 55 and 60.8. based on Heather’s maternal matches.

Chromosome 16

I hope that this Chromosome goes more smoothly than the last one:

I don’t see any uploaded Jarek matches on the spreadsheet. I have used Peter before as a Jarek side match:

That gets things started on the maternal side:

The 55 above is closer to 54.8. That is cutting it close, but JJ has this maternal match:

Heather’s match with KP ends slightly sooner:

So I will give Heather the crossover at 54.8:

JJ has many matches going through 82, so I will give the crossover to Heather again:

I couldn’t find a clear answer to the two segments on the left of Chromosome 16:

Chromosome 17

Here Heather gets a full dose of Hartley DNA from my father:

 

A match with Robert on the Jarek side shows that Heather has the first maternal crossover from Jarek to Cavanaugh:

 

JJ matches Cavanaugh side Martha here:

That means that Heather must match on the Jarek side in that area:

A Little Detective Work to Fill in the Last Part of Chromosome 17

I noticed that on Heather’s list of matches from FTDNA, she has one with a Polish sounding last name:

The match goes through positiion 72.7. I need to know if this is a paternal or maternal match for Heather. I checked Heather’s in common matches at FTDNA and did not see any paternal matches. That tells me that this match is likely on Heather’s maternal side. From what I can tell, this is the right answer for Heather and JJ’s Chromosome 17:

Chromosome 18

I’lll conclude this Blog with Chromosome 18:

This project would have been much more difficult without my mother’s Rathfelder DNA.

Jarek Cousin Robert has a match that goes to position 53:

The match looks like it goes over the crossover line, but I don’t trust the accuracy of it.

Cavanaugh Cousin Martha matches Heather here:

There were no obvious snags in Chromosome 18:

This would be a good Chromosome to look for Cavanaugh side matches – especially on Heather’s side.

Summary and Conclusions

• It looks like I was able to finish the visual phasing for each of Chromosomes 13-18
• The smaller higher number chromosomes are generally considered easier to visually phase compared to the longer chromosomes
• I find it interesting that when I passed my DNA on to my children, I was really passing down my parents DNA to them and combined my children recieved the DNA from their four grandparents.

In my previous Blog, I started working on visually phasing the first 6 chromosomes of my two children. Normally, visual phasing is done with three or more siblings. However, it should not be too difficult to visually phase Heather and JJ’s chromosomes. I have tested their paternal grandmother. Because of that, their paternal side is basically phased.

Chromosome 1

Here is how far I got previously:

It would be helpful to put a few position numbers in at the end of the Chromosome. Specifically, the beginning and the end of the last green HIR would be helpful. The end should be around 216.6M where the last black non-matching area starts:

I’ll call that 215.5. Here is the beginnning of the FIR:

I’ll call that 203.6M.

Segment Search for Maternally Phased Kits of Heather and JJ

Here are some of the results for segment details for the maternal part of JJ’s DNA:

Near the bottom, JJ matches Heather from 237.5M. However, his match with *sly goes past that match to 238.9M. This is a likely indication that Heather has a crossover at 237.5M. Unfortunately, we first need to find out who has the crossover at 203.6.

Heather has this match which I don’t see on JJ’s match list:

Betty likely matches Heather on the Cavanaugh side. Gedmatch indicates that Betty tested at Ancestry, but I am having trouble identifying her test. So it looks like I am stuck, unless I download more match information from FTDNA and MyHeritage for Heather and JJ.

Chromosome 2

Here, I’ve added a few position numbers:

Let’s see what Heather and JJ show around positions 115 and 231M. I couldn’t find anything obvious, so I need to find the end of the first green FIR:

I’ll call that 20.7M. Heather has many maternal matches that pass through 20.7M:

So, I’ll give the crossover to JJ:

Next, I’ll add two more positions:

 

However, when I do that, I notice a problem with the segment map. I see that this is the result of a missplaced paternal crossover:

It’s a good thing I am checking this. The crossover from Rathfelder to Hartley should be at 83:

JJ shows a match going through 47.7 which is the beginning of the second green HIR:

That means that Heather gets the crossover there:

This is an improvement over what I had. In this case, it helped to check.

Chromosome 3 Check

Here I added some easy position numbers:

I’ll look at Heather and JJ’s maternal matches around position 2 and 168.3M. Heather’s first match goes beyond 3M:

The first position above should have been a 3:

So I am giving the crossover to JJ.

JJ has many matches that go through 168.3:

So I give this crossover to Heather:

Heather and JJ do not have many maternal matches around 183.1, so I will leave this Chromosome as is.

Chromosome 7

Chromosomes 4-6 are in good shape, so let’s check on Heather and JJ’s Chromosome 7:

Here, JJ’s match with his paternal grandmother didn’t quite match up with his crossover point, so I put his grandmother’s match at the closest crossover.

Here, I’ll add Leeanne’s match on the left side of Chromosome 7:

Here is Heather’s match with Cavanaugh side Martha:

This match fills in 2 Cavanaugh segments for Heather:

Due to the HIR and FIR, JJ is Jarek and Cavanaugh below Heather. JJ’s match with Martha brings his Cavanaugh DNA to the end of his Chromosome 7:

Next, it would be nice if JJ or Heather had some maternal matches going through position 80. Heather’s maternal match Charles meets that requirement:

Next, I am focusing in on 56.1:

JJ’s match with the same Charles appears to go through 56.1:

That leaves the very left of Heather and JJ’s maternal side. The next position I am interested in is at 5.7:

JJ has two matches going through that position. That should finish Chromosome 7:

However, it doesn’t. Two segments after the red one above should be red and not green. If there is no match there, then the two Hartley segments cannot be right there. Remember when I guessed on JJ and Heather’s grandmother’s ambiguous match position? I guessed wrong.

Here is the easiest, though perhaps non-scientific way to fix the problem:

I moved JJ’s Rathfelder segment right to 80. I then moved JJ’s Jarek segment left from 80 to 76.3. This is the intuitive, logical solution. By non-scientific, I mean that I didn’t look at all of Heather’s and JJ’s matches in that region to double check the crossovers. The yellow/green/red segment map checks out.

Chromosome 8

Things have been going fairly smoothly so far. Let’s hope they continue that way.

Here are two complications. The first situation has a FIR going into a region with no matches. In order for that to happen there has to be two crossovers. The second arrow points to a region where there appear to be two crossovers fairly close to each other, but the match to Heather and JJ’s paternal grandmother shows as being between the two crossovers.

The start of the FIR is at 101.6:

Using the closest rule, I’ll go with the 99.2 crossover.

I left the little paternal segment blank on JJ’s side as there are two very close changes there. The segment is so small, it doesn’t matter. I will just need to have a HIR there when I am done.

Mat1’s matches give some Jarek segments to Heather and JJ:

This seems to be what the match with Jarek relative Mat1 is telling me:

The next step is to find some more crossover locations for this Chromosome.

Next, I’ll check Heather and JJ to see what their matches look like in the vivinity of 12.9, 72.1, 106 and 137.5.

Downloading Heather and JJ’s Segments

However, instead of looking at each chromosome, I will download Heather and JJ’s segment information for their top 1,000 maternal matches at Gedmatch. I did this, but could not find any easy clues as to their crossovers on this chromosome.

Chromosome 9

Chromosome 9 looks interesting:

For one thing, the Heather and JJ’s matches with their grandmother do not line up with the first crossover I have. I went back and compared Heather with JJ at a resolution of 3 cM:

3 cM is the smallest increment allowed. It is good that the smallest is not 4 as I would have missed two crossovers at 10.2 and 13M. Now this makes more sense:

Matches with Robert point out two maternal crossovers:

It seems like JJ should have a crossover to Jarek at 98.1.  When I lower the threshold for JJ’s match with Robert, I get this:

This is what I expected, so JJ does have a crossover at 98:

That leaves only 4 maternal segments. Here is a match that Heather has with Martha on the Cavanaugh side:

Next, I’ll look at Heather and JJ’s maternal match list at around 133.6M. Heather has a lot of maternal matches that go through that crossover. That means that the crossover must belong to JJ:

Here is what I end up with:

Chromosome 10

Here is my initial interpretation:

Chromosome 9 had to HIRs. Chromosome 10 has a small one shown in green above.

Robert has a small match with JJ:

Robert is on the Jarek side, so Heather must have Cavanaugh DNA in her corresponding maternal segment. Heather’s match with Martha on the Cavanaugh confirms that:

 

Heather also matches Martha at the right hand side of Chromosome 10.

Next, I am looking for the position number for the beginning of the HIR:

I’ll call that 114.6.

Heather and JJ’s maternal matches at Gedmatch are primarily between 13.8 and 79.2 for Chromosome 10, so I am stuck for now:

Chromosome 11

Here is my start:

JJ’s matches don’t align perfectly with his paternal grandmother. Robert matches Heather and JJ on the Jarek side:

When I put this in, I notice that there is a Fully Identical Region (FIR) going to a non-match. That means that there needs to be an extra crossover there.

Leanne matches JJ and not Heather on the right hand side:

Here is the beginning of the first FIR in green:

I’ll ignore the three yellow lines and call the start of the FIR 57.4M.

Heather has maternal matches that go through 123.6:

 

Because there is already a paternal crossover at 115.8, I can also move the two Cavanaugh segments to the left.

JJ has two matches that go through 102.5:

Heather would not have a super small Cavanaugh segment at 95.8:

Checking around FTDNA, I see that JJ has a match with Peter, who is in common with Robert and Leeanne from the Jarek side on my spreadsheet:

Thanks to Peter, I can finish Chromosome 11:

Other matches at FTDNA and MyHeritage would also help in completing chromosomes.

Chromosome 12

Here is my starting point with my children’s Rathfelder grandmother added:

I was suspicious of the segment at the right hand side, so I looked at the match between Heather and Gladys at a lower resolution:

Here we see Heather has a small amount of Rathfelder at the end of her paternal side. I don’t see any standard Jarek matches, so I’ll check on Martha on the Cavanaugh side:

JJ has two good matches with Martha:JJ

JJ’s other match with Martha appears to extend to the left of 96.1, but I’m not sure:

Heather’s maternal match with Bryan at Gedmatch clarifies this:

JJ also has matches that go through position 15.3:

In order to get more match information, I will download Heather and JJ’s segment data from FTDNA. The problem with this is that it takes a little work to figure out whether the matches are paternal or maternal.

Summary and Conclusions

• I have now looked at about half of my childrens’ chromosomes and have done an initial mapping out of their segments, sorting them out to where they got their DNA from their four grandparents where I could figure that out.
• I found an additional Jarek side match named Peter at FTDNA which helped out on one chromosome
• I downloaded additional segment information from Gedmatch and FTDNA. The Gedmatch segments are more helpful as I can download just the maternal side segment imformation
• So far, the detailed segment information from FTDNA has not been helpful as many matches are on the paternal side or small and I can’t be sure on which side they are (or perhaps they could be false matches).