Visual Phasing My Two Children with the Fox Spreadsheet: Part 2

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).

 

 

 

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