Visual Phasing Six Siblings with the Fox Spreadsheet: Part 1 – The X Chromosome and a Deceptive Cousin Match

My brother Jim was the last of six siblings to have his DNA tested. As a result, I am behind on phasing his DNA. The Visual Phasing process puts your DNA into four categories. Those four categories correspond to the DNA that you got from your four grandparents.

First I used the Steven Fox Visual Phasing Spreadsheet. I downloaded information from gedmatch using that spreadsheet. The program timed out, but it looks like I have enough to get started. Usually, Visual Phasing is just done with three siblings at a time, but I thought I’d try it with all six.

Starting with the X Chromosome

Some people like to start with the X Chromosome. Part of the reason is that it is already phased between maternal and paternal. Females get two X Chromosomes, but males get one. The one that males get is from the maternal side. I had already looked into Jim’s X Chromosome. I compared it without the Fox Spreadsheet and got this:

Here is the complicated six sibling comparison:

In this comparison, Jim is V, Jon is F, and Joel is D. V&F, V&D and F&D correspond to my three brother comparison above. My three sisters have two X Chromosomes, so they have a maternal and paternal side. The paternal side is the same for all three sisters, so they are at least half identical in all places. Yellow is the half identical areas. Red is no match and green means that my sisters match on both the maternal and paternal sides.

I have set the crossover points here:

Next I need to figure out who owns each crossover. It looks like the first one belongs to Heidi:

Every time there is a change in one of the comparisons, Heidi is involved. In three sibling visual phasing, Heidi would be involved in match changes with two other siblings. In six sibling visual phasing, she shows the changes with each of her five siblings. This gives more certainty to setting crossover lines.

Second Try at Building the Chromosomes

I tried to build the chromosomes a second time without all the added cousins as that was slowing the process down. The spreadsheet allows you to add them later. Here is the assuring message I got:

I can add the cousins in later.

An Apparent Jim Crossover That Is Not

Note that at about position 23, it appears that Jim should have a crossover, but it actually goes to his two brothers:

This is a little easier to see in the six sibling comparison:

Jon (F) is in purple and Joel (D) is in orange. These two crossovers are not in the same place but are very close to each other. Joel’s is first at about 23M and Jon is next at about 23.3M.

Another Close Set of Crossovers: Jim and Lori

Here Jim’s crossover is at 87.5M and Lori’s is at 87.7M. That means I need to add another Line for Lori. Now I have 13 crossovers for six siblings:

Adding Cousins

I would like to add cousins to the spreadsheet, as I took them out earlier to make the spreadsheet build run smoothly. Now I will add them back in. I went through Steve Fox’s instruction manual. I added back in cousins and hit the ‘add’ button. I had added my father’s cousin Jim and the program didn’t like that as my brother is also Jim, so I changed my father’s cousin’s name to James and the program was happy. I added 17 cousins, so it could take the spreadsheet a while to add in 17 cousins for 6 siblings. Based on the progress, this process should take about an hour if nothing times out. Actually, it did time out or Excel hung up and I wasn’t happy with the results. So I deleted the cousins and added them in in two batches after closing unneeded programs and Excel spreadsheets.

Here is another assuring announcement:

After this, I ran the other 9 cousins and I successfully completed the build. This build process took a while but should be well worth it.

Back to Visual Phasing of the X

Heidi, Sharon, and Lori will all have their X DNA from their paternal grandmother – Frazer.

I put Frazer on the bottom. That means the maternal side will go on top. For that, I just need to see a few cousin matches. When I choose ‘all cousins’, I see that Anita and her sister have the best X Chromosome matches with my family:

Anita matches Jim, Sharon, Heidi, and Lori on the right. Anita has smaller matches near the middle of the Chromosome with Sharon and Lori . By comparing the chromosomes on the right, it looks like I can see a crossover for Sharon (at 68M) and Lori. For some reason, the position numbers for the matching comparisons are not all showing at the left.

Remember, I said that Lori had a crossover on the right hand side? It shows as my crossover (D or Joel). That means I probably missed a crossover for Lori.

Here is a comparison between Lori and Jim that shows where Lori’s crossover is:

Every carat mark is one million, so Lori’s crossover is at 142M.

Anita above represents Rathfelder, so I just need to put in Rathfelder everwhere that Anita matches my family.

The spreadsheet has a function called Extend, but it didn’t work for the Rathfelder entries for some reason. I’ll just extend Rathfelder manually to the crossovers:

A Problem for Sharon

I extended Jim, but ran into a problem with Sharon:

If I extend Sharon to the right, it goes through a crossover line. A crossover line is where there should be a change from Rathfelder to Lentz. That means that something is wrong. I’ll just visually phase the brothers:

Then I will go segment by segment from Jim to his sisters to see where the change is needed.

It turns out that I was doing it right, but the two small matches with Anita and Inese were wrong. The common wisdom is to ignore X Chromosome matches under 15 or 20 cM. In my opinion, this is especially true between two females. I find this a bit confusing as three cousins match on those two segments of Sharon and Lori.

So that was supposed to be the ‘easy’ Chromosome!

Here is another way of looking at the X Chromosome and cousin match:

Jim (V) matches Lori and Sharon at segment S-F as shown by the blue bars above. Sharon and Lori match cousins Anita, Inese and Catherine at the same segment. However, James does not match cousins Anita, Inese or Catherine at the same segment. That is further confirmation that the X Chromosome match Anita has with Lori and Sharon is not good for use in Visual Phasing.

Checking the Segment Map

The Fox Spreadsheet also has a Segment Map. This is a check to see if your final results match up with the original Gedmatch comparison. It is not a proof that the visual phasing is right. However, if it does not match, it is pretty good proof that something went wrong.

For the X Chromosome, it only works for the three sisters.

The top part is the Gedmatch comparisons with my three sisters. The bottom spreadsheet part should mimic the topgedmatch comparisons if the Visual Phasing is done correctly. Also in Chromosomes other that the X, there will be red sections where there is no matching. When three sister always match on the paternal grandmother, there is no place on the X Chromosome where there is no match.

Summary and Conclusions

  • I had never visually phased my brother Jim except for the X Chromosome. I decided to start the process by working with the Steven Fox Visual Phasing Spreadsheet.
  • I had never clearly understood why a crossover that looked like it should belong to one sibling could belong to the other two. Using six siblings, it was visually clear how that could happen. The other two siblings have crossovers that are close to each other. In this example, Joel and Jon had crossovers near each other. As a result, they both matched Jim in those close crossovers. This made it look like Jim had one crossover when the three sisters were not considered.
  •  A match that three of my sisters had with three cousins made the visual phasing confusing. By re-checking the crossovers and the match between my brother Jim and my three sisters, it became clear that the X Chromosome matches with my sisters that was around 10 cM was either not valid or too ancient to be helpful. In order for these 10 cM cousin matches to be valid there would have had to have been a match with these cousins and my brother Jim also.
  • Visual Phasing of the X Chromosome is simple in that there are only three grandparents to consider and one grandparent is always the sisters’ paternal grandmother’s DNA unrecombined. However, there are other issues that can make the visual phasing of the X Chromosome complicated.
  • I used the segment map to check my work.
  • The Steven Fox Visual Phasing Spreadsheet is a great tool for Visual Phasing. It is time-saving and a great way to organize your work. For six siblings, it shows the results for those siblings all in one location.
  • I’m ready to Visually Phase Jim and the other 5 siblings for Chromosomes 1-22.

 

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