In Part 1, I downloaded the Steven Fox Spreadsheet and built up the information for six siblings and 17 cousins. Then I did the visual phasing on the X Chromosome. In Part 2, I finished Chromosome 1 for 6 siblings, with a heavy dependence on cousin matches.
Visual Phasing Chromosome 2
Here are the 15 comparisons for my six siblings. There are 5, 4, 3, 2, then 1 comparison. I think that is where the 15 comes from.
I don’t see too many odd things here.
Here I added a bunch of crossovers. I don’t know if it is better to put in too few and add later or too many and erase later. I’m not too worried if I have them perfect as I will be checking them against cousin matches.
I’ll start with cousin Maury. I think that’s how his name is spelled. Where we match represents the DNA I got from my paternal Hartley grandfather:
I need to stick the blue matches above for Jim, Joel, Heidi and Lori. I see one crossover for Heidi where her Hartley DNA stops and above and below her, Jim and Lori’s Hartley DNA continues on to the right. To the right of Heidi’s crossover, the only other choice on the paternal side is Frazer, so I’ll add that in.
I have the first crossover identified. It is for Heidi, it is paternal and it is at position 53.5M. I’ll put this into a spreadsheet as it is helpful information to have if you ever do raw data phasing or if you want to add your grandparents to Gedmatch:
[The M for Heidi is wrong. It should be a P.]
I could also infer that the segments above and below the Hartley matches would be Frazer matches. I’ll add those now. If I’m wrong, I can correct them later. However, again, on the paternal side, there are two choices from where the DNA came from.
Adding a Maternal Cousin Match to Chromosome 2
Cousin Anita is a Rathfelder cousin.
It looks like there are few crossovers here. However, the representations of where the relative positions of the matches are can be misleading. I think that I will try assign as many crossovers as I can. Here is what I get from Anita’s matches:
Here is a summary of the crossovers from the first two cousin matches:
I didn’t get a position number for Jim’s crossover as they are not displaying correctly on the spreadsheet.
Next, Check the Gedmatch Comparisons
Here is one issue I see right away:
In the Gedmatch comparison between Heidi and Lori, there is a no match area between Segment H and F in red. The answer appears to be that Heidi has an additional crossover in the area of the L and F maternal crossovers at 103 and 105M. The Heidi crossover should be at about 104, based on the Heidi and Jim (V) comparison:
In Lori’s crossover, she went from Rathfelder to Lentz. In order for Heidi and Lori to continue not matching, Heidi needs to change from Lentz to Rathfelder.
The above gedmatch comparison is Lori compared to Heidi. Between crossovers L and H there is a very short segment where Lori and Heidi are HIR. They don’t match H to L. Then L to H they match on Lentz (green) only. Then Heidi and Lori go back quickly to not matching again.
Cousin Joyce on the Hartley Side
Cousin Joyce has some Hartley segments for the left side of my family’s Chromosome 2:
These matches start at about zero and go to 9M. That is at about the third vertical line above (crossover) belonging to D who is me (Joel). This causes a problem as it goes through Sharon’s crossover. When I look more closely, I see that Sharon’s crossover is at 9M and mine is at 12M:
That means I have to bring back the orange one small segment:
While I was working on this, I made a guess that I (D) had a paternal crossover right after Sharon. I put this into my spreadsheet:
At 7M, I have a crossover for Lori, but I don’t know if it is maternal or paternal yet. I also looked up the last crossover position for Jim at gedmatch.
It looks like Joyce could help clean up the right side of Chromosome 2:
The bottom blue bar is for Heidi and it shows her crossover. Heidi’s crossover is at 226M. Note that I show three crossovers in a row above, but only have two initials. I’ll say that the extra crossover is for Heidi:
The circled areas are in the comparison of Jim (V) to Heidi and Jon (F) to Heidi. Heidi is common in both. I had mentioned in a previous Blog that a change from no match to FIR or from FIR to no match could indicate a crossover for a person on a paternal and maternal side in close succession. That appears to be the case here.
The spreadsheet is important, because the visual part of visual phasing can throw you off. That means that the visuals don’t always line up well, so it is important to depend on the position numbers. This is especially important where the crossovers are close together.
Here are Heidi’s crossovers on the right:
This creates another problem as Heidi’s Lent in Green has to get back to purple Rathfelder on the left, and I don’t have any crossovers for Heidi between the two. This means that either Heidi doesn’t have a crossover on the left or she needs another in the middle. Confused? You bet I am. I’ll worry about this later.
Deciphering the Right End of Chromosome 2 – Paternal Side
Hartley cousin Beth helps figure out the right hand side of the Chromosome. Ends of Chromosomes can be difficult to interpret.
Lori’s match is off by about one half million positions from the other three matches. I don’t know if that is significant. It may indicate a crossover that I don’t have.
Here is how I started to fill in the right hand side of Chromosome 2:
- JIm’s crossover was on the maternal side, so I filled in the rest of his Hartley DNA.
- I show Sharon with a crossover. If she has one, it needs to be on the paternal side.
- This leaves Lori. If her match with Beth is right, then Lori needs another crossover – probably at 239M.
Here is Lori’s crossover:
This shows that Lori’s crossover is right before Jim’s.
Tiny Segments at the Chromosome Ends Are Not That Important
First, thanks Beth. The tiny segments at the end for Sharon and Jim are not that important in practice. However, if you want to fill out your Chromosome Maps it is fun to figure them out. Note Sharon’s small Hartley segment at the right end. This does not show up on the cousin match. It is just too small. If I lowered the thresholds at Gedmatch, it should show.
As my mom would say, “So there”.
Paul’s Frazer DNA
Here I just show the right side of Chromosome 2, where Paul matches my brother and three sisters:
These segments don’t align well, but the numbers show that they are pretty close to each other vertically.
I filled in the Frazer segments and Hartley segments where Paul didn’t match:
Jim likely has a paternal crossover at V. He needs one to match the paternal Frazer at the left.
Cousin Linda’s Maternal Lentz Matches
Linda points out two crossovers on the maternal side:
These are at 222M for me and 228M for Heidi:
I already had Heidi’s crossover listed, but here is mine added.
Gedmatch Sibling Pair Comparisons and Reconciliations
Next, I want to compare my Sibling Chromosome Map with what Gedmatch shows:
For example the comparison between Sharon and Lori shows that they have an FIR that means that Sharon should have Lentz DNA on her maternal side. Lori has two crossovers in a row, so the second should be Frazer to Hartley. Because I am looking for a crossover for Heidi, somewhere in the middle, I’ll fill in the other siblings, but not Heidi:
As I fill in the blanks, I see that I have more problems:
- Looks like Jim (V) needs another crossover. I believe that should be near the third V above.
- Jon has two crossovers, but if I put in Rathfelder in the blank area on Jon’s maternal side, that would solve that.
- Sharon needs to go from Rathfelder (purple) to Lentz (green) but has no crossover.
- Heidi has the same issue.
- Lori has a crossover but no apparent need for one. By looking at the Gedmatch comparisons, the L should be an H and S. This should solve the above two problems.
Jim’s Double V
Here Jim has crossovers on the maternal and paternal side:
These don’t line up that great visually. These two Jim Crossovers are at 191 and 192. I don’t know which crossover is maternal and which is paternal at this point.
Replacing One Lori Crossover with One Sharon and One Heidi Crossover (Or How to Solve Two Problems by Correcting One Crossover)
The problem in doing this is, which Crossover goes first? Here is the Lori Crossover I want to replace:
This shows where they both match with me (D). The Sharon crossover is at 173M and the Heidi crossover is at 172M, so Heidi goes first.
My list of crossovers is getting quite long:
These two crossovers need to be on the maternal side to make the map work. I don’t know if this is right, but it seemed to work:
Some Eye Excercise
This is a side by view of what it is from Gedmatch versus what I came up using the Fox Spreadsheet. I think they agree. All I have to do now is fill in Jim’s double crossover and some small segments on the left hand side of the Chromosome.
Jim’s Double Crossover
This should be easy.
In the little gap between 191 and 192M, Jim has no match with Jon (F), Sharon and Lori.
Jon, Sharon and Lori have a blue/purple combination, so I’ll give Jim a no-matching orange/green combo:
If everything else is right, this just falls into place.
The Left Side of Chromosome 2
This looks really confusing. I have five crossovers in short succession and one not assigned. I could give up now, but I would like to finish this Chromosome and move on to 3-22. First, I took out the unassigned crossover.
I’ve circled all the cases where there is a no match going to an FIR or FIR going to a no match. They include three V’s, three F’s, three H’s and three L’s. I think that means that I need to add an F and H crossover to what I already have. That includes all six siblings. The other question is whether these are all double crossovers. If that is the case, then I could need to add up to five crossovers.
I can start by filling in some paternal side in the first segment:
Next, I need to make use of my spreadsheet.
These are the crossovers I have already. Next, I’ll look for some more position numbers.
Here Jon has a 10.4 crossover. It seems to line up well with his other matches.
Jim and Heidi match here:
That looks to be about the place of Heidi’s crossover.
I’ll start filling out the map based on the above, but I feel like there is at least one double crossover somewhere:
I did a quick segment map check:
The resolution is off, but it looks to be not too bad a comparison.
Could This Be the Map?
I think it looks good for a wrap.
Comparing Chromosome 2 with Previous Analysis
Here is what M MacNeill did for me previously:
This was for three siblings. The interesting par is that this shows DNA that was missing on my father’s side. My mom has been tested, so is missing no DNA. DNA is missing for my paternal grandmother on both ends. DNA is missing for my paternal grandfather in the middle of Chromosome 2.
Now no Hartley DNA is missing (paternal grandfather). Also no paternal grandmother is missing thanks to Jon. He has a full Chromosome 2 of paternal grandmother. This is interesting because Jon also has a full Chromosome 1 of Frazer (paternal grandmother). That’s a lot of Frazer. Let’s say Jon was trying to prove he was related to a Hartley who had huge segments of Hartley DNA on Chromosomes 1 and 2 but nowhere else. Jon would show that he would not be related to this Hartley by DNA.
Summary and Conclusions
- I continued on with the same method I used for Chromosome 1. That was to use cousin matches and to identify crossovers by cousin matches. I map those matches and crossovers and what I can infer from the gedmatch comparisons. I then check the Segment Map to see if it agrees with the gedmatch comparisons.
- I still like using the cousin matches first as it sets the maternal and paternal side right away. The crossovers from the cousin matches seem quite certain and give me a good start on visual phasing.
- I make sure I keep at least the close crossovers in a spreadsheet, so I can know which crossover goes where. Special attention is given to the position numbers as they can give clues to how many crossovers there are.
- At the end of my visual phasing, I was looking for double crossovers, but they were not there.
- For Chromosome 1, I consulted with some of my previous work. For Chromosome 2, I did not look at any previous work I had done or had done for me.
- Finally, I looked at my results compared with previous results.