In this blog, I plan to look at the previous analysis I had done on my Chromosome 1 based on comparing my DNA to my 2 sisters. That was done in atDNA Under the Hood: Segments and Crossovers. I will break that down further using phased results. I have had my mother tested for her autosomal DNA. As a result on gedmatch.com, I have been able to produce 2 kits for each person. Those kits split out the results into the DNA I got from my mom and the DNA I got from my dad.
Recap On My Chromosome 1
Before I wrote my blog, I tried using a technique proposed by Kathy Johnston to show where all my segments had come from. Gedmatch is used to compare 3 siblings. Vertical crossover lines are established and DNA segments from contributing grandparents are established. This was my preblog placement of crossover lines and who they were assigned to using initials.
Note all the close crossover lines on the right side. This was a bit confusing. Here is my first try at assigning those segments to my two sisters and me.
In my blog, I simplified the crossovers a bit.
I came up with these segments.
However, in at least one way, I noted on my Chromosome (J), there was a mistake. I had a large known match with someone that was likely on my Hartley (green) line that went through the short orange segment I had. So I knew that had to be wrong.
Assigning Segments With Phased Results – Paternal Side
As mentioned above, I have 3 phased paternal kits for my 2 sisters and myself. These are based on the testing of my mother. A computer program essentially subtracts out the DNA I got from my mother and assigns the rest of my DNA to my father. I took the 3 paternally phased kits and compared them. So this will represent the precursor to the paternal orange and green segments that I developed (shown above).
See how much simpler this is than comparing the whole DNA with the maternal and paternal side. This shows just the paternal side where the siblings do and do not match each other. Plus this clearly shows that these crossover points are specifically paternal crossover points. Sharon, Heidi and Joel each have 2 of them. This also points out mistakes I made in my previous analysis on the paternal side. Notice the 2 J’s at position 23 and 237. I take this to mean that I have a very large segment from one paternal grandparent in the middle and 2 short ones on the end. I’ll take the results from my previous blog and adjust that accordingly – taking out that tiny segment I already knew was wrong. I also added a ‘P’ after these 2 J’s at the top of these 2 vertical lines to show that they were my paternal crossover points.
Aah, much better. Heidi is matching me between 77 and 205, so I got that right. Remember, I’m just looking at the top half/paternal part of the chromosome at this point. Also I had it right that Sharon and Joel match from 190 to 237. Except I had it as 186. That difference may be from the effect of phasing. Between 19 and 23 all three siblings match. So Sharon’s orange Frazer segment gets moved a little to the left there. Also in the 1st segment, we shouldn’t all match. I had guessed wrong there. Heidi and Joel match, but not Sharon.
Note the following:
- On each paternal line (green and orange) there are 2 paternal cutoff points producing 3 segments
- The original full comparison (maternal and paternal) had 12 crossover points vs. the 6 paternal ones here
- These segments alternate between my 2 paternal grandparents.
- Between the 3 siblings we could match a descendant of my grandmother Frazer’s ancestor at any point except between 186 and 205. Looking up and down at that point, there will be no orange representing Frazer
- On the 3 spreadsheets of matches for these siblings, I can assign with confidence, Frazer ancestor or Hartley ancestor to each of the paternal matches in the regions indicated above. This is a huge step forward in DNA analysis.
At this point, I could go back to the original full comparison and adjust the maternal segments or look at the maternally phased sibling comparisons. I’ll do the latter, to complete the picture.
Assigning Segments With Phased Results – Maternal Side
Here we have 10 maternal crossovers Vs. the 6 previous paternal ones. This is the complicated side. I had trouble assigning crossover points. These should be assigned to people who have 2 changing areas along the vertical line. For example, Sharon gets an ‘S’ for the first vertical line (crossover point) because of the defined segment she has in the comparison between her and Heidi in the first row and her and Joel in the second row. At the first question mark crossover point, there is one change shared by only Heidi and Sharon. Also there is a weird region between 204 and 206. I’ll ignore that section for now. I would like to start on the right, because I have a match with a known Lentz relative there (my maternal mother’s line). The very last segment doesn’t make sense because it shows that Sharon matches Joel and Heidi matches Joel but Sharon doesn’t match Heidi. We’ll ignore that and keep my segments the way they are as they make sense by the original gedmatch full comparison. Moving from the right to the left, the next segment in makes sense. On the third segment from the end, all 3 siblings should have the same maternal grandparent. I’ll have to change that to Lentz for Heidi. So I’ll put a purple section in the middle of my blue Rathfelder grandfather on the bottom right:
As I have mentioned previously, Chromosome 1 should be the hardest to analyze, as it is the longest. If I can get this one right, all the others should be a walk in the park. 160 to 204 is all the same maternally, so that makes sense. What doesn’t make sense is segment 77-160. Again the maternally phased comparison has Sharon matching Joel and Heidi matching Joel but Sharon and Heidi not matching. However, in the original full comparison Heidi and Sharon are opposites and the other matches are half matches, so we’ll stay with what we have. I note this non-sensical sequence 6 times on the maternal side. Not good. Also notice that Heidi has a maternal crossover at 77. Some crossovers for Heidi and others are both maternal and paternal. This appears to be one of them. That means there should be a change from Lentz to Rathfelder here. But when I check the original full comparison, I see that Heidi Vs. Joel should be opposite, so I’m tempted to leave it the way it is here. Hopefully, this will get easier.
Segment 23-40: Here, I need a paternal correction as it shows the same paternal match for all three siblings. In my paternal phased gedmatch comparison, it shows that Sharon and Heidi match from 23-77, but I don’t match either of my sisters paternally. This is fixed by moving my green Hartley segment to the left (J Row).
This gives me even more Hartley segment in green. Next I notice in the 5th segment (40-77) that Heidi to Joel was supposed to be opposite in the full comparison. I can fix this by moving Heidi’s Lentz segment to the left. Talk about tedious.
At any rate, that’s a bit more aesthetically pleasing. Now there’s another problem at 23-40. The original full gedmatch comparison has Sharon to Joel as opposites which is now right, but Sharon to Heidi and Heidi to Joel as half matches and I have them as full. I don’t want to mess with the Sharon-Joel opposite match here, so I’ll skootch the Lentz a little more to the left.
Segment 19-23 – Only 3 more segments to go (hopefully). The full comparison has Sharon and Joel as full matches (FIRs) and the other 2 as half matches. That looks good.
8-19: Sharon to Heidi are opposites and the others are half matches. Giving Sharon a bit more purple will fix that. Plus Sharon has a maternal crossover there, so it makes sense.
Home Stretch. Sharon to Joel needs to be opposite in the first segment. No correction needed here. This is as good as I can get Chromosome 1 right now.
The Frazer DNA Project Connection
Here is where the Richard Frazer Triangulation Group is:
Here was my earlier attempt at chromosome 1 without phased DNA. This was from last week when I was younger and more foolish. It’s off, but not totally.
Summary
- It was a long blog, but who wants short blogs with wrong answers?
- Using phased DNA (paternal and maternal) made the answer more clear, but the process was no easier.
- My paternally phased comparison behaved better than the maternal. However, if you knew my mom, you would understand why.
- It took a combination of the full sibling comparison plus the phased paternal and maternal comparisons plus known relative matches to complete the diagram
- For anyone that matches me or my siblings on Chromosome 1, I should now be able to tell which grandparent they match
- This blog has been approved by the FDA as a cure for insomnia