In my previous Blog, I went back and solved Chromosome 6 which had given me problems.
Chromosome 9
I like seeing the clean palette before any work has been done:
First, I move the vertical lines to match up with changes in the sibling comparisons:
I would like to look at the circled area as it is a confusing area of congested crossovers.
The Congested Crossovers
Here is my detailed analysis of the positions of the changes between siblings between in the congested area:
Here is the sorted version:
I was right to think that a lot was going on. There are six crossovers and possibly seven as there are a lot of V’s for Jim. The last comparison appears to be an anomaly or part of the V crossover. For now, I’ll assume that all the V’s indicate two crossovers – one at about 22M and one at 23.5M. Here is the summary:
Cousin Matches
Next, I’ll look for cousin matches. Initially, I’ll look in the area of congestion that I just focused on. Frazer cousin Emily matches just Jim:
She matches him up to 23.1M which is between the two V crossovers that I had for Jim. The next match is with Frazer cousin Paul:
Neither of these help a lot with the confusing crossover sections. I may be able to work both sides of the congested area into the middle.
Cousin Maury helps fill in some Hartley:
Looking for Maternal Cousin Matches
Rathfelder cousin Catherine gives me one of my maternal crossovers:
Cousin Judith fills in some Lentz DNA:
Lentz Cousin Joan adds some maternal DNA for Jon and suggests a crossover for Jon:
Moment of Truth with the Segment Map
Before I get too far down the road, I would like to check the Segment Map:
This shows I am on the right track.
Next, I’ll solve my second to the last crossover. According to the comparisons, I have an FIR with Lori, so that means a Hartley/Lentz combo. I’ll add that and move my DNA to the left side.
Next, I’m curious as to whether Jim has a double crossover in the congested area:
I can fill in the S-L segment for Jim.
Jim shows opposite to Jon (F) and Joel (D) and the same as Sharon. That means he does have a double crossover in that area as I supposed.
Perhaps I can fill in the rest of the Chromosome now:
Here is the quality check:
It looks like I need some work on the right side.
A Closer Look at the Last Four Crossovers
Here are the last four crossovers:
From the Fox Spreadsheet, I can tell where Lori’s crossover is, but not the other three. Actually, Jon (F) appears to be at 130.6.
One issue that is see is that the VL comparison has an NIR to FIR change which means there is a quick segment of HIR in between the NIR and FIR.
This is what V&L looks like at full resolution:
It looks like there are actually four changes here. There is a small FIR near 130 (based on other comparisons also) and then the transition from NIR to FIR is two changes.
However, if there is an FIR at 130, that would be a double change also (from FIR to HIR to NIR), so that gets confusing.
I was hoping that the detailed analysis would give me easy answers:
This means that if I did this right, there are a lot of crossovers in this area. I had V-F-L-V. By the above, it could be F-V-D-L-D-F-L-L-V. This seems overly complicated.
An FIR at 130M?
The other option is to assume that the green segment at 130M is not an FIR:
A Third Option – Look at the Sibling Comparisons
I think I’ll go this route as it seems easier right now.
First, I’ll try to correct the little VF segment between Jim (V) and Jon (F). I have it as red and it appears to be green in the Gedmatch comparison. It could be that I have the V and F crossovers in the wrong order.
That worked. It makes sense as having two crossovers in the wrong order results in two changes in the F-V segment.
The next area I’m interested in is here:
In segment V-L, Jon is off in his matches to Joel (D) and Sharon, but not to Jim (V), Heidi and Lori. I don’t see how a change would fix this.
Any Help From Hartley Cousin Maury?
Here Maury matches Jim, Joel and Sharon. However, it could be that if I lowered the thresholds at Gedmatch, that Jon would match Maury also.
I took Maury and Jon down to a 2cM threshold and saw no match in the area I am looking at – around 130M. That suggests to me that Jon’s crossover is on the maternal side. When I changed Jon’s crossover to Maternal, that solved segment VL.
Here is the next segment to solve:
Hopefully, this is the last problem. Each mistake is with Jim (V). I think that if I change his crossover from maternal to paternal, that could solve the problem.
It did:
Good News, Bad News
The good news is that the right side of Chromosome 9 appears to be finished. The bad news is that I forgot to finish the left side. I’ll try this as a solution:
I don’t see any obvious errors in the comparison:
Summary and Conclusions
- I may have over-analyzed the right hand side of Chromosome 9. I was seeing a small FIR where there was not. This was remedied by a segment by segment approach to correct mistakes.
- It looked liked I would have saved time by going directly to the segment by segment approach on the right hand side of the Chromosome. Making the Segment Map larger helped in seeing the problems and solutions.
- Sharon has a full Frazer paternal Chromosome 9.
- Heidi has a full Hartley paternal Chromosome 9.
- All four grandparents’ DNA appear to be covered by the six siblings.