I need an easy Chromosome after Chromosome 9.
Chromosome 10
Here is my first shot at crossover lines:
I have crossovers very near the beginning and end of Chromosome 10. The D-D-H-V crossovers near the right end are a little confusing – partly due to the misalignment of the changes below. If I get stuck, I’ll go back and take a closer look at those crossovers.
A Dose of Hartley DNA – Thanks to Joyce
I can see based on Joyce’s paternal Hartley matches that I need to add a paternal crossover for my brother Jim (V):
The above has the crossovers for Jim and Lori, but not for JIm. Here is where I go to my supplementary spreadsheet to keep track of the crossover positions:
Now I can add in Joyce’s Hartley DNA to my map:
While adding Joyce’s results, I had some questions on the circled crossovers.
The crossovers of S and D do not match up will with some of the changes, so I would like to do a more detailed analysis at around 30.5M on the Chromosome. When I look up all the changes and sort the positions, the results are clear:
The crossover I had as S should be V. Here is the full resolution comparison between V and D:
The small red line at about 30.5M indicates how close the V and D crossovers are on either sides of the red line. I’ll say V is 30.4 and D is at 30.5.
A match with Frazer cousin Paul gives Jon a paternal crossover:
Maternal Lentz Cousin Carolyn
Carolyn adds a lot of green Lentz to the map:
Jim’s crossover is implied by his lack of Lentz match after his V crossover. I added a maternal crossover for Lori at the beginning, but I will need to check it later for accuracy.
Ready to Fill in the Blanks
I’m ready to give a shot at filling in the blanks:
I moved the DNA from left to right to each siblings’ crossover. Next, I’ll check the Segment Map.
The Segment Map shows some disparities which I have highlighted in pink. The problems start at the close-together D-S-L-V crossovers.
D-S-L-V High Resolution Analysis
I’ll use Gedmatch to look at this area of the Chromosome between 56 and 61M. Here are the results of my analysis:
The bottom line is that I don’t see the V crossover. D is the clearest. S gets three votes between 59.1 and 59.9. Then L gets three votes between 60.8 and 61.1. The last column shows the difference from the previous position. The 0.9M indicates a likely break.
But What About Jim’s Match with Joyce?
Above, I showed a crossover based on Jim’s match with Joyce. Here is how Joyce matches my siblings and me on Chromosome 10:
This would indicate that I have the right crossovers, but that I could switch Jim and Lori.
Segment By Segment Analysis
In my previous Blog, when I got stuck, I used the segment by segment analysis. Here I have picked up the resolution of the Segment Map for easier comparison:
Perhaps pink isn’t the best color, but this points out the problem is with me (Joel -D). The comparisons between me and JIm (V), Jon (F), Sharon, Heidi and Lori are off by one change. Theoretically, that would be fixed if I took out the crossover that I (Joel) have or add a crossover. Seeing as my 56.6M crossover is super-clear, perhaps I need to add a crossover:
In this scenario, both Jim (V) and I (Joel-D) have two comparison changes in common plus our match with each other. If I take the average of the position changes that I have with Jim, Sharon and Lori, I get 60.1M. Or perhaps I don’t need this at all. I just looked at the map and see this:
I show a crossover at D, but no change on my Joel Chromosome. So that must be the error. When I moved the DNA to the right above, I moved it through my own (Joel) crossover. That was a mistake.
Fixing the Mistake
There are bound to be mistakes. I’ll pull back my DNA to my D crossover:
Based on the sibling comparisons, I am opposite to Heidi in segment L-F:
That means that my crossover is on my maternal side.
Now that I have agreement between the Segment map and Gedmatch comparisons, I can continue on solving the Chromosome:
On the right-hand side, I wasn’t so sure of the crossovers D, D, H and V, so I’ll look up those positions at Gedmatch.
Detailed Analysis Around 120M of Chromosome 10
When I looked up the position numbers of the changes for the sibling comparisons and sorted them by positions, I got this:
Here I clearly have crossovers for D, D, L and V. Notice that H has two possible crossovers in two locations. I think that these are valid, because I ignored two FIRs. Here is one of the FIRs for the F & H comparison:
This starts at 119 and ends at 121.5. Those are the areas of the two H crossovers above. The S & H comparison should show the same thing:
That means that instead of D, D, H, V crossovers, I have D, H, D, H, L, and V crossovers.
The two inserted crossovers look like this on the Chromosome Map:
I would like to solve the large next to last segment first and work back. However, it seems like the Jim, Jon and Sharon comparisons with Joel, Heidi and Lori are all HIRs. That means that these cannot be determined. However, I had erased some of the cousin matches. I need to add them back in:
James is a paternal Hartley cousin. This shows Heidi and Lori’s paternal crossovers as well as one I already had for Jim. James’ match with Heidi starts at 121.3. That is her second crossover:
That means Heidi’s first crossover must be maternal:
With that information, I can fill in up to here:
I interpret the green at the right end of the Jim and Heidi comparison as an FIR:
This is at about 135.1M.
Meanwhile Jon (F) and Joel (D) have a FIR for Joel’s first blank segment:
The FIR appears to go further, but the position numbers say otherwise. I would solve the rest like this:
Here is the hopefully correctly solved Chromosome 10:
Checking the Segment Map
This looks right.
Summary and Conclusions
- The detailed analysis got me out of trouble in this Chromosome. I recommend using this method in any area where there are questions on close crossovers or the alignment of changes between siblings is not good.
- Mistakes are inevitable. I made one mistake here that slowed me down.
- If I mapped Lori right, she is almost all Lentz on her maternal side except for a tiny segment of Rathfelder at the beginning of the Chromosome.
- Frazer, Lentz, and Hartley DNA are covered. For some reason, Rathfelder DNA has been missing in more than one Chromosome. Fortunately, my DNA-tested mother can fill in the details.
- There are 21 crossover here and if I count right, 22 in the previous Chromosome 9. That means that the number of crossovers are going down as they are supposed to as we get to the shorter chromosomes.
- I should be about halfway done mapping the six siblings’ DNA as I’ve already mapped the X Chromosome and the chromosomes are getting smaller.