My Son’s AncestryDNA Results Are In

I recently got an email saying my son JJ’s DNA results were in. JJ shows this on his main AncestryDNA page:

There is a third box for DNA Circles, but those take a while to form after JJ’s DNA is linked to a tree. Here is how JJ compares to his sister Heather:

Both JJ and Heather come out as mostly England, Wales and Northwestern Europe. However, JJ’s #2 Ethnicity is Eastern Europe and Russia and Heather’s #2 is Germanic Europe. Another thing that stands out is that JJ has about 150 more 4th cousin or closer matches.

JJ and Heather’s Ethnicity

One would think that the ethnicity would come out the same for Heather and JJ as siblings, but it doesn’t. Here is what JJ shows:

JJ shows 3% Baltic within the larger Eastern Europe and Russia.

Heather doesn’t show the 3% Baltic but has 3% France instead:

The overall effect is the same.

JJ and Heather Each Have One SubRegion of England

These are subtle differences. JJ has Yorkshire & Pennines within Northern England and the Midlands:

Heather has the SubRegion of Northern England & the Midlands, but doesn’t have it broken down further like JJ has:

That means that while JJ and Heather both have the subregion: Northern England & the Midlands, JJ has the sub-sub region of Yorkshire & Pennines.

JJ and Heather At Gedmatch Genesis

As siblings, JJ and Heather match each other in a way that they match no one else. Here is how JJ and Heather compare to each other on Chromosomes 19-21:

We each have a male and female copy of our chromosomes. However the results don’t distinguish which is which and combine the two. On the bottom of each chromosome above is a blue or black region. Blue is where JJ and Heather match each other and black is where they don’t match. On the top part, there is either green, red or yellow. Red is where there is no match. The yellow above the blue is called a half match also known as an HIR. The green is called a Fully Identical Region (or FIR).

What Do These Three Regions Mean?

No match means no match. However, a good way to look at this is in terms of grandparents. JJ and Heather got their DNA from their four grandparents: Hartley, Rathfelder, Jarek and Cavanaugh.

  • No Match – An example would be if JJ got his paternal DNA From Hartley and maternal DNA from Jarek in a no match region, that would mean that Heather must have gotten her paternal DNA from Rathfelder and her maternal DNA from Cavanaugh
  • HIR – These regions are a little trickier. This means that if JJ and Heather both got their paternal DNA from Hartley and JJ got his from Jarek, then Heather got her maternal DNA from Cavanaugh in that half matching region.
  • FIR – This means that if JJ got his DNA in this region from Hartley and Jarek, then Heather also would have to have gotten her DNA from Hartley and Jarek.

Visual Phasing for JJ and Heather

Visual Phasing is more difficult for two siblings than for three or more, but let’s try it on Chromosome 19. First I put some information onto a spreadsheet, but it is just a place for phasing:

In the middle no match, I represented the four grandparents as four different colors:

There looks like there may be a tiny match in the middle of the non-match, but I am ignoring that for now.

Cheating on the Rathfelder Side

JJ and Heather’s Rathfelder grandmother has been tested so this should be a big clue. Here is how JJ and Heather match their paternal grandmother:

What does this mean? This means that Heather matches her paternal grandmother on the whole length of the Chromosome. Again, I’m ignoring the non-match in the pink area (called the centromere).

In the chart above, I had Heather’s paternal as blue in the middle region. Let’s call blue Rathfelder.

 

The places where I have the vertical lines in the spreadsheet above correspond the changes in the ways that JJ and Heather match each other. These are called crossovers. That means that at these spots the DNA that they got from one grandparent will cross over to the DNA that they got from another one. These crossovers are either maternal or paternal.

Already, I also know that JJ’s Yellow will be Hartley. That is his only other choice for a paternal grandparent. Next I put the JJ’s Rathfelder DNA in:

Now JJ has two paternal crossovers. His paternal DNA goes from Rathfelder to Hartley and then back to Rathfelder. JJ’s crossover is at 7 Million, because that is where the DNA match with is Rathfelder grandmother stops.

Next, because JJ has a paternal crossover at position 46, that means that he probably doesn’t have a maternal crossover at the same spot. Because of that, I’ll move JJ’s green DNA a little to the left and all the way to the right:

On the right hand side there is a half match. That half match is blue, so the orange can extend to the right on Heather’s maternal side:

Using the same logic for the small segment on the left, I can move the orange a little way to the left:

 

Now I am stuck on the left HIR segment. I don’t know if the maternal crossover goes to Heather or to JJ. If it goes to Heather, then that means that the left maternal segment for JJ will be green. If JJ has the crossover, it will be orange. A maternal cousin match could solve this.

Painting JJ’s Chromosomes

I’ll come back to visual phasing later. Now I’d like to paint JJ’s chromosomes. I had painted Heather’s previously. This shows Heather’s known maternal matches on her Jarek side:

These appear to be four siblings or close relatives. They are not relatives that Heather knows, but relatives with known Jarek ancestors. I could use this information for visual phasing as these chromosomes should be easier to visually phase.

The Same Matches But Matched To JJ

Back To Visual Phasing

JJ has a pretty good match on Chromosome 18, so I’ll try that one next:

Here we have almost the same scenario as in Chromosome 19, except that there is one more crossover on the right. I put in numbers at 9.8 and 53 to give a general idea of where we are. These correspond to where JJ and Heather match each other.

Here is how JJ and Heather’s paternal Rathfelder grandmother match them on Chromosome 18:

This time JJ gets a full dose of Rathfelder DNA.

 

I put in Heather’s Rathfelder DNA also.

Next, I want to visually phase Heather and JJ’s first maternal side DNA. Actually, I phased it on Chromosome 19, but I couldn’t identify it due to lack of DNA matches with known ancestry. Now we can do that. My guess is that green will be Jarek and orange will be Cavanaugh. By eye it looks that way.

JJ’s match with one Jarek descendant goes from 33 to 53.8, so that is the case.

I filled in the yellow Hartley for Heather as it should go up to where Heather matches her Rathfelder grandmother. Now I am stuck, but I have identified a Cavanaugh segment for Heather based on JJ’s Jareck DNA.

Chromosome 4 – Some Cavanaugh DNA for JJ

From DNA Painter, here are JJ’s Jarek DNA matches:

Here are Heather’s Jarek DNA matches:

Heather has extra Jarek matches that JJ doens’t have. That means that JJ probably has Cavanaugh DNA where Heather has her first two Jarek DNA matches.

Unfortunately, Chromosome 4 is longer and will have more crossovers:

This time I’ll start at the FIR. That means that JJ and Heather have the match on the same two grandparents on their paternal and maternal sides. I’ll have to switch the colors to keep them consistent. I said that JJ should be going from Cavanaugh to Jarek:

Here is JJ’s first identified maternal crossover.

Next, I’d like to add in the Rathfelder DNA:

The blue is Rathfelder. The matching segments information is how Heather and JJ match their grandmother. This is the same as the blue Rathfelder segments above. Where there isn’t blue Rathfelder DNA, I have put in yellow Hartley DNA.

Heather’s first Jarek descendant match goes from 85M to 109M:

At this point, I am stuck again:

There is a maternal crossover at 85, but I can’t tell if it belongs to JJ or Heather.

A Spreadsheet For JJ and Heather Using Gedmatch Genesis

At Genesis, I used JJ’s and my own DNA to make two more kits for JJ. One has an M1 designation and one is P1 for maternal and paternal. Genesis has a utility called Segment Search. I’ll use this once for JJ’s maternal matches and once for his paternal matches.

JJ’s Maternal Matches

Here are some of JJ’s maternal matches. I downloaded about 1,000 of them:

I made them pink for maternal. The green matches are the ones over 15 cM. JJ’s largest match above is with Heather. Note that JJ has maternal matches on Chromosome 4 between 80 and 89M. That means that he should not have a maternal crossover at 85M. That means that Heather should have the maternal crossover at 85M. Let’s look at Heather’s maternal results next.

Heather’s Maternal Matches at Genesis

Here are Heather’s Chromosome 4 maternal matches:

Notice that Heather has no matches going through position 85. Actually, Heather has matches going up to 84.3 and then starting again at about the same spot or at 85M. This tells me that Heather has a maternal crossover where I thought.

If I did this right, I should find Cavanaugh ancestor matches for Heather and JJ in their orange areas and Jarek ancestor matches in their green areas of Chromosome 4. Unfortunately, Heather and JJ have small matches in their orange areas which means that the relationships represented by those matches could be quite distant.

Near position 14, there aren’t a lot of matches, so I would be guessing more than usual there as to where the crossover goes. What about the right side of Heather and JJ’s Chromosome 4? First I need to figure out where the crossover is. For that I need to look at how JJ and Heather match each other at full resolution:

Each  ^ is 1M, so the change from all green to more yellow is at about 167.6M. Again, neither JJ nor Heather have good matches in that area, so I can’t tell where their maternal crossover is using that method.

Summary and Conclustions

  • I started looking at JJ’s AncestryDNA test results. I first compared JJ’s ethnicity with what his sister Heather showed. JJ shows a more detailed sub-region in England compared to Heather. JJ shows a Baltic region that Heather doesn’t show and Heather shows a France Region that JJ doesn’t have. The overall effect is the same, but the smaller details vary a bit.
  • I looked at how JJ and Heather compare to eatch other with HIRs, FIRs and no-match areas. Using these, I was able to start to visually phase Heather and JJ. I haven’t been able to identify matches along JJ and Heather’s Cavanaugh maternal grandparent side, so that made the phasing a little more difficult. JJ and Heather’s paternal side is already phased by comparing their results to their Rathfelder grandmother.
  • I downloaded JJ and Heather’s maternal matches from Gedmatch Genesis. Some of these matches were helpful in assigning maternal crossovers for their visual phasing maps.
  • Some other things that I could do would be AutoClustering JJ’s AncestryDNA results, more DNA Painting and more match identification. I would still like to figure out at least one match on JJ or Heather’s Cavanaugh side.

 

 

 

 

 

 

 

Visual Phasing Six Siblings with the Fox Spreadsheet: Part 20: Chromosome 19

I feel like I’m getting near the end of this series. So far, I have been able to solve the first 18 Chromosomes plus the X Chromosome.

Chromosome 19

Here is my first cut at crossover lines assigned to me and my five siblings:

The crossovers seemed straightforward. Actually, I think that there is an additional crossover for Jon (F) at the very end.

Adding Position Numbers to the Crossovers

Next I add the position numbers to the crossovers:

I didn’t have any easy position answer for the first and last crossovers. I could get this from Gedmatch.

Cousin Matches

I hope that I have enough cousin matches to solve Chromosome 19. I need at least one paternal match and one maternal match to solve the Chromosome. It looks like I should have one of each, so that is good. One of the best cousin matches is with Rathfelder cousin Anita:

This is a conservative rendition of her match. Jim, Jon and Sharon will also have Lentz DNA where they do not match Anita (in the area where Anita matches Heidi).

Here is Hartley cousin James’ matches with my family:

This may be enough to solve Chromosome 19:

Note that Jon and Sharon have a HIR for most of the Chromosome:

This is true except for the very ends of the Chromosome where Sharon has a crossover on the left and Jon has one on the right. Here is how that works out:

To be HIR, that means that two siblings have the same DNA from one grandparent and that they have different grandparent DNA on the other side. It turns out that Sharon and Jon share the same Lentz DNA but Jon has Hartley DNA and Sharon has Frazer DNA on the paternal side.

I got this far:

I don’t think that Jon really has a crossover on the right. Here is a close-up of the comparison of Jon (F) and Sharon on the right side of the Chromosome:

Jon and Sharon were HIR for most of the Chromosome. If Jon has a crossover, then their comparison would have to to either FIR or NIR. If this is a NIR, then I should see some red and I don’t. Now, I’m changing my mind back. Perhaps Jon does has a small FIR. If Jon has a Fully Identical Region with Sharon, then he would have a HIR with his other siblings:

 

The F & S comparison looks greener on the end compared to the other F comparisons.

This image doesn’t give enough detail to see the small crossovers, but shows that overall, I had the right idea with the visual phasing:

Summary and Conclusions

  • Heidi had a full Frazer Chromosome.
  • Jon and Sharon both had a full Lentz Chromosome.
  • Jon either had a full Hartley Chromosome or nearly full Hartley Chromosome.
  • I spent some time figuring out whether or not Jon had a crossover near the end. It was a judgement call and amounts to bug dust as it is such a small inconsequential piece of DNA.
  • Anita was our only maternal match, so she was very important for the solving of this Chromosome.

 

 

 

Visual Phasing Six Siblings with the Fox Spreadsheet: Part 18: Chromosome 17

In my last Blog, I looked at Chromosome 15. This is because I took Chromosome 16 out-of-order by mistake. On to Chromosome 17,

Chromosome 17

Here is my first cut:

The first four crossovers are fairly close together. However, Chromosome 17 is much smaller than Chromosome 1. The spreadsheets are all the same width. That means that the spacing is further apart on the higher numbered chromosomes. That makes the crossovers easier to see.

Next, I take a second look and enter the crossover positions in a spreadsheet:

I needed the first four positions during my first look to get the order of the crossovers right.

Cousin Matches

I like this part of the process as it makes things go faster and shows crossovers. Hartley 1st cousin once removed Joyce is the best match for these six siblings:

Joyce’s matches point out two paternal crossovers for Jon and one for Lori. This is what I get for Joyce’s matches:

[Note here that I added orance Hartley on the Lori’s first segment by mistake. This is corrected later in the Blog.]

I didn’t fill in between Lori’s L and L segment. That is because Lori has two crossovers and could go from Hartley to Frazer and back to Hartley again. Sharon and Heidi had only one crossover each and would have needed two to go from Hartley to Frazer to Hartley. As they only had one crossover each, I filled in the gap between the two Hartley areas of DNA with more Hartley DNA. Jim had no crossover in that area, so I was able to fill in his gap with Hartley DNA also.

A Maternal Match

If I have a maternal match, it may be enough to solve the Chromosome. Lentz cousin Judith matches three siblings on the right-hand side of Chromosome 17:

There are not many crossovers, so I can expand the DNA to the right. I also gave Rathfelder DNA to Sharon, Heidi, and Lori on the right as they didn’t match Lentz cousin Judith.

Lori has the most crossover, hence a few blanks. To fill in the blanks I go vertical. That means I go up to where the Gedmatch sibling pair comparisons are. However, before I do that, I take a glance at the Segment Map. It looks like I have at least one mistake. By reviewing my map, I see this:

I missed a crossover for Jim (V) at the pink circle. I was going from right to left, so I’ll erase Jim’s maternal DNA to the left of the circled crossover. I had already added Hartley to the left of the V crossover based on a match with Hartley cousin Joyce. That means that the crossover at the circled area should go from Rathfelder to Lentz going right to left.

I can shrink the Segment Map very small to see that I have fixed the problem:

Going Vertical for Lori

Now I can go above for Lori to fill in her missing DNA with FIRs and NIRs. Here is an issue:

The Jon (F) and Lori comparison has a green FIR at the top of the image above for the first segment. That means that Lori should have Frazer/Lentz DNA, but I have her with Hartley DNA already. I had added that above by mistake. Lori does not match cousin Joyce in that segment and should have Frazer DNA there:

Next, if I have Lori’s paternal side right (which I didn’t before), she should go from Lentz to Rathfelder  and then back to Lentz on her maternal side. Then at the last L crossover above, she would go back to Rathfelder.

On my computer, this is the solution to Chromosome 17 at 40% size:

To quote an old joke, “I thought I made a mistake once, but I was wrong”. I thought I saw an error, but I’m not used to this comparison. When I look more closely the top and bottom of the image above match.

 

My Previous Attempt at Chromosome 17

I first started working on Chromosome 17 in January of 2016. This is what I came up with:

At the time, I was working with three siblings and didn’t have as many cousin matches.

Here is the new analysis. The colors are different and the maternal and paternal are reversed. Not only that, the sibling order is different:

There are also more crossovers in the newer version due to twice as many siblings. However, despite all the differences, the results were the same. It seems a bit ironic that I used the same colors that Fox adopted for his spreadsheet.

Summary and Conclusions

  • I missed one of Jim’s crossovers, but was able to fix it.
  • I wrongly assigned Hartley DNA to Lori, but I was able to find that error and fix it.
  • Jim, Sharon and Heidi have full Hartley DNA on the paternal side of their Chromosome 17.
  • Joel has  a full paternal copy of Frazer.
  • Sharon and Heidi have full Rathfelder maternal copies of Chromosome 17.
  • When looking for Frazer or Hartley matches on Chromosome 17, I know the best people to go to to look for matches.
  • Between all six siblings we recieved the full amount of DNA from our four grandparents.
  • A comparison with an earlier attempt I did at solving Chromsome 17 for three siblings matches with my current results.

 

 

 

 

Visual Phasing Six Siblings with the Fox Spreadsheet: Part 17: Chromosome 15

I went a bit out of order as my last Chromosome solved was Chromosome 16. That just shows how easy it is to make a mistake or get mixed up.

Chromosome 15

On the right, on a separate spreadsheet, I write down the initials and the locations of the crossovers. The three locations in yellow indicate that I am not sure of the order of the crossovers. I was also not sure of the last crossover. However, I have convinced myself that there is one there:

I believe that the last segment is a small HIR in the V & D and the V &L comparisons. This last crossover will go to Jim (V).

Next, I go through the crossovers again and write down the position numbers:

This gives me a second look at the crossovers. I think I have this right now. I am missing the last position number which is not a big deal. I can get it from the full resolution comparison between Jim (V) and Jon (F):

The beginning of the match is at 95.5M. Each ^ is 1M, so the beginning of the FIR (and thus the crossover) is as 99.4.

Cousin Matches

This Chromosome should be easy to solve. Here are matches with Hartley cousin Patricia:

My first match ends at 41.4 while Jon and Lori’s matches end at 43.7M. That seems to indicate a crossover that I didn’t see on the paternal side. However, my match with Hartley cousin Beth clears that up:

Beth shows my match goes way beyond 41.4 to 53.9M. Here is how I fill in paternal DNA based on Beth’s match with me and my siblings:

Here I have assumed that a no-vote for Hartley is a vote for Frazer.

Match with maternal Rathfelder cousin Inese may be enough to solve the Chromosome:

Next, I should be able to finish by extending DNA to the crossovers and comparing the sibling pairs from Gedmatch:

 

However, when I get to the right-hand side, I see that I have done something wrong. The Joel (D) and Lori comparison show an FIR in the next to last segment. However, to do that would require a double crossover for Lori and she only has one. Perhaps the Segment Map will show my mistake:

Here I boxed some areas that are right in the sibling comparison, but wrong in the Segment Map (which represents my Chromosome Map). Interestingly, the first mistake is at V but at the F & D comparison.

The Segment Map pointed out exactly where the problem was. I have a crossover at V which doesn’t make sense. I should only have crossovers at D. I’ll take that V crossover out and carry it over to my next crossover:

After my next crossover, I see I have an FIR with Lori. That means that my crossover has to be on my maternal side (Lentz).

Next I won’t outline all the problems, but I do see one at the top:

This one starts with Jon (F). There should be an FIR, but I have NIR. I can fix this by reversing Jon’s crossover at F. This is confirmed by an FIR between Jon and Heidi:

When I reverse Jon’s crossover, I see that I have corrected the two errors:

Here is what I get for a finished Chromosome 15:

This looks like a match:

Summary and Conclusions

  • Two mistakes were solved by comparing the Segment Map to the Gedmatch sibling pair comparisons.
  • Joel and Lori have recieved a full dose of Hartley on their paternal sides.
  • Sharon has a full dose of Frazer. Jim has 99% Frazer DNA on his paternal side of Chromosome 15.
  • A bit of Rathfelder is missing.
  • So far, it seems like the paternal Hartley and Frazer are the most popular for full Chromosomes. Maternal Rathfelder is least likely to be represented across the chromosome for some reason.  This may have to do with the fact that females tend to have more crossovers than males on average.

 

 

 

 

 

Visual Phasing Six Siblings with the Fox Spreadsheet: Part 16: Chromosome 16

The last two Chromosomes (13 and 14) went well. We will see what is in store for Chromosome 15. Actually, I see that I have been working on Chromosome 16, so I’ll go with that.

Chromosome 16

After a break with the two easy Chromosomes, it looks like I am back to a bit of a challenge:

I have two difficult areas, signified by lack of siblings’ initials.

Cousin Matches – the Easy Way Out

It is my hope that cousin matches will define some of the confusing crossover areas. I’ll start with Hartley cousin Maury:

Maury shows that Jim has a crossover at 72.3 in the second problem area.

 

Once I saw that crossover, it appeared that there was only one other crossover (for S). This is what I get:

Back to Maury

That is what I get out of Maury’s match. I note that the end of Maury’s first match with Lori is at 20.1M and the end of the other matches is at 21.1, so there is a possible crossover for Lori there. I’ll hold off on that for now until I find other information.

Matches with Rathfelder cousin Anita fill in some maternal DNA:

Matches with Lentz cousin Joan give the other side of the maternal coin:

Figuring Out the Two Missing Crossovers with a Detailed Analysis

The first step is to look at the V & H comparison at Gedmatch full resolution:

This gives the positions of the crossovers at 20.4 and 21.6.

The V & L comparison has two very close changes:

This is because Jim (V) and Lori go from NIR and quickly to an FIR with a small FIR in the middle.

Here are the results:

The FD and DL are for the crossover for Joel (D) that I already have. I interpret the other matches to mean that there is a close double crossover for Jim (V). One is at 20.3 and the other is at about 21M.

Expanding Around the Double V Crossover

My next strategy is to work around Jim (V). This is because I’m not totally sure of the two crossovers.

I’ll use the gedmatch sibling comparisons to expand the DNA more:

At this point, I see that Jim (V) and Heidi are NIR in the larger missing segment above. That means that Jim needs to be Hartley /Rathfelder there which agrees with the proposed double crossover for Jim (V).

I don’t know how to fill in the little V-V segment. This would have to be either Frazer/Rathfelder or Hartley/Lentz. If it was Hartley/Lentz, then Jim would be FIR with Jon, Joel and Sharon in that little segment.

Here is Jim and Jon:

Here’s Jim and Joel:

Here’s JIma and Sharon:

The question is: Is there a FIR between about 20.8 and 21.2M? I can’t tell, but I’ll say there is:

 

Basically, it is not a big deal either way, so it’s a judgement call.

Here’s my crossover list:

After working the DNA a bit, I get this:

This comparison between the Segment Map and the Gedmatch sibling chart confirms Chromosome 16

Summary and Conclusions

  • Once the crossovers are accurately identified, it is fairly easy to solve the Chromosome.
  • Lori and Joel got a full dose of Hartley. Heidi got a full dose of Frazer.
  • There is a small segment of Rathfelder DNA missing.

 

 

 

Visual Phasing Six Siblings with the Fox Spreadsheet: Part 6: Chromosome 5

I’ll jump into Chromosome 5. Using the Fox Spreadsheet, I’ll make some potential crossover lines, assign them to people and put the crossover positions into a spreadsheet. As I start to do this, I see an issue already. It looks like I have a crossover near the very beginning of the Chromosome. I can find the position of the crossover by comparing myself with my sister Sharon at a low resolution:

My crossover with Sharon is at position 1.2M:

Here is my first try at assigning crossovers:

I had a bit of trouble figuring out the two crossovers in red:

In my spreadsheet, I called the trouble crossovers F/S and D/H.

Time to Look at Cousin Matches

This is one of my favorite parts of the process. I’ll start with two Hartley cousins. These will show some paternal crossovers:

Actually, they show the same crossover twice for Sharon at either 35.1 or 34.7. This solves the mystery of the first unknown crossover. It belongs to Sharon. I’ll show that on my spreadsheet:

I could tell that that crossover was Sharon’s first crossover as the one in question was at position 35M. Sharon’s next crossover that I had identified was at 39.5M.

Next, I’ll add all the cousin matches to the Chromosome Map:

Adding Maternal Matches

Next I’ll add maternal matches to see how I compare with the Segment Map. Cousin Carolyn on the Lentz side has some good matches:

I can see a maternal crossover for me (Joel) and one for Heidi. Here is a conservative rendition of Carolyn’s Lentz matches:

 

Catherine’s Cousin Matches and Two Inferred Crossovers

Here is how Joel, Sharon and Lori match Catherine on our Rathfelder side. Lori has a match to the left of where Joel and Sharon match Catherine. That implies crossovers for Joel and Sharon. Because there is no overlap between the match and the crossovers, I can’t exactly see the crossovers. However, I do know that both crossovers for Sharon and Joel are on the maternal side which is a big help.

Lori would need two crossovers to go from Rathfelder to Lentz and back to Ratchfelder and I only show one. I’ll assume that the one crossover for Lori on the right hand side of the Chromosome is right for Lori and say that belongs to her paternal side.

Check Your Work

This must be a saying I learned from High School. I have this:

Gedmatch has this:

That is a problem. I’ll add a Frazer match for Jim and then take another look:

The places I circled are D &S and D & L comparisons. The common denominator is me, Joel (D). I’ll fix that by just erasing my segments on the right side of the Chromosome.

Next, I work from the middle of the Chromosome where the DNA agrees with Gedmatch and work to the right:

This is the section to the right of the crossover that I haven’t put a name to yet. I didn’t have some information for Heidi also, so I didn’t fill her in. This looks to check with the segment map:

Next, I’ll fill in Heidi and Joel using the Gemdatch comparisons.

This points out the problem. I need another crossover near Lori’s last crossover. This crossover can be seen here:

The crossover is at the third line – currently for Lori. As I am D, this is clearly a Joel (D) crossover as there is a D in these three comparisons. In order to find the position of my crossover, I have to look at a full resolution image at Gedmatch. I’ll pick my match with Sharon and look around Lori’s crossover which is at 167.5M.

The left side of the bar is at 160M. Each ^ is one M. I’ll say the FIR ends at 167.3 which is right before Lori’s crossover at 167.5. Here is my list of crossovers:

The comparison for the right side should work as I used Gedmatch to produce the map:

Problem solved – for the right side of the Chromosome.

I’ll use the same principle for the left hand side. The unnamed crossover is based on the comparison between Joel and Heidi. I’ll fill in the other four siblings and then fill in Joel and Heidi based on the other four and see what happens.

Here, Heidi does not need a crossover, but I need a maternal one to go from purple to green. Here is my pre-fact checked answer:

The Moment of Truth

This is like comparing your test results to the answer sheet on the right:

Summary and Conclusions

  • I find it helps to work from the known to the unknown. To fix discrepancies, I identify where and who the discrepancy belongs to. I erase those results. I fill in other siblings around the discrepancy. This usually corrects the problem.
  • My brother Jim filled in a lot of missing Frazer DNA. This could be important for Frazer matching.
  • This is the first Chromosome with some missing grandparent DNA. There is a small segment of Rathfelder DNA missing between crossovers H and L or between 55.4 and 61.5M. Fortunately, my mother has been DNA tested, so it isn’t really missing. It was just not passed down to any of her six children.
  • The run of full non-recombinied grandparents continues. This time Jon has a full Hartley paternal Chromosome. Jim has a full Frazer paternal Chromosome. I have heard that males have fewer crossovers than females. This seems to confirm that.
  • My crossover position spreadsheet still comes in handy – especially for the crossovers that are close to each other.
  • I used the Gedmatch full resolution chromosome browser to find one close crossover and one crossover very near the beginning of the Chromosome.

Visual Phasing Six Siblings with the Fox Spreadsheet: Part 5A: Chromosome 4

I’m working on Visually Phasing myself and my five siblings. In my previous Blog, I took Chromosome 20 out of order. Now I am back on track.

Setting the Boundaries for Chromosome 4

First I look for crossovers and try to assign a person to the crossover.

I do the best I can, but will likely need some adjustments as I go along. For this Chromosome, I made a chart to keep track of the crossovers:

Here I had problems at positions 21.4 and 40.

Both these problem areas were in the comparison between Jim (V) and Lori. It didn’t seem like the ends of their first two matches lined up with changes in the other sibling comparisons. Undaunted, I shall continue. If I do everything else right, this will sort itself out.

Adding Cousin Matches

As I look down the cousin matches that I have in the Fox Spreadsheet, I see that I only have Hartley matches on the paternal side. I don’t see any maternal side matches. I can speed things up by looking at three Hartley cousin matches at once:

I have circled crossovers for (left to right) Joel, Jim, Heidi, Jim and Lori. The first crossover for Jim erases a question mark I had. I can see Jim’s crossover now zig zagging accross the ? Line:

Jim’s crossover as shown by match with Hartley cousin Maury is interesting:

This shows that I need another crossover for Jim (V) or my Joel (D) crossover is wrong. Jim’s crossover is at 114.3M. I had my Joel crossover at 114.6M. I’ll say that they are separate crossovers. That means I solved a problem I knew I had and solved one I didn’t know I had. That leaves one other known problem.

Adding Paternal DNA to Chromosome 4

Based on the three Hartley cousin matches above, I get this:

I would put in Frazer to either side of the Hartley crossovers and above and below the orange segments.

In Need of Maternal Cousin Matches

Seven out of seventeen of the cousin matches that I brought into the Fox spreadsheet are maternal. Time to search for more. I searched around on my mom’s one to many list at Gedmatch and found one match with Lentz cousin Joshua:

Chances are my mom sent down some of this Lentz DNA to at least one of her six children:

My mom’s segment only made it down to Heidi.

Add Joshua to the Fox Spreadsheet

Joshua is helpful, so I’ll add him to the Fox Spreadsheet. I went to the first tab and typed in his information at the bottom of the CousinTable:

Note that there is no box to the left of Joshua which means that he has not been incorporated into the Fox Spreadsheet yet. Under the Action drop-down menu, there is a place for Add which I assume is appropriate. The leads me to type in my Gedmatch password. This opens Internet Explorer and compares Joshua to me and my six siblings automatically. Joshua may be a help for other chromosomes, but he is critical for Chromosome 4.

I had missed a Jim (V) crossover near the beginning of this Joshua match, so I added that in. Then I added Joshua’s Lentz shared DNA on Heidi’s maternal Chromosome 4 segment. Next, I filled in some Rathfelder DNA:

  • Jim did not have his first crossover above on the paternal side, so it must be on the maternal side
  • Jim’s second crossover was on the paternal side so the maternal purple Rathfelder will carry through there.
  • I didn’t carry the Rathfelder to the right on my maternal chromosome as I have a crossover there.

I’ll make other similar assumptions:

Thanks to one little match between Joshua and Heidi, I have the middle of Chromosome 4 mapped. I stopped extending to the left as I have a question mark there.

Checking the Segment Map

Before I go on, I’d like to know if this part is right:

Here I have the images reversed. The left side represents the mapping I did. I want it to match the right side. The Gedmatch comparisons are on the right. The two sides look to match.

Chromosome 4 Right Side

I’ll continue on to the right, as I have no question mark on that side:

Jim, Heidi and Lori had no crossovers to the right, so I continued their segments to the right unchanged. Sharon and Heidi have a FIR. That means I can copy Heidi’s DNA to Sharon’s. That puts Sharon’s crossover on the paternal side. I have three crossovers.

I finished Sharon’s right hand side. She had another crossover before the end. After that she had an FIR with Lori which put Sharon’s last crossover on her maternal side.

I have FIRs with Heidi and Sharon in my first unmapped segment. That puts my first crossover on my maternal side:

I am opposite of Heidi on the right:

For the last segment, I match my brother Jim (V):

So close:

At this point, I would like to work the left side back to the question mark. I will also stay away from Lori and Jim as that is where the issue of the question mark was:

Progress Check

This tells me I am on the right track:

I’ll fill in from the left to right:

This is interesting as the top row shows that Jim needs another crossover. It also appears that there will be a Jim maternal crossover where the question mark is. Lori already has a crossover to get her from Lentz to Rathfelder.

Adding JIm’s First Crossover

Jim’s first crossover is at 6.4M which is right after Sharon’s at 6M:

This gets us to a small segment for Lori at the beginning. However, I note that Heidi and Lori don’t match in the Gedmatch comparison. That puts Lori’s first crossover on her paternal side. I’m hoping this fully filled out Chromosome 20 will be the right answer:

The Final Fact-Checker

It’s difficult to see every tiny comparison at once, but this looks overall OK.

Summary and Conclusions

  • The maternal part of this map would not have been possible without one match between Heidi and Joshua. He is my 2nd cousin twice removed. I would have had to have put in just maternal grandparents one and two.
  • So far every chromosome has had one sibling  who has inherited a a full the length of the chromosome from one grandparent. These are cases where recombination does not take place. On this Chromosome, Jon has all Frazer on his paternal side. He appears to have the record for non-recombined Frazer DNA.
  • I tried to work the areas that I was more sure of first and then the unsure areas solved themselves with the good areas that were confirmed by the Segment Map from the Fox Spreadsheet.
  • I used a spreadsheet of crossover positions for each sibling to keep these straight and in the correct order.

 

 

 

 

 

 

Visual Phasing Six Siblings with the Fox Spreadsheet: Part 5 – Taking Chromosome 20 Out of Order

I’m taking Chromosome 20 out of order. This one has been a problem Chromosome in the past in that I have had so many matches. And they have all seemed to triangulate. Blaine Bettinger had a recent poll on Facebook on how many new matches people had at Gedmatch. I had 41, but my largest new match was on Chromosome 20. My previous free-hand mapping showed this:

However, my match spreadsheet seemed indicate I had Hartley DNA at the start of my Chromosome where the new match was:

Putting the Fox Spreadsheet to Work

I start with a blank slate on the Chromosome 20 tab and quickly go to the ‘all cousins’ option at the bottom left. I like this option as I can go from the known to the unknown. I’ll start with the first Hartley cousin on my list – Joyce. This view will immediately point out crossovers for five siblings:

From this, it already appears that I either have no Hartley DNA at the beginning of the Chromosome or very little. Certainly not between 2 and 10M where Jon has Hartley DNA. I have circled crossovers for all siblings except for Lori. Based on my old mapping, Lori had all Frazer DNA on her paternal side of Chromosome 20.

Setting the Crossover Lines

I forgot to do this first. I made some lines, though I may have missed a few and they didn’t all line up perfectly:

Above, I put in orange Hartley above for Joyce’s Hartley matches in blue on the lower half of the image. Then on the other side of the Hartley crossovers, I put in Frazer as that is the only choice on the paternal side. Above and below where there was no Hartley match, I also put in Frazer. I’ve mapped quite a bit of the paternal side already. However, some quality control will be needed.

Maternal Lentz Cousin Carolyn Mapped

Carolyn’s match ends at 56.2M. Jon’s crossover is at about the same place, so I shouldn’t go past that crossover. I’ll add in Rathfelder above and below where there are no Lentz matches:

Next, I’ll carry some of these matches to the left and right based on the crossovers that I have:

Here I have a problem already. Lori is on the bottom row above. She shows a crossover, but no changes in her maternal or paternal side DNA.

Quality Check with the Segment Map

This shows I am off:

I went back and erased the extra maternal DNA I mapped. Then I focused on the sections from V to F:

Obviously the comparisons with Lori (L) in them were wrong. Next, I compared Lori with Joyce and Carolyn at Gedmatch and got this match with Carolyn:

This second match is right at Lori’s crossover: 53.7M. I take that to be more than a coincidence:

This solves the problem at Lori’s crossover.

Next, I’ll extend all siblings over to the right except for Jim and Jon – as they have crossovers to the right:

A glance at the segment map compared to the Gedmatch comparisons seems to show I am on the right track. Then I filled in JIm and Jon based on the Gedmatch comparisons:

Here is the check. It shows that the right side of Chromosome 20 was mapped correctly.

Finishing the Left Hand Side of Chromosome 20

The above represents the right hand side of Chromsome 20 for the six siblings. Next, I can either go with the Gedmatch comparisons or look at more cousin matches. I’ll try cousin matches. Judith is another Lentz relative:

The blue lines don’t line up well, so it is best to look at the match numbers. Judith matches Sharon up to position 6.6M. She matches the others up to 8.4M. That means Sharon has a crossover from Lentz to Rathfelder at 6.6M.

That brings up a potential problem as I had it that Sharon had another crossover between purple and purple. However, as I look at the Gedmatch comparisons again, I see that the Sharon crossover should be a Lori (L) crossover. I’ll change this and try filling in the rest:

I got this far, but didn’t finish filling in Jim (V). He has three crossovers in the blank area and I only have need for two. If all the other segments are right, I can fill in Jim’s missing segments using the Gedmatch comparisons. Now I have it down to here:

[Note: In review, I see that here I should have just carried the Lentz through the first V crossover to the second V crossover. That would have saved time and made the corrections below unneccessary.]

That corresponds with these comparisons:

V&S is FIR, that would put Rathfelder in the narrow segment for Jim. That would mean that Jim (V) has no crossover after L. That gives me this:

Just looking at this, I see a mistake on Lori’s maternal bottom Chromosome 20. She goes from Lentz (green) to purple Rathfelder on Jim’s crossover, so I need to fix that. Next, I’ll do a final quality check:

This shows I still have Jim’s outlined segments wrong. That’s all right, because Jim is the last DNA tested sibling. I want to get his right. By Gedmatch, V-L should be all HIR. I have four no matches and one FIR. I see that there is a problem on the left side of the boxed area. I have green to red and red to green with no transition. There has to be a small HIR between a red no match and a green FIR. The other issue is here:

I show Jim having a double transition with only one transition or crossover line. I know from Jim’s match with Joyce that his crossover should be on the paternal top side. That means that there should not be a maternal change at V above. It also means that I should not have taken out the other Jim (V) crossover.

The Final Answer for Chromosome 20?

These two images below should now agree:

Summary and Conclusions

  • I was able to map Chromosome 20 using the Fox Spreadsheet after a few corrections.
  • It is easy to make mistakes with all the crossovers and segments.
  • Each of the four grandparents are fully covered between the six siblings.
  • I (Joel) have a full maternal Chromosome 20 of Lentz and no Rathfelder on Chromosome 20.
  • The comparisons don’t always line up visually. You have to look at the actual position numbers.
  • I was able to confirm earlier mapping I had done.
  • Using the Steven Fox Segment Map helps to correct any mistakes that I may have made.

 

 

 

 

 

 

 

Visual Phasing Six Siblings with the Fox Spreadsheet: Part 4 – Chromosome 3

I’m ready to start visual phasing of Chromosome 3.

I’ll start with some rough crossover lines:

I try to look at the crossovers and names at the same time to make sure I have enough crossovers. One unusual thing is that on the right hand side, I have five crossovers for Jon (F) in relatively close proximity.

Putting Cousins on the Map

Next I look at the All Cousins function on the Fox Spreadsheet. The first best candidate is James, my father’s cousin. I’ll put some Hartley paternal grandfather DNA in the slots where James matches my family.

Here’s something I want to keep on top of. The right hand side of the matches (in blue) is wandering on each side of a crossover line. I need to start my crossover spreadsheet to keep track of where these crossovers are.

This shows that the Jim (V) crossover is at 39.8 and the Hartley cousin match goes up to 38.6, so we are OK to put Hartley up to the Jim crossover.

The three paternal crossovers on the left fell right into the spots that I had predicted, so I’m off to a good start.

Maternal Cousin Carolyn

Carolyn matches our family on our Lentz grandparent side. Here is my grandmother, speaking of Lentz:

She was born in 1900.

I started mapping Lentz DNA, but ran into a question on the right hand side of Chromosome 3:

Actually I may all right, as I show a crossover for Joel and Sharon on the very right and that is consistent with our match with Carolyn. Here is what Gedmatch -shows for Carolyn:

The right-hand crossovers for Sharon and Joel are really close. Sharon is at 195.80 and Joel’s crossover is at 195.82. I can go with these numbers, but I’ll have to change the crossover order. It also look like, from Gedmatch, that Jon has a crossover at 186M. I’ll write this into my spreadsheet:

Here is how the right hand side of Chromosome 3 mapped out:

Checking out the position numbers at Gedmatch helped me find the crossover for Jon (F).

This is what I get from looking at the first two cousin matches:

Rathfelder Line Cousin Inese

Inese is from Latvia. Here are her matches with my family:

Inese is picking up maternal crossovers for Joel and Lori:

Inese’s matches do not span the crossovers but the two crossovers are implied by the crossover lines above.

Joyce – Another Hartley Match

Here I add in some more orange Hartley based on Joyce’s matches:

Emily – A Frazer Side Match

Here the paternal Frazer match goes through a Lori crossover. That means Lori’s first crossover must be maternal.

I checked a few more cousins and came up with this:

What’s Next? Gedmatch Comparisons

Next, it would make sense to look at the FIRs at Gedmatch and the no-match sibling comparisons, to fill in some blanks above. I did that plus I extended the DNA to the easy looking crossovers. That means the crossovers I wasn’t expecting problems with.

I filled in all but this area on the right hand side of Chromosome 3:

This looks right for Jon as he has two crossovers in this area. However, I have none. I need to add one in there. At the top of the image above, it shows that the comparison between Heidi and Joel (D) shows no match on either side of the Chromosome in that little segment. That means that I would be Frazer (blue) and Lentz (green). That means that my crossover should be near Jon’s first F.

I need to look around 160.9 for my crossover.

This could be it at 156.7:

Here’s some more information from Gedmatch:

The first circled match is my match with Heidi and the next two circled matches are between me and Lori and Jim. I’ll call my crossover 156.2.

Here, I’ve added my paternal crossover:

Placing Jon’s Two Sequential Crossovers in the Right Order

Next, I’m curious as to Jon’s (F) two crossovers. Which is maternal and which is paternal? I ran Jon against 5 siblings and two maternal first cousins and got this:

#6 is Cousin Cindy. My guess is that her match is the maternal crossover for Jon (F). This is at 165.7M which is where I had Jon’s second crossover:

Of course, that makes Jon’s preceding crossover at 160.9M paternal:

Comparing My Work to Gedmatch with the Segment Map

I don’t see any obvious errors. The places on the right that are small and yellow indicate small HIR matches that didn’t show as blue matches on the left because the resolution was not low enough. Here is one example:

That was relatively painless. I tried to be careful with my work, so I wouldn’t have to fix a lot of things later.

The Final Result

I forgot to show my results:

 

This is the first time my brother Jim’s Chromosome 3 has been phased. I don’t think that I had phased Lori before on the Chromosome either. This time, Jim and Lori have full paternal side Frazer Chromosomes. That’s good for the Frazer DNA Project I am working on. Between the six siblings, there is full coverage for all the grandparents. Without Jim and Lori in the mix, I would be missing a lot of Frazer DNA on Chromosome 3.

Summary and Conclusions

  • I tried to be more methodical with my work this time and plan ahead for areas that could cause problems
  • One problem area is nailing down crossovers that are near other crossovers. A spreadsheet giving the position number of the crossovers helps.
  • I used a first cousin maternal match to find a maternal crossover for Jon. This was necessary because Jon had two crossovers in a row.
  • As in all Chromosome Maps, this information should be helpful in finding matches along one of four grandparent lines.

Visual Phasing Six Siblings with the Fox Spreadsheet: Part 3 – Chromosome 2

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.