Category: DNA General

I’m trying to visually phase my DNA as well as five other siblings’ DNA. It is taking a while.

Chromosome 13

Here is a quick try at crossovers. I didn’t see any obvious problem areas. If I did these crossovers right, then Joel (D) and Heidi don’t have any crossovers. None of the crossovers are too bunched up. I predict an easy solve.

Bring On the Cousins

I am seeing huge amounts of Hartley DNA in my first three cousin matches.

These point out three paternal crossovers. One is for Sharon and two are for Lori:

It seems safe to map out all the paternal DNA based on these three Hartley matches. The one exception is Jim’s (V) last segment as that is quite small.

Next, Carolyn is a Lentz (maternal) cousin. Based on her matches, I’ll make an attempt at finishing the Chromosome:

If I have this right, this could be the fastest Chromosome mapped yet. However, I see a mistake already. The person I mapped was actually Catherine who is a Rathfelder cousin, not Lentz.

I think that fixed it.

Note above that Joel (D) and Heidi both had full Hartley/Rathfelder Chromosomes. As a result, they have full D and H comparison FIRs (all green).

Summary and Conclusions

• Solving this Chromosome took under an hour – including the time to write this Blog. That makes Chromosome 13, the lucky one.
• All four grandparents’ DNA is covered except for a small segment of Frazer on the right-hand side of Chromosome 13
• As with all chromosomes, I can use this information to fill in a grandparent column on each of these six siblings’ match spreadsheet.

 

 

 

Here is Chromosome 12 from the Fox Spreadsheet:

I have made a guess at placing crossovers and assigning them to my siblings and me. In fact, in places, I am quite sure these crossovers are not right.

Cousin Matches Ferret Out Crossovers

Here are some matches with Hartley cousin Joyce:

These matches represent a paternal crossovers for Jon at 106.7 and Heidi at 75M.

I expect that Joel, Sharon and Lori will also have Frazer DNA in this area. I also note that I have not given Jim any crossovers. If this holds true, he will have full chromosomes of one grandparent on the maternal and paternal sides.

Here’s some more Hartley DNA from my father’s first cousin Maury:

When I compare Maury’s match to me compared to the crossover positions I have, I see that I have the D and F crossover lines backwards:

I gave myself (Joel) a big dose of Frazer after the Hartley crossover.

Matches with Frazer cousin Gladys give crossovers to Lori and Heidi:

Maternal Cousins – A Problem Have I

Unfortunately, I have imported 8 maternal cousins into the Fox Spreadsheet and none of them match me or my 5 siblings on Chromoosme 12. What to do? I can go further down the list.

Rathfelder Cousin Otis

Otis matches on my Rathfelder side. Here is his match with me and my siblings on Chromosome 12:

So not only does he match, but he points out two crossovers: Joel at 46.4 and Lori and 45.4M. Thanks to Otis, I get this:

Frazer Cousin Paul and Lori

Here we see a few things. I forgot to add Sharon’s Frazer DNA. The other thing is that Frazer DNA goes by Jon and Lori’s crossovers. That means that their crossovers need to be on their maternal sides.

Checking the All-Important Segment Map

The Segment Map compared to the Gedmatch sibling pairings keep me on track:

Filling in the Left Side of Chromosome 12

If the crossovers are correct on the left side of Chromosome 12, I’ll be able to fill that side in with no problem.

I don’t show Sharon or Jim with crossovers. I moved Sharon’s DNA to the left. However, I see a problem already as Sharon and Lori are FIR in the first section. That means that if Sharon’s first segment is right, Lori should also have Frazer and Rathfelder DNA. However, Lori shows a crossover which would indicate a change going left from her already Frazer/Rathfelder DNA.

I’m not reallys sure of the DLFD area, so I’ll take a detailed look.

Detailed Look at the DLFD Crossover Area of Chromosome 12

The V & S comparison shows a change at 16.8M, but I don’t show a crossover for V or S:

Before I looked at this in a more detailed way, I have a few observations:

I don’t see changes for L. I do see that V has two changes at 16.8M. This may be the difference. Another thing I see is that there doesn’t appear to be a need for the first D crossover. I’ll take that out.

I’m trying to avoid the detailed analysis, so I’ll see how this works out:

Here is the all-important comparison:

A Problem with Crossovers at 111M

I had a problem figuring out things around S, L, and H on the right-hand side of Chromosome 12:

The changes don’t align well. Also there is a change between V & D at 111.6M, but no crossover for V or D. That means that I should start at 111M and go up to 118 in my analysis:

By just looking at the Jim (V) comparisons, it appears that the S crossover should be a V and that the H and L may be right. But I need to continue on. The final sibling comparison that I do is here between Heidi and Lori:

This shows an NIR going to an FIR. That means that there must be a small HIR between the NIR and FIR. Here is the close-up version at Gedmatch:

This shows two changes between about 117.3 and 117.7.

After I look up all the comparisons, I sort by position number:

Unfortunately, the results are not as definitive as I would have liked. The F at the top was not in question. The last L and H seem clear. The other crossovers are probably V and S.  L and H are not needed in the first unboxed areas, as they are already combined with either V’s or S’s.

Here is my interpretation of the above analysis:

Here, I erased Jim’s Lentz DNA on the right as I have him with a crossover now. I’ll try solving the Chromosome with my new crossover arrangement:

The comparison looks about right:

However, if I look too long, I get eye fatigue.

Summary and Conclusions

• The problem areas for the crossovers were where I thought that they would be.
• I was able to solve one problem area without doing a full detailed analysis.
• Solving these Chromosomes mostly comes down to solving the problem areas. These are where the crossovers are close and difficult to determine.
• Jim, who was the last sibling to have his DNA tested, had all Hartley DNA on his paternal side. This is important as the other siblings were missing Hartley DNA in a large section of the Chromosome.
• This Chromosome has full coverage for all four grandparents.

 

 

 

 

 

 

 

In my previous Blog, I was hoping for and easier Chromosome to visually phase. I don’t think that Chromosome 10 was more difficult than Chromosome 9, but a mistake I made gave me some problems.

Chromosome 11

Here is a first shot at drawing DNA lines.

The first line is for me (Joel – D). This will be where I have a change in DNA. The next three lines were confusing, so I’ll wait to figure those out. I put my original findings into a spreadsheet:

I need the spreadsheet to keep track of the locations of the changes. The yellow parts and the question marks are areas that need work or further analysis. Some of these area may be more clear once I look at our cousin matches.

Cousin Matches

Cousin Maury on my Hartley side gives two crossovers, in an area where I was confused:

This shows that Jim (V) has a crossover at 16.9M and Heidi has one at 17.5M. This saves me some time. I’ll give the third question mark to Jim (V). Jim has changes in his five sibling comparisons. These can be seen in the first five comparisons below:

Next, I find a crossover I missed for Joel (D) thanks to matches with Hartley cousin Joyce:

This crossover is at 77.4. This describes another confusing area that I had noted on my spreadsheet:

I’ll replace the ? with a D at 77.4.

Hartley cousin James has some huge matches with me and my siblings on Chromosome 11:

I could have inferred more Frazer DNA from the Hartley matches, but I haven’t added them in yet. For example, Jim will have a lot of Frazer DNA as he doesn’t match James on the Hartley side. I have already filled in all of Heidi’s paternal Chromosome 11 with these three Hartley matches.

Inese adds in some Rathfelder DNA:

Here I made a few assumptions. I assumed that I had the right crossovers. I assumed where the paternal side DNA went through a crossover, that the crossover belonged to the maternal side. In doing this, I completed Lori’s Chromosome 11. However, I have not checked the work.

Next I’ll look at Lentz cousin Judith:

 

While looking at this match, it appeared that I had a crossover for Jon in this area that didn’t belong, so I took it out. I have the H crossover at 122.3. That means that Judith’s matches start before the H crossover which is at about 122.8

However, I added Lentz DNA in for Heidi at that location. She needs Lentz DNA there due to her crossover. My assumption is that due to her crossover, her match with Judith went below the reportable level of 7cM. This should be easy to check:

This is Judith’s matching with Sharon, Jon, Jim, Heidi (#4), Lori and Joel. The pink match with Lori appears to be a false match.

Checking the Segment Map for Peace of Mind

I’ve gone a way without checking the Segment Map. Here is the comparison between the Segment Map and the Gedmatch sibling comparisons:

This is a bit of an eye workout. I put purple around what appears to be the problem areas. This area starts with a Heidi crossover. The three problem areas have Lori in common. The positions are around 120 to 122M.

Detailed Analysis

Before I do a detailed analysis, I’ll do a semi-detailed analysis:

These are the sibling pairs where I am seeing the changes. It seems like there are a lot of H’s and L’s. It could be that I will need to add another L crossover. That would also be consistent with the mistakes that I outlined in purple above. Without even finishing my detailed analysis, I can see what is going on:

V, F and D are each matching with H once and L twice. That means that H has one crossover and L has two. I finished the analysis and sorted by position:

I had taken out an F crossover above that should have been an L crossover. Here is the production update:

Here is the revised Segment Map/Gedmatch comparison:

This shows that I am back on track.

Next, I’ll try to solve the Chromosome:

This needs to be checked:

This looks OK.

Summary and Conclusions

• There is a segment of Lentz DNA missing from the first third of Chromosome 11.
• There is a bit of Rathfelder missing from a small middle segment. Both of these can be filled in with DNA from my mother.
• There is a tiny bit of Frazer DNA missing from the next to the last paternal segment.
• Large matches from my father’s three first cousins were helpful in solving this Chromosome.
• I was able to see where the extra needed Lori crossover came in before finishing my detailed analysis.

 

 

 

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.

 

 

 

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.

 

 

 

 

I had tried to solve Chromsome 6 previously, but had problems. Since then, I have solved Chromosome 7 and 8 for my 5 siblings and myself. I tried being more analytical in listing all the changes in problem areas for crossovers. I hope that using that same technique for Chromosome 6 will solve this Chromosome.

My Previous Problems with Chromosome 6

Here were some of the problems I had at the right side of Chromosome 6:

The problem areas where the Segment Map didn’t match the sibling comparisons were circled.

This was the map I had done previously:

There were a lot of confusing crossovers.

Looking at the Major Crossover Bunch-up

I need to look at this area in more detail:

Here is my spreadsheet of that area within the box below:

I previously didn’t have the Heidi Crossover on my spreadsheet, so I added her.

A More Detailed Approach

For example, in the first sibling comparison of Jim (V) and Jon (F), I can see this in the full resolution Gedmatch comparison:

I record those changes in my spreadsheet here:

I continued on with the positions and sorted the positions to get htis:

These results were not as conclusive as I had hoped. Sharon’s first crossover appears to be in two different or three different places. JIm (V) has a clear crossover. Jon (F) probably has two crossovers. I don’t see any obvious indication of a crossover for Heidi.

Help from Rathfelder Cousin Inese

I’ll look for help from Inese:

Based on matches with Jim and Sharon, these matches seem to indicate that Jim has a crossover at 35.1 and Sharon at 35.6. Those matches give me something like this:

Jon’s Hartley Match with Maury in the Jungle of Crossovers

This shows where Jon’s paternal crossover is. That means his next close crossover should be a maternal one.

A Lentz Cousin Clue

Here Jon’s Lentz DNA continues on, so that makes me think I got his Maternal crossover right. These matches don’t line up well and there is a space in the middle of the matches for some reason. These matches with Joan line up a little better at Gedmatch:

This appears to show three of Lori’s crossovers. She goes from Lentz to Rathfelder at 25.2 and from Rathfelder back to Lentz at the next L and then back to Rathfelder at 56.3M. This also shows Jim and Sharon’s maternal crossovers again at 40.38 and 40.43M. Those are close crossovers.

Trying to Get the Left Side Right

Using more cousins, crossovers and sibling comparisons, I got this for the left side of Chromosome 6:

I need to check this as I’m skeptical:

Here the comparison looks better than I thought it would. The lowest rectangle may not be a discrepancy. Gedmatch is reading that area on the S&L Row as an NIR and it is probably an HIR. The S&H discrepancy is a matter of alignment as I had the HIR to FIR change at 35.2M. This would correspond with Sharon’s Crossover. I think that the top rectangle is also a matter of alignment. I have the V crossover at 34.5 which is the first crossover in the bunch. However, the image shows the V&D change from HIR to FIR to be on the right of the bunch of crossovers. My detailed analysis of the crossover positions has given me confidence to override what my eyes see above.

Another Bunch of Crossovers

The next bunch of crossovers is here:

I want to look up the full resolution locations for all the changes above. The last change is a double change as it goes from NIR to HIR to FIR.

A Detailed Analysis of the Second Bunch of Crossovers

 

I looked up all the changes in the above area and sorted by position:

Previously, I had five crossovers. Now I have either three or four. I need to take out Jon and Sharon and add in Heidi. The first position is for the double crossover that I had mentioned above.

Here is the simplified crossover bunch of H/L/D:

I moved Jim, Sharon and Lori to the right through that crossover bunch as they are not involved in those crossovers. Then based on the sibling comparisons above, I filled in the D-H section:

Now I can see where the crossovers will be for Heidi, Lori and Joel (D):

Next, I can assume my old crossovers are right or do the detailed analysis. I ventured out to the right without looking up all the position numbers:

Segment Map Check

If the Segment Map matches the sibling comparisons, that means that my map is right:

This comparison shows my map went off at the V crossover on the right. I’ll go back and do the detailed analysis that has worked so well so far. I don’t feel so sure about the last three crossovers either, so I’ll include those. For example, in the V&L comparison, I see this at the end of the Chromosome when I lower the thresholds:

This shows a change from NIR to an HIR at the right. This doesn’t show unless I lower Gedmatch thresholds.

Detailed Analysis of the Right Hand Side of Chromosome 6

I feel that I can conquer this Chromosome. My detailed analysis takes a while, but it seems to be getting results:

Above is what I had before. I had a Jim (V) crossover at 152.5. Then I had others but wasn’t sure of the positions. Below are the position numbers I looked for each of the sibling comparisons. Next I sort those by position and the answer should be clear:

Compared to original analysis, I need to take out the first Jon (F) and add a Sharon at 155.5. The analysis confirmed a crossover for Jon at the end of the Chromosome.

I erased the right hand side starting with the new Heidi crossover and moved the DNA segments to the right to their correct crossovers:

I filled in the blanks by looking at the sibling comparisons. I’m hopeful that this is the right answer and have merged the segments:

I don’t see any obvious mistakes in the Segment Map:

Summary and Conclusions

• I recommend charting every change in DNA for sibling comparisons for difficult crossover areas. Then sort by position number and it should show who has each crossover and where it is.
• The above method is a little time-consuming but easier than trial and error.
• My above map is missing some Rathfelder DNA, but my mother is tested and should be able to fill that in. All other three grandparents are covered by the six siblings’ DNA.
• My sister Sharon and I are opposites on the paternal Chromosome. I have all Frazer DNA and Sharon has all Hartley DNA. This knowledge could be helpful when looking at unknown matches.

 

 

 

 

 

 

 

 

First, I’ll take a rough cut at setting the crossovers for Chromosome 8. Things went fairly smoothly until I got to the last S Crossover:

At F&L and H&L, we go from an HIR to an NIR (Non-Identical Region). My guess is that Lori has a double crossover in this area. This may be where a spreadsheet of crossovers could help. This is as far as I got:

For the boxed area above, I want to create an even more detailed spreadsheet of all the changes. Some of the positions, I can get off the above image:

The first column has the initials of the two comparisons. The second column has the position of the changes from HIR, FIR, or NIR. The third column is who I think the crossover goes to. In blue, DH and HL are both at 104. These both have H in them, so it appears that the crossover could go to Heidi. Above, VL and FL both are at 103.1 and have L’s, so it appears to be a Lori crossover, but there is a change in the FD comparison at 103, so I want more information before I decide. To fill in the other positions, I need to look at the full resolution comparisons at Gedmatch. The first is Jim and Jon (VF).

Each ^ is one M, so this is at position 103M.

To me, it looked like there were two changes in the Jon and Sharon FS comparison:

The first is at 101.5M and the second at 103M. That means that Jon (F) may have a crossover at 103M.

I also see two changes between F and H:

They are at 103M and about 103.8M.

Here is the change from FIR to HIR to NIR between F and L:

 

Again, I see 103M and about 103.2M.

Here is DL (Joel and Lori compared):

This change is just past 103M, so I’ll call it 103.1M to distinguish it from all the other 103 changes.

For Sharon and Heidi, it is a little difficult to read the changes:

It looks like the first change is at 100.5M, but it is actually at 101.4 as there is a quick ^ after the 100M mark. That means I have to change the other 100.5’s on my spreadsheet to 101.4’s.

I double checked all the positions and sorted the results by positions. That gave me this:

This gives me confidence that I have crossovers S, F, L and H – in that order. I had mentioned the possibility of a double crossover for Lori, but I’ll add that later if needed. That was a bit of work, but it gives me some confidence in who has what crossover and where. Here are the crossovers I get:

Hartley Side Cousin Joyce

Cousin Joyce’s matches line up with the crossovers that I had. However, the match numbers suggest that the S and H crossovers are in the wrong order for Sharon and Heidi. I suppose to know for sure, I need to look up more full resolution comparisons:

Unfortunately, the results are less than conclusive. However, I would say that the H should be before the S. This is based on matches with Joyce and most of the comparisons above. I’ll say that Heidi is at 11.3 and Sharon is at 11.5. Here is what I finally fill in from Joyce’s match:

I made some assumptions that there would be Frazer DNA where there was not a Hartley DNA match.

More Hartley Cousins: Maury and James

Here I see a crossover for Jon in the Cousin James matches. I also see that my (Joel’s) Hartley DNA carries through the middle of the Chromosome.

The Frazer DNA probably carries to the middle of the Chromosome for my siblings, but I have not added that DNA in yet.

Lentz Cousin Carolyn

Carolyn gives me some maternal Lentz DNA on the right hand side of Chromosome 8:

Again, I filled in Rathfelder for those who did not match on Lentz.

 

Lentz Cousin Linda

Linda adds some green to the middle of the Chromosome:

Jon Matches Two Rathfelder Cousins

Both cousins match Jon in the same place so I only show Cousin Catherine:

Checking the Segment Map

This is the non-controversial middle part of the Chromosome, so I would suspect that I would have agreement between the Segment Map and the Gedmatch Sibling comparisons:

Working to the Left of the Chromosome

Getting Through Four Crossovers in a Row

Assuming my four crossovers were right:

I see only one obvious mistake:

The F&H Line is off starting at the H (Heidi) Crossover. Also the S&H comparison line is off. And they are off by quite a bit. They should be FIRs and they are NIRs. Heidi should have the same DNA as Jon (F) and Sharon, but I show her have the opposite DNA on the paternal and maternal sides.

It occurs to me that Heidi’s  Paternal Crossover should be a Maternal Crossover.

If I make that change, then Heidi would match Jon and Sharon:

The Final Answer for Chromosome 8?

I don’t see any obvious errors:

Summary and Conclusions

• My mother didn’t pass down some of her Rathfelder DNA to any of her six siblings, so we will have to depend on her DNA results for those areas.
• I looked up full resolution positions for changes between sibling comparisons in areas where there were multiple crossovers or close crossovers. This helped resolved problems.
• I hope to use this technique to solve my problem Chromosome 6
• I found out that changing one crossover from paternal to maternal could be the difference between an FIR and NIR comparison between two siblings.

 

 

Previously, I was working on Chromosome 6, but it was too much of a headache, so I’m skipping that chromosome for a while and starting with a fresh Chromosome: 7. I do have partial sibling results based on the raw data for Chromosome 6, but that seems like cheating.

Adding Crossovers

Some people call these by a different name. They are the vertical lines that need to be assigned to a sibling to show where they have a change in their inherited DNA.

I try not to spend too much time on these initially as they may change.

Lentz Cousin Carolyn

Carolyn is a maternal cousin match on my Lentz side:

By Carolyn’s matches, it looks like I have Jim’s (V) crossover right, but that my Joel (D) crossover should be a Jon (F) crossover. As I look back, I see I made a mistake:

Based on the matches with Carolyn, I came up with this maternal configuration at the start of Chromosome 7:

My Frazer Cousin Susan

Susan shows I was on the right track with Lori’s crossover here:

Here is how I map the matches with Susan:

I don’t want to imply too much with Sharon yet as she has a crossover in this area.

Hartley Cousin Maury

Maury will help map Hartley onto the middle of the Chromosome for 5 siblings:

Hartley Cousin James

Here James’ match with Jim (V) stops at 147.3. I need to add a crossover for Jim (V) there. I’m going to change the L I had there to a V. The start of the match for Joel appears to affirm the crossover I had there.

I also added another D crossover about 1/3 of the way from the beginning of the Chromosome.

Rathfelder Cousin Catherine

This tells me Jim (V) needs another crossover:

Jim’s match with Catherine ends at 72.7M and the others end at 75M. Also my match with Catherine is off of the other matches and probably indicates a maternal crossover for me:

Cousin Beth to Fill in More Hartley

The first L Crossover will be paternal going from Hartley to Frazer. Sharon will also have a Hartley to Frazer crossover at the corresponding S above (123,5M).

The Segment Map

Before things get too far out of hand, it is a good idea to check the Segment Map:

This shows that I am on track as far as I have gone. At this point, I would like to fill in the missing segments using the Gedmatch comparisons:

In the F-V Segment, Sharon and Heidi have an FIR, so I filled in Rathfelder for Heidi there. However, Heidi needs another crossover to go from Rathfelder to Lentz going from right to left.

That crossover is at 36.5M:

Heidi’s crossover looks to be between D and V. Here I did some extending:

However, I ran into a problem with Lori as it looks like she has a double crossover, but I don’t think she should.

More Segment Map Checking

Here, I’ve circled a few problem areas. At least they are only in one section of the Map.

Here is one problem:

Heidi and Lori have a FIR in green. Going from that FIR to the left is an HIR. In order for that to happen, either H or L should have a crossover and there is no H or L crossover there. I think the D crossover above should be an L.

This looks better. However, now I see another problem I didn’t see before:

This is an area that has Jim in common (V). I see that a V crossover is needed for Jim around here:

When I add this crossover, the Chromosome is solved. At least the right hand side:

The Gedmatch comparisons and the Segment Map match each other:

Here is the completed Chromosome:

I was unable to use the Merge function as I added some columns to the left. This shows that I (Joel) have the Frazer DNA near the middle of the Chromosome and the other five siblings do not. Lori carries Lentz DNA in some places where the other five siblings carry Rathfelder DNA. There is coverage of all four grandparents in each section of the Chromosome.

Summary and Conclusions

• I moved on to Chromosome 7 after having trouble with Chromosome 6
• I was able to find missing or mis-attributed crossovers by comparing the Segment Map to the Gedmatch sibling comparisons.
• I am fortunate to have many Hartley side relatives who have tested. This made the work go more easily,
• I am still keeping a list of crossovers with their positions. I am highlighting the rock solid crossovers as the landmark ones that I am really sure of. This helps get the positions right when there are many close crossovers.