Category: DNA General

The way this is going, I am heading for a 24 part Blog on visual phasing.

Chromosome 18

Here’s a bit of glitch with Chromosome 18:

The fourth sibling comparison doesn’t line up with itself. I tried to go out of my spreadsheet without saving it to see if that would fix it and then lost my last 3 solved Chromosomes. Well, I should be able to recreate them easily by checking back on my Blogs.

Charting the Crossover Locations

I go through the crossovers again and put some numbers on them. This often results in changes to the crossovers that I originally put in:

The yellow indicates crossovers that I am unsure of.

Cousin Matches

Next, I’ll see which cousins match me and my siblings on Chromosome 18. It turns out that Catherine matches all six siblings:

I have circled all the crossovers. They all appear to agree with what I have except for Sharon’s first of three maternal crossovers. Also Jim’s first crossover appears to be on my line. However, these crossovers agree with my spreadsheet above. It turns out this was a good check as I need to update the chromosome map. I took out the D on the Chromosome Map above, but I feel there will need to be another crossover in that area eventually.

Here is my interpretation of Catherine’s matches with my family:

Looking for a Paternal Cousin

I have a few Frazer cousins that match in the same area. Here is Emily’s match from 35 to 52M:

This is the first time I haven’t had Hartley cousins to help me out:

Next I would like to fill out as much as I can to the left of the V and S crossovers. These are the ones I was unsure about. However, before I do that, it appears that I have a problem with what I have done above. Sharon should have Frazer DNA, but not Lori. Good thing I caught that. I did a glance on the Segment Map and that pointed out something was wrong.

This looks pretty good as far as I have gone:

This is my ‘all in one’ view.

Next I need to fill in to the left of the V-S crossovers.

I filled in Jon (F) based on him having a FIR with Heidi from the F & H comparison at the top. That means that he should have a Frazer/Lentz combination. However, I see that I missed a change for Jon on his F crossover to the right. I fixed that, and it looks like the crossovers were right as I had them:

This now agrees when I fill in the rest:

Summary and Conclusions

• Jim has a full paternal Hartley Chromosome
• Joel has a full Frazer Chromosome
• I wonder why Jim had not Hartley cousin matches given his full Hartley Chromosome.
• I made it through the problem areas without too much difficulty.
• Most of the problems were of my own making. I found and corrected two of my own mistakes.

 

 

 

Chromosome 13 was easy to solve. Let’s see how easy Chromosome 14 is.

Chromosome 14

I start with trying to find crossovers and assigning them to siblings:

Then I put these crossovers into a spreadsheet and try to get position numbers from the match numbers to the left of the above.

This gives me another chance to check out the crossovers. I’m not sure on the position numbers of H and V near the end. I may find that from cousin matches. This should be another easy chromosome to solve.

Rathfelder cousin Anita shows Jim’s crossover, but the position number is still not given:

I’ll just log in to Gedmatch and get the position number there:

That means that the 94.9M crossover that I had for Heidi belongs to Jim.

These two Hartley cousins fill in a lot of orange DNA:

However, I see a problem. Between Heidi’s Frazer DNA and the Hartley on the right, she only has one crossover and that has been used up on the maternal side. However, Heidi has a crossover on the right with no maternal or paternal change, so that is wrong. Heidi must have a paternal crossover on the right:

That also makes sense because the H &L comparison shows a green FIR, so Heidi must have Frazer on the paternal side. I am now close to solving this Chromosome.

I’ll check matches with Lentz cousin Judith:

I just need to fill in the left and check for accuracy.

The HIR Problem

Lori has an HIR with each of her five siblings in the first segment:

That means that we may not be able to solve Lori’s last remaining segment:

Fortunately, my Hartley cousin Patricia uploaded her DNA to Gedmatch:

Patricia does not match Lori in that first segment, so the inference is that Lori has Frazer DNA there as do Jim, Jon and Joel:

That puts Lori’s crossover on her maternal side.

Here is the final comparison:

Summary and Conclusions

• These higher number chromosomes are shorter. However, on the Excel spreadsheet, they take up the same amount of room. That means that they are spread out more and easier to see. In addition, the larger chromosomes have fewer crossovers, making them easier to solve.
• There is also the chance that, on these shorter chromosomes, there will be fewer matches. That has not been a problem up to this point. I’m sure it helps that I have six siblings.
• In Chromosome 14, Jim gets a full dose of paternal Frazer DNA.
• There is DNA coverage on the paternal grandparent side. Some Lentz DNA is missing on the maternal side. We could get that from my mom, but would have to figure out which of her DNA is maternal and paternal.

 

 

 

 

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.