Adding Some Ancestors to DNAPainter

DNA Painter is a fun and helpful tool created by Jonny Perl. I discussed DNA Painter in a previous Blog. Since then, DNA Painter has come out with a new dividing line in the key. At the time I started using DNA Painter, I was so happy with the software, that I didn’t care about the key. However, now I have organized my key.

The Key to the Key

Here is the way I had my key:

By choosing the area to the right of the ancestral name, these names can be dragged up or down. Here is my new key:

I have sorted the names into paternal and maternal. Then within paternal and maternal, I have sorted the names in a way that makes sense to me – basically by grandparent line. In order to add the above line, I chose T Clarke:

Then I choose Edit Group:

In that screen, I have circled where there is an option to add a dividing line below the group. I have checked this option.

Mining My Blogs for More DNA to Paint

Here is what the DNA Painter shows for me right now:

I recall Blogs tha I have written where I found other ancestors.

Adding Abraham Howorth, Born 1768

Old Abraham goes back a ways. He lived in the Bacup area of Lancashire with his wife Mary. I was able to Identify his DNA thanks to a match with Anne on Chromosome 4. Now I have to remember how to add Anne’s DNA to DNA PainterFirst I find the match at Gedmatch. Here is my match with Anne:

Now to get this on to the Painter. At the top right of the software is a software that says “Paint a new match”. This sounds like a good choice:

Above, I copied Anne’s matching chromosome information into the box provided. I then click on the blue box [save match now] to get this screen:

In the top blank box I put the match’s name and Gedmatch number. In the bottom, I’ll put in Abraham Howorth and Mary. This is on my paternal side. Here is the new painted segment on Chromosome 4 in blue:

I’m not totally happy with the color as it is not too distinctive from my paternal T Clarke:

So I chose Abraham in the Key above and then chose Edit:

There I chose a different color for Abraham. I didn’t like that either, so I chose a brighter green:

This will do for now. Next, I want to move Abraham down one slot on the key:

When I choose the area to the right of the name, I get a double arrow and I can move the name down one space.  Howorth is the second surname on my paternal grandfather’s side.

Adding a Maternal Rathfelder Segment

I discuss this Rathfelder find in more detail in a set of Blogs called My German Success Story. The DNA match was with Astrid, and I was able to trace the match back to Hans Jerg Rathfelder born in 1752.

I wonder if Hans Jerg had a sense of humor as he named two of his sons Johann Georg that were born four years apart. His own name was a bit similar to these two sons. One son went by Johann and the other went by Georg.

Here is my match with Astrid:

Here is where these Astrid/Rathfelder segments show up on my maternal chromosome:

I used the same color as Howorth as it is OK to repeat colors as long as the last time I used this color on Chromosome 4, it was on the paternal side.

Next, I moved Han Jerg down on the key to where I want him:

Here is the Linden Church in Latvia where Hans Jerg and Juliana got married:

The odd thing is that it looks like it could be a New England scene with children sledding on the hill of the church. However, this is in the middle of Latvia.

Part of my impetus to paint is the header at the top of the DNA Painter. It shows how much of my chromosome is mapped. Right now it shows:

  • 33% mapped – 166 segments
  • Paternal: 46% mapped – 109 segments
  • Maternal: 20% mapped – 57 segments

This exercise hasn’t raised the overall mapping from 33%. It takes quite a bit of DNA to go up one percent.

A Maternal Lentz Add

This is a match I have with Radelle that goes back to John Lentz, born in Philadelphia in 1792. Here is my share of John Lentz:

Oops, I forgot to tell DNA Painter that this match was on my maternal side, so it put the lilac color across the maternal and paternal side. This is easily fixed.

There, that looks better.

DNA Painter puts the new ancestral couple at the top of the key, so I’ll move them down to where they belong:

There is some confusion as to who Eliza was and whether John had one or two wives, so I’ll just leave it as Eliza for now. John and Radelle got me up another percent on my maternal side:

It like a game trying to get these numbers up.

The X Chromosome and My Cousin Cindy

I am only mapping my great grandparents and further out. Right now, I only have a small segment mapped. However, there may be a way to get further back on the X Chromosome. My plan involves my first cousin Cindy. Here is how I match Cindy on the X Chromosome:

On Chromosome 1-22, we would match on either Alexander Rathfelder or Emma Lentz. However, on the X Chromosome, we only match on Emma Lentz. That is becuase Cindy’s father Bob only got and X Chromosome from his mother.

Emma in turn, got her X Chromosomes from her two parents: Jacob George Lentz and Ann Eliza Nicholson. This only works for a female cousin where I am also related to her father.

Now I will map my matches with Cindy to J.G. Lentz and A.E. Nicholson:

Perhaps this will get my percentages up. I click the refresh button for my statistics and get this:

I’m looking for more than one perent increase on my maternal side:

There. I got a 2% increase thanks to my cousin Cindy. Actually it was two percent from before I started the Blog.

Cindy is the 2nd from the left and I am on the right.

The Big Picture

Next, I add two more lines to the key:

The four divisions are paternal grandfather, paternal grandmother, maternal grandfather and maternal grandmother. A few observations:

  • I have only identified two ancestors each on my paternal and maternal grandfather sides so far.
  • The darker green Hartley/Snell DNA represents 17% of my DNA. This is half of all my identified DNA. This is due to the fact that I have a lot of relatives on the Hartley side of the family. The theoretical average amount of DNA I would get on my Hartley/Snell side would be 25%. By identififed, I mean DNA that I can put ancestral names to.
  • I don’t have any 2nd cousins tested on my paternal grandmother side (Frazer). I do have a Frazer DNA Project which partially makes up for that.
  • Two second cousins on the Rathfelder side account for 4% of my DNA.
  • DNA for Lentz/Nicholson acounts for 3% of my DNA. This includes my X Chromosome match with my 1st cousin Cindy.
  • My Nicholson/Ellis matches account for another 4% of my DNA. This is a case where a more distant ancestral couple is more accounted for than a closer ancestral couple. This number could get higher as I have run into quite a few DNA-tested descendants from this Nicholson/Ellis line.
  • That leaves 6% for the identified DNA I got from the other ancestors listed above.

Summary and Conclusions

  • Jonny Perl’s DNA Painter remains a highly respected and useful tool for DNA analysis
  • I enjoy looking a the percentage statistics
  • I can see where the mapped DNA is relatively complete and where it is lacking
  • The DNA Painter gives insight into my DNA’s origins and spurs me on to further discovery

 

 

Using Visual Phasing

I did some visual phasing for Jane and her two siblings. Now Jane wants to see how the visual phasing can be used.

Mr Gray’s 8.5 cM Match

Jane’s first question came from a Mr Gray. He matched Jane and her two siblings at about 8.5 cM. Jane had this conundrum:

For me the match points to Beckham, for Heather it points to Beckham but for Alex it points to Hamilton. Unless it is on Mum’s side as indicated by Jackson for all three of us, but then why wouldn’t Mum share DNA with Mr. Gray?

Here is the right side of Jane’s Chromosome 2 Map. Jane is in the middle bar and her maternal side is on the top bar.

Here is where Jane matches Mr. Gray:

The answer for this one is that this is not a real match. Jane’s mother has tested and Jane has two sets of phased results based on her mother’s results. I ran Mr. Gray against Jane’s paternal and maternal kit and got no results. This means that the match is not real. Different analyses have been done for the chances of a certain size match being real or not. Here is one from Roberta Estes:

These studies seem to show that there is about a 50% chance of a 7 cM match being real. This goes up to a 66% chance of being real for an 8.5 cM match. It looks like Mr Gray fell into that 34% range. The only other possibility is that Jane’s mother could have had a false negative match with Mr. Gray. All in all, I would say that these results would be inconclusive. For me, I tend to say if there is no match on the two phased kits, then there is no match.

Second Example: An Adoptee at 23andme

Only Jane and her mom tested at 23andme. Here is how the adoptee matched Jane:

Chromosome 1:     108 to 151     26 cM

Chromosome 2:     225 to 230     8 cM

Chromosome 3:     104 to 145     41 cM

Chromosome 17     5.7 to 9.3      9 cM

By looking at the Visual Phasing Spreadsheet, Jane deduced that this was on her Beckham Line:

Jane is in the middle bar. The bottom of that bar is her paternal side where Bekham is in blue. I assume that Jane’s mother did not match this adoptee at 23andme.

I have Jane’s Chromosome 2 above where she matches Beckham between 225 and 230 on her paternal side.

The match is significant for Jane as the  match between 104 and 155 goes through her maternal crossover at position 110M. That would confirm that this is a paternal side match on Beckham.

Here is Chromosome 17:

It looks like I had trouble identifying the maternal grandparents, but Jane matches this adoptee in her paternal Beckham region. So I would agree with Jane that this match is on her Beckham side. It would help if this adoptee uploads his/her DNA results to gedmatch.com.

Peggy’s Maternal Match on Chromosome 13

Jane reports these results for Peggy’s matches to her and her siblings:

Heather     74 to 103     31.5 cM

Jane          74 to 91       14 cM

Alex – no DNA

Without looking at Jane’s map, it appears that Jane should have a maternal crossover at around 91M.

Jane has a maternal crossover at 90 on the map where her DNA goes from Adair to Jackson. Alex is on the top row. He has a large maternal Jackson segment which explains why he has no match with Peggy. Jane has determined correctly that this match is along the line of her maternal Adair grandmother.

A Paternal Hillock Match on Chromosome 2

This match has a similar pattern to the previous one. Here Hillock matches:

Jane     40 to 79         41 cM

Alex      119 to 208      8.4 cM

Heather – no DNA

Two siblings match Hillock and one does not. However, in this case, the two siblings match at different locations on Chromosome 2.

Jane again is shown on the middle bar. The paternal side is on the bottom where she matches on her Hamilton grandfather. The match with Alex on the top shows that he should be matching on the Beckham paternal grandmother. However, this is a small match. It is time to check Alex’ paternal phased kit against Hillock.

I forgot that I had lowered the threshold and was surprised to come up with this result:

The location of this match is within the orange Hamilton segment for Alex’ top bar. The match that Jane reported for Alex should have been 199-208 (unphased). That means that my red circle above on Alex’ bar above is not correct.

Summary and Conclusions

  • Jane is fortunate to have a mother whose DNA could be tested. This gives her paternal and maternal matches for Jane and her two siblings.
  • It is important to know first whether the match is on the maternal or paternal side.
  • If there is no maternal or paternal match, I consider that to not be a match.
  • Jane’s conclusions appear to be correct as far as on which grandparent line her matches are on. However, it is important to make sure that the position numbers of the matches are correct to match up with the right grandparent.

 

Visual Phasing of My Canadian Frazer Relatives

One of the Canadian Line of Frazers descends from my 2nd great-grandfather’s brother. His name was Richard Frazer born 1830 in Roscommon County, Ireland:

My 2nd great-grandfather was George William Frazer, born about 1838. Here are the two lines as shown with their descendants that have taken a DNA test:

Visual Phasing

Visual Phasing is comparing the DNA results of three siblings (or more) and figuring out from which of their four grandparents they got their DNA from on each of their chromosomes. I did that with myself and my four tested siblings. Now on the yellow line we have Susan, Doreen and Ken who have all had their DNA tested. I am 4th cousins to Susan, Doreen and Ken. However, by figuring out where we got our DNA from, it will be almost like comparing our grandparents to each other. Richard Price “Pat” Frazer will be compared with my grandmother, Marion Margaret Hartley. These grandparents would have been second cousins to each other. Now we didn’t get all our grandparents’ DNA, but what we did get, we will be able to identify and compare.

Steven Fox’s Excel Spreadsheet for Visual Phasing.

If you do a Google search for Steven Fox and Visual Phasing, you will find a lot of information and blogs of other’s that have used his spreadsheet. It is possible to do Visual Phasing without his spreadsheet, but his spreadsheet makes it easier, more organized and more standardized.

Jumping in with Chromosome 22

Chromosome 22 is the shortest, so some people start with that one. There should be fewer crossovers on this Chromosome. The downside is that there are also usually fewer cousin matches on this short Chromosome.

This image is small but if you click on it, it should get larger. The top bar compares Ken (K) and Susan (S). The vertical lines represent crossovers where DNA received changes from one grandparent to another. The location of these changes or crossovers are important. It is also important to know to which sibling these crossovers get assigned to. The first crossover is found where the match between Ken and Susan goes from HIR or FIR. HIR is Half Identical Region. That means that Ken and Susan both got the DNA from one of their 4 grandparents at that segment. The problem is, we don’t know which grandparent. After the crossover, represented by the first vertical line, Ken and Susan have an FIR. This is a Fully Identical Region. That means that Ken and Susan both got their DNA in that segment from two of the same grandparents. One matching grandparent was on the maternal side and one was on the paternal side.

Finding the Location for the First Crossover

The second crossover is easy to find, because it is at the same place where Susan and Doreen go from no match to a match. This spot is recorded by Gedmatch at 23,564,890. I could call that 24M or 23.6 depending on how exact I want to be. In the case above, I called it 23.6. To get the first crossover, we have to look at the comparison between Ken and Susan at full resolution at Gedmatch.

Here is the first part of Ken and Susan’s comparison at Chromosome 22:

This says that the beginning of Chromosome 22 doesn’t even start until position 14.5M where M is million. Every little ^ is one million. So counting back from 20M, Ken and Susan go from HIR to FIR between 15 and 16M. I’ll call it 15.7M. The pink part is a centromere. Usually this would be at the center of the chromosome, but there must be information at the very start of Chromosome 22 that isn’t used.

One Crossover or Two on the Right Side of Chr22?

Here is a blowup of the last two crossovers. On the top bar, there is a spot where Ken and Susan go from HIR to FIR. However, this does not line up with position 45.4M where Ken and Doreen go from no match to an FIR. However, to be sure, I need to know where Ken and Susan go from an HIR to an FIR.

According to Gedmatch, the end of Ken and Susan’s match is at 49.5M. That means the last ^ is 49M. That means that Ken and Susan’s change from HIR to FIR is between 45 and 46. I’ll say 45.7. This is pretty close to 45.4, so a judgement call. I’ll just leave it as I had it.

Assigning the Crossovers

The crossover usually gets assigned to the person that is in two of the changes. This is easier to see in the second crossover. There is a change in the top and bottom comparisons. The first comparison is Ken and Susan. The last comparison is between Susan and Doreen. Susan is the common denominator, so she gets the crossover.

I gave the first crossover to Ken:

I had forgotten why. Now I remember. I think that there is actually a very small match that doesn’t show up between Ken and Doreen at the beginning of the Chromosome. It is very subtle, but I’d say that there is more green in the beginning of the K&D comparison compared to the S&D comparison. These crossover assignments can be a bit of an art. If I had lowered the match resolution it should have shown up as a blue match there.

The last two crossovers were not easy either:

These changes have to come in pairs. That means that I had to treat the little segment between D and S as an FIR on the bottom comparison. That means that there are two changes for Doreen first making that her crossover. Then there are two changes for Susan (top and bottom comparisons).

Working on the Segments

This image is the end result, but I will say how I got there. First I started with K&S. They have a FIR for the second segment. This shows as dark green. In the image above, that means that Ken and Susan have two of the same colors. They match with one maternal grandparent and one paternal grandparent. Because Ken has no crossover to the right of the second segment, I can extend that DNA all the way to the right end of the Chromosome on both Ken’s maternal and paternal sides. Also in the second segment, Doreen has no matches with Ken or Susan. That means she has the spouse of the other two grandparents in that slot. So instead of orange and purple, she gets blue and green there. She has no crossover to the left and none on the right until near the end of the Chromosome.

At some point I have to deal with a HIR. I did that with Susan after the second segment. Susan has a HIR to Ken and Doreen. I made Susan match Ken’s purple but not his orange. We already knew that Ken and Doreen had no match in the third segment, so Doreen got the opposite colors there.

The last three bars in the image above represent Gladys’ match with Ken, Susan and Doreen. She shows a match with only Ken and not Doreen nor Susan. This has to be in Ken’s orange section as that is the only place along the match with Gladys that one of his segments is different than Doreen’s or Susan’s.

Gladys and Ken only match on the Frazer Line. Gladys has no Gray DNA. That means orange has to be Frazer. The only other paternal side is Gray so blue has to be Gray. I don’t have specific information on Ken, Susan and Doreen’s maternal side, so those are just labeled G3 and G4 for now. Actually, they should be M1 and M2 for maternal grandparents:

Ken and siblings’ father’s name is Stefansson and their mother’s surname is Gudmundsdottir.

How to Use Visual Phasing

Now that we know where Ken, Susan and Doreen got their DNA from on most of their Chromosome 22, what can we do with this information?

Part of the information is educational. Knowing how our DNA recombined by way of our grandparents is interesting. It is a kind of snapshot of what went into our makeup at conception.

Another part has to do with DNA matches. This focus us as to where our matches are. However, there is still one hitch. We still need to know if our matches are on our maternal or paternal side. If we don’t have a parent to compare our matches with, then it is possible to compare matches with known relatives.

Use of Crossovers

The exception to this is if Susan were to have a match that started before her crossover at 23.6 and continued beyond it. For a match that goes through a crossover, it has to be on the other side. So for such a match for Susan, this could not be a Frazer match but must be on her mother’s side.

These visual phasing maps work best when you have downloaded all your matches. Then you will know for every Chromosome which grandparent they will match depending where in the Chromosome your match is. If you have a lot of matches that end at a certain place and then other matches that start up again at that spot, that could be indicative of a crossover.

Separating Real Matches from Far Away or False Matches

Another way to use these results is to tell if a match is real or not. Here is part of mapped Chromosome 22 showing a small match between Doreen and Michael of the Frazer Project:

It shows that Michael only matches Doreen and not Susan nor Ken. Michael’s match is indicated by a blue bar at the bottome right of the image above. However, Doreen has no Frazer DNA in that segment. She only has Gray DNA on her paternal side. So, it may mean that Doreen matches Michael on the Gray line going way back or less likely on the Icelandic Line. But Michael could not be matching on the Frazer Line assuming I have mapped this correctly. As I mentioned, this is a small match of 5.6 cM. Matches under 7 cM have more than a 50% chance of not being real matches.

Comparison with My Visual Phasing

Here is my Chromosome 22. It is mapped along with three of my siblings. I didn’t get around to mapping Lori.

When I compare the two maps, I can see where my siblings have the potential to match with Ken, Doreen and Susan along the Frazer Line. It doesn’t mean we have to match there. For example, my Frazer grandparent DNA also has Clarke and McMaster DNA that Ken, Doreen and Susan don’t have. Likewise, Ken, Susan and Doreen have other DNA in their Frazer line that I would not share.

Extra Chromosome Mapped

While I was at it, I mapped Chromosome 12:

This was a little easier, because more cousins matched on this Chromosome. One interesting thing about this Chromosome is that between about 88 and 104M, there is no Frazer DNA. That means that if any of these siblings have a match in that area, it could not be a Frazer match.

This map had three spots that appeared to go from a no-match to a FIR or from a FIR to a no-match. This is impossible, so there needs to be a HIR transition. That is why there are three places where the crossovers are close.

Summary and Conclusions

  • Visual Mapping shows the process of our makeup based on how our grandparents’ DNA combined to form us
  • This mapping can be helpful in identifying DNA matches
  • Special attention should be made to crossovers. That is where DNA on one side of our Chromosome changed from one grandparent to the other.
  • If a match goes through a maternal crossover, for example, it means that match must be on the paternal side.
  • A lot of genetic genealogy is about separating out the DNA and visual phasing goes a long way in doing this.
  • Other sorting can be done by names or location of matches. As Ken, Doreen and Susan’s mom is Icelandic a clue as to the matches’ names, locations or genealogy can be a hint as far as placing them.
  • Visual Phasing works best when there are good cousin matches on all four grandparent sides.

 

 

 

 

 

My Mother’s Best Lentz DNA Match

I’ve been in touch with Radelle for a while. First, we were in touch over Lentz genealogy without the DNA part. Some of the Lentz genealogy that I had done in the past was helpful in Radelle finding parents for her ancestor Eliza Lentz. Radelle later took the AncestryDNA test and recently uploaded those results to Gedmatch.com.

Lentz Genealogy

I have made a Lentz tree for those that have had their DNA tested and uploaded the results to Gedmatch. There would be a bigger tree of those who haven’t had their DNA tested.

I’m on the left side of the chart. Radelle is on the right side of the chart. Radelle, Al, and Stephen descend from Eliza and William Andrew Lentz. Note that Al and Stephen’s great grandfather is Phillip Miller Chappell. Phillip Miller is discussed below as the 2nd husband of Eliza who married John Lentz at the top of the chart. Phillip Miller most likely raised the young Lentz family. Judy, Joshua, my mom and her children and my 1st cousin Cindy descend from Jacob Lentz b. 1818. Because Jacob George Lentz b. 1866 married Annie Nicholson, I can’t tell for sure if the matches with Judy, Joshua and Cindy are on the Lentz side or Nicholson side. Radelle and my mom are 4th cousins. Radelle is 4th cousin once removed to everyone else except for Joshua. Radelle is 4th cousin, 3 times removed to Joshua.

I had a difficult time nailing down John Lentz years ago when I was working on Lentz genealogy. I wasn’t sure if there were one or two John Lentz’s in the area at the time. From what I could tell, John died and his wife Eliza married Phillip Miller. Here is an 1877 death notice for Eliza:

Notice that the funeral reception was at Eliza’s daughter in law’s house. Mary A Lentz was my 3rd great grandmother, the wife of Jacob Lentz b. 1818. Eliza was Jacob Lentz’s (b. 1818) mom, so Mary A Lentz his wife was Eliza’s daughter in law. Based on the above death notice, Eliza would have been born about 1796.

Who Was the Eliza Lentz Married to John Lentz and Phillip Miller?

I see that Radelle has a possible name for Eliza:

 

This record was from Trinity Church, Oxford. According to Wikipedia:

Old Trinity Church, also known as Trinity Church, Oxford, is a historic Episcopal church founded in 1698 in Oxford Township, Pennsylvania, which is now part of Philadelphia

Here is another hint that came up for me at Ancestry. This is from Kensington

This may fit in better as far as the date goes. This would mean that Eliza was married at about age 26. The first marriage, Eliza would have been married at about age 17.

However, having said that, it does appear that Radelle is right as I have that the three sons of John were born before December 1st 1822. Perhaps Elizabeth Refford died in childbirth at the birth of Wiliam Andrew Lentz who was born 13 May 1822. John would have had no one to take care of his young family. So perhaps he remarried Eliza Rihl later that same year. Something to think about. However, then John Lentz died in 1823. Eliza marries Phillip Miller in 1825. If I have my facts right, then the Lentz children were raised by a step mother and a step father.

The DNA Part

I said that Radelle was my mom’s largest Lentz DNA match. Here is how they match at gedmatch:

Their estimated common ancestors are at 4.4 generations based on the DNA match. Their actual ancestors are 5 generations back, so that is a bit more than average DNA that they share. Here are some more matches Radelle has with my family:

Heidi and Jon are my siblings. Gladys is my mom. Heidi got the same match with Radelle that my mom had. Jon and I got less. My two sisters Lori and Sharon don’t match Radelle.

Mapping My Family’s DNA onChromosome 2

I have my DNA mapped. That mapping shows where my siblings and I got our DNA based on how our four grandparents contributed. Any match with Radelle should be on the Lentz grandparent side.

This shows why Jon and I had less than a fuill dose of Lentz DNA from our mom. My mom matches Radelle between 171 and 212M. I have a crossover at 186. That means on maternal Chromosome 2, my Lentz DNA ends at 186M and the Rathfelder DNA takes over. Lori is has all Rathfelder DNA in that area (from my mom’s dad) so she doesn’t match Radellether. Jon has a Crossover at 180M, so he matches Radelle’s Lentz DNA less than I do. Here is a close-up of the area where Radelle matches me and my brother Jon:

We match Radelle only in the yellow Lentz segments. I didn’t show Heidi, but she has a longer Lentz segment than Jon or me in this area of Chromosome 2.

DNA Matches to My Mom and Radelle

At Gedmatch, there is a way to find common matches to two people. I did this for my mom and Radelle. When those matches are on the same segment, that tells me that these people should share the same ancestors. Here is how my mom matches Radelle and four others on Chromosome 2:

#3 had a tree at Gedmatch.

A Lanz/Lantz family may be a link to the Lentz family.

Another Chromosome Map

Kitty Munson has a chromosome mapping utility at her web site. Using my new match with Radelle, I get this:

The new match with Radelle translates to the DNA I got from John Lentz b. 1792 (or his wife who appears to be Elisabeth). That new piece of DNA appears in pink on my maternal side Chromosome 2. This map is different from the mapping I did with Chromosome 2 above that only has my grandparents. This map uses matches from actual people with known ancestry. The DNA match with Radelle pushed back what I had on the Lentz family over 70 years.

Other Matches?

Unfortunately, I didn’t see other matches between Radelle and other Lentz descendants. It may be that the relationships are too distant and the DNA dropped out. However, Radelle matches my mom and three out of five of her children. My mom matches others on the Jacob George Lentz branch. That implies that the DNA match between my mom and Radelle also applies to them:

Here are the chances of matching a specific level of cousin:

Summary and Conclusions

  • Radelle is my mom’s biggest identified Lentz DNA match. This helps solidify the genealogy that Radelle and I have done.
  • With previous Jacob George Lentz descendants matches, I couldn’t tell if the DNA represented Lentz or Nicholson. The match with Radelle would be the first Lentz-only identified DNA match.
  • I was able to add a late 1700’s Lentz DNA segment to my Chromosome map
  • Radelle got me thinking again about John Lentz, Elisabeth and Eliza. I came up with a possible scenario for this family which had the children being raised by two step-parents.
  • Radelle does not match other Lentz desendants by DNA. This may be due to the distance of the relationships. After fourth cousin level, the chances of matching by DNA drops off.
  • I’ll be waiting to see if we find other Lentz DNA matches. These matches seem to be a bit rare.

 

 

Two Person Hartley Visual Phasing

I’ve had a FTDNA kit hanging around for my father’s elderly cousin. I’ve had it since last Summer, but haven’t gotten in touch with my second cousin Lisa to see if I could get her uncle tested. This would be important, because I have test results for Lisa’s dad Jim and her Aunt Joyce. The third sibling Ralph would make it easier to perform Visual Phasing.

Visual Phasing

Visual Phasing is comparing siblings’ DNA results in a Chromosome Browser. By looking at changes and comparisons in the Browser as well as matches to known cousins, it is possible to find out what portions of the siblings’ DNA came from which grandparent. For me, this is important as I am interested in separating out matches between my great grandparents Hartley and Snell. Jim and Joyce’s maternal grandparents were James Hartley and Annie Snell. Annie’s ancestors went back to SE Massachusetts Colonial times. James ancestors were from NE Lancashire. I’m stuck on Hartley genealogy in Trawden, Lancashire around 1800. This is due to the fact that there were too many Hartleys in the area at the time to tell one from another based on vital records. Finding Lancashire Hartley ancestor DNA matches may help me break down my Hartley genealogical brick wall.

Joyce and Jim’s Genealogy

The goal of visual phasing is to figure out what parts of Gurney, Rounesville, Harltey and Snell contributed to Jim and Joyce’s DNA. In doing this, it would help to have matches from fairly close (but not too close) relatives on all four lines.

Comparing Jim to Joyce on Chromosome 11

I’ll just jump in and start with Chromosome 11. This is midway between 1 and 22. Here is the comparison between Jim and Joyce:

  • The blue line is where Jim and Joyce match each other
  • Within the blue line there are two types of matches
  • The yellow area is a single match. This is also called a Half Identical Region (HIR). This means that Joyce and Jim get their DNA from one shared grandparent A, but don’t match on grandparent B, C or D. We don’t know now if granparent A is on the maternal or paternal side.
  • The green is a double match. That is called a Fully Identifal Region or FIR. In that area they got the same DNA on their maternal and paternal side of Chromosome 11. That also means that they share the DNA from the same maternal grandparent and the same paternal grandparent
  • The grey, non-blue area (below) and the red area above is where Joyce and Jim do not match. That means that Joyce gets DNA from Maternal grandparent A and Paternal grandparent C while Jim gets his DNA in that area from Maternal grandparent B and Paternal grandparent D
  • At each vertical line above, there is a crossover where Jim or Joyce’s DNA goes from one grandparent to another.

Let’s Start Two Person Visual Phasing

Here is a start. In about the middle of the Chromosome there is a green FIR. That means that Jim and Joyce got their DNA from the same maternal and paternal grandparents. Those grandparents are represented by blue and orange segments. There are crossovers on the right and left of these segments, but we don’t know if the crossovers are for Jim or Joyce (or one for Joyce and one for Jim).

It would be nice to know where the changes take place, so I go to gedmatch.com for that. At gedmatch I compare Joyce to Jim in the chromosome browser at full resolution.

The pink area is the centromere of Chromosome 11. Every ^ is one million places. The start of the green HIR counting back from 60M is 57M.

Here I added the 57 before ‘Chromosome 11’ above. I also added some other crossover locations.

Cousin Matches

I am stuck already in my analysis, so I need some cousin matches. These would ideally be at the level of second cousin matches. At the level of second cousin, you match on only one grandparent. Most known matches matches share Hartley and Snell grandparents, so that is a problem.

Shared Ancestor Hints (SAHs) at AncestryDNA

Joyce’s results are at AncestryDNA. There, she has Shared Ancestor Hints. Those Hints are where Joyce has a family tree match and a tree match. Here is an SAH that Joyce has with Chuck:

Chuck is at the perfect level as he is a 2nd cousin. However, he has not uploaded his DNA to gedmatch for comparison. Ancestry does not show on what Chromosomes you match, so that is a problem. We need chromosome match information for DNA mapping.

Back to Gedmatch

Because many at AncestryDNA don’t upload to Gedmatch, I’ll go back to Gedmatch and look for matches there.

Here is a very interesting match that Sumner and Heather have with Joyce at Gedmatch. This shows that Joyce has an estimated by DNA common ancestor between 3.7 and 3.9 generations away. They also share autosomal DNA and X Chromosome DNA. These two are also at Ancestry and show up on Joyce’s Shared Ancestor Hints.

Here, Joyce and Sumner are 4th cousins by shared trees. However, note that this is only hint 1 of 3. HInt two also goes back to Joyce’s Rounseville grandparent at firth cousin twice removed. Here is Hint 3:

This Snell connection is at 7th cousin once removed. There has to be a very low chance of a DNA match that far out – especially compared to a 4th cousin match . However, this is interesting as it shows that Joyce has two paternal matches with this person and one more distant maternal match.

Here are the important details of the match between Joyce and Sumner:

This shows that Joyce and Sumner match on four different chromosomes, but not Chromosome 11. OK, back to the drawing board. I’ll start over with Chromosome 7. Sumner and Joyce have a pretty good match there.

Chromosome 7 Visual Phase Two Person Map

Note that Joyce’s Chromosome 7 match is from 149 to 158M. That is at the right side of Chromosome 7. It is possible that the 149M could mark Joyce’s paternal crossover. I am going to start from the right of the Chromosome and give Jim and Joyce four different colors there. This will represent all four of their grandparents. I can do that because Jim and Joyce don’t match each other at all in that segment.

Here I have put Joyce in for a possible to likely crossover at 149. Remember that Joyce and Jim don’t match each other at all after 149M. That means that Jim won’t match Sumner either. I checked gedmatch and he doesn’t as expected. Next, I’ll assign Sumner’s match to Joyce on either her green or brown side. I’ll randomly choose green. That puts the paternal side on the top for Jim and Joyce:

Becuase Joyce’s green paternal segment is Rounesville, that means that Jim’s orange segment must be the paternal husband, Gurney.

Next, I would like to check the paternal crossover for Joyce. The recommendation at the Facebook Visual Phasing side is to look for ‘stranger matches’.

Stranger Matches

If I see that Jim has a match or matches that go across the 149 crossover line, then I can assume that he has no crossover there. The hitch is that the match going over the 149 line needs to be on Jim’s paternal side on the top of his Chromosome 7.

Here is a spreadsheet of Jim’s matches on Chromosome 7. Jim’s match with Tim goes clearly from 138-155M. That meets one requirement. Is this a paternal or maternal match for Jim? My thought was that if this match was maternal, then Tim should match my sister Heidi at the top and me at the bottom of the list in blue. I checked and Tim only matched Jim. That means that the crossover belongs to Joyce and is likely on her paternal side. The only thing I didn’t rule out is that the crossover could possibly be on Joyce’s maternal side.

Here I went with my original guess that Joyce’s crossover was on her paternal Gurney/Rounesville side. Because I gave the crossover to Joyce’s paternal side, that meant that there was no other crossover at 149 and I moved the maternal segments to the left. I still have figured out whether Hartley or Snell is blue or brown. Next note that the segment from 110 to 126M is a no-match segment. That means that there must be a maternal crossover next. The reason for that is that no-match means four different colors. Jim and Joyce already have different colors on the maternal side. If we change one of those colors with a maternal crossover, there will be a match between 110 and 126M.

In order to get a no-match from 110-126M, Jim or Joyce’s DNA must be Rounseville from 110 to 126M.

Stranger Match or More Cousin Matches?

I really should go with both, but I’ll start with the stranger match. Jim has matches between 105 and 134 showing no crossover there. When I look at one of those matches and run those that are in common, I get this:

#1 is Jim’s sister Joyce. 2-6 are the strangers and #7 is actually a 2nd cousi of mine, but it could be from a match on another line. So Jim is matching the strangers in that 105 to 134M area. However, he is matching Joyce starting at 126. That gives me the impression that it is Joyce that has the crossover. On the other hand, I don’t see any of Joyce’s matches on her match list that go through 126M.

i am moving slowly from right to left on Chromosome 7. The segments that I am really interested in, I have no information on – except that one is Snell and one is Hartley and they appear to be relatively large segments, so far.

Phasing by Geography

I had mentioned that Snell’s ancestors were from SE Massachusetts going way back. The Hartleys came to the US from Lancashire in the last half of the 1800’s. As far as I know, the Gurneys and Rounesvilles have been around SE Massachusetts for several hundreds of years also. When I look at Joyce’s matches at Chromosome 7, I see some interesting emails. Between 155M and the end of Chromosome 7, Joyce has three small matches with people three people that have nz, au or uk in their email addresses. That gives me the opinion that at least from 154M to the Joyce could have Hartley DNA. That also brings up the question as to whether Joyce has a maternal or paternal crossover at 149M. If I go with what we had already, I would get this:

Starting to Visually Phase Chromosome 8

I can come back to Chromosome 7 at some time. I’m looking at Chromosome 8 as I wrote a Blog about a Lancashire matcher here. Here is how Anne matched Joyce and two of my second cousins:

The important part is that Anne matches Joyce from about 17 to 59M. That is a pretty good match. Here is the common ancestor:

The other important thing is that even though the match points back to Howorth, this is on Joyce and Jim’s Hartley grandparent line.

Here is how Jim and Joyce match each other:

Here I did something different. I started by mapping a HIR or Half Identical Region. That means that one grandparent matched and the other two did not. We know that Joyce matched on the Hartley segment and Jim did not.

That means that the maternal Hartley/Snell side is on the bottom of their Chromosome 8. From here, we can logic a few more segments. Going from HIR to the no-match left, that means the top part will have to change for there to be no match at the beginning of Chromosome 8. Using similar logic, for all to match (in the HIR region), the crossover will have to be on the bottom of Chromosome 8.

Next, on Joyce’s match list, I picked someone who she matched that went through the 70.7M crossover.

I picked the 18 cM match. Then I picked people that matched both Joyce and the stranger’s 18 cM match.

#1 is Jocye’s match to her brother Jim. The next three matches go up to 74, so they go through the crossover. #5 is our stranger, Sheila with the 18 cM match. There is another interesting thing about Match #2. That is Jo who is on Ancestry with a private tree. However, when I click on her name, it says she is from Lancashire, England. Someone with a tree at Ancestry and DNA at gedmatch is good news to me, so I wrote an email to her.

Here is another piece of the puzzle:

I don’t know what the orange represents, but I don’t match Joyce and Jim on that side, so it isn’t as important to me. I was interested in separating the green DNA from the blue – or the Snell from the Harltey DNA. I was able to do that thanks to visual phasing and a match with Anne.

Wrapping It Up

  • It is possible to do some visual phasing with only two siblings. However, cousin matches, and stranger matches are needed.
  • Geographical phasing is also important. I like the use of email extensions to identify non-US matches.
  • Mapping my father’s two cousins is important in separating my Lanchashire ancestors from my colonial Massachusetts ancestors.
  • Work is needed to get AncestryDNA testers to upload their results to gedmatch.com
  • More matches could be found by checking FTDNA
  • More work is needed in tracking down genealogies of gedmatch mathes. This would help identify segmens of visually mapped chromosomes.
  • Attention to mapped segments of interest (in this case Hartley) can lead to matches to follow-up with.

Mapping James Frazer born 1804 and Violet Frazer born 1803

In my last Blog, I wrote about Doreen’s results. Doreen and I have the common ancestors of likely first cousins, James Frazer b. 1804 and Violet Frazer born 1803. For some reason, I don’t believe that I have ever mapped this couple out using Kitty Munson’s Chromosome Mapper.

Descendants of James and Violet Frazer

The people in bold have all taken autosomal DNA tests. That is, except for Rick who took the YDNA test. If I compare myself to Susan, Doreen, Pat, Gladys and Bill, the DNA that we share would represent either James or Violet Frazer.

Kitty Munson’s Utility requires the information be put into a CSV File like this:

I share the first and last segments with Doreen. The second I share with Pat. I share rows 3, 5, and 9 with Susan. I share rows 4 and 8 with Gladys. I share rows 6 and 7 with Bill. However, they are the same segment. One is as reported at FTDNA and one is as reported at Gedmatch.

Here is my map of just these two ancestors:

This is just my map. The map for each of my siblings and my cousin Paul would look different. Also The map for each of the people in the yellow part of the James/Violet Tree would also look different.

Here is the blue James/Violet segments  (now showing as navy blue or black) with other segments I have identified:

Next, I would like to put the ancestors in a better order. They appear randomly, but I am guessing that the first chromosome gets the first color, etc. as I have my table sorted by chromosome. My four grandparents are Hartley, Frazer, Rathfelder and Lentz. So I would like to sort them by these four grandparents. Then I would like the older ancestors in each line first. That is, except for Annie Snell. I have her listed separately as I must have figured out some of my DNA was from her. However, her dark green is overshadowed by the blue Hartley/Snell segments.

My new order will be:

Hartley:

  • Esther Howorth
  • Otis Snell
  • Annie Louisa Snell
  • Hartley/SNell

Frazer:

  • Richard Frazer
  • James/Violet Frazer
  • George Frazer/Margaret McMaster

Rathfelder

  • Hans Jerg Rathfelder/Juliane Bietenbinder
  • Rathfelder/Gangnus
  • Rathfelder/Lentz

Lentz

  • Nicholson/Stanisforth
  • Nicholson/Ellis
  • Lentz/Nicholson

That configuration gives me this:

I like the colors better. However, Annie at the first part of Chromosome 16 is still subsumed in Hartley/Snell in dark green. Also Otis Snell is a tiny segment at about 4cM. I think I’ll take out Otis and Annie:

I like this version the best. I have a lot of Hartley/Snell as this couple had 13 surviving children. As a result, I have a lot of 2nd cousins with matches. Hartley/Snell is now light blue. James/Violet Frazer is now dark green. My goal is to split up the light blue into Hartley and Snell.

Summary and Conclusions

  • I added some important James Frazer/Violet Frazer segments to my Chromosome Map
  • This couple was born in 1803/4.
  • Mapping points out where you have cousin matches and where those matches are missing
  • I hope I haven’t missed any other important ancestor segments on my map

My First Try at Two Sibling Visual Phasing

I recently had my wife’s Aunt Elaine’s DNA tested. She is the only sibling of my mother in law Joan. I would like to try to visually phase these two. Fortunately, they have have a half Aunt Es wasther. She is related on only one of their grandparent’s sides. That side is Upshall from Newfoundland. I am hoping that Esther’s DNA results will be helpful in visually phasing.

Aunt Esther’s Upshall DNA

Here is how Elaine matches Aunt Esther:

Here is how my mother in law Joan matches Esther:

It looks like Esther will be a big help in identifying Elaine and Joan’s maternal grandfather side.

Chromosome 1

I’ll just jump in and try Chromosome 1. That is the big one.

Already I have a bit of a problem. There is some green within the second HIR or Half Idendical Region (yellow area). I am ignoring it for now. This graphic shows that Joan and Elaine have no FIRs on Chromosome 1.

Next I add Esther’s DNA to the mix:

This is interesting. I see two maternal crossovers for Joan. Joan’s maternal grandparents are Upshall and Daley. Esther represents Upshall. So at 17.4M, Joan must go from Upshall to Daley. I say this because Elaine continues to match Esther (Upshall) after 17. 4M. The same thing happens at marker 117.6. Now look at Esther. She must have a maternal crossover between 70 and 117.6M.

Actually, it looks like I made a mistake. My first comparison of Joan and Elaine is the same as Esther and Joan, so I must have done it wrong. I’ll make sure I have Joan and Elaine this time and lower the levels to 3 cM and 300 SNPs. Now my results look more reasonable.

That looks a lot better. Forget my comment about there being no HIRs. There are at least five green HIRs between Elaine and Joan. Things didn’t line up perfectly, but I tried to fudge them in. Upshall is shown in orange which corresponds to the matches with Aunt Esther. Next, I add in some more Maternal segments for Elaine and Joan:

Again, the orange pretty much mimics the matches that Joan and Elaine have with Esther. The difference is with Elaine’s last orange segment. That goes more to the left as I don’t show a crossover there. There should also be a maternal crossover for Elaine to the left of her second orange segment. That means that to the left of that middle orange segment, there should be some green Daley.

The Paternal Part of the Puzzle

It would help to have some paternal matches at this point. Melissa is one match that I have mentioned in at least one previous Blog.

I like Melissa’s matches, because she doesn’t show any obvious Rayner in her ancestry. A Rayner would mess things up as that is Elaine and Joan’s maternal grandmother’s name. Jane would also be a good choice here.

Melissa adds some information. She represents the Ellis side. She matches Joan, but not Elaine. As Melissa does not match Elaine in this location, I have put down the paternal grandmother Daley in Elaine’s segment below Joan’s Ellis segment:

[Edit: the reddish paternal segment on Elaine’s bar should actually be Rayner.]

Now I have a little bit of paternal informatiion, but I appear to be at an impasse. Next, I will look at Joan’s Excel spreadsheet of matches. I see a Hayley there that matches through the Dicks Line. Dicks is a mother of Upshall, so that counts as an Upshall for my purposes.  Here is Joan’s match with Hayley:

This does not help as Esther already matches in this area. However, it does point out that I missed a crossover at the beginning of the Chromosome where the FIR (green) between Elaine and Joan goes to HIR (yellow).

I’ll take a break for now and move on to another Chromosome.

Mapping the X

I mentioned that Chromosome 1 was the largest Chromosome. The X Chromosome is fairly large also. There are some advantages to mapping the X Chromosome. One advantage is that Elaine and Joan’s paternal X is already mapped to their father’s mother (Daley).

See, I already mapped both of their paternal side X Chromosome. Joan and Elaine both get the same X Chromosome from their dad. This is the same one he got from his mom (Elizabeth Daley). Here is the genealogy:

See, that is why I check. Joan and Elaine’s dad was an Ellis and his mom was a Rayner, so I got that backward.

That leaves Upshall and Daley for the maternal side. I mapped three maternal crossovers, but there may be more that I don’t see.

Again, Esther will represent Upshall and not Daley. That is because Elizabeth died in the flu epidemic. Fred Upshall remarried a Shave and had Esther.

When I check Esther’s X against Elaine’s, I get no match. Joan and Esther, however, do match:

In fact, Joan’s matches with Esther line up with the crossovers I have. That is good news. Here I also changed the color of Rayner to be consistent with Chromosome 1.

 

I’m pretty sure the end result should look like this:

Back to Chromosome 1

In the Dicks DNA Project I have been working on, I have a Triangulation Group Summary. The mother of Fred Upshall was a Dicks, so Dicks helps to identify Upshall DNA.  Here is a partial shot of that Summary for Chromosome 1:

I have not added Elaine to the Summary yet. This shows that Cheryl, Charles, Joan and Elaine match on Chromosome 1. Here is how Cheryl matches Esther, Elaine and Joan:

Adding Cheryl and Position Numbers

I got the numbers on the top of the Joan/Elaine comparison from Gedmatch’s full resolution option on their chromosome browser. A few observations:

  • Cheryl’s matches confirm Elaine’s crossover at 94 and Joan’s at 118M
  • Cherlys’s match with Joan also indicates a likely Paternal crossover for Joan at 70M
  • Elaine and Esther match to 158M. That means that Elaine likely does not have a crossover at 152
  • Due to the centromere of Chromosome 1, the two browsers align very poorly around 152M. Note on the original comparison between Joan and Elaine how quickly the numbers go from 118 to 152M.
  • As mentioned above, Elaine’s Upshall segment should go past 152, but then there is a FIR. That means that Joan will have an Upshall segment above Elaine’s. That means that her Daley segment will look tiny, but it will actually go from 118 to 152M which is not so small.

Based on my above observations, I have this new map:

I gave Joan a paternal crossover at 70.5M. I also gave her a paternal crossover at 152M. This leads to another observation. The area between 60.5 and 70.5M is a FIR. That means that for Joan and Elaine, their paternal grandparent and maternal grandparent have to match. That means that at 60.5M, Joan’s Ellis DNA has to turn into Rayner DNA or Elaine’s Rayner DNA has to turn into Ellis DNA. Either way, there will be a Paternal Crossover for either Elaine or Joan at 60.5M. That means that there is not a maternal crossover at 60.5M for Elaine nor Joan. That will expand the maternal Daley to the left for Elaine and Joan:

This leads to more observations:

  • One I could have noted before. Betwen 17 to 26.6M Elaine and Join do not match each other. Elaine has Upshall DNA there, so Joan has to have Daley there.
  • Elaine has a Maternal Crossover at 26.6M. That means that there is no Paternal Crossover there. That means that I can move the two paternal segments to the left.
  • The fact that Elaine has a Maternal Crossover at 26.6M means that Joan has no maternal crossover there, so the Daley segment can be moved to the left also for Joan.

Moving the Daley segment to the left for Joan created a Maternal Crossover for her at 17. That means that there is no Paternal Crossover there and the two Paternal segments can be moved to the left:

So Chery’s matches were a help.

Summary and Conclusion

  • A first shot at two person visual phasing has shown promise.
  • Chromosome 1 is a difficult one, but I got a start on it
  • The X Chromosome was mapped for Elaine and Joan.

 

 

 

Visual Phasing: My Father in Law’s Chromosome 22

Looking through the visual phasing of my father in law’s family, I notice I am missing a map for Chromosome 22. Chromosome 22 is the easiest and hardest Chromosome to visually phase. It should be the easiest because it is the shortest Chromosome and should have the fewest number of crossovers. It should be the most difficult because it should have the fewest cousins matches. I assume that I haven’t visually phased Chromosome 22 because of the hard part.

Gedmatch One to One Comparisons

To do visual phasing, I need to compare my late father in law Richard to his two sisters in the Gedmatch Chromosome browser. Here is how Richard matches one of his sisters, Lorraine:

This shows that Richard matches his sister Lorraine all along the Chromosome except for a little segment between 43.6M and 43.8M. Hopefully this is accurate. Other comparisons should bear this out. By comparing siblings, we are looking at how many grandparents’ DNA they share. Green means that Richard and Lorraine share two grandparents’ DNA. More specifically, they share one maternal grandparent and one paternal grandparent.

Yellow means they share one grandparent on a maternal or paternal Chromosome and don’t share the grandparent on the opposite Chromosome. For example, if they share the DNA from a maternal grandparent, that means that they don’t share DNA from the same grandparent on the paternal Chromosome. This is all important information for visual phasing.

Finally, above the break in the solid blue line above is a red area. That means that in that little segment, Richard and Lorraine share DNA from neither of their grandparents. This is important information. Richard’s paternal grandparents are Butler and Kerivan. His maternal grandparents are LeFevre and Pouliot. So say Richard gets his DNA from Butler and LeFevre in that red area. That means that Lorraine must get her DNA from Kerivan and Pouliot in the red area. Those are the rules for Visual Phasing.

Next I put the three comparisons into Excel.

Then I look for changes in the colors on the Chromosome Browser. These changes should come in pairs. The first two changes are in the first two bars. The colors go from green to yellow. That means that the shared DNA goes from two grandparents to one. Lorraine’s name is associated with both those comparisons, so we say that Lorraine has a crossover there. A crossover is where Lorraine’s DNA changes. Before the crossover, she is getting DNA from one grandparent, and after the crossover, she is getting her DNA from another grandparent.

Again, these crossovers show up in pairs. A top/top pair assigns the crossover to Lorraine. A top/bottom pair goes to Richard. A bottom/bottom pair of changes assigns the crossover to Virginia. Above, Lorraine and Virginia got 2 crossovers each and Richard got three crossovers.

Next, I show the two Chromosomes that everyone has – in this case for Chromosome 22. Unfortunately, I don’t know which side is maternal and which side is paternal at this point.

These two copies of Chromosome 22 are blank for each sibling right now, but I’ll fill them in with four colors representing the DNA they got from each of their 4 grandparents. When the DNA changes from Butler to Kerivan on the paternal copy, for example, that is where the crossover is for a particular sibling.

Visual Phasing

Richard and Lorraine share a large green area. That means that they got the same DNA from one grandparent on the maternal side and the same DNA from one grandparent on the paternal side. The DNA from those two shared grandparents will be represented by two colors.

The blue and orange colors represent the DNA that Richard and Lorraine both share from the same grandparents: the same maternal grandparent and the same paternal grandparent. Unfortunately, I don’t know which side is maternal or paternal at this point and which grandparents they share. I just know they share the same grandparents.

Note also that Richard has a crossover at the beginning and end of this colored-in segment. We don’t know if his crossovers are on his maternal Chromosome 22 or paternal Chromosome 22 – or it could be that one crossover is maternal and one is paternal. That means that we will keep his blue and orange segments where they are – for now. However, Lorraine’s first crossover is to the left of the green shared area. That means her blue and orange DNA segments can move to her first crossover. The same segments can also be moved to the right up to Lorraine’s next crossover. No crossover means no change in the DNA.

This show that Lorraine got two pretty long segments of DNA. Let’s say she got them from Grandparents A and C.

Next we need more grandparents. We only have two out of the four. In the middle of Chromosome 22, notice that Lorraine and Virginia have no match. There is a large break in the dark blue line. That means that in that area, If Lorraine has DNA from Grandparents A and C, Virginia has DNA from grandparents B and D. Now we need two different colors:

To check notice that Richard and Virginia also have no match in a smaller area, therefor they also show two different colors in that area. Virginia has the last crossover, so I move the brown and green segments to that crossover.

Richard and Virginia have a smaller green area starting at position 43.8.

Richard has no crossover that prevent the brown and green segments from going to the end of Chromosome 22. That is as far as we can go with the bright green areas (which are also called Fully Identical Regions or FIRs) and the red non-matching areas. At this point we could look at the yellow areas which are also called Half Identical Regions or HIRs. Or we could look at cousin matches to see if they give any hints. I’ll look at cousin matches.

Cousin Matches

A first cousin should sort out the maternal or paternal side. I pulled up Virginia’s spreadsheet where I have a lot of her matches. On Chromosome 22, I notice 2 of Virginia’s maternal 1st cousins, Joe and Pat:

 

In Virginia’s spreadsheet, I have these positions in pink for Virginia’s maternal side. Next, I checked out some of the matches at Gedmatch and got this:

Here, #1 is John, a nephew. Nephews are not as helpful as they can be related on the maternal or paternal side. Note also that something seems to be going on around 25.4 M. This could be Virginia’s maternal crossover. In fact, I think that is more likely than having four other people having their crossovers there. #2 and #3 are Pat and Joe.  #4 is a maternal 2nd cousin once removed named Sandra. More about her later. Now that I know where there is a likely maternal crossover at 25-1/2M, I’ll go back to the visual phasing.

Visual Phasing HIRs

So far with the visual phasing, everything is equal on the chromosomes. That is because, we have only dealt with FIRs and no matches. HIRs upset that balance and make us choose sides. Because the HIR creates an imbalance of one copy of the Chromosome vs. the other, we only get one shot at doing that. I don’t know if my reasoning is right, but because I have some information already for the left side of the Chromosome (Sandra), I will choose an HIR on the right side. I will choose the small HIR Lorraine and Virginia have starting at 43.5M.

Here on one copy of Lorraine’s Chromosome 22, the blue goes to brown while the other copy remains orange. Next, I see that Lorraine has no more crossovers, so I can move the DNA colors over to the right.

In addition, Lorraine and Virginia have an FIR on the right, so I can copy Lorraine’s colors onto Virginia’s maternal and paternal side. Now I have a lot of Chromosome 22 mapped out, but I still don’t know which side is maternal and which is paternal. Here is how Pat matches with Virginia, Richard and Lorraine:

Remember that Pat is a maternal cousin. It is important to note that Pat matched Virginia and Richard but not Lorraine. The yellow pattern of Pat matching Virginia and Richard matches the green above that I mapped out. That tells me that green and orange are the maternal side and brown and blue are the paternal side.  So thanks to Patricia, my in-law’s have identified maternal and paternal sides. Yay.

Next I bring back some cousin matches:

I had guessed that Virginia had to have a maternal crossover due to cousin matches at about position 24.5M. #4 above is Sandra. She is one of my in-law’s top maternal Gedmatch matches. She also is a match at AncestryDNA. She doesn’t have a public tree but she told me who their common ancestors are:

 

Sandra is a 2nd cousin once removed to Lorraine, Richard and Virginia. As such, they share only one of my in-law’s grandparents’ lines which is LeFevre.

Here is how Sandra matches Virginia and Richard:

Now I can add in LeFevre in the green segments.

Once I know green is LeFevre, then orange has to be Pouliot.

Next, I was pretty sure that Virginia had a maternal crossover at 25.5. Knowing that, I can fill in the rest of the puzzle:

  • Note that on the left had side of Chromosome 22, there are three FIRs in a row going from top to bottom. That means the three siblings have their DNA from the same two grandparents. They all have Pouliot on the maternal side and either Butler or Kerivan on the paternal side.
  • The maternal side is French Canadian.
  • The paternal side is Irish.
  • There aren’t as many paternal cousins matches to fill in the blue and brown as there are maternal matches. I’m looking for cousin matches to fill in the blanks
  • Virginia has DNA from only one paternal grandparent shown in reddish brown.
  • Lorraine has DNA from only one maternal grandparent – Emma Alphonsine Pouliot
  • There will be parts of the Chromosome where there is no DNA representation from one grandparent. For example, no one got green LeFevre DNA at the beginning of the Chromosome. No sibling got blue paternal grandparent DNA at the beginning or at the end of Chromosome 22.

 

 

Part 7 – Raw DNA From 5 Siblings and a Mother – DNA From Mom

I’ve spent my last 6 Blogs on this topic finding out which alleles came from my dad. In this Blog, I would like to work on finding my siblings’ and my alleles that come from mom.

The Ironic Step of Phasing – Mom Alleles from Dad Alleles

I call this ironic step in that it was my mom that was tested for DNA. Based on her results we found out a lot of the alleles that her children got from our dad who passed away quite a while ago. Now, we use those alleles we got from dad to figure out which alleles we got from mom. From the Whit Athey Paper referenced at the ISOGG Web Page on Phasing:

If a child is heterozygous at a particular SNP, and if it is possible to determine which parent contributed one of the bases, then the other parent necessarily contributed the other (or alternate) base.

 

First I copy my FillinOne Table to a MomfromDadOne Table. Then I’ll do a query on that.

This says where I am heterozygous, and I have an allele from dad, I want to see where I’m missing one from mom.

I have over 50,000 of these which will be easy to update. I will want to put Joelallele2 in the blank where JoelfromDad = Joelallele1. Then I will want Joelallele1 in the JoelfromMom space when my allele from Dad is Joelallele2.

I ran this query twice for each sibling, so 10 times. This updated 50-60,000 alleles per sibling, so about a quarter of a million alleles altogether.

Finding Mom Patterns

Now that I have filled in more alleles from Mom, it should be easier to find Mom Patterns. Here is a Query to find Min and Max for the AAAAB Pattern:

Results in:

This saves a lot of time and gives me the start and stop positions of all the AAAAB Mom Patterns. In my previous look which I now see as premature, I only found 2 AAAAB Patterns. Now thanks to my MomfromDad update above, I have at least 17 AAAAB Patterns. The only drawback is that if there is more than one AAAAB Pattern within a Chromosome, it will not show that. However, if I run all the Mom Patterns, and find overlapping Patterns, that can be reconciled later. In fact, I see an overlap already:

The first AAAAB Pattern I found was 162-233M which I did see as large. I already had found an AAABA Pattern from 192-249M. This could mean that AAAAB goes from 162-192 and that the 233M AAAAB pattern was just an outlying singleton.

I also recall that I want ID’s, so I’ll add that to my query:

Because I have so much new information, I’ll put this into a new spreadsheet:

AAABA Mom Pattern

I just have to change the Query slightly to get the AAABA Mom Pattern:

The results of this Query go into the new spreadsheet. This spreadsheet will be sorted by Chromosome later.

I added a column for IDEnd minus IDStart:

Where this is zero, it would indicate a single Pattern.

I went through all the Mom Patterns and got a spreadsheet of 194 rows that need to be reconciled. Here are Chromosomes 1 and 2 sorted:

Reconciling Chromosome 1

I have added in a column for possible assignment of a crossover to a sibling. Note that up to about 20M everything looks OK. There are discrete Patterns. ABBBA to AABBA is a change in the second position which belongs to Sharon. The change from AABBA to AABBB goes to Lori. Then the AABBB is the same as BBAAA which goes to ABAAA. That would be my crossover [Joel].

I did a Query showing where all the alleles were filled in for the Mom Patterns:

This shows where my Crossover is at ID # 8984. I have added a few more columns to my Mom Pattern Spreadsheet to add the more refined cut points:

Next I’ll look at 77M.

As best I can tell, there are two single AABAB’s in the middle of an AABBB Pattern. Next I will want to find the start of that AABBB Pattern. To find that I do a query to look for the AABBB Pattern in Chromosome 1. That Query results in more AABBB Patterns.

A Problem

I have a problem in that it appears that the Mom Patterns of AABBB and AABAB appear to overlap each other on Chromosome 1. I assume that means that I did something wrong.

refilling the dad patterns

That means that I should go back and fill the Dad Pattern back in:

First I recreate a Fill-in Table using the old Three Principles Table. Then I do update queries on that. Hopefully these numbers will work:

Back to Mom Patterns From Dad Patterns

Just so I’m not going backwards, I’ll redo this step. I copied my revised fill-in Table to a revised Mom from Dad Table. This time I’ll keep track of the alleles for fun:

So in retrospect, I don’t know if I made a mistake with the Dad fill-in’s or in the Mom fill-in from the Dad Pattern. Hopefully, there were no mistakes this time.

 

Part 6 – Raw DNA From 5 Siblings and a Mother – Filling In Paternal Blanks

In my last Blog, I said that I would work on the Maternal Patterns and then fill in blanks. However, my Maternal Pattern Table is not very filled. After some thought and re-reading the Whit Athey Paper on Phasing, on which I base this work, I decided to:

  1. Fill in the Paternal Blanks
  2. Use the Paternal Data to fill in the Maternal alleles
  3. Fill out the Maternal Pattern Table
  4. Fill in the Maternal blanks based on the Maternal Pattern Table

Filling In Paternal Blanks

I might as well start filling in the AAAAA Patterns. On my Dad Pattern Excel Spreadsheet, I can filter for that pattern:

However, I now need a formula for Excel including all the ID positions above. This was the point of my starting this project over – to get those IDs. The formula will be in the form of “Between A And B OR Between C And D OR…” So first I need a formula in Excel to create the formula in Access. That formula is called Concatenate. According to a Google search, concatenate means to “link (things) together in a chain or series”. The symbol in Excel for concatenate is simply the ampersand (&).

Here is my formula and the outcome:

However, I have another idea. I can concatenate the concatenation. First, I add an extra space on the end of my “Or”. Then I drag down the formula to fill in the other chromosomes. Then I take off the last “Or”.

That gives me this helpful string of AAAAA Positions:

This will save me a lot of cutting and pasting in Access.

Back to Access

First I copied my old Table to a new one called tblFillInOne. I will create an Update Query for that Table.

I am only updating Dad alleles from other Dad alleles, so I import those 5 alleles plus the location ID. Then I use the expression builder, to paste in the location of the AAAAA Patterns in all 22 chromosomes. So now I have the Pattern and the location, but I need some more criteria. I would like the criteria to say if there is any allele in any of the five columns and any blanks in those columns, then replace the blank space with one of the existing alleles.

Here is a simple Update Query:

This says, that if my allele is null and Sharon’s isn’t, then replace mine with Sharon’s. The problem is that this would take four separate Update Queries. With 5 siblings, that would be 20 queries.

Another risky Update Query would use this form:

Here I am saying if any allele is not null (other than mine) replace that in my slot where I have a blank. The thing I don’t know if the Update To: field can have a variable criteria. I’ll try it. When I run this as a Select Query, it puts a bit of a strain on my computer. Eventually, it gives me 18,385 rows. When I run the View function on the Update Query, I get the same number of rows, so I’ll hit the Run button and hope for the best.

If I run this Select Query again, I should get no results if everything updated.  I did get no results, so I assume that it worked. I want to save this Update Query and use it for the other four siblings.

Filling in Sharon’s missing alleles from the AAAAA Paternal pattern

I used the same logic for Sharon:

Now she has all the Is Null values and I don’t. I moved the Update To: criteria over to Sharon. I took out Sharon’s allele and added mine in her place. Again, this gives my old computer a workout. I get 18,315 rows again which seems suspicious. I see the problem. I appears that Access updated my results with a (-1) rather than with an allele.

That means that I just have to do 20 Queries. However, they should go quickly.

Back to the Simple AAAAA Query

Due to all the Update Queries, I’ll make a Spreadsheet to keep track of each Update Query I do:

It turns out that it is easier to run this Update Query sorted by ‘From’:

That way, I can just move Sharon’s allele from Dad and the Is Null along the Update Query:

With these fast 20 Update Queries, I updated over 100,000 alleles:

AAAAB Fill-in

This could be a little easier. For this one, we don’t want to touch the last ‘B’. The last B represents Lori, so we will only be filling in to and with the other four siblings.

And then we need the fill-in locations.

AAABA and AAABB Fill-in

AAABA is about the same as AAAAB except the B in the AAABA corresponds to Jonathan. He is all alone as a B so he gives no alleles and takes no alleles. The other siblings share their AAAA’s in this Pattern.

In an AAABB Pattern, the three A’s will share with each other and the two B’s will share with each other. This happens to break down along V1 and V2 lines, so I expect there will not be as much sharing as between AncestryDNA versions.  The sharing of A’s and B’s looks like this in my Fill-in Tracker:

I have darkened out the areas where an A cannot share their A with a B and a B cannot share their B with an A. As I predicted, the AAABB filled-in alleles were less:

All the other patterns filled in

All the other patterns will be of the same type. There is one AAAAA which is all the same. The other combinations are four of one type and one of the other or three of one type and two of the other.

There are 20 fill-in’s for AAAAA. As a quality check, there are 12 fill-in’s for a 4-1 Pattern and there are eight fill-in’s for a 3-2 Pattern. I would recommend using a fill-in tracker to make sure all the combinations are being covered. The specific numbers of alleles being filled in for each combination of each Pattern are not all that important, but they are interesting.

Fixing an abbab mistake

When I was filling in the ABBAB Pattern, I noticed a mistake I made. I filled in 3754 rows of Joel alleles into Heidi blank spots. In an ABBAB Pattern, I am only supposed to be filling in my alleles into Jon’s blanks. Here is the mistake:

That means in those positions, I’ll have an ABAAB Pattern where I should have an ABBAB Pattern. Oh no. So how do I fix that? I need a fix query. Under Pos ID, I’ll put in all the locations that are supposed to be ABBAB. Then I’ll make sure the first position isn’t the same as the second:

That results in only 103 rows.

If I update those 103 rows to Null, that should be a start:

Next I set the first position to be different than the last in this ABBAB Pattern:

That fixes another 212 rows. That may be all the rows to fix. I looked for more JoelfromDad = Heidi from dad where JoelfromDad <> LorifromDad and where JonfromDad <> LorifromDad, but didn’t see anything. The other updates must have been in areas with AAAAA by chance areas. In the meantime, I copied the first two columns on the left to the right, so I don’t lose my place when I am scanning across the spreadsheet.

Dad Pattern Fill-in First Round

The dark blue areas are the ones where there should not be any filling in based on the Pattern.

Summary

  • The Fill-in Step is a major part of phasing. In this step I filled in over 1 million paternal alleles in my DNA and in my 4 siblings’ DNA.
  • I noticed a mistake I made along the way, but figured out a way to fix it.
  • I figured out a shortcut to describe the different patterns by way of ID’s. The shortcut involved using a concatenation of a concatenation.
  • I haven’t yet filled in the random AAAAA Patterns that are within the other patterns. I imagine that would be important to do at some point. I know that David Pike has a utility to find Runs of Homozygosity. I suppose that would be useful for filling in alleles.