Wednesday, June 24, 2020

Y-DNA reveals unsuspected relationships



Sometimes Y-DNA reveals unsuspected relationships between men with different surnames and in different locations. It in only by researching all of them that we can find the answers we have been seeking. 

This case is a great example. I have an ancestor named Henry Gragg who was born 1763 in South Carolina. After exhaustive research, I was no closer to finding his parents. Y-DNA was the best option to find his father. I might even be able to extend this line several generations further.

If you are new to Y-DNA testing, please review Y-DNA STRs, SNPs, and Haplogroups. The page will open in a new window so that you don't lose your place here. 



First Y-DNA test


A man with the surname of Gragg took a Y-DNA test from Family Tree DNA. He is a descendant of Henry Gragg from South Carolina. When Y-DNA results are returned, there is a list of people with similar results. Here was Gragg's list of matches at 37 markers [The given names have been erased by me to protect privacy]:



FTDNA match list
37-marker match list
Mr. Gragg's closest STR matches appear to be a Craig and two men named Smith. Two of the men on the match list had family trees, and they were both descendants of an ancestor Edward Gregg, born 1722. He lived in the same area of South Carolina as Henry Gragg did. Could these men be related? 

I have researched the Graggs in South Carolina for years. As it turns out, in this area of South Carolina there was no other Gragg, Gregg, Grigg, or other man with a variant surname except Edward Gregg. Edward Gregg arrived in South Carolina in 1752 with his wife and four children. Although no documentation has been found of the children of Edward Gregg, it appears that Henry was his son. Y-DNA supports this supposition. 

Here is the Gragg tree with Edward Gregg added as Henry's father. Note that Henry's descendant is also descended from the James Mullins discussed in a previous post, Y-DNA: Big Y test solves STRs and convergence.


Descendant of Christopher Gragg

Here are the family trees of the two descendants of Edward Gregg:



Descendant of John Nelson Gregg


Descendant of Daniel Gregg


These two Gregg men are more closely related to one another than they are to Mr. Gragg. However, one of them is a genetic distance of two from Mr. Gragg, and the other is a genetic distance of four. There are also Craigs and possibly Smiths who appear to be related. The Genetic Distance column is not enough to determine the relationships.


Craig, Gragg, and Gregg: 
How are men with these surnames related?


After seeing that Edward Gregg was a possible ancestor to Mr. Gragg there were various routes that could be taken to learn more. One is to upgrade the results to see more STRs. Another is to upgrade to Family Tree DNA's Big Y test which includes 111 STRs and much more. Mr. Gragg and a descendant of Edward Gregg [through Edward's great-grandson John Nelson] took the Big Y-500 test to find the most information about their relationship. The Big Y-500 test was the test available in 2018.


More STRs


Included with the Big Y test is an upgrade to 111 STRs.  At 67 markers, the two descendants of Edward Gregg are still showing the same genetic distances. This means no new mutations occurred in the 38-67 marker panel. 


Y-DNA matching
67-marker match list

At 111 markers there is only one match, and he is the Gregg who has taken the Big Y-500 test. We should be able to find him on Mr. Gragg's Big Y match list.




111 Y-DNA marker matches
111-marker match list

But we also need to see why one of the Gregg descendants is a genetic distance of two and the other is a genetic distance of four from Mr. Gragg. The Y-DNA match list only shows us the total genetic distance. It does not show the details. For this we need to join surname or other projects.


Joining Projects


To join a project, click myPROJECTS at the top of the screen, then select Join A Project:


Join a Y-DNA Project
Join a Project

You will see various categories of projects. We will look for a Gragg surname project. In the Surname Projects category, click on the letter G.


Family Tree DNA Project links

There are no Gragg or Gregg projects, but there is a Grigg surname project. Click the name of the project, then click Join on the next page. There is no charge to join a project, and you can join as many as you wish. 


How to make results visible in projects


The primary reasons to join projects are to compare STRs, see matches that do not appear on your match list, get advice from project administrators, and advertise your results to encourage others to do DNA testing or to upgrade their results. But many people do not realize that your project administrator and other members of the project may not be able to see the results. This defeats the main advantages of projects. This is the most important part: Update your account settings.

Hover your mouse over your name in the upper-right of your screen. A drop-down menu will appear. Click on Account Settings:


Account Settings

You will next see the Account Settings screen with several tabs. It is essential that you click on each tab. We will just look at the Project Preferences tab right now.


Project Preferences


On the next screen you will see the Group Project Administrator Access. Be sure to "Opt in to Sharing" at the bottom of the screen:



FTDNA Privacy settings
Group Project Preferences


Edit each project by clicking the pencil icon on the right. Select the Access level you want to give the Project Administrators. In most cases "Limited" is the recommended choice.


FTDNA project access
Determine Project Administrator access

When you have finished, see the left side of your home screen where you will see the projects you have already joined. 


myProjects
Family Tree DNA Projects

Click on any project name to go to its website. 


Surname Projects

Here is the Grigg surname project. Click on Colorized Chart to see the full list of STRs with the differences highlighted for each man. 


Y-DNA project
Grigg Surname Project

Even though I clicked on Colorized, these results were found in an ungrouped section that did not have modal values. Because there are no modal values, there are no colorized differences. 



FTDNA surname project
Grigg Surname Project Results

The two descendants of Edward Gregg are listed immediately above the descendant of Henry Gragg. It is difficult to see the genetic distance in the above image, but here is a closeup: 



non-matching STRs
STR differences

The first results shown are from the descendant of Edward through John Nelson Gregg. He is a genetic distance of four from Mr. Gragg [listed third]. He is off by three alleles at DYS576 and one at DYS442. Because of this three-allele mutation at DYS576, he is also a genetic distance of four from his much 
closer cousin, listed second in the table above. The second man [the descendant of Edward through Daniel Gregg] is a genetic distance of two from Mr. Gragg: one at CDY and one at DYS442. 

Mr. Gragg is also in the Craig surname project. One reason for joining multiple projects is to find more matches. Here are the results from the Craig Surname Project. The first man, who is descended from Edward Gregg, has a mutation of 16 in the last column where all the rest of the men have a 19. This column is DYS576. Because we believe that Henry Gragg and John Gregg are both sons of Edward Gregg, Edward probably had a 19 which was mutated to a 16 in the descendants of the line of John Nelson Gregg. 


Y-DNA surname results
Craig Surname Project Results


Evaluating Big Y Results


Now, let's look at the Big Y results. We cannot verify that Henry was the son of Edward without examining the mutations of several Gregg-related men taking the same test. But with just the Big Y results of these two men, we can verify that Henry Gragg and Edward Gregg have a common male ancestor. 

When the Gragg and Gregg Big Y tests were completed in 2018, Mr. Gragg had two unnamed variants. This means that these mutations occurred in his line, and not in the line of Mr. Gregg. 


Unnamed Variants
Unnamed Variants

When we clicked on the matching tab, we saw the following: 



Gragg Big Y Matching, 2018

There was only one match, and he was Mr. Gregg, descendant of Edward. There is no question now--these men share a common ancestor. Since their ancestors Henry Gragg and John Gregg both lived in the same area, the genealogical and DNA evidence indicate that they are highly likely to both be sons of Edward Gregg.

The Non-Matching Variants column shows that they are not very distantly related. There were three variants listed: 12031913, 14331435, and 22256644. The last two appear on Mr. Gragg's list of Unnamed Variants, so this means that those mutations occurred in the line of Henry Gragg. 

The mutation 12031913 occurred in the line of John Gregg (son of Edward). We can verify this by clicking the Private Variants tab, then entering the mutation 12031913 into the Position Search box.  


private variants
Verifying unnamed variants

The results will appear below the search box. It says,"Currently no results" which means that Mr. Gragg does not have this mutation.



Uploading to other databases

Often you can find out more about your DNA results by uploading to other databases. Multiple databases show additional details about your DNA results. They may also have the results of men who tested at other DNA companies. The VCF file for Mr. Gragg was uploaded to The Big Tree by Alex Williamson. At that time, Gragg had no close matches. He is listed in the last column with four other men.


Alex Williamson Big Tree
Gragg Y-DNA results in The Big Tree at ytree.net, 2018

Mr. Gragg's results were also uploaded to YFull. Again, he had no close matches. His Most Recent Common Ancestor with these men was dated at about 3500 years ago. 


Results in Y Tree at YFull.com, 2018


Mr. Gragg needs to get more matches on the Big Tree and at YFull!


A new match with a different surname


In 2019 one of the Smiths took the Big Y-700 test. This test is more comprehensive than the Big Y-500 taken by Gragg and Gregg. 

Here is how Mr. Gragg's Big Y match list now appears:


Big Y matching
Gragg Big Y Matches, 2020

You will first notice that the screen has changed from the 2018 version. Now there is a blue link to "View Big Y Block Tree." What can be puzzling is the Non-Matching Variants. The STR results made it appear that Smith was more closely related to Gragg than Gregg was. However, the Big Y non-matching variants seem to indicate that he is much more distantly related. What is going on?

The variants with only numbers, such as 14332435, 22256644, and 14767685, are all unnamed. They are unnamed because they were not seen in the tests of the other men. Like Mr. Gregg, Mr. Smith does not have the variants 14332435 and 22256644 that Mr. Gragg has. Mr. Gragg does not have the variant 14767685, but Mr. Smith does. 

Why does Gragg have such a large list of Non-Matching Variants with Smith in the Big Y results? The reason for the differences is that Mr. Smith took the Big Y-700 test. This test will show variants that the previous Big Y-500 did not.


Big Y-500 vs. Big Y-700 


Named variants start with a letter, and unnamed variants are all numerical. Therefore, the variants that start with the letters BY are all named, but they were not determined to be matches in the Big Y-500 tests of Gragg and Gregg. Each of these variants was either not read at all in the test of Gragg or Gregg, or it were not read with enough confidence in both tests to be called a match at that time. 

We can determine why some of the named variants were not called in the Big Y-500 test of Mr. Gragg by clicking the Named Variants tab, and individually entering the names of each of the named variants in the SNP Name Search box. In the screenshot below, one of the non-matching named variants, BY28663, was entered into the SNP Name Search box.


SNP name search
SNP Name Search box in Named Variants tab


When the named variant is entered, a line will appear below the search box to show the results. The "Derived?" column is the most important one.

If the results for a position are derived, this means there is a mutation there, and it is not the ancestral value. So this column tells you whether or not a mutation was found in the test results. In this case, in the "Derived?" column the answer is Yes. This is baffling because this means that Mr. Gragg apparently does have this variant. If Mr. Smith also has it, why is it showing up as a Non-Matching Variant between the two men? If we click the blue link for BY28863, we can see this variant in the Chromosome Browser.


Chromosome Browser for BY28663

The Chromosome Browser is showing that Mr. Gragg has a T in this position, and the Reference Sequence has a G (the ancestral value). This means that Mr. Gragg seems to have this variant. When we look at the Chromosome Browser, however, we can see that each read is notated with the quality of that read. This position only has two high quality reads, and this was not good enough to call this SNP as a match to Mr. Gregg in the Big Y-500 results. 

Although Mr. Smith has several named variants that were not called in Mr. Gragg's Big Y-500 test, the SNP name search reveals that  Mr. Gragg likely does have all of these.



The Big Y Block Tree

The best way to see the relationships between Gragg, Gregg, and Smith is to go the Big Y Matching tab and click on the link to "View Big Y Block Tree." 


View Big Y Block Tree

The Block Tree was based on Alex Williamson's Big Tree. All shared variants will be listed in the tree in the order in which they occurred. If more than one variant is shown in any block it means that the order of the variants is not yet known, and they will be listed in alphabetical/numerical order.


As you can see below, Mr. Gragg, Mr. Gregg, and Mr. Smith share a very long list of mutations that have not yet been seen in anyone else. These shared mutations are shown in the white block in the screenshot below. The unnamed "Private" variants, such as 14331435, are not listed.


Matches in Family Tree DNA Block Tree


The results for all three Big Y tests of Gragg, Gregg, and Smith have now been submitted to Alex Williamson's Big Tree. The results show quite a difference from the previous version where only Gragg's results were in the tree. The three of them are shown in their own branch in the fourth column from the right.



Gregg, Gragg, and Smith in the Big Tree at ytree.net, 2020



Two of the results are now on YFull where their common ancestor is estimated at 225 years before present.

Y Tree at YFull.com, 2020



Finding the common ancestor

We now know from the Big Y results that Gragg, Gregg, and Smith share a common ancestor. I contacted Mr. Smith, and he told me that according to family tradition his ancestor George Smith was born out of wedlock, and that his father's name was Gragg. I have traced his lineage, and I believe I know the name of George's father. The father lived in North Carolina. There were Craigs and Graggs in the same county, and it looks likely that George's ancestor was a Craig. He married and had sons after George was born. We need to find a descendant of this man who will be willing to take a Y-DNA test. We may then be able to tell his relationship to Edward Gregg.



What's next?


In addition to the Craig family in North Carolina who appear to be related to George Smith, there are also a large number of Craigs who are showing up as STR matches to Gragg, Gregg, and Smith. Some of these Craigs appear to be coming from the same area of North Carolina as the Craig family of George Smith.

1. Find a male descendant of the North Carolina Craig family and, possibly of the North Carolina Gragg family, and see if they are willing to take a Y-DNA test so that we can prove the parentage of George Smith. 

2. Ask one of the Craigs on the list of STR matches to take a Big Y test. If the Big Y connects these men to Gragg and Gregg (as I suspect it will), there is a good possibility of tracing all these lines much further back than we now have them.



Summary


One mistake made by beginning family history researchers is ignoring variant spellings of their surname because, "My ancestor didn't spell his name that way." In the past, there was no standardized spelling of surnames. In addition, when a large proportion of the population was illiterate no clerk asked your ancestor, "How do you spell your name?" The clerk wrote whatever he thought he heard. You may even find the clerk spelling the surname in multiple ways in the same document. Sometimes you must be quite creative in finding records of your ancestors. For example, one census enumerator spelled the surname Jonas as Yonus because this is how he heard a German immigrant pronounce that surname. In this post we saw variant spellings of the surname Gragg, and these alternates cannot be ignored.

The ancestry of Henry Gragg can only be resolved by researching the DNA relationships and family trees of the men with the surnames Craig, Gragg, Gregg, Smith, and perhaps others. This story is not over! We are now going to recruit some men with different variations of the surname Gregg to see what we can find.

I have made more significant breakthroughs in my family tree with Y-DNA than with any other test. We will soon be seeing several of these, all in different stages of research. It gets great.

________________________________________
Disclosure
Links to Family Tree DNA appear in the sidebar. I receive a small contribution if you make a purchase, but clicking through the link does not affect the price you pay. 

Monday, October 14, 2019

Advantages of submitting to YFull


For Y-DNA testing, I have seen a lot of questions about how to evaluate Next-Generation Sequencing (NGS) tests such as Family Tree DNA's Big Y test, and similar tests at Full Genomes Corp, YSEQ, and extracted Y-DNA results of full genome tests from companies such as Dante Labs. If your Y-DNA company gave you good results, why would you want to download your results and upload them to a third-party site such as YFull? 

I previously wrote a post about the advantages of YFull, but that post was written when I took my original Big Y test. Please review What are the benefits of YFull?  The benefits are much more extensive now that YFull has added new tools and especially since I've also ordered the Big Y-700 test. So, what are the advantages of submitting to YFull?



What is YFull?


YFull is not a DNA testing company. YFull is an analysis and comparison service for Y-DNA Next Generation Sequencing and full mitochondrial DNA sequences. These interpretation and comparison services are more comprehensive than those found at any DNA testing company.



 Y-DNA analysis and comparison


In this post we will discuss Y-DNA only. Since most people at the present time have tested with Family Tree DNA, let's focus on a portion of the Big Y-700 results from Family Tree DNA and compare these to the YFull evaluation of the same results.

We will examine the Private Variants from a Big Y-700 kit at Family Tree DNA. Private Variants are those that have supposedly only been seen in your kit. Once they have been seen in more than one kit, you will find them in the Named Variants. However, note that I said "supposedly."  Sometimes positions appear in your Private Variants list that have been seen in other kits, but FTDNA hasn't yet discovered this. This will especially be the case if your results have just arrived and haven't been fully evaluated.

Log into the Family Tree DNA account and go to Big Y Results. There are three tabs for Named Variants, Private Variants, and Matching. Here are the first ten Private Variants for a Big Y-700 kit. There are a total of 19 private variants, but only the first ten are displayed below. They are listed by their hg38 position number:


Big Y-700 Private Variants


Let's look at the first SNP on the list, position 10053444. If we click on the blue link for that position, you will be taken to Family Tree DNA's chromosome browser and see the following:



Big Y chromosome browser


This SNP is considered by FTDNA to be high quality. The Reference Sequence has a G at this position, but this kit had a C. The chromosome browser shows us how many times the position has been read, but we have to count each line. No further information is available. Now let's see what we can discover about this same position at YFull.



Novel SNPs at YFull


In YFull, "Private variants" are called "Novel SNPs." Here again, the SNPs may not truly be novel.  Other companies may have found these variants, but YFull hasn't discovered them yet. To see a list of your novel SNPs, view the menu at the left side of the screen, and click on Novel SNPs. 


Click Novel SNPs

At YFull, SNPs are categorized by quality and divided into separate tabs. The tabs are Best qual [best quality], Acceptable qual, Ambiguous qual, Low qual, One reading, and Indels.

Below is the Best qual tab. You will see the SNPs listed by both their hg19 and hg38 positions. Notice that at FTDNA we only saw the hg38 position number. To see if we can find anything new about the position we examined at FTDNA, find 10053444 on the Best qual screen. 



List of Novel SNPs at YFull


You can see that 10053444 has been named FGC65817 by Full Genomes Corp, but we did not see that at FTDNA. The red check mark on the line means that this SNP is available for verification by Sanger testing at YSEQ. This is another piece of very useful information, as we will see later.

Now click View BAM on the right side of the screen to see several versions of the BAM viewer.  This one is similar to the one we saw at FTDNA:



One version of YFull chromosome browser


We can see even more by clicking the yellow magnifier icon on the left side of the screen:



View position in BAM


We will then see this information:



SNP information


The above screen tells us the kit number and haplogroup [on the first line, but much of it is erased in this image] and the Y-chromosome position numbers in hg19 and hg38. The red arrow next to the hg38 position shows that we are looking at a test that was aligned to hg38. This position was read 22 times in the Big Y test, and all the reads showed a C instead of the G found in the Reference Sequence. We also see that the SNP has been named FGC65817, it is available for testing at YSEQ, and it is listed in YBrowse.

The right side of the above image was cropped to make it more readable. However, another useful part of this screen is that you can not only see the position number, but you can see where this position is situated on the Y chromosome. This can help you determine how reliable this SNP may be. As shown below, position 10053444 is found in the Yp11.2 combBED region:



Y-chromosome regions


Notice that the fourth position below has been given the SNP name FT86640. SNPs beginning with FT are ones that were discovered by Family Tree DNA from the Big Y-700 test. Since it was not discovered in the previous Big Y test, let's see if this could be a valid SNP. Click the magnifier.



YFull Novel SNPs



This SNP had consistent results for 39 reads, so that's a good sign.



Search in BAM file


If we click the Ambiguous qual tab, we see the following. Let's examine the first listed position to see why it's on the ambiguous list. Again, click the magnifier on the left.



Evaluate an ambiguous SNP


On the next screen we see that this SNP was only read two times, so it's a less reliable SNP. 



A SNP with two reads


Family Tree DNA does not show this position in its list of Private Variants because it was only read two times. YFull considers the above SNP to be ambiguous for the same reason, but they do list it. If you want to know if any SNP is a valid one, you can verify it by ordering Sanger Sequencing at YSEQ for this position (along with any other doubtful SNPs). YFull does not indicate that the 9686527 SNP is available for testing at YSEQ, so go to yseq.net, and check to see if it's been added to their list of SNPs. If not, submit the position to YSEQ's Wish A SNP:



YSEQ Wish a SNP


On the next page, you will see full instructions for making your SNP available for testing.  Notice that the price is only one dollar.



YSeq Wish A SNP order


If this SNP is in a region that can be reliably tested, you will receive an email from YSEQ when your SNP is available. Because 9686527 was only read twice in the Big Y test, it is a questionable SNP, but once it's available for testing you can submit a DNA sample to YSEQ to verify that you actually have a novel SNP at this position. The ability to verify questionable SNPs is very important when comparing your results to someone else.



How do I download my Big Y results and submit them to YFull?


Log into your FTDNA account, and go to Big Y Results.  Click the blue Download Raw Data link at the upper right of the screen:



Download Raw Data


If you haven't already done so, you will first have to request the BAM file.  In a few days your BAM file will be ready. When it is, click Share BAM. then copy the link that appears.



Share BAM file


Now go to YFull.com and click Order Now:



Order YFull interpretation


The cost is $49, but you will not be charged until the results are ready.  If you have previously submitted another kit for the same person (for example, you previously submitted Big Y-500, and now you're submitting Big Y-700), add a comment to your order that "This is the same kit as [YFxxxxx]" and insert your old YFull ID number. You will get a new ID number for your Big Y-700 results, and it will be cross-referenced to your old ID number in the YFull tree. If you have ordered a mtDNA Full Sequence test for the same person, those results can also be uploaded at no additional charge.



Comparing STRs


To be sure you have the most complete results in your YFull account, you will want to upload a STR file as well as your BAM file. This is because the STRs are not as reliable from NGS tests as they are from Sanger testing. Family Tree DNA does Sanger testing to get the first 111 STR markers, but the BAM file you uploaded does not include the Sanger-tested results. Be sure to upload not only your BAM file (as shown above), but also upload a separate STR file. No matter what company you used for your NGS test, you can order a STR test from Family Tree DNA or from YSEQ.

If you ordered a STR test from FTDNA (it was included in any Big Y-700 results), log into your FTDNA account and go to your Y-STR Results page:



FTDNA Y-STR Results


Scroll all the way to the bottom of the page, and click the orange CSV button at the bottom right of the screen:



Download CSV file of STRs


In your YFull account, click the Upload STRs link.



Upload STRs


Depending on whether you received your STRs from YSEQ or FTDNA, on the next page either click Upload STRs - FTDNA or Upload STRs -YSEQ:



Upload FTDNA or YSEQ STRs


Notice above that there are two kits in the account. No CSV file of STRs has yet been uploaded for the first kit on the list. The FTDNA CSV file for the second kit has been loaded. The green check mark means that the CSV file passed the quality check. The red X is an option to delete the file. The Re-upload link is so that you can upload another CSV file if you get any additional STR results for the same kit from FTDNA. You can also upload a STR file from YSEQ for the same account. The STR uploads are free.



YFull Groups


With your STR CSV file uploaded, you will get better results from YFull Groups. "Groups" at YFull are similar to "Projects" at FTDNA. You can submit a request to form a new group by sending an email to YFull. 


Joining a Group

To join a YFull group, click Groups Y. [In the current mobile version it's called Groups.]


YFull Y-DNA Groups


On the next page, find the group of interest and click the name of that group. You will be taken to the Group page where you can submit a request.



Request to join a group



The Join request form looks like this:



Request form to join a YFull Group



Select the correct sample ID [if you have more than one sample in your account], then submit a comment. The comment field is currently required, but it is not used, so you can put anything in it [even an x]. Check the "I agree" box, and click Send. You will receive an email as soon as your request is approved.


Advantages of Groups

Once you have joined a group, you can see the group results. Below are the first lines of the results from the R-L21 group.  Notice that only twelve markers are displayed. This is the default, but you can display 12, 25, 37, 67, 111 or ALL markers. Family Tree DNA only displays the first 111 markers in projects because the STRs from the Big Y tests are less reliable than the first 111 markers tested by Sanger testing.



YFull R-L21 STR results


Notice above that some of the STRs are missing or questionable in the test results. This means that the NGS test returned reliable results for some positions and not others. However, if these were results from Family Tree DNA all of the first twelve markers should have solid results because FTDNA does Sanger testing on the first 111 markers. In the above screen, the people who have missing or questionable results loaded their BAM file, but they did not load their STR file.

We can display all STRs by clicking the All view button as shown above.

The results below are some of the additional STRs received from the Big Y-700 test that are not compared at Family Tree DNA.



YFull Comparison of all STRs


In the above screen we can see that the NGS tests do not return all STRs for all people. This is one reason why FTDNA does not compare them, but if so, what is the benefit of showing them at YFull? One reason is that if you discover missing STRs, you may be able to order these from YSEQ and have them added to your account. We will examine this procedure later in this post.

Although FTDNA projects are generally much larger than YFull groups, YFull groups have a few major advantages. The first is your ability to contact anyone in the group whose results interest you. [For example, let's say that you see that someone else appears to be an STR match to you, but his test did not show results for many STRs that you have. Has he uploaded his STR file? Would the two of you be willing to do Sanger testing for any STRs that you both agree are particularly important?] Simply click the PM (Private Message) envelope icon next to the kit number in the group results.  A message screen will pop up:



Sending a private message in YFull


Notice that you are sending a message to Kit YF06227 who is recipient 6227. We do not know this person's name or email address. However, once you send the message it will appear in that person's YFull account, and they will have the option to respond. 

A second advantage is that YFull groups have results from not only Family Tree DNA, but also from other companies. This will be increasingly important as the price of Full Genome testing continues to come down. More and more people are extracting Y-DNA results from Full Genome tests and uploading the results to YFull. In addition, YFull group administrators can add results from scientific studies. See the "Add science sample" below.



Add science sample to YFull Group



A third benefit of YFull groups is the ability to search for SNPs to find everyone in the project who might share your SNP of interest. 



Search for SNPs


You can search by SNP name using the Y-Results tab or by position number using the Y-Browser tab.  Although the Group's scientific samples may not show in the STR table (because the STRs were not included in the scientific report), they will show up in the SNP search. 

Searching by "View Y-SNPs", people who have the SNP we're looking for will show up in the results list with a + sign like this:



Positive SNPs



Of course, if any SNP is one of particular interest, we could send a Private Message to another person who has this SNP.

The results will be less likely to show positive results when searching for something like an ambiguous novel SNP. Using the Y-Browser, we searched by position.  The results will show every sample in the Group.  Only the first three results are shown in the image below:



Search by Position number


These results show that the Reference Sequence had an A at position 14239619. The first ID had a N which means this position had no reads in the Big Y test. The second ID had an Error. The error is because the position had only two reads, and they were both T.  The third ID is a scientific sample. The sample had an A in this position. If we hover the mouse over the A, we can see that this position was read five times in the test.

The ability in Groups to search by SNPs is another tool that can verify SNPs and find variants that can identify recent lineages.





What if I have taken more than one test?


One really great thing about YFull is the ability to load several test results for the same person. Your previous results do not disappear. For example, I ordered a Big Y test for a kit in 2017.  In 2019, I ordered the Big Y-700. The Big Y-700 is an entirely new test, not just an upgrade from the previous Big Y. YFull indicates multiple tests for the same kit on their tree. The new kit is displayed along with the old kit number.



Two YFull kits for the same person


When the Big Y-700 test was finished in 2019, Family Tree DNA removed the original Big Y test results and replaced them with the Big Y-700. With the results from the first test gone, there is no way to compare the two. But at YFull, the original test remains and can be compared to the linked Big Y-700 results. I have also ordered a Full Genome test from Dante Labs. When those results come in, I can compare all three tests. If we click Comparisons in the YFull menu, we can see the following Statistics tab that compares the original Big Y to the Big Y-700 test for this kit. The original Big Y was aligned to hg19 [this was before the Big Y-500 test], and the new results were aligned to hg38:



Big Y vs Big Y-700


The Novel SNPs tab below is especially fascinating.  Position by position we see the hg19 and hg38 position numbers, all names that have been given to each SNP, and the calls from the two tests. We can hover the cursor over any item to see an explanation. For example, hovering the cursor over the green 1 shows that this is a Best quality SNP.



Novel SNP comparison between Big Y test and Big Y-700 test


We want to examine one of these positions that was discovered in the Big Y-700 test but not in the original Big Y. Click on the yellow magnifier.



 New SNP discovered in Big Y-700


We can see that although this position was not discovered in the original Big Y, it was read 28 times in the Big Y-700 and has been given the SNP name FT85878.



More information about newly-discovered SNP


We can also compare the STRs from the two tests. The STR name is on the left, then the STR results from the first Big Y test for this kit, and finally the results for the same kit from the Big Y-700 test (the column on the far right). Notice that on this first screen the STR results are the same for both tests:



Compare Big Y and Big Y-700 STRs


However, as we move further down, we can see that they are not all the same:



Missing STRs in two versions of Big Y tests


In the above screen there were results for some markers in my original Big Y test [the second to last column], but no results for the same markers in the most recent Big Y-700 test. The same is true with the new test showing results for some markers that the older test did not. Without being able to compare the two tests at YFull, I would not know about the missing results at any position. But I what can I do about it?  I may be able to order a test for a specific STR at YSEQ.



YSEQ STRs


YSEQ can test a single STR or a panel of STRs. To order a single STR, click STRs in the menu on the left of the screen, then search to see if the STR is available for testing.



YSEQ STRs


We can order a test for the DYS518 STR that was discovered in the original Big Y test, but lost in the Big Y-700:



Order YSEQ STR 


Once you have received STR results from YSEQ, you can upload them to YFull and add them to the results you already uploaded. First click Upload STRs:



Upload STRs to YFull


Now click UPLOAD STRs-YSEQ:



Upload YSEQ STRs


The ability to combine STRs from FTDNA and from YSEQ is wonderful.



SUMMARY: Why should I upload to YFull? 
Here are 10 reasons


Although we did not cover all of the benefits of YFull including SNP matches, STR matches outside of projects, estimating the dates when SNPs occurred, and many others, here are ten benefits that we did discuss:

1. You will not be charged for your upload until the results are ready, and you can add mtDNA Full Sequence results and multiple STR files for the same person at no additional charge.
2. You can find additional information about your private variants including the names that have been given to this variant, the region of the Y-chromosome where it appears, whether it is available for Sanger testing at YSEQ, and more.
3. You can compare your results to people who tested at other companies.
4. You can compare your own results from different NGS or Full Genomes tests you've taken.
5. YFull Groups can display and compare all STRs (not just the first 111).
6. You can find SNP matches in YFull Groups, not for just your terminal SNP, but for any named or unnamed variant.
7. You can contact other people in your YFull Groups.
8. If you discover questionable SNPs or STRs in your NGS test, you can verify them at YSEQ and add them to your test results.  
9. If some SNPs or STRs did not appear in your test results at all, you can order new SNPs or STRs from FTDNA or YSEQ and add them to your results.
10. Your results will not be wiped out, no matter how many versions of the same test you take.

You get a new, more comprehensive interpretation of your data. The benefits increase as YFull adds more features and more people submit results. Please seriously consider adding your results to YFull.