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Advantages of submitting to YFull - Part 2

Tags: karnes yfull snps

In my previous post Advantages of submitting to Yfull, I discussed mostly what you can find in YFull even if you don't have any close matches. In the summary I mentioned that the post 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." In this Part 2 we will discover many of these benefits that may not be immediately obvious. 


Matches missing from Family Tree DNA


Although I did previously mention that if you tested at Family Tree DNA (FTDNA) you would be able to find matches at YFull who tested with other companies, I did not mention that you would be able to find missing matches from FTDNA. You may think, "What missing matches? FTDNA has the most comprehensive database." Yes, FTDNA has the largest database, but their matching algorithm prevents you from finding many of them. Here's a very frustrating example.

In The amazing power of Y-DNA I showed how Y-DNA results gave me the clues I needed to trace the ancestors of Michael Karnes back to Germany. This would not have been possible without Y-DNA. Two Big Y tests showed matching results for two Karnes descendants. The ancestry of one of them is known, but we needed to test more Karnes descendants to find how the other man connects.

After that post, another Karnes descendant agreed to take the Big Y-700. I knew his ancestry, and he is a descendant of Michael, son of Nicholas Karnes. Fantastic! To protect their privacy we will call the three Big Y testers Mr. Carnes, John Karnes, and Robert Karnes. John and Robert share a known ancestor. "John" Karnes had taken the Big Y-500, and "Robert" Karnes would be taking the Big Y-700. The results of Robert should match those of John and possibly give us a SNP that only occurred in the line of Michael. 

Here's the paternal ancestry of the two Karnes men:


Karnes Family Tree
Tree of John Karnes



Karnes Family Tree
Tree of Robert Karnes


STR Results

The Big Y test includes a separate test of 111 STRs. These STR results for Robert came in before the Big Y results, and proved that he is biologically related to both Mr. Carnes and John Karnes.

I regularly checked the Big Y results to see if anything had changed, but these results seemed to be taking a long time. Then I was looking at the STR results in the Kern project, and I noticed that Robert's haplogroup had changed. He now had the same haplogroup as Mr. Carnes and John Karnes:


STR comparisons
Kern DNA Project


Yes! His Big Y results are in! I could hardly contain my excitement. 



Big Y matches


I was now on the track to make some great discoveries. I immediately looked at the Big Y matches for John Karnes.

 
Big Y match list
One Big Y match at Family Tree DNA


Nothing had changed. This was the same match, Mr. Carnes, that I've seen since April 2018. I checked day by day to see if the results for the new Karnes match would show up. Nothing. I know he's related, and I even know the exact ancestor, but he is still not on the match list. I can imagine how disappointed Robert must have been when his Big Y-700 results showed that he had no matches at all.

The only thing I could think of was that the number of SNPs from Robert's Big Y-700 must have increased enough from the former Big Y-500 tests to keep him off the match list of his two Karnes cousins. 

Luckily, John and Robert were both in the Kern surname project at FTDNA. So I looked up the SNPs in the Kern Project. Here's the SNP list for John Karnes who tested Big Y-500:



SNP table
Big Y-500 SNPs


Here's the SNP list for Robert Karnes who took the Big Y-700:


Big Y-700 SNPs
Big Y-700 SNPs


Well, that's definitely enough to throw him off the match list! Unless FTDNA changes their matching algorithm we may never be able to compare these men at FTDNA. If fact, if Robert had a few more STR mismatches, he wouldn't have shown up on that list either, and we never would have known anything about this match. 



The Big Y Block Tree



Although Robert Karnes does not appear in the Big Y match list, I checked the FTDNA Block Tree for John Karnes. It appears that there are three results for J-BY45500, but only one name is showing. This is Mr. Carnes who was a match to John Karnes with the Big Y-500 test. FTDNA only shows the names of the people who appear on your match list. There is no way to obtain the identity or contact information for any person in the Block Tree other than the one named man.


Karnes SNPs
Karns/Carnes Block Tree



Matches at YFull


YFull does not have the same restrictions for displaying SNP or STR matches. If Robert loads his results to YFull, we'll be able to compare SNPs, STRs, and maybe even find a SNP that occurred with our common ancestor Michael Karnes. Mr. Carnes and John Karnes are already in YFull, so we will examine what we can find about their ancestry.

Here is how Karnes and Carnes, the two Big Y-500 testers, appeared in the tree at YFull. YFull does not always use the same names for haplogroups as FTDNA does. The men appear under the haplogroup J-Y145902. 


YFull haplogroups
YFull Tree



Notice that one of the IDs is in italics. This is because he submitted a VCF file. The rest of the men on this portion of the tree submitted BAM files.

Haplogroup J-Y145902 shows three SNPs next to it. The first one is BY45499/Y145904. BY45499 is the name given by FTDNA, and Y145904 was the name given by YFull. The third SNP has only Y145906 because this SNP was not called by FTDNA. As shown in the above Block Tree FTDNA had a total of 13 SNPs for this block, and YFull has 15. YFull named several more potential SNPs that they have not yet included in the YFull tree.

The YFull tree contains similar information to the Block Tree with SNPs and countries. The difference is that you can see the ID number for every person on the tree. You can contact any of them if they are on your lists of SNP or STR matches (which are far less restrictive than FTDNA's) or are in a YFull group.


In one of the Y groups, we can see four of these IDs all together, but the best part is the envelope next to each ID number. 


YFull ID
Private Messaging


Click that envelope, and you can send a PM (Private Message). You will never know the name of the person or the person's email unless he responds to you and gives you that information. If you wish to retain your privacy while discussing distant ancestry, you can continue to use the PM feature. 

YFull does not restrict you from contacting more distant matches. You can contact anyone from your list of close and distant SNP matches, STR matches, and people in YFull Groups. We'll see how this is important in the next section.




YFull tools for extending ancestral lines


If we want to find out more about your ancestral past, YFull has some great tools.



STR matches


In addition to finding STR matches by joining a group, YFull also has a table for STR matches. Here is an example:


Y-DNA match list
YFull STR matches


There are two tabs: one for close matches, and one for distant matches. You can see the country of origin reported by each match. This is great for extending ancestral lines. There is a Private Message envelope included, so you can contact any match. For example, you can use this feature to ask a match to join a group so you can compare the full list of STRs. As I explained in my post The Advantages of Submitting to YFull, YFull groups display all STRs, not just the first 111.


The advantages of the private messaging system


The really cool part about the private messaging is that I have been in contact with a match who comes from a town in the Czech Republic that is not far from the town in Germany where the Kern ancestor was born. This man does not appear on the list of SNP or STR matches at FTDNA, but he does appear in the match lists at YFull. Matches were contacted through the private messaging system and asked to join a Y Group, so they are all in one group where deeper comparisons can be made. Of course, most of us are not close matches, but now the members of that group are continually finding new information about our common ancestry. We know the approximate dates for our common ancestors. One of the members is doing some incredible research by recruiting people for Y-DNA testing to determine more about the migration path of the ancestors.


SNP dating


YFull results include age estimations to help determine how closely various men are related. In the Age estimation link the haplogroups are shown starting with the most recent known haplogroup, and continuing back in time. Estimated ages are included.


SNP age estimates
YFull SNP age estimates


Notice that there are multiple tabs. The Known SNP tab, for example, shows the known SNPs that were used to estimate the age of the haplogroups. This is another feature that can be very useful for extending ancestral lines.


STR dating


While YFull does not estimate a date for STRs, they do display something similar. The STR variants table shows the STRs in the approximate order in which they occurred and shows the STR values for the various haplogroups.


STR variants
YFull STR variants


Here are the results for another test to show how the list appears when there are closer matches:


YFull STR variants
STR variants




Decision time



The above information from YFull can tell us much more about the ancestral past of the Karnes line. Is there a SNP or STR that identifies the line of Michael Karnes? We cannot compare the Y-DNA results of John Karnes to Robert Karnes at FTDNA. So, to compare the Y-DNA of John and Robert Karnes and find out more about the Karnes lineage, there are two choices:

1. We can just have Robert Karnes upload his BAM file to YFull and be done with it. We can see all the STRs and SNPs we need to make this match, and can make multiple comparisons. This will not involve any expenditure of money for more tests.  

2. Have John Karnes upgrade to Big Y-700. There is no option for Mr. Carnes, the Big Y-500 match. He is now deceased and therefore cannot provide a new sample for the Big Y-700 test. He has no close male relative. Here are reasons for John to upgrade:

a. It is clear that John Karnes is missing a lot of SNPs that Robert has. Some of those may be important in determining Karnes lineage. John will never know about those unless he upgrades to the Big Y-700. 

b. Because of FTDNA's matching algorithm if any future Karnes man does a Big Y test, he will not show up as a match to John. We may never know about it. 

c. It is not good enough for a match to be in only one database whether that database is YFull or any testing company. We want several options for people to be able to find more about our Karnes ancestry. We've seen too many DNA companies go out of business, and companies that are still in business wipe out their databases. Examples: Ancestry acquired SMGF and removed its online database, Ancestry discontinued Y-DNA testing and removed its database, FTDNA wiped out YSearch and Mitosearch databases, National Geographic's database is no longer available, and many others.

The decision was made to upgrade the test of John Karnes to Big Y-700.



Family Tree DNA Big Y-700 results


The Big Y-700 results for John Karnes were recently completed. Here is his new match list at Family Tree DNA:

Big Y matches
Big Y-700 match list for John Karnes


Although Robert Karnes did not show up as a match at all before the upgrade, he is now the first match on the list. There are three Non-Matching Variants: 21610971, 14852433, and 16995971.

If we look click the tab for Private Variants, we can see which of these John has.

Big Y-700 private SNP
Private variants for John Karnes


This shows that John has 2161071. Therefore, Robert has 14852433 and 16995971.


Big Y Block Tree


In the Big Y match list, the non-matching variants for Mr. Carnes make it look like he is very distantly related. To see a more accurate picture, we have to look at the Big Y Block Tree. From the Matching tab, click the blue box "View Big Y Block Tree."


FTDNA Y Tree
Big Y Block Tree of John Karnes


Compare this tree to the previous one shown above. When Mr. Carnes and John Karnes took the Big Y-500 test, only the first 13 SNPs appeared in the Big Y Block tree. All the ones after that were discovered by FTDNA from the Big Y-700 test. In the past, SNPs discovered by Family Tree DNA in the Big Y test were given names starting with the letters BY. Beginning with the Big Y-700, FTNDA now names the SNPs starting with the letters FT. So, in the above Big Y Block Tree, the SNPs BY45500, etc., were discovered by FTDNA with the Big Y-500 test, the SNPs FGC33683, etc., had already been discovered by Full Genomes Corp., the SNPs FT113124, etc., were discovered by FTDNA with the Big Y-700 test, and the SNPs Y145902, etc., had already been discovered by YFull.

The Block Tree is showing that the average number of private variants is 1. The previous version showed the average number as 17. Many "private" variants have now been resolved, and the mismatching variants of Carnes appear to be due to the difference between the Big Y-500 and the Big Y 700 results.

The results show that it was definitely worthwhile to upgrade to Big Y-700.



YFull comparison of Big Y-500 to Big Y-700


The results from the Big Y-500 test of John Karnes are no longer available at Family Tree DNA. They were replaced by the Big Y-700 results. This makes it difficult to compare the results of someone who took a Big Y-500 to the results of a Big Y-700 tester. However, at YFull you can have results from multiple tests at several different companies, and all tests results can be compared. The comparisons include Known SNPs and Novel SNPs from all tests, STR comparisons from all tests, and Statistics.

My favorites are the Novel SNPs and the STRs. Here's a portion of the Novel SNPs tab comparing John's Big Y-500 results to his Big Y-700 results.

Novel SNP comparison
Novel SNP Comparison between Big Y-500 and Big Y-700



In the above screen we can see novel SNPs that were discovered in the Big Y-500 test, but not in the Big Y-700, as well as those discovered only in the Big Y-700. We can find more information about any item in the chart by hovering over the item in question. We can see details about any variant by clicking the yellow magnifier icon. 

Mr. Carnes only took the Big Y-500, and Robert Karnes only took the Big Y-700. So having this list of comparisons from John Karnes can be important in comparing all three Carnes/Karnes tests at YFull. If any variant appears to be significant, it can be verified at YSEQ and added to the YFull results.



Ongoing research


The Big Y-700 BAM file of John Karnes was only recently loaded to YFull. YFull's SNP dating is updated every month, so we can't see the new age estimation yet. The STR file of John Karnes is still being evaluated. New DNA testers are being recruited to find out more about the Karnes ancestry, and ongoing discussions are occurring. So, we will continue to find new information.


Summary: The advantages of submitting to YFull


The advantages from the previous post were combined with the ones described in this post to create the following list. So, here's why you want to submit to your Y-DNA results to YFull:

1. You will find matches that did not appear in the results from your testing company. 
2. You can compare your results to people who tested at other companies.
3. You can compare your own results from different NGS or Full Genomes tests you've taken.
4. You will be able to see all variants discovered in your test, including novel ones that had only one or two reads. 
5. You can find additional information about your private variants incl


This post first appeared on The Ultimate Family Historians, please read the originial post: here

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Advantages of submitting to YFull - Part 2

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