An Update on an Irish Butler’s Big Y

Not too long ago I wrote about my Butler father in law’s Big Y results here. I found it a bit frustratinng that FTDNA changed their matching criteria. Richared is I2 on the YDNA nomenclature and his terminal SNP is now I-A427. Here are the matches shown at FTDNA:

However, there was a catch to the matching. Now Richard has a match if:

A person is considered a match if they have 30 or fewer differences in SNPs with you, and their haplogroup is downstream from your haplogroup or downstream from your four closest parent haplogroups.

Since my last Blog, I uploaded Richard’s VCF file to YFull.

I made sure to show that his ancestor was from Ireland, as I didn’t see any other Irish Flags. Now Richard is in an I-A427 group with no further branching along with two other YFull people. I’m hoping that once the next Y Tree comes out, that Richard will be on a new branch of the Y Tree. But back to the matching. If I count the id’s above, I get 17 other than Richard that are positive for I-A427. Yet Richard has no A427 matches by the FTDNA criteria. And that holds true for the four branches above A427 even though there are likely many more people that are positive for those SNPs.

Once Richard was on YFull, I joined him to the I-M223 Group. That way, group adminsters can see his results there and do any needed analysis.

FTDNA’s SNP Tree

I was unable to get FTDNA’s SNP tree working for my last blog. Here is how it looks for Richard:

I have a little trouble reading the FTDNA tree. I went two levels above A427 to P78. It looks like the two branches under P78 are the larger S25733 and the smaller Y7219. Under S25733 there is A427 and PH2670.  This leads me to modify the tree I had drawn in my previous Blog:

This was drawn to show that FTDNA may be ahead of YFull in some aspects and YFull may be ahead of FTDNA in others. The yellow level and down don’t  apply to the Butler/Whitson I-M223 Branches. Peter from the Project and Richard have both tested negative for S23612. That means that they are awaiting to be put in a  new branch below A427 that is parallel to S23612.

Here is where I expect the new branch to be:

Eventually, there should be additional branching below this yellow level. I would expect there to be more than just Butlers and Whitsons in this branch as this branch could still be over 4,000 years old. Note that probabably due to planned family testing, the Y24488 Branch got down to as recent as 150 years ago for their common ancestor.

VCF and BAM files

The two files that are generated when your Big Y results come in are the VCF and BAM files. FTDNA has not been generating the BAM files due to their conversion from HG19 to HG38. Due to a better understanding of YDNA a new standard was needed as new locations were found on the Y Chromosome. Thus the new HG38. For example, here is a list of some of Richard’s Novel SNPs:

YFull shows the HG19 position and the HG38 position.

The BAM Files are much larger than the VCF files. Other than that I don’t know a lot about them. YFull used to only accept the BAM files, but now that BAM files are held up, they wisely decided to accept VCF files. They get their money ($49) and we get most of the analysis. The rest of the analysis is done for free once the BAM file is available. Here is YFull’s ad:

Note they state that they only get about 50-70% of what they need from the VCF file. Also note that no age estimation is done without the BAM file. That is one of the most popular features of YFull. So I will definitely send YFull my BAM link once it is available.

Any Shared SNPs at YFull?

Again, no. YFull doesn’t do SNP sharing on old SNPs. Isn’t that age discimination? This is from the YFull site:

Q: What is YFull’s “SNP matches” methodology?

A: The methodology is reflected in the SNP matches table, which provides information about Shared SNPs and Assumed Shared SNPs of compared samples. The table is limited to SNPs having an estimated age of 3500 ybp or younger (using TMRCA from the YTree), with a maximum of 100 lines of information.

I-A427 has a TMRCA of 4700 years before present. That is ancient. Richard is only off by 1200 years.

Are the Novel SNPs At YFull the Same As the Unnamed Variants At FTDNA?

I think so. From my last Blog, FTDNA showed that Richard had 33 Unnamed Variants of High Quality. YFull shows 18 Novel SNPs of best quality and 11 of acceptable quality. That adds up to 29 which is two off from FTDNA’s 33 Novel SNPs and Unnamed Variants appear to be the same thing. However, based on differing interpretations different Novel SNPs were reported at different reported qualities:

This is a partial listing of all of Richard’s Variants. YFull is on the left and Big Y is on the right. I lined everthing up by the position numbers. YFull reports two Novel SNPs as ‘Ambiguous Quality’ that FTDNA reports as High Quality. Then FTDNA has 7 Novel SNPs rated at High that YFull does not even report. Again, it’s good to have a second opinion.

Any Shared Novel SNPs at YFull?

I think so. I copied all the Noved SNPs into Excel and filtererd all the ones that said ‘shared’ on them:

Here is what I gather:

• Even though these 14 Novel SNPs are shared, I can’t tell who they are shared with
• There are an equal amount of low quality Novel SNPs shared as well as Best Quality Novel SNPs
• One Novel SNP is new as there was no HG19 Position given
• All these Novel SNPs have been named except for two. The YF designation is a YFull numbering system, but as far as I know, not a SNP naming designation.
• I expect these Best quality and acceptable quality shared Nove SNPs to form a new branch or branches.

Summary and Conclusions

• The Big Y Results have gotten tbe ball rolling for the I-M223 Group of the Whitson/Butler YDNA Project
• Once the BAM file is available from FTDNA it will be uploaded to YFull
• Richard’s Big Y VCF file has been uploaded to YFull. I expect new branching once a new Y Tree comes out. These seem to come out about every two months. The last one came out at the beginning of January.
• FTDNA’s I-M223 administrators will also be looking at the Big Y results and the Y Full results for Richard, to see if further branching of A427 is warranted.
• One or two others from the Witson/Buter I-M223 Branch have expressed interest in taking the Big Y test. These tests could get to how the Butlers and Witsons are related. This may also give some geographic information on common ancestors. The Butlers were known to be in Ireland? Were the Whitsons also there? If so, when?