PSHG Haplotree and SNP Detail

In a previous blog post, we defined what a SNP is and discussed the haplotree upstream of the PSHG SNPs. In this post we take another look at the PSHG Haplotree by introducing a new page and taking a dive deep. We’ll also talk a little bit about SNP naming.

For those new to genetic genealogy or Y-DNA analysis, the concept of SNPs can be intimidating. One of the reasons may be seemingly abstract SNP names which represent the mutation of an allele at a very specific numeric position on the Y Chromosome.

SNPs are named when a researcher or DNA testing company identifies an unnamed variant in a test kit’s results, validates that it’s viable for genetic genealogy, and is able to develop a primer for it. You can easily identify each testing company by looking at the SNP prefix.

A – named by YSEQ (see Partner Profile post)

BY – named by FTDNA (see Partner Profile post)

FGC – named by Full Genome Corp (see https://www.fullgenomes.com/)

S – named by James F. Wilson, D. Phil of Edinburgh University

Therefore, we know the PSHG SNP of FGC13609 was named by Full Genome Corp. What else can we find out about this SNP? We turn to the ISOGG YBrowse tool (http://ybrowse.org/gb2/gbrowse/chrY/?). Enter FGC13609 into the “Search Landmark or Region” field and click Search. With the default resolution set to “Show 1 bp” we see below a diagram and location of the SNP on the Y Chromosome and a reference scale.

In case the image is too small, click the image to browse to the page.

Click on the yellow & red highlighted FGC13609 in the middle of the page to see SNP details. Here we can find:

Position at 20919447
Mutation from T to G
Comment including position downstream of DF96
Named (ref:) by Full Genomes Corp. (2016)

Sometimes a SNP is named by multiple companies. Take A16447 which is also known as BY16815. Search for it in Ybrowse and notice that while it has two names, the chrY position and allele mutation are the same.

Multiple SNPs can also be grouped together. For example, the group FGC13609, FGC13605, FGC13601, and A1230 are all SNPs shares by 2 PSHG members who have taken the BigY test from FTDNA. These SNPs will remain grouped together until a test new BigY test taker comes along having one or more, but not all, of those SNPs. If and when this happens, we learn more about the branches of our Haplotree as it evolves based on the results of additional testing and analysis.

Our website has a new page for keeping an updated haplotree including a table of Y-SNPs from FGC13602 including name, position, and base mutation. Please visit PSHG Haplotree Technical Data!

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