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Re: STRs & SNPs and what you can do with them


 

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That was about as helpful as anything I've read re: some direction in understanding this puzzle.

Thanks,

Roy Graves


From: R1b-S6881@... on behalf of avalea3@... [R1b-S6881]
Sent: Monday, January 30, 2017 6:57:33 PM
To: R1b-S6881@...
Subject: [R1b-S6881] STRs & SNPs and what you can do with them
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This group is pretty new and we have a lot of new members so I thought I would write a series of posts over the next few weeks on topics covering some genetic genealogy terms and concepts. I¡¯ll put these in our files section after I write them so future members can find the information. I¡¯m going to keep it simple and high level so I will gloss over some details. If anyone wants to ask questions or correct something I¡¯ve said please speak up. I¡¯m just trying to help everyone get the most out of their testing. And if there is something you would like to see explained please ask. I might not know the answer but we can find someone who does.

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In this one, I'm going to cover a simplified explanation of STRs and SNPs and what you can do with them.

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STRs (short tandem repeats) are kind of like stutters in our DNA. It's where you have copies of a sequence, like ATAATAATA, and FTDNA tests at certain locations for how many times the sequence repeats. They use that number to decide if people match closely with each other at that location (or marker).?The count of how many repeats you have at each marker is where the numbers come from (i.e. DYS534=14) in your Y-STRs results. You can see your results under the Y-STRs results tab on your kit page. On your Matches?tab,?you can see who you match up with and how closely. So if my kit has a 14 and yours has a 15 at DYS534 we would have one genetic difference at that marker. If yours had 16 then it would be 2 genetic differences. Calculating these numbers is a little more complicated than I am making it seem so if you really want to get into the nitty gritty of how they calculate these numbers contact me and I¡¯ll give you more information. FTDNA adds up all your differences on the markers for each panel tested and that's how you get a total of say 8 differences out of 111 markers with your match. They only report closer matches so if someone exceeds the threshold of mismatches for that panel they won¡¯t report them as a match. These STR repeats are passed on genetically but over time they change. There can be more or less repeats. Some markers are very stable and stay like they are for a long time but others change more quickly. We can predict someone's haplogroup by how closely?they match to others and how many repeats there are?at?certain markers. A big one for U106 is a result of?13,?or for S6881 a result of 14, at DYS492.? ?

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SNPs (single nucleotide polymorphisms, pronounced ¡°snip¡±) are mutations at a certain place on the DNA. If ancestrally the nucleotide has been C at that location but has now mutated to T then it would be said that you are positive for that SNP. With these positive?SNPs,?we can form a sort of tree, building up from the most ancient SNPs to the ones that are mutating in our own families as we have a new child and that nucleotide changes. On average you get a new mutation about every 150 years. It is possible for a father with 2 sons to have one son with a new mutation and the other son not. We can use SNPs to figure out branching within families.?But remember the 150 years is just an average so there can be fewer years or more years between mutations. And they don¡¯t happen like clockwork, they happen totally randomly. The good thing about SNPs is that they are passed on from father to son and they rarely mutate back like STRs can do.?

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So STRs can help?predict?how closely related you are to someone and what your haplogroup might be. But it's the testing of SNPs that tells you exactly what your haplogroup is, not just a prediction. And that shows who you are really related to at some point in time. In your list of?matches,?you probably have people who look like they might match you but are really on a different branch of the tree. SNP testing answers that question. If you¡¯ve done no SNP testing your kit probably predicts a haplogroup of M269 and is written in red. So FTDNA is predicting you will be at least that haplogroup from your STR results. But that SNP is very, very old (like probably 6,000 years ago). So you want to find SNPs that are younger so you can see who you might be related to in a later time period. Some people in your matches will have a green haplogroup. That means it is no longer a prediction, he actually has tested to that result. But that SNP could still be very old and he would need to do more testing if he wants to find a younger SNP that others will?match to. That¡¯s where the BigY or other NGS (next generation sequencing) test comes along. These tests help you find SNPs up to the ones occurring in your own family.

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If you find that you are having problems with so many Y-STR matches that you can¡¯t figure out where to start that is because R1b is a huge group (U106 is a piece of that group). Having a WAMH badge on your kit will make it even harder to find the best matches. WAMH (Western Atlantic Modal Haplotype) is the most common (modal) result of STRs over a certain set of markers. My kit has this badge and because it is modal you will match to so many people that it is hard to figure out any pattern. For all those people who have kits?where you have few matches, you¡¯d probably wish to have too many. But it is actually easier to figure out who you match to with fewer matches. You just don¡¯t have as many choices. It¡¯s a good strategy to test out to at least 67 or 111 STRs to narrow down the matches. They might look like a close match at fewer STRs but as you test out more STRs that person may drop off your matches. The other thing to remember is that most of these matches may be pointing to a point in time before they had adopted surnames. So matching to your own surname isn¡¯t a requirement. You will probably find closer matches if you do match your surname but it doesn¡¯t mean you can¡¯t find a match without sharing the name. The match is just going to be further back in time. (We are going to skip adoptions and what they call NPE (not the parent expected) in this discussion). The interesting thing is there seems to be a pretty good amount of people in this subset of S6881 that were in the area of Lancashire in England before surnames were set or are from there now. So there may have been one man there who we all descended from or maybe a group of brothers. It's hard to tell but kind of fun and exciting.?

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You have probably heard both the terms haplogroup and terminal SNP. They are both referring to the youngest SNP you have?tested to. Terminal SNP is a bad term in that there is really nothing terminal about it unless you have matched all your SNPs to someone (which would mean your common ancestor would be within probably the last 300 years). What you really have when you haven¡¯t matched them all is what I refer to as your last shared subclade. If you have done testing like BigY you'll then have a handful of SNPs leftover that we call singletons that we still need to find someone closer related to us to match to. ?While this can break a wall for people and get into genealogical time only some of us are there. My kit¡¯s last shared SNP is probably from the 900s. But we have others in our small group who are sharing SNPs from probably the 1800s. So it just matters who you can find to test with that might share your SNPs.?

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