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Re: STRs & SNPs and what you can do with them
开云体育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. ? In this one, I'm going to cover a simplified explanation of STRs and SNPs and what you can do with them. ? 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.? ? ? 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.? ? ? 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. ? ? 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.? ? 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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Re: STRs & SNPs and what you can do with them
开云体育I will try to post this week about how to use the FTDNA BigY Match screen and what to ignore as well as the best things to do with your BigY results. I'm glad the information I posted today has helped you.? Chris On Jan 30, 2017, at 8:01 PM, Peter Latham peter.latham1@... [R1b-S6881] <R1b-S6881@...> wrote:
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Re: STRs & SNPs and what you can do with them
? ? ? ? ? ? ? ? ? ? ? 31 January 2017 Thank you for this helpful and timely posting for a beginner like myself who is awaiting my Family Tree Big Y test results in February to supplement my Y DNA 67 results. ?I am currently reading Dr Blaine Bettinger's October 2017 book 'Family Tree' to get up to speed. Peter Latham. ? |
STRs & SNPs and what you can do with them
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. ? In this one, I'm going to cover a simplified explanation of STRs and SNPs and what you can do with them. ? 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.? ? ? 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.? ? ? 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. ? ? 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.? ? 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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Re: S6881 Panel at YSEQ
I haven’t had chance yet to look at the results from the Xmas Big Ys so if you have suggestions for improving the panel please let me know. Ray, ? ?It looks like there are five new blocks under the SNPs you were testing.I believe only the Sexton/Graves block has been analyzed by a third party for their opinion on how good the SNPs are. The Brooks block is currently being analyzed. All of the other blocks have not been analyzed by anyone other than the U106 crew, as far as I know. So I'm sure it would be good to use one SNP from each of these blocks but I'm not sure which ones would be your best bets at this time. Chris On Sat, Jan 28, 2017 at 2:58 AM, Ray Warburton ray2warburton@... [R1b-S6881] <R1b-S6881@...> wrote:
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Re: S6881 Panel at YSEQ
That’s a fair summary Chris.
I haven’t had chance yet to look at the results from the Xmas Big Ys so if you have suggestions for improving the panel please let me know. The target audience for the panel is anyone who is predicted to be S6881 and wants to know where they fit in the S6881 tree. My view is that multiple Big Y tests will have diminishing returns as more SNPs are uncovered, but the panel will let anyone determine their (and their extended family’s) place in the tree. Saying I funded setting up the test sounds grand, but it was under $10. Regards Ray Ray Warburton Warburton Website: |
Re: S6881 Panel at YSEQ
I actually answered a long time ago but it never posted. So I tried again and it didn't post. When it finally posts I guess it will post twice :) On Fri, Jan 27, 2017 at 4:25 PM, prosperity200220815@... [R1b-S6881] <R1b-S6881@...> wrote:
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Re: S6881 Panel at YSEQ
It's kind of weird. I replied to this but it never showed up. Here's what I said:
He's really telling me because I asked him for this information. Ray commissioned and paid for YSEQ (a third party company) to put together a panel of SNPs that he chose to represent a good test?for people wanting to see if they were positive for the SNP S6881 and some of the clades under it. This SNP (or some right under it) seems to originate in someone who lived in the area around Lancashire so it fit in well with his project group. All of us in this S6881 project who?are at least S6881 positive are related to this person.? The panel he put together was pretty current until our most recent Christmas BigY blitz when we blew up the tree with new results :) YSEQ is an alternative to testing at FTDNA. It is cheaper but the downside is that your new result will not show up on your badge on your FTDNA homepage or in the projects. You would either have to be happy to just leave those not updated or buy a test at FTDNA for just the last SNP you tested positive for at YSEQ to get everything updated. Since it is a cheaper solution it is something to keep in mind when you are trying to figure out where people in a line might end up. Ultimately, only the BigY or another NGS test is going to tell you your own family SNPs so anyone wanting that should just save up and get that instead of spending money on SNP testing and then paying for it again with the NGS test. But if you are testing close family members, there is no reason for multiple NGS tests since they will come out pretty much the same so you could just test for certain SNPs instead. Chris |
Re: S6881 Panel at YSEQ
He's really telling me because I asked him for this information. Ray commissioned and paid for YSEQ (a third party company) to put together a panel of SNPs that he chose to represent a good test?for people wanting to see if they were positive for the SNP S6881 and some of the clades under it. This SNP (or some right under it) seems to originate in someone who lived in the area around Lancashire so it fit in well with his project group. All of us in this S6881 project who?are at least S6881 positive are related to this person.? The panel he put together was pretty current until our most recent Christmas BigY blitz when we blew up the tree with new results :) YSEQ is an alternative to testing at FTDNA. It is cheaper but the downside is that your new result will not show up on your badge on your FTDNA homepage or in the projects. You would either have to be happy to just leave those not updated or buy a test at FTDNA for just the last SNP you tested positive for at YSEQ to get everything updated. Since it is a cheaper solution it is something to keep in mind when you are trying to figure out where people in a line might end up. Ultimately, only the BigY or another NGS test is going to tell you your own family SNPs so anyone wanting that should just save up and get that instead of spending money on SNP testing and then paying for it again with the NGS test. But if you are testing close family members, there is no reason for multiple NGS tests since they will come out pretty much the same so you could just test for certain SNPs instead. Chris On Fri, Jan 27, 2017 at 3:58 PM, wiredmarys@... [R1b-S6881] <R1b-S6881@...> wrote:
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Re: S6881 Panel at YSEQ
Mary, there is a company, Yseq, where we can given them a list of SNPs that are in our clade. These SNPs are examined by them are either determined to be of good quality or not. There are a minimum number of 7 good quality SNPs needed to create a Panel. As you can see this S6881 Panel is made up of SNPs from both our lines where we connect with the Warburtons. Make sense??
Chris check if I said that well enough.? |
Re: S6881 Panel at YSEQ
开云体育Chris can you tell me what Ray is referring to here?? I don’t
understand what he’s tell us.
Mary E
? From: Chris Noble avalea3@... [R1b-S6881]
Sent: Friday, January 27, 2017 3:46 PM
To: R1b-S6881@...
Subject: Re: [R1b-S6881] Re: S6881 Panel at YSEQ ?
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Thanks, Ray. I've marked it down so I'll remember.
?
Chris ?
On Fri, Jan 27, 2017 at 11:44 AM, Ray Warburton
ray2warburton@... [R1b-S6881] <R1b-S6881@...> wrote:
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Re: S6881 Panel at YSEQ
Thanks, Ray. I've marked it down so I'll remember. Chris On Fri, Jan 27, 2017 at 11:44 AM, Ray Warburton ray2warburton@... [R1b-S6881] <R1b-S6881@...> wrote:
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Re: S6881 Panel at YSEQ
开云体育
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Re: New file uploaded to R1b-S6881
开云体育Well bummer.? You are right he is basically a first cousin because we
are only considering the male line. duh
?
Will have to regroup.? Thank you so much.? I’ll leave the
airwaves quiet for a while.
? From: Chris Noble avalea3@... [R1b-S6881]
Sent: Thursday, January 26, 2017 2:30 PM
To: R1b-S6881@...
Subject: Re: [R1b-S6881] Re: New file uploaded to
R1b-S6881 ?
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The one you are considering is too close. He's just a first cousin to Keith
if I understood it correctly. He's Keith's uncle's son so they share a
grandfather. They usually recommend a 3rd or 4th cousin, meaning your common
ancestor is either your gg grandfather or ggg grandfather. You'll have to search
a bit probably. I have the same issue on one line. All the boys either didn't
have children or they had all girls. I'm too familiar with that :(
Chris On Jan 26, 2017, at 10:56 AM, kgnmeg@... [R1b-S6881] <R1b-S6881@...> wrote:
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Re: New file uploaded to R1b-S6881
开云体育The one you are considering is too close. He's just a first cousin to Keith if I understood it correctly. He's Keith's uncle's son so they share a grandfather. They usually recommend a 3rd or 4th cousin, meaning your common ancestor is either your gg grandfather or ggg grandfather. You'll have to search a bit probably. I have the same issue on one line. All the boys either didn't have children or they had all girls. I'm too familiar with that :(? Chris On Jan 26, 2017, at 10:56 AM, kgnmeg@... [R1b-S6881] <R1b-S6881@...> wrote:
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Re: New file uploaded to R1b-S6881
Thanks again Chris.
I appreciate your quick answers. ?I had our sons 111 completed but figured a Big Y would not benefit anything. I had thought of asking Keith's brother but figured he wouldn't anyway. Then I wondered how about a half cousin and what you send above sounds to me like he might be the ticket. You can weigh in on that please if you agree or disagree. This Graves cousin is the son of Keith's fathers half brother. ?Same father, different mother. ?I've been wishing he would test, but he apparently hasn't of if he has there is a problem because there has never been a match with him. I do have contact with him and can explain what is going on as he is in the Graves group. Just hasn't tested as near as I know. We really have no one else that I know of. Dad was the only living child of his father and mother. They divorced and he remarried. ?Granddad did have other boys but from what I have found there were no other boys that would be living in this line. Going back a generation, I could do some more paper research to see if those boys had boys etc and see if I could contact them. Would any of those be distant enough do you think? |
Re: S6881 Panel at YSEQ
Thanks, Ray, yes I remember you set this panel up but I don't remember what SNPs it covers. Can you tell me again? I recommended to Cynthia that she think about using it to weed out the Graves and Warburtons to find the ones she wants. And yes, we've been doing a lot of testing so new SNPs all the time. It's a blessing and curse. :) Chris On Thu, Jan 26, 2017 at 9:03 AM, ray2warburton@... [R1b-S6881] <R1b-S6881@...> wrote:
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Re: New file uploaded to R1b-S6881
Well, the questionable singleton will usually come from being in a hard to read area or not a good read so they aren't sure if it's real. The kits that these appear on can be analyzed by a third party and see if they feel that it is a strong SNP. I usually use both of them (FGC and YFull) as they don't always agree with each other and I want the most eyes looking at the data that I can get. So you can't really solve it but you can get a second or third opinion on how good of an SNP it is. If you had money to burn you could always get another NGS (next generation sequencing) test that covers more area. BigY is an NGS test but there are tests that test more area than BigY but they are also more expensive and their results don't show on the FTDNA page to match with other customers. It's a choice to be made when getting the tests. There are people who have done both but most people pick a test and only do the one. As for getting more of the singletons matched on your husband's kit, you are going to need to find relatives who are distant but not so distant as John. So someone who shares a common ancestor with Keith more towards today but not a close relative. A son, brother, cousin, uncle are all probably going to match exactly. That would get all the rest of the singletons matched right off if you used a close relative but you are trying to see approximately where in time the mutation appeared so you can use that to break up lines. If your?ggg grandfather passed down a mutation to one son and not the other you can use that information to figure out who is matching to which line. Does that make sense? Chris On Thu, Jan 26, 2017 at 7:58 AM, kgnmeg@... [R1b-S6881] <R1b-S6881@...> wrote:
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S6881 Panel at YSEQ
Just wanted to make you aware of the S6881 panel at YSEQ which I created as a cheap way to fit likely or confirmed S6881 people into the S6881 tree. However I note Chris's tree has some extra SNPs. If it is possible to improve the panel I expect this can be done. 7 is the minimum SNPs for a panel, and I only have 7 and YSEQ weren't happy about the quality of one of them. On the other hand adding SNPs would make the test (currently $103) more expensive. A replacement strategy would be a way to go. In time I would expect to see panels below the S6881 panel to address single name groups e.g. a Warburton panel, or a Graves panel based on their currently known singletons. The role of BIG Y is to do 1 or 2 to identify enough singletons, and then panels to fit the majority of people. |
Re: New file uploaded to R1b-S6881
First let me say THANK YOU....that is a wonderful explanation. It helps a lot and seemed very understandable to me.
In hoping that I did understand correctly, I'd like to ask a couple more questions regarding this subject. 1. When you say his 1 singleton is questionable, I did see the code meanings top left, I wondered why it would be questionable and if that needs to be solved some way or can it be solved? 2. As I see what you are saying about my husbands kit, who is the 232994 Graves, needs at least 4 more matches to reach his terminal SNP. Is there a suggestion as to how we get those 4 other matches? Who would best be able to tell us our most likely possibilities, if indeed there are any available at this time.? As I look at this chart some more, I'm sure I'll have more questions but thank you so much for what you have told me so far. It has helped a lot to be able to understand what I'm seeing. Mary ? |