Page 4 of 5 FirstFirst ... 2345 LastLast
Results 31 to 40 of 45

Thread: Big Y Block Tree view

  1. #31
    Registered Users
    Posts
    562

    Quote Originally Posted by mwauthy View Post
    Pardon my ignorance but I am still sort of a noob at this. Are you saying that some of the SNPs that Ftdna use to create branches are phantom and would disappear if someone’s data were run twice?

    Also, since you are knowledgeable maybe you can answer a few questions I have about Yfull’s aging system. First, why does Yfull use the same amount of SNPs in their age calculations for two SNPs that are downstream from each other? For example, Yfull is saying I have 13 SNPs downstream of I-S10350 and 13 SNPs downstream of I-Y125947 even though S10350>Y125947. Shouldn’t they include 1 more for S10350? Also, Yfull uses the same averages for faster mutating paternal lines as for slower mutating paternal lines. As a result, S10350 is dated to be younger than Y125947 even though S10350>Y125947 forcing Yfull to ascribe Y125947’s age to S10350.

    Lastly, I am actually S10350>Y125947>BY149414. There are 4 phyloequivalent SNPs for I-BY149414 so I figured they would use 9 SNPs to date it (13-9) but instead they use 10. Not sure why?
    Ok I was able to figure out the answer to part of my question. I-Y125947 and I-BY149414 are not included in Yfull’s age calculation because they are not in the combBED regions of the Y chromosome.

    My question is why are they given 5 star ratings and are given subclade names on Yfull’s Haplotree if they aren’t good enough to be used in the age calculations?

  2. #32
    Registered Users
    Posts
    243
    Sex
    Location
    Wisconsin, USA
    Nationality
    American
    Y-DNA
    R1b-FGC29071
    mtDNA
    U5a1b1g*

    Ireland England Netherlands Germany France
    Quote Originally Posted by mwauthy View Post
    Ok I was able to figure out the answer to part of my question. I-Y125947 and I-BY149414 are not included in Yfull’s age calculation because they are not in the combBED regions of the Y chromosome.

    My question is why are they given 5 star ratings and are given subclade names on Yfull’s Haplotree if they aren’t good enough to be used in the age calculations?
    The criteria to include a SNP in age calculation has nothing to do with call quality. Call quality is nothing more than a likelihood estimation based on number of reads, alignment fit for the read, and base likelihood from the sequencer.

    Age estimation SNPs must appear in the regions defined by what Big Y is designed to target and the filter from the Poznik paper: http://science.sciencemag.org/content/341/6145/562

    They cannot use everything in Poznik’s filter because there are 2 million bases not seen consistently in Big Y. This leads to very large error ranges when compared with samples that do look there. Basically, you have to use the least common area covered for this type of calculation.

    SNPs outside that are can be perfectly fine as phylogenetic markers.
    Last edited by JamesKane; 01-28-2019 at 01:15 AM.

  3. The Following 3 Users Say Thank You to JamesKane For This Useful Post:

     JMcB (01-28-2019),  Mikewww (01-30-2019),  wlk (01-30-2019)

  4. #33
    Registered Users
    Posts
    562

    Quote Originally Posted by JamesKane View Post
    The criteria to include a SNP in age calculation has nothing to do with call quality. Call quality is nothing more than a likelihood estimation based on number of reads, alignment fit for the read, and base likelihood from the sequencer. Age estimation SNPs must appear in the regions defined by what Big Y is designed to target and the filter from the Poznik paper: http://science.sciencemag.org/content/341/6145/562

    They cannot use everything in Poznik’s filter because there are 2 million bases not seen consistently in Big Y. This leads to very large error ranges when compared with samples that due look there. Basically, you have to use the least common area covered for this type of calculation.

    SNPs outside that are can be perfectly fine as phylogenetic markers.
    Thanks for the reply! It makes sense to me now.

  5. #34
    Registered Users
    Posts
    3,841
    Sex
    Y-DNA
    R1b
    mtDNA
    H

    Quote Originally Posted by rms2 View Post
    Personally, I don't find the "myOrigins" part of the new Big Y Block Tree all that important, at least not to me. Most of one's autosomal dna comes from places other than the single line of males who comprise the y-chromosome line. Even really close Big Y matches can differ significantly on autosomal dna depending upon what this or that ancestor's mother was like...
    We have to look ahead to see where this is going. This is version 1.0. They need roll-up or aggregated for myOrigins at different layers of the tree. They need more granularity or sub-regional discernment more like what LivingDNA is doing in the Isles.

    I can’t copy/paste this because it is private but I’ve seen a couple of cases that provide tremendous insight. In one case you can see very clearly that at one particular branching layer Jewish at DNA was introduced. It came in on the maternal side right there but it is pretty much pinpointed.

  6. The Following User Says Thank You to Mikewww For This Useful Post:

     Robert1 (02-12-2019)

  7. #35
    Senior Member
    Posts
    176
    Sex
    Omitted
    Y-DNA
    I - L338/YSC261
    mtDNA
    V

    England Ireland Denmark Sweden Norway
    If I could easily open and view the new tool would be wonderful. Very slow to load, if it does at all. Not all computers/laptops handle the graphics as well, definitely not my work computer and my home one is pretty slow. I much prefer Alex W The Big Tree, at least I can open and navigate easily.

  8. #36
    Registered Users
    Posts
    112
    Sex

    Indeed, for some reason companies intentionally make things very hard to use. You need to use
    a million clicks to see a good size view.

    WHY do they make things so hard? WHY? I use the Williamson code to draw trees for my project.

    You can see everything at a glance.

    The same is true for genealogical trees for Family Finder.

  9. The Following 2 Users Say Thank You to dtvmcdonald For This Useful Post:

     JMcB (05-10-2019),  rivergirl (02-13-2019)

  10. #37
    Registered Users
    Posts
    5,068
    Sex
    Ethnicity
    Polish
    Y-DNA
    R1b-Z2552
    mtDNA
    W6a

    Poland Poland Pomerania European Union
    I don't understand why it shows 0 autosomal Origins for my father's sample considering that he also has Family Finder autosomal results?
    Last edited by Tomenable; 05-10-2019 at 08:07 PM.

  11. The Following User Says Thank You to Tomenable For This Useful Post:

     JMcB (05-10-2019)

  12. #38
    Registered Users
    Posts
    562

    Quote Originally Posted by Tomenable View Post
    I don't understand why it shows 0 autosomal Origins for my father's sample considering that he also has Family Finder autosomal results?
    I think you need at least two people who have done Family Finder for it to pop up on the Block Tree.
    I1> DF29> Z58> Z59> Z2041> Z2040> Z382> S26361> S16414> FGC24354> FGC24357> FGC24356> S10350> FGC75802> Y125947> S21197> BY149414> BY188003> BY188570

    YFull id: YF15884

  13. The Following User Says Thank You to mwauthy For This Useful Post:

     Tomenable (05-11-2019)

  14. #39
    Registered Users
    Posts
    5,068
    Sex
    Ethnicity
    Polish
    Y-DNA
    R1b-Z2552
    mtDNA
    W6a

    Poland Poland Pomerania European Union
    Quote Originally Posted by mwauthy View Post
    I think you need at least two people who have done Family Finder for it to pop up on the Block Tree.
    My father and me both have Family Finder. But only one of us has Big Y.

  15. #40
    Registered Users
    Posts
    562

    Quote Originally Posted by Tomenable View Post
    My father and me both have Family Finder. But only one of us has Big Y.
    Yeah I think you need at least 2 big Y kits that also have family finder.
    I1> DF29> Z58> Z59> Z2041> Z2040> Z382> S26361> S16414> FGC24354> FGC24357> FGC24356> S10350> FGC75802> Y125947> S21197> BY149414> BY188003> BY188570

    YFull id: YF15884

Page 4 of 5 FirstFirst ... 2345 LastLast

Similar Threads

  1. Replies: 2
    Last Post: 02-12-2019, 10:43 AM
  2. The L51 SNP Block - Revisited in 2018
    By Earl Davis in forum R1b Early Subclades
    Replies: 7
    Last Post: 07-21-2018, 09:02 PM
  3. Replies: 0
    Last Post: 05-17-2016, 02:00 PM
  4. Current view on origins of L2, etc
    By MattL in forum L2
    Replies: 6
    Last Post: 05-01-2016, 07:19 AM
  5. 3D View of Richard III's Grave.
    By JohnHowellsTyrfro in forum History (Medieval)
    Replies: 0
    Last Post: 03-22-2016, 10:07 AM

Posting Permissions

  • You may not post new threads
  • You may not post replies
  • You may not post attachments
  • You may not edit your posts
  •