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3234Re: {Disarmed} Re: [J-mtDNA] J1c1 missing and extra mutations

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  • Josh Weinstein
    May 18, 2014
    • 0 Attachment
      Actually, the criteria were from Phylotree. The same private mutation (s) must be found in three different full genome sequences----emphasis on different sequences.
      On Sunday, May 18, 2014 11:01 AM, "Josh Weinstein jgw111@... [J-mtDNA]" <J-mtDNA@yahoogroups.com> wrote:


       
      I don't mean to confuse anyone, but if enough individuals from different families share the same private mutation. it can serve as the basis for a new subclade. The specific criteria for defining a new subclade are at ISOGG-- i don't remember the details.

      On Sunday, May 18, 2014 10:12 AM, "Josh Weinstein jgw111@... [J-mtDNA]" <J-mtDNA@yahoogroups.com> wrote:


       
      Mutation 315.1c was specifically excluded from being used as a subclade defining mutation by Phylotree. The ( ) marks around it indicate that it was an  inconsistent locus. But it is not private

      On Sunday, May 18, 2014 9:53 AM, "Josh Weinstein jgw111@... [J-mtDNA]" <J-mtDNA@yahoogroups.com> wrote:


       
      Good that your results were confirmed. I have not seen any data on the average number of private mutations for full sequence testing.  Mutation 315.1c is not private---it simply does not distinguish between subclades

      On Sunday, May 18, 2014 5:28 AM, "'Petr Soucek' petr@... [J-mtDNA]" <J-mtDNA@yahoogroups.com> wrote:


      Thak you Josh, now I used http://dna.jameslick.com/mthap/ - they use
      rCRS and PhyloTree Build 16 and their result is the same:

      1) J1c1
      Good Match! Your results also had extra markers for this haplogroup:
      Matches(27): 73G (228A) 263G 295T 462T 482C 489C 750G 1438G 2706G
      3010A 3394C 4216C 4769G 7028T 8860G 10398G 11251G 11719A 12612G
      13708A 14766T 14798C 15326G 15452A 16069T 16126C
      Mismatches(0): (185G)
      Extras(6): 198T (315.1C) 7735G 8848C 12007A 16422C 16431A

      So still the same 6 extra markers.

      Is it nomal to have so many extra markers?

      As far as I know my maternal line comes from Carinthia, border area
      between Austria and Slovenia.

      Best Regrads,

      Petr

      On 13 Apr 2014 at 10:52, Josh Weinstein wrote:

      > Petr, I hope the following is not confusing for everyone, it is
      > FTDNA's fault. To determine your mutations, FTDNA compares your
      > pattern with a reference pattern known as RSRS. This is not standard
      > practice and is under debate. Most everyone else uses the reference
      > rCRS----the systems provide different  mutation results.  You can
      > choose the rCRS option on your Results page.  Phylotree's main
      > option provides rCRS results. It does provide an option for RSRS
      > results. (My own preference is for RSRS, but I think rCRS will
      > remain the standard)
      >                                              
      >                       Josh
      > On Sunday, April 13, 2014 1:28 PM, Josh Weinstein <jgw111@...>
      > wrote:

      >  
      > That should be Phylotree
      > On , Josh Weinstein <jgw111@...> wrote:

      > Petr, It is quite possible that your additional mutations could be
      > related to a future new subclade. Thanks to new research, often
      > involving FTDNA, new subclades appear all the time. I often have not
      > been up-to-date regarding the changes. The change could be major,
      > e.g. J1a was reclassified to J2a-----Wikipedia remained incorrect on
      > this issue.  Phylogree has provisional new trees at recent
      > intervals--it is just a matter of checking.
      >                                              
      >                                              
      >        Josh
      > On Sunday, April 13, 2014 1:11 PM, Petr Soucek <petr@...>
      > wrote:

      >  
      > Hello,
      >
      > FTDNA has determined my mtDNA haplogroup as J1c1 with:
      >
      > Extra Mutations: C198T, 315.1C, 522.1A, 522.2C, A7735G, T8848C,
      > G12007A, T16422C, C16431a, C16519T
      > Missing Mutations: G185A
      >
      > The missing mutation G185A is at http://www.phylotree.org/ in
      > brackets, so this note is relevant to it: "Mutations between
      > brackets
      > () are recurrent/unstable within the respective clade, or are yet
      > uncertain based on current data."
      >
      > At http://www.phylotree.org/ is written: "The mutations 309.1C(C),
      > 315.1C, AC indels at 515-522, 16182C, 16183C, 16193.1C(C) and 16519
      > were not considered for phylogenetic reconstruction and are
      > therefore
      > excluded from the tree."
      >
      > OK, then the following extra mutations remain:
      > C198T, A7735G, T8848C, G12007A, T16422C, C16431a
      >
      > Does this mean that in the future there may be haplogroups like
      > J1c1i, J1c1j, J1c1k etc. and that these extra mutations would
      > determine them?
      >
      > Best Regards,
      >
      > Petr Soucek

      >
      >
      >
      >
      >
      >




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