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RE: [R1b-P312-Project] Geno 2.0

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  • vernade didier
    What I was looking for was rather a comparison. It might need 3 files :One file outside DF27 ; L21 or U152 would do a file of the SRY2627 brancha file of the
    Message 1 of 39 , Jun 1, 2013
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      What I was looking for was rather a comparison. It might need 3 files :

      One file outside DF27 ; L21 or U152 would do

      a file of the SRY2627 branch

      a file of the M153 branch

      The question would be : how many SNPs in common between SRY2627 and M153 , AND not shared by L21 (or U152) ?  This is targetting the segment at the root of DF27 branch.


      Didier


       

      I've seen and run comparisons on several p312 Geno 2 files but I'm not systematically collecting them.

      If you're wondering about a specific SNP I can look to see if its in my most recent Geno 2 files.

      Sent from Yahoo! Mail for iPhone


      From: vernade didier <didier.vernade@...>;
      To: <R1b-P312-Project@yahoogroups.com>;
      Subject: [R1b-P312-Project] Geno 2.0
      Sent: Sat, Jun 1, 2013 2:35:44 AM

       

      List,


      I noticed that Geno 2.0 L21  results are collected by someone, the same for U152, but I am not sure there is someone collecting systematically the DF27 results. I know that SRY2627 is checked but what about the whole DF27 group ?

      In turn, I would like to know how many SNPs equivalent to upper SNPs like P312 and L11 are on Geno 2.0.


      Didier Vernade

    • Mikol Ryon
      Cool, I suspected as much but wanted to be sure. thanks. ... From: David Carlisle Subject: Re: [R1b-P312-Project] Geno 2.0 (vs
      Message 39 of 39 , Jun 12, 2013
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        Cool, I suspected as much but wanted to be sure.

        thanks.


        --- On Wed, 12/6/13, David Carlisle <davidcar801@...> wrote:

        From: David Carlisle <davidcar801@...>
        Subject: Re: [R1b-P312-Project] Geno 2.0 (vs FullGenomes.com)
        To: "R1b-P312-Project@yahoogroups.com" <R1b-P312-Project@yahoogroups.com>
        Date: Wednesday, 12 June, 2013, 18:19

         

        What we were saying is that you are at the top of the branch that terminates at M153, even though you're not M153.


        From: Mikol Ryon <mikolryon@...>
        To: R1b-P312-Project@yahoogroups.com
        Sent: Wednesday, June 12, 2013 9:51 AM
        Subject: Re: [R1b-P312-Project] Geno 2.0 (vs FullGenomes.com)

         

        Sorry if I've not understood you correctly but I am actually M153-.


        --- On Sat, 1/6/13, David Carlisle <davidcar801@...> wrote:

        From: David Carlisle <davidcar801@...>
        Subject: Re: [R1b-P312-Project] Geno 2.0 (vs FullGenomes.com)
        To: "R1b-P312-Project@yahoogroups.com" <R1b-P312-Project@yahoogroups.com>
        Date: Saturday, 1 June, 2013, 14:06

         
        The only SNP in Geno 2.0 in that category is Z195.  The last word on the subject may soon be available if there is someone in the M153 branch and the SRY2627 branch that signed up for the FullGenomes.com test.  If so, those results could be compared with David Reynolds L21 FullGenomes test to give you an essentially final answer.

        I compare Geno 2.0 raw files with a reference U106 file, so that reference plays the role of a comparison with a kit outside DF27.

        One kit near the top of the M153 branch is the Mikol Ryon kit.  A kit near the top of the SRY2627 branch is the Bisbey kit, which is Z198/L176.2.  The comparisons with U106 for each of those kits is as follows, which shows the only commonality at Z195+ and U106-:

        Comparing _U106_Reference_NEW.csv and Z220_MikolRyon_NEW.csv

        SNP: P135  T <> -
        SNP: PF3346  T <> -
        SNP: U106  T <> C
        SNP: Z195  G <> A
        SNP: ColD_Z210  C <> T
        SNP: ColE_Z210  C == C
        SNP: ColD_Z215  G <> A
        SNP: ColE_Z215  G == G
        SNP: Z220  G <> A
        SNP: Z268  T <> G
        SNP: Z274  C <> G

        The following numbers must be equal
        Total  Y-Counts: 12064 = 12064
        Synced Y-Counts: 12064 = 12064


        Comparing NEW_U106Ref_Feb27.csv and Bisbey (P312 Z198)

        SNP: CTS10855  G <> A
        SNP: CTS7095  T <> C
        SNP: F3515  C <> -
        SNP: L618  T <> -
        SNP: U106  T <> C
        SNP: Z195  G <> A
        SNP: Z198  G <> T

        The following numbers must be equal
        Total  Y-Counts: 12058 = 12058
        Synced Y-Counts: 12058 = 12058


        From: vernade didier <didier.vernade@...>
        To: R1b-P312-Project@yahoogroups.com
        Sent: Saturday, June 1, 2013 4:21 AM
        Subject: RE: [R1b-P312-Project] Geno 2.0

         


        What I was looking for was rather a comparison. It might need 3 files :
        One file outside DF27 ; L21 or U152 would do
        a file of the SRY2627 branch
        a file of the M153 branch
        The question would be : how many SNPs in common between SRY2627 and M153 , AND not shared by L21 (or U152) ?  This is targetting the segment at the root of DF27 branch.

        Didier

         

        I've seen and run comparisons on several p312 Geno 2 files but I'm not systematically collecting them.

        If you're wondering about a specific SNP I can look to see if its in my most recent Geno 2 files.

        Sent from Yahoo! Mail for iPhone


        From: vernade didier <didier.vernade@...>;
        To: <R1b-P312-Project@yahoogroups.com>;
        Subject: [R1b-P312-Project] Geno 2.0
        Sent: Sat, Jun 1, 2013 2:35:44 AM

         
        List,

        I noticed that Geno 2.0 L21  results are collected by someone, the same for U152, but I am not sure there is someone collecting systematically the DF27 results. I know that SRY2627 is checked but what about the whole DF27 group ?
        In turn, I would like to know how many SNPs equivalent to upper SNPs like P312 and L11 are on Geno 2.0.

        Didier Vernade




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