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Total: 4/4
    1. Re: [yDNAhgI] I2a2b and PF3514
    2. DNAresults

    3. John, I might be missing something here, but I agree with Obed -- I am I2b1c (I-P78) and I have PF 3514 derived (+) from GENO 2.0 as do all the I1d (I-L22) members of my surname project who tested with GENO 2.0. I don't have immediate access to the call right now to see if it shows a "C" but I believe it does. So, no new SNP eh? Richard Brewer On Wednesday, January 8, 2014, Obed W Odom wrote: > John, I wouldn't call PF3514=C a new SNP. I am I1-Z138 and also have C. In > fact, the ISOGG Y browser says this SNP is at the IJ level in the Y tree so > probably all I and J people should have it. The problem seems to be that > the original reference for PF3514 showed A to G instead of A to C. All of > the next-generation-sequencing results that I have seen for I1 and !2 > people show C. > > > On Wed, Jan 8, 2014 at 2:21 PM, John O'Grady <[email protected]<javascript:;> > >wrote: > > > Bernie, > > The reason that the Geno 2.0 chip didn't work is that the PF3514 mutation > > is A to C, not A to G. The good news is that, according to Full Genomes, > I > > am PF3514=C+. So we have a new SNP for L161-Isles. > > John O'Grady > > > > > > ------------------------------- > To unsubscribe from the list, please send an email to > [email protected] <javascript:;> with the word > 'unsubscribe' without the quotes in the subject and the body of the message >

    01/08/2014 07:00:46
    1. Re: [yDNAhgI] I2a2b and PF3514
    2. John O'Grady

    3. Richard, I am always looking for new SNPs. Sometimes I get a little overenthusiastic. I will be right one of these times. John O'Grady > > John, > > I might be missing something here, but I agree with Obed -- I am I2b1c > (I-P78) and I have PF 3514 derived (+) from GENO 2.0 as do all the I1d > (I-L22) members of my surname project who tested with GENO 2.0. I don't > have immediate access to the call right now to see if it shows a "C" but I > believe it does. So, no new SNP eh? > > Richard Brewer

    01/08/2014 07:20:51
    1. Re: [yDNAhgI] I2a2b and PF3514
    2. DNAresults

    3. Well, here is a little update on my own GENO2.0 results since I arrived home and was able to go back and find the raw data call and I see that in my November 2013 data the report was derived but showed PF3514 as A->G in both my I2 raw results and the I1 raw results for the others in my project. I see that that is just old news now and is exactly what Obed wrote. Sorry to have bothered you with unhelpful data. It did point to an upstream position which is now nicely confirmed by the data Magoon has provided for all of us. Thanks Richard On Wed, Jan 8, 2014 at 2:00 PM, DNAresults <[email protected]> wrote: > John, > > I might be missing something here, but I agree with Obed -- I am I2b1c > (I-P78) and I have PF 3514 derived (+) from GENO 2.0 as do all the I1d > (I-L22) members of my surname project who tested with GENO 2.0. I don't > have immediate access to the call right now to see if it shows a "C" but I > believe it does. So, no new SNP eh? > > Richard Brewer > > > On Wednesday, January 8, 2014, Obed W Odom wrote: > >> John, I wouldn't call PF3514=C a new SNP. I am I1-Z138 and also have C. In >> fact, the ISOGG Y browser says this SNP is at the IJ level in the Y tree >> so >> probably all I and J people should have it. The problem seems to be that >> the original reference for PF3514 showed A to G instead of A to C. All of >> the next-generation-sequencing results that I have seen for I1 and !2 >> people show C. >> >> >> On Wed, Jan 8, 2014 at 2:21 PM, John O'Grady <[email protected] >> >wrote: >> >> > Bernie, >> > The reason that the Geno 2.0 chip didn't work is that the PF3514 >> mutation >> > is A to C, not A to G. The good news is that, according to Full >> Genomes, I >> > am PF3514=C+. So we have a new SNP for L161-Isles. >> > John O'Grady >> > >> > >> >> ------------------------------- >> To unsubscribe from the list, please send an email to >> [email protected] with the word 'unsubscribe' >> without the quotes in the subject and the body of the message >> >

    01/08/2014 08:11:28
    1. Re: [yDNAhgI] I2a2b and PF3514
    2. G. Magoon

    3. For what it is worth, an A->C mutation at the site of PF3514 is placed on the IJ branch of the automatically generated phylogeny described in http://biorxiv.org/content/early/2013/12/13/000802, consistent with Obed's observations: > > For the branch from node 3 to node 37 with length 2507.00: > 3074753 REF->ALT (A->T); # of mutations in tree = 1 (weighted = 35) > 3110127 REF->ALT (C->G); # of mutations in tree = 4 (weighted = 4) > 3256504 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > SITEOF(['PF3503']) > 3496739 REF->ALT (G->A); # of mutations in tree = 3 (weighted = 15) > 3573860 REF->ALT (C->A); # of mutations in tree = 1 (weighted = 35); > SITEOF(['PF3504']) > 3850621 REF->ALT (C->A); # of mutations in tree = 3 (weighted = 15); > SITEOF(['PF3505']) > 4050542 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > SITEOF(['PF3506']) > 4366933 REF->ALT (C->A); # of mutations in tree = 1 (weighted = 35); > SITEOF(['PF3507']) > 4486612 REF->ALT (C->A); # of mutations in tree = 1 (weighted = 35); > SITEOF(['PF3508']) > 4520730 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35); > ['PF3509'] > 4843178 REF->ALT (A->C); # of mutations in tree = 6 (weighted = 0) > 4860686 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35); > ['PF3510'] > 5006360 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35); > SITEOF(['PF3511']) > 5173195 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > SITEOF(['PF3512']) > 5558718 REF->ALT (A->T); # of mutations in tree = 1 (weighted = 35) > 5578919 REF->ALT (A->C); # of mutations in tree = 2 (weighted = 70); > SITEOF(['PF3514']) > 5585882 REF->ALT (G->A); # of mutations in tree = 2 (weighted = 70) > 5625159 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35) > 5756437 REF->ALT (T->C); # of mutations in tree = 2 (weighted = 70); > SITEOF(['PF3515']) > 5818984 REF->ALT (C->T); # of mutations in tree = 2 (weighted = 70); > SITEOF(['PF3517']) > 6607318 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35); > SITEOF(['PF3518']) > 7190277 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35) > 7316588 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['CTS1292'] > 7694266 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35) > 7922133 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > SITEOF(['PF3522']) > 7923823 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > SITEOF(['PF3523']) > 8222299 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35) > 8558969 REF->ALT (A->T); # of mutations in tree = 1 (weighted = 35); > ['P130', 'PF3525', 'S22'] > 8590752 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['P127', 'PF3526'] > 8888300 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35) > 8906357 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > SITEOF(['PF3528', 'F1460']) > 9921164 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35) > 10002861 REF->ALT (G->T); # of mutations in tree = 1 (weighted = 35); > SITEOF(['PF3529']) > 13370245 REF->ALT (C->T); # of mutations in tree = 2 (weighted = 70); > SITEOF(['PF3530']) > 13617770 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > SITEOF(['PF3531']) > 13637759 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > SITEOF(['PF3532']) > 13676377 REF->ALT (G->T); # of mutations in tree = 1 (weighted = 35); > SITEOF(['PF3533']) > 13901813 REF->ALT (AC->A); # of mutations in tree = 1 (weighted = 35) > 13906393 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > SITEOF(['PF3534']) > 14031334 REF->ALT (T->A); # of mutations in tree = 1 (weighted = 35); > ['M429', 'P125', 'PF3535'] > 14144593 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['P129', 'PF3536'] > 14214957 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['CTS2197', 'PF3537', 'YSC0001258'] > 15055079 REF->ALT (A->T); # of mutations in tree = 1 (weighted = 35) > 15554989 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > ['F4188', 'PF3539'] > 15887617 REF->ALT (C->G); # of mutations in tree = 1 (weighted = 35) > 16244914 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > SITEOF(['CTS5387', 'PF3541']) > 16422613 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['L775', 'PF3542', 'YSC0000265'] > 16540552 REF->ALT (G->C); # of mutations in tree = 2 (weighted = 70); > ['CTS5899'] > 16674560 REF->ALT (A->G); # of mutations in tree = 2 (weighted = 70); > SITEOF(['CTS6101', 'PF3543']) > 16839810 REF->ALT (C->T); # of mutations in tree = 2 (weighted = 70) > 16966024 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35) > 17012180 REF->ALT (C->A); # of mutations in tree = 1 (weighted = 35); > ['L748', 'PF3546', 'YSC0000289'] > 17040447 REF->ALT (C->A); # of mutations in tree = 1 (weighted = 35) > 17200869 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35) > 17513178 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > SITEOF(['CTS7507', 'PF3549']) > 18519121 REF->ALT (C->G); # of mutations in tree = 3 (weighted = 15) > 18633084 REF->ALT (C->A); # of mutations in tree = 1 (weighted = 35); > ['F2794'] > 18769674 REF->ALT (C->G); # of mutations in tree = 1 (weighted = 35); > ['CTS9240'] > 19038302 REF->ALT (A->C); # of mutations in tree = 1 (weighted = 35); > ['P124', 'PF3553'] > 19166861 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35); > ['F4281', 'P123', 'PF3554'] > 19324937 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['CTS10200'] > 19331026 REF->ALT (T->A); # of mutations in tree = 1 (weighted = 35); > ['CTS10223'] > 21040853 REF->ALT (A->C); # of mutations in tree = 1 (weighted = 35); > SITEOF(['PF3556', 'F3102']) > 21220741 REF->ALT (T->C); # of mutations in tree = 1 (weighted = 35); > SITEOF(['PF3557']) > 21225770 REF->ALT (C->G); # of mutations in tree = 1 (weighted = 35); > SITEOF(['PF3558']) > 21321273 REF->ALT (A->T); # of mutations in tree = 1 (weighted = 35); > SITEOF(['PF3559', 'YSC0001320']) > 21337651 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['PF3560'] > 21389837 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35); > SITEOF(['PF3561']) > 21461202 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35); > ['PF3562'] > 21669123 REF->ALT (T->A); # of mutations in tree = 1 (weighted = 35); > SITEOF(['PF3563']) > 22319648 REF->ALT (T->G); # of mutations in tree = 2 (weighted = 70) > 22325279 REF->ALT (T->A); # of mutations in tree = 2 (weighted = 70) > 22484240 REF->ALT (G->T); # of mutations in tree = 3 (weighted = 15) > 22883286 REF->ALT (G->A); # of mutations in tree = 1 (weighted = 35) > 22909101 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['F3368', 'PF3566', 'YSC0001317'] > 23069523 REF->ALT (A->G); # of mutations in tree = 1 (weighted = 35) > 24080237 REF->ALT (A->C); # of mutations in tree = 4 (weighted = 4) > 24426007 REF->ALT (C->T); # of mutations in tree = 1 (weighted = 35); > ['F3629', 'PF3568'] On Wed, Jan 8, 2014 at 5:00 PM, DNAresults <[email protected]> wrote: > John, > > I might be missing something here, but I agree with Obed -- I am I2b1c > (I-P78) and I have PF 3514 derived (+) from GENO 2.0 as do all the I1d > (I-L22) members of my surname project who tested with GENO 2.0. I don't > have immediate access to the call right now to see if it shows a "C" but I > believe it does. So, no new SNP eh? > > Richard Brewer > > On Wednesday, January 8, 2014, Obed W Odom wrote: > > > John, I wouldn't call PF3514=C a new SNP. I am I1-Z138 and also have C. > In > > fact, the ISOGG Y browser says this SNP is at the IJ level in the Y tree > so > > probably all I and J people should have it. The problem seems to be that > > the original reference for PF3514 showed A to G instead of A to C. All of > > the next-generation-sequencing results that I have seen for I1 and !2 > > people show C. > > > > > > On Wed, Jan 8, 2014 at 2:21 PM, John O'Grady <[email protected] > <javascript:;> > > >wrote: > > > > > Bernie, > > > The reason that the Geno 2.0 chip didn't work is that the PF3514 > mutation > > > is A to C, not A to G. The good news is that, according to Full > Genomes, > > I > > > am PF3514=C+. So we have a new SNP for L161-Isles. > > > John O'Grady > > > > > > > > > > ------------------------------- > > To unsubscribe from the list, please send an email to > > [email protected] <javascript:;> with the word > > 'unsubscribe' without the quotes in the subject and the body of the > message > > > > ------------------------------- > To unsubscribe from the list, please send an email to > [email protected] with the word 'unsubscribe' > without the quotes in the subject and the body of the message >

    01/08/2014 10:14:27