Yes, I can see how a revertant might be mistaken for the ancestral, under some circumstances. Is that the case for CTS12173 here, i.e. is the derived CTS12173 under M222 a revertant (C>A>C)? Mike On Apr 27, 2014, at 12:28 PM, Iain Kennedy <ikennedy_msdn2@hotmail.com> wrote: > Sometimes there is confusion about what the ancestral value is - the PF2640 being a good example where hg19 conflicts with the information posted the other day; IGV and YFull are both reporting me as ancestral. > One thing to bear in mind is that the human reference genome is based on a mixture of people rather than someone at the root of the Y tree. So the value in href might be derived. > > By way of example, we all descend from hg A1 which is defined by L985. That's an A->C transition at 7374927. Now look at GRCh37: > http://www.ensembl.org/Homo_sapiens/Location/SequenceAlignment?db=core;g=ENSG00000114374;r=Y:7374927-7374927 > > and it shows a 'C'. IGV shows me as C and ancestral. But I'm actually derived of course. > I have also noted a couple of times when IGV and YFull report conflicting ancestral reference values. > > Iain

No I didn't mention back mutations. As far as I can see every source (not counting FTDNA!) is in agreement that C is the ancestral value for CTS12173 and that is what I have in my old Geno file and my BAM file and so does everyone else I've looked at so far. For example Bob Degnen's BAM file shows a C at that position and that conflicts with his project display for the SNP that has him as derived. Name: CTS12173 Type: snp Source: point Position: ChrY:28505799..28505799 (+ strand) Length: 1 ISOGG_haplogroup: not listed YCC_haplogroup: not listed allele_anc: C allele_der: A Homo_sapiens > chromosome:GRCh37:Y:28505799:28505799:1 Homo_sapiens 1 C 1 VENTER 1 . 1 WATSON 1 . 1 Degnen: Total count: 16 A : 0 C : 16 (100%, 16+, 0- ) G : 0 T : 0 N : 0 --------------- project display: CTS12173+ > From: kullfarr@gmail.com > Date: Sun, 27 Apr 2014 12:49:20 -0700 > To: dna-r1b1c7@rootsweb.com > Subject: Re: [R-M222] The 24 FTDNA SNPs below M222; Locations proposed for PF3292 and Z70, and rough locations for others. > > Yes, I can see how a revertant might be mistaken for the ancestral, under some circumstances. Is that the case for CTS12173 here, i.e. is the derived CTS12173 under M222 a revertant (C>A>C)? > > Mike > > > On Apr 27, 2014, at 12:28 PM, Iain Kennedy <ikennedy_msdn2@hotmail.com> wrote: > > > Sometimes there is confusion about what the ancestral value is - the PF2640 being a good example where hg19 conflicts with the information posted the other day; IGV and YFull are both reporting me as ancestral. > > One thing to bear in mind is that the human reference genome is based on a mixture of people rather than someone at the root of the Y tree. So the value in href might be derived. > > > > By way of example, we all descend from hg A1 which is defined by L985. That's an A->C transition at 7374927. Now look at GRCh37: > > http://www.ensembl.org/Homo_sapiens/Location/SequenceAlignment?db=core;g=ENSG00000114374;r=Y:7374927-7374927 > > > > and it shows a 'C'. IGV shows me as C and ancestral. But I'm actually derived of course. > > I have also noted a couple of times when IGV and YFull report conflicting ancestral reference values. > > > > Iain > > > ------------------------------- > To unsubscribe from the list, please send an email to DNA-R1B1C7-request@rootsweb.com with the word 'unsubscribe' without the quotes in the subject and the body of the message