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 > From: kullfarr@gmail.com > Date: Sun, 27 Apr 2014 11:35:46 -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. > > Hello, > > I am the Farrell who FTDNA has now listed as CTS12173+ (N112356). > > However, I think perhaps the rather random assortment of men (based on their previous snp assignments) that have now been identified as CTS12173+ may be due to FTDNA/Geno2 misidentifying some of us. I looked up CTS12173 on YBrowse today and found that C is the ancestral nucleotide at this position and A is derived, which is odd since my Geno2 raw data, both the original file and the file I downloaded yesterday, indicates that I have the ancestral C nucleotide at this position. I’m not sure how this kind of mistake might happen but it seems fairly clear that I am not CTS12173+. > > Mike > > > > > > ------------------------------- > 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

In addition to Iain's remarks, let me add that there were calls in both Geno2 and Chromo2 that seemed to make NO sense. There are several possibilities... 1. Being a back mutation that is very rare but does happen...if something like this was the case one could expect to see the same value for that SNP in a linear lineage since the Y is inherited from father to son even if it may be different among others. Like I said, though, back mutations are rare. 2. The second and most likely possibility that the Illumina technology being used by both scanning arrays isn't interpreting the data correctly. A similar issue seems to be the case with sequencing technology to some extent as well for slightly different reasons (the Illumina technology although different technology is used for sequencing processes). 3. Some SNPs apparently for what ever reason behave more like STRs. Some speculate that these that behave this way aren't truly SNPs. I wouldn't know. Jim Wilson is an accomplished and professionally respected geneticist and he has represented that certain SNPs that are truly SNPs do not behave as we expect they should and used the phrase specifically "behave more like STRs" In all circumstances above, validating the information with Sanger technology for the most part settles the call, and if the call is truly correct and conflicting with what is expected then the geneticist can interpret the reason, generally. IMCO Geno2 has had its issues that have not been addressed in the same manner that BISDNA addressed seemingly the same issues with Chromo2. I cannot speculate FDDNA has or hasn't done to mitigate the observational information that was forwarded to them; however it seems that the variable calls continue. Susan On 4/27/2014 3:28 PM, Iain Kennedy 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 > > > > > >> From: kullfarr@gmail.com >> Date: Sun, 27 Apr 2014 11:35:46 -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. >> >> Hello, >> >> I am the Farrell who FTDNA has now listed as CTS12173+ (N112356). >> >> However, I think perhaps the rather random assortment of men (based on their previous snp assignments) that have now been identified as CTS12173+ may be due to FTDNA/Geno2 misidentifying some of us. I looked up CTS12173 on YBrowse today and found that C is the ancestral nucleotide at this position and A is derived, which is odd since my Geno2 raw data, both the original file and the file I downloaded yesterday, indicates that I have the ancestral C nucleotide at this position. I’m not sure how this kind of mistake might happen but it seems fairly clear that I am not CTS12173+. >> >> Mike >> >> >> >> >> >> ------------------------------- >> 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 > > > ------------------------------- > 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 >