On Sat, Dec 12, 2015 at 9:33 PM, David Schroeder via < genealogy-dna@rootsweb.com> wrote: > Can anyone explain why I have no 'AT' SNP pairs in my AncestryDNA raw data > file? > I checked my 3 ancestry raw data files, one had no ATs, one had 1 AT, and the other had 3. So I suspect this is something in how they present the data An AT actually is an AT and a TA - the company only reports one part of the base pair.The basis for reporting an AT as opposed to a TT or an AA appears to be something called orientation which can change from build to build (e.g.build 36 to 37 and to 38). Reading about orientation, I see that the A of the first AT and the T of the second AT are each on the "forward" or "plus" strand In other words you are given 2 of the 4 letters at that location. Each chromosome having a base pair of its own. Here is sort of an explanation at SNPedia. The term is orientation http://www.snpedia.com/index.php/Orientation --------------------------------------------------------------- Kitty Munson Cooper, web developer,programmer, San Diego,CA genetic genealogy blog at http://blog.kittycooper.com/ family history and genealogy at http://kittymunson.com
Kitty, I did flip the orientation as I noticed there were C-Gs and G-Cs on AncestrDNA files when I loaded them to a database. 23 only had C-Gs so I wanted it to look like 23 raw data. I see there is more to it than a simple ordering. I did not flip the orientation back when I recreated the fixed ANCDNA file. I wonder if that causes any issues? David From: Kitty Cooper [mailto:kittymcooper@gmail.com] Sent: Thursday, December 17, 2015 1:16 PM To: David Schroeder; genealogy-dna Subject: Re: [DNA] My Raw Data Files - Comparison 23andme vs AncestryDNA On Sat, Dec 12, 2015 at 9:33 PM, David Schroeder via <genealogy-dna@rootsweb.com> wrote: Can anyone explain why I have no 'AT' SNP pairs in my AncestryDNA raw data file? I checked my 3 ancestry raw data files, one had no ATs, one had 1 AT, and the other had 3. So I suspect this is something in how they present the data An AT actually is an AT and a TA - the company only reports one part of the base pair.The basis for reporting an AT as opposed to a TT or an AA appears to be something called orientation which can change from build to build (e.g.build 36 to 37 and to 38). Reading about orientation, I see that the A of the first AT and the T of the second AT are each on the "forward" or "plus" strand In other words you are given 2 of the 4 letters at that location. Each chromosome having a base pair of its own. Here is sort of an explanation at SNPedia. The term is orientation http://www.snpedia.com/index.php/Orientation --------------------------------------------------------------- Kitty Munson Cooper, web developer,programmer, San Diego,CA genetic genealogy blog at http://blog.kittycooper.com/ family history and genealogy at http://kittymunson.com
GEDmatch "tokenizes" the data in an attempt to make it more uniform across platforms, so that should not be an issue for most SNPs. All C's are converted to G's and all A's are converted to T's (or maybe the opposite direction, but you get the idea). That fixes any strand orientation problems, but it introduces a few cases where the alternative alleles are also complementary base pairs in the double helix. The next effect of that is to give you a free ride for those few SNPs where you and your match are really opposite homozygotes. You speak of fixing errors -- I assume you're referring to no-calls rather that outright errors (miscalls). No-calls don't break up segments, just opposite homozygotes (e.g. CC in one party and TT in the other party). GEDmatch doesn't give any credit for the SNP threshold (although 23andMe and FTDNA do). For that reason, I predicted you might have a small increase in the number of matches, and I am puzzled as to why you saw a decrease. Ann Turner On Thu, Dec 17, 2015 at 11:39 AM, David Schroeder via < genealogy-dna@rootsweb.com> wrote: > Kitty, > > > > I did flip the orientation as I noticed there were C-Gs and G-Cs on > AncestrDNA files when I loaded them to a database. 23 only had C-Gs so I > wanted it to look like 23 raw data. I see there is more to it than a simple > ordering. I did not flip the orientation back when I recreated the fixed > ANCDNA file. I wonder if that causes any issues? > > > > David >