Geno 2.0 Errors?

[tbartold]

Has anyone else found errors in their Geno 2.0 results?

I compared my yDNA Walk Through the Y results from 2011 to my Geno 2.0 Y alleles, and found 32 mismatches.

I can't believe that I've personally mutated that much in just 2 years.

One example is the L1 mutation.

My Geno 2.0 download shows:
SNP Chr Allele1 Allele2
L1 Y G G

My WTY download shows:
Sample Marker Allele Position
GRC10032905 L1 C- ChrY:13025258..13025258

Does WTY really show me as an unmutated C? And does Geno 2.0 really show that (both of) the allele(s) are G?

Since the L1 mutation is normally C->T according to the ISOGG Y-DNA Index, does it even make sense that I'd have a different mutation there?

Am I reading the Geno 2.0 results completely wrong? What else could "L1 Y G G" actually mean?

[ScooterCat]

...
What else could "L1 Y G G" actually mean?

It could actually mean "C C" if read on the complementary DNA strand. Without knowing which strand is being read, you can't say for sure which it is.

Bases that are read on the complementary strand show:
A <-> T
C <-> G

[tbartold]

It could actually mean "C C" if read on the complementary DNA strand. Without knowing which strand is being read, you can't say for sure which it is.

Bases that are read on the complementary strand show:
A <-> T
C <-> G

I guess that I should have added more examples. Here's a couple more C's from my WTY.

If I look at L11, I see that they are both reporting 'C' for the mutation.
L11 Y C C
GRC10032905 L11 C+ ChrY:16353412..16353412

So it would seem that they both have the same result for L11, but differing results for L1.

But in this case it's a positive mutation, so may it's not the same?

How about L10? Both report 'C' for not mutated:
L10 Y C C
GRC10032905 L10 C- ChrY:20616712..20616712

Both report 'C' in both cases. Why would Geno 2.0 report a 'G' for L1?

It really appears that Geno 2.0 insists that my L1 mutated in the last 2 years, doesn't it?

My confusion derives from the fact that just 32 of the WTY results differ from the Geno 2.0 results. The other 900+ results are the same. If they really did choose to report the complementary results instead, then these 32 might be correct, but the other 900+ would be wrong, wouldn't they?

Since I'm pretty sure i don't have the L1 mutation, especially since the mutation that Geno 2.0 reports is not the standard mutation, I'm more willing to trust the WTY results.

I really think that my Geno 2.0 results are messed up. Either that or the WTY results were flawed. Where should I complain?

[Ann Turner]

The GenoChip is not necessarily consistent about reporting plus or minus strands. That's definitely the case for mtDNA.

Have you transferred your results to FTDNA and joined a haplogroup project? The SNP tab of the project website will list the SNPs that Geno calls as positive, and the administrator may have access to raw data files for further refinement.

[Wing_Genealogis]

The GenoChip is not necessarily consistent about reporting plus or minus strands. That's definitely the case for mtDNA.

Have you transferred your results to FTDNA and joined a haplogroup project? The SNP tab of the project website will list the SNPs that Geno calls as positive, and the administrator may have access to raw data files for further refinement.

Actually, the project administrator would NOT have access to an individual's raw data. Instead, we ask the individual to voluntarily send us a copy of their raw data (which they have to download). In return, we have been finding where the Geno webpage does not actually identify the terminal SNP about 30% of the time, as well as other technical glitches.

[Ann Turner]

Actually, the project administrator would NOT have access to an individual's raw data. Instead, we ask the individual to voluntarily send us a copy of their raw data (which they have to download). In return, we have been finding where the Geno webpage does not actually identify the terminal SNP about 30% of the time, as well as other technical glitches.

Yes, you're quite correct. I didn't word that clearly when I said "may" -- I was thinking of several admins who have collected files.

[tbartold]

So it appears that Geno reports some markers 'reversed' from what WTY reported. So, if the Geno result is reversed from the WTY result, that marker is one of those.

But what other markers are reversed? Is there a list anywhere that tells which markers Geno 2.0 chooses to reverse?

[ScooterCat]

... Is there a list anywhere that tells which markers Geno 2.0 chooses to reverse?

The only thing I've seen is a list of differently reported alleles between Geno 2.0 and FTDNA WTY.
https://dl.dropbox.com/u/92587284/WT...Mismatches.csv

[tbartold]

The only thing I've seen is a list of differently reported alleles between Geno 2.0 and FTDNA WTY.
https://dl.dropbox.com/u/92587284/WT...Mismatches.csv

Thanks ScooterCat!

That's basically much what I have. 32 alleles that are reported differently between WTY and Geno 2.0. Wherever we have mismatches, we all have the same mismatches. For example, we all had 'C' for L1, on WTY, and all have 'G' in Geno 2.0.

The only one that I did not have a mismatch on was P321. For that one, I got a 'G' from both WTY and Geno 2.0. However, the both 173880 and 193834 reports a 'C' from WTY, and a 'G' from Geno 2.0. So in this case there probably really was an error for the other 2, but not for me. And it was not just a bizarre way of interpreting reversed results.

Of course, now I have another mystery. Did I really get a 'G' for P321 from WTY, and, if so, why was that not flagged as a mutation?

Where did that list come from? Was there any explanation of whether this is true for everybody, or just for a lucky few?

[ScooterCat]

The list is from Dave Reynolds' website:
http://daver.info/geno/

He hangs out in the R1b-L21 Project Yahoo group:
http://tech.dir.groups.yahoo.com/group/R1b-L21-Project/
and would definitely be the person to ask about differences in reporting between WTY and Geno 2.0.