Mistakes in the ISOGG Y-SNP index

The Y-SNP calls in my last post implied that Stora Förvar 11 was O3a1a. But notice that Ajvide 58 also had a positive call for O3a1a-DYS257_2/P27.2_2, and Ajvide 58 definitely wasn’t O3a1a.

There appear to be one or more mistakes in the ISOGG Y-SNP index for the SNP at position 8620377.

According to the index, there’s a T → C mutation at 8620377 that defines O3a1a. But the allele at that position in the human reference genome is C, and Ensembl shows that all of the following genomes also have the C allele at that position:

VENTER
WATSON
AK1
YH
Misha Angrist
Henry Louis Gates Sr
Henry Louis Gates Jr
Rosalynn Gill
Anonymous Irish Male
Marjolein Kriek
Stephen Quake
Palaeo-Eskimo Saqqaq individual HC
Palaeo-Eskimo Saqqaq individual
SJK
1000GENOMES:pilot_2_trio:NA12891
1000GENOMES:pilot_2_trio:NA12892
1000GENOMES:pilot_2_trio:NA12878
1000GENOMES:pilot_2_trio:NA19239
1000GENOMES:pilot_2_trio:NA19238
1000GENOMES:pilot_2_trio:NA19240

So the C allele is definitely the ancestral allele, and Stora Förvar 11 wasn’t O3a1a.

Also according to the index, a C → T mutation at 8620377 defines P. But Venter and Watson are both R1b-U106, and R1b is descended from P. Since Venter and Watson are both C at 8620377, there has to be a mistake in the index.

There’s another mistake in the index I found. Notice that Ajvide 70 and and Ajvide 58 both had positive calls for O3-P198. According to the index, there’s a T → C mutation at 17053771 that defines O3. But the allele at that position in the reference genome is C, and Ensembl shows that all of the above genomes also have the C allele at that position, except for AK1, which is a Korean genome. And dbSNP shows that only the C allele is found in Caucasoid and Negroid populations, while the T allele is only found in Mongoloid populations. So the mutation for O3-P198 should be C → T, not T → C.

But I didn’t find any mistakes for F2-M427, so maybe Ajvide 70 really was F2. It might be that F2 originated in the Veddoids of India, and then ended up in both the Caucasoids of Europe and the Mongoloids of East Asia, just as C1a did. If that is what happened, then F2 must have died out in Europe, because it hasn’t been found in modern European populations.

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