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Wing Genealogist
10-21-2019, 12:47 AM
Many Ancient DNA papers utilize a 1240K panel (roughly 12 million nuclear DNA SNPs) rather than the more comprehensive (and more expensive) shotgun approach.

The David Reich Lab of the Harvard Medical School has posted a listing of all the SNPs included in this panel https://reich.hms.harvard.edu/downloadable-genotypes-present-day-and-ancient-dna-data-compiled-published-papers

I have extracted the 32,670 Y-SNPs (called Chromosome 24 in the original spreadsheet) and created a Google Docs spreadsheet at:https://docs.google.com/spreadsheets/d/1wCWqyy8-jWU5-ZtNjKXXU1k-rTh8TZNO4tl6W2mE-pQ/edit?usp=sharing

Unfortunately, the original spreadsheet did not include the actual SNP name for the vast majority of Y-SNPs. Most are listed under their Reference Sequence (rs) name, or even by a label combining the SNP "number" (24) with the position on the Y Chromosome.

I have quickly tried to identify the R1b-U106 Y-SNPs and would like to grant Editor access to individuals who would be willing to identify SNPs for other clades.

deadly77
10-21-2019, 10:48 AM
Many Ancient DNA papers utilize a 1240K panel (roughly 12 million nuclear DNA SNPs) rather than the more comprehensive (and more expensive) shotgun approach.

The David Reich Lab of the Harvard Medical School has posted a listing of all the SNPs included in this panel https://reich.hms.harvard.edu/downloadable-genotypes-present-day-and-ancient-dna-data-compiled-published-papers

I have extracted the 32,670 Y-SNPs (called Chromosome 24 in the original spreadsheet) and created a Google Docs spreadsheet at:https://docs.google.com/spreadsheets/d/1wCWqyy8-jWU5-ZtNjKXXU1k-rTh8TZNO4tl6W2mE-pQ/edit?usp=sharing

Unfortunately, the original spreadsheet did not include the actual SNP name for the vast majority of Y-SNPs. Most are listed under their Reference Sequence (rs) name, or even by a label combining the SNP "number" (24) with the position on the Y Chromosome.

I have quickly tried to identify the R1b-U106 Y-SNPs and would like to grant Editor access to individuals who would be willing to identify SNPs for other clades.

Thanks for digging into this. I've been through some 1240K SNP captures of ancient samples and a lot of SNPs are no call because of a lack of coverage. Cutting down on the number of SNPs that I need to look for would be very helpful (and save me a lot of time) so I do appreciate this.

If you're interested in having the SNPs for the I1 haplogroup identified, I'd be happy to help out. I have them in spreadsheets for hg19 position that I've used for looking at the BAM files of ancient I1 individuals.

Wing Genealogist
10-28-2019, 01:41 PM
The spreadsheet at: https://docs.google.com/spreadsheets/d/1wCWqyy8-jWU5-ZtNjKXXU1k-rTh8TZNO4tl6W2mE-pQ/edit?usp=sharing has been updated with the help of others.

Hg 38 position has been added for all SNPs
I1, R1b-U106 and R1b-M269+/U106-/P312- SNPs have been identified and named
More SNP names have been added throughout the spreadsheet

I am still looking for volunteers to add information on other subclades, including the various subclades before P312.