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spanjool
10-06-2013, 01:13 PM
I compared the SNPs found by Geno-2 in 6 CTS4065 cases with my WGS Y results.
Aside from CTS4065 I shared only 4 of the 52 CTS SNPs which all of them shared.
I checked visually my Bam file at the position of these SNPs; but none were derived.
Any explanation?
Hans

razyn
10-06-2013, 05:35 PM
One possible explanation would be 48 (out of 52) erroneous calls (i.e. "false positives") by the Geno 2 chip. That seems extreme, even for it; but I think your WGS (from DNA-DTC) has been pretty reliable about all the things we are otherwise able to verify. Something seems very out-of-synch, in these results.

Are the four CTS SNPs that agree with your results known to be farther upstream? I believe you had previously determined that CTS4065 is your "terminal" SNP, among those that have been given names.

spanjool
10-08-2013, 04:20 AM
One possible explanation would be 48 (out of 52) erroneous calls (i.e. "false positives") by the Geno 2 chip. That seems extreme, even for it; but I think your WGS (from DNA-DTC) has been pretty reliable about all the things we are otherwise able to verify. Something seems very out-of-synch, in these results.

Are the four CTS SNPs that agree with your results known to be farther upstream? I believe you had previously determined that CTS4065 is your "terminal" SNP, among those that have been given names.

The 4 CTS markers that I share with the CTS4065 terminal SNP clade are pointing to the haplogroups R1b1a, R1b1 and P.
The same disagreement was found with YSC markers.
But all the Z markers were in agreement.
I screened the SNP markers against the Finch2 SNP database (after conversion to build 37) and also the Compendium for position as well as derived allele.
Is there a possibility to approach the Geno group about this?