While 95% of the Y-chromosome does not have comparable alleles on the X, the tips of the X and Y do recombine. These are called pseudoautosomal regions; and, from the standpoint of inheritance, they behave like autosomes: https://en.wikipedia.org/wiki/Pseudoautosomal_region Could these have something to do with the reporting of two alleles on a Y test? Diana > From: Obed W Odom > Sent: Thursday, January 16, 2014 8:29 PM > To: [email protected] > Subject: Re: [yDNAhgI] CTS11651 in I1 L22+ Sector > > As far as I know, the Y should be identical in every somatic cell of an > individual. It is true that parts of the Y have internal repeats of > sequences, but I would think these regions would be avoided by the Geno 2.0 > chip.

Yes, the pseudoautosomal regions of the Y could show 2 alleles on the Geno 2.0 chip, but I would think the chip would avoid these regions since, due to their frequent recombination with the X, they are not useful for the Y phylogenetic tree. There is another region of the Y which is thought to have been copied from the X long ago and whose sequence is therefore very similar to the X. I think this region includes at least positions 3.5 to 6.0 million on the Y (corresponding to 89.3 to 91.8 million on the X). It rarely if ever recombines with the X so some useful Y SNPs are in this region, and these might also show the X allele on the Geno 2.0 chip. On Thu, Jan 16, 2014 at 10:27 PM, Diana Gale Matthiesen <[email protected]>wrote: > While 95% of the Y-chromosome does not have comparable alleles on the X, > the > tips of the X and Y do recombine. These are called pseudoautosomal > regions; > and, from the standpoint of inheritance, they behave like autosomes: > > https://en.wikipedia.org/wiki/Pseudoautosomal_region > > Could these have something to do with the reporting of two alleles on a Y > test? > > Diana > > > > From: Obed W Odom > > Sent: Thursday, January 16, 2014 8:29 PM > > To: [email protected] > > Subject: Re: [yDNAhgI] CTS11651 in I1 L22+ Sector > > > > As far as I know, the Y should be identical in every somatic cell of an > > individual. It is true that parts of the Y have internal repeats of > > sequences, but I would think these regions would be avoided by the Geno > 2.0 > > chip. > > > > ------------------------------- > To unsubscribe from the list, please send an email to > [email protected] with the word 'unsubscribe' > without the quotes in the subject and the body of the message >