Male DNA genotyped with Illumina GSAMD gives two alleles for certain loci within sex chromosomes

I have a tab-separated file (the columns are rsID CHROM POS GENOTYPE) generated by Diganomics with Illumina GSAMD (v2.2) from male DNA, and there are a few hundred loci within X or Y chromosome that contain two alleles, even heterozygous, e.g.

[cut]

rs28463388  X   191998  TT
rs28669107  X   195014  GC
rs6655397   X   201935  GG
rs7890186   X   202458  TG


[skipped]

rs1016793029    Y   8619592 GA


[skipped]

rs527288580 Y   8771750 GA


[skipped]

rs917158084 Y   14871973    TG


[…etc]

There are 1270 such double alleles (7 in Y chromosome and 1163 in the X chromosome) from a total of 734162 number of lines, or 0.17%. What is remarkable is that these 1163 doubles within the X chromosome tend to be clustered, i.e. come consequently one after another mostly, but the 7 in the Y were sparse single lines.

• Do you have a link to the manual for the Illumina caller you used? I searched a bit for it but couldn't find anything. Aug 23 '20 at 7:39
• Could it be related to the pseudoautosomal regions of the chromosomes? Aug 24 '20 at 3:45
• @JamesSchinner It seems that you are right. For example, rs28463388 is in the PLCXD1 gene which is a pseudoautosomal gene. Aug 24 '20 at 17:47
• @JamesSchinner, here is a relevant reply: snpedia.com/index.php/Talk:Gs266 Aug 24 '20 at 17:53
• Nice, first time my Biomedical Science degree has been useful! Aug 25 '20 at 6:08