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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.

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  • $\begingroup$ 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. $\endgroup$
    – user438383
    Commented Aug 23, 2020 at 7:39
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    $\begingroup$ Could it be related to the pseudoautosomal regions of the chromosomes? $\endgroup$
    – James Schinner
    Commented Aug 24, 2020 at 3:45
  • $\begingroup$ @JamesSchinner It seems that you are right. For example, rs28463388 is in the PLCXD1 gene which is a pseudoautosomal gene. $\endgroup$
    – Maxim Masiutin
    Commented Aug 24, 2020 at 17:47
  • $\begingroup$ @JamesSchinner, here is a relevant reply: snpedia.com/index.php/Talk:Gs266 $\endgroup$
    – Maxim Masiutin
    Commented Aug 24, 2020 at 17:53
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    $\begingroup$ Nice, first time my Biomedical Science degree has been useful! $\endgroup$
    – James Schinner
    Commented Aug 25, 2020 at 6:08

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