Body: <p>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.</p>
  <p>[cut]</p>
  <pre><code>rs28463388  X   191998  TT
  rs28669107  X   195014  GC
  rs6655397   X   201935  GG
  rs7890186   X   202458  TG
  </code></pre>
  <p>[skipped]</p>
  <pre><code>rs1016793029    Y   8619592 GA
  </code></pre>
  <p>[skipped]</p>
  <pre><code>rs527288580 Y   8771750 GA
  </code></pre>
  <p>[skipped]</p>
  <pre><code>rs917158084 Y   14871973    TG
  </code></pre>
  <p>[…etc]</p>
  <p>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.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-08-23T07:39:07.880Z
Comments.Text: 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.
Comments.UserDisplayName: user438383
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-08-24T03:45:59.533Z
Comments.Text: Could it be related to the pseudoautosomal regions of the chromosomes?
Comments.UserDisplayName: James Schinner
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-08-24T17:47:00.907Z
Comments.Text: @JamesSchinner It seems that you are right. For example, rs28463388 is in the PLCXD1 gene which is a pseudoautosomal gene.
Comments.UserDisplayName: Maxim Masiutin
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-08-24T17:53:40.343Z
Comments.Text: @JamesSchinner, here is a relevant reply: https://www.snpedia.com/index.php/Talk:Gs266
Comments.UserDisplayName: Maxim Masiutin
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-08-25T06:08:18.923Z
Comments.Text: Nice, first time my Biomedical Science degree has been useful!
Comments.UserDisplayName: James Schinner
Tags: <genotyping>
Title: Male DNA genotyped with Illumina GSAMD gives two alleles for certain loci within sex chromosomes
ThreadText: # Male DNA genotyped with Illumina GSAMD gives two alleles for certain loci within sex chromosomes
  
  (Asked by: username_0 on 2020-08-22)
  
  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.
  
  **Tags:** genotyping
  
  > **Comments:**
  > **username_1**: 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.  
  > **username_2**: Could it be related to the pseudoautosomal regions of the chromosomes?  
  > **username_0**: @username_2 It seems that you are right. For example, rs28463388 is in the PLCXD1 gene which is a pseudoautosomal gene.  
  > **username_0**: @username_2, here is a relevant reply: https://www.snpedia.com/index.php/Talk:Gs266  
  > **username_2**: Nice, first time my Biomedical Science degree has been useful!  
  
  ---
  
  ## 0 answers
  
  