Body: <p>I am working with an Illumina-generated final report file from human genotyping; the MEGA chip I believe. It's in a massive .csv file I've been 'exploring' via unix commands on a compute cluster, something I'm fairly new to.</p>
  <p>For a particular SNP (an APOE variant, rs429358, ancestral allele T with the C MAF presumed to be ~15% in this population of ~160 genotyped persons), though, I'm seeing seemingly non-sensical reads. (Table of first two sample IDs' results at bottom.)</p>
  <p>I've been trying to make sense of this, and I think the R 1-5 indicates 5 reverse reads and F1-15 indicate 15 forward reads. This also makes sense as to why the R reads would be A-G in the name since that would be the opposing strand of the T-C of the forward reads.</p>
  <p>But, as you can see, literally everything on both reads is T-T. This is true for every single person in the sample, everyone is T-T, which even if not for the forward/back mismatch, would still be mathematically virtually impossible.</p>
  <p>This is my first time working with raw final report files large enough that I can't simply open them and look at them, and so I'm having trouble determining if there's something wrong with the file, or something wrong with how I'm reading it. Is there any explanation that more experienced people know of for what I'm seeing here? (I will turn to the organization that did the genotyping soon, but I wanted to see if I could figure it out on my own or get as much info as possible to help <em>them</em> troubleshoot first!)</p>
  <hr />
  <div class="s-table-container"><table class="s-table">
  <thead>
  <tr>
  <th>SNP Name</th>
  <th>Sample ID</th>
  <th>Allele 1 - Forward</th>
  <th>Allele 2 - Forward</th>
  </tr>
  </thead>
  <tbody>
  <tr>
  <td>19:45411941-A-G</td>
  <td>001</td>
  <td>T</td>
  <td>T</td>
  </tr>
  <tr>
  <td>19:45411941-A-G-R1</td>
  <td>001</td>
  <td>T</td>
  <td>T</td>
  </tr>
  <tr>
  <td>19:45411941-A-G-R2</td>
  <td>001</td>
  <td>T</td>
  <td>T</td>
  </tr>
  <tr>
  <td>19:45411941-A-G-R3</td>
  <td>001</td>
  <td>T</td>
  <td>T</td>
  </tr>
  <tr>
  <td>19:45411941-A-G-R4</td>
  <td>001</td>
  <td>T</td>
  <td>T</td>
  </tr>
  <tr>
  <td>19:45411941-A-G-R5</td>
  <td>001</td>
  <td>T</td>
  <td>T</td>
  </tr>
  <tr>
  <td>19:45411941-T-C</td>
  <td>001</td>
  <td>T</td>
  <td>T</td>
  </tr>
  <tr>
  <td>19:45411941-T-C-F1</td>
  <td>001</td>
  <td>T</td>
  <td>T</td>
  </tr>
  <tr>
  <td>19:45411941-T-C-F10</td>
  <td>001</td>
  <td>T</td>
  <td>T</td>
  </tr>
  <tr>
  <td>19:45411941-T-C-F11</td>
  <td>001</td>
  <td>T</td>
  <td>T</td>
  </tr>
  <tr>
  <td>19:45411941-T-C-F12</td>
  <td>001</td>
  <td>T</td>
  <td>T</td>
  </tr>
  <tr>
  <td>19:45411941-T-C-F13</td>
  <td>001</td>
  <td>T</td>
  <td>T</td>
  </tr>
  <tr>
  <td>19:45411941-T-C-F15</td>
  <td>001</td>
  <td>T</td>
  <td>T</td>
  </tr>
  <tr>
  <td>19:45411941-T-C-F2</td>
  <td>001</td>
  <td>T</td>
  <td>T</td>
  </tr>
  <tr>
  <td>19:45411941-T-C-F3</td>
  <td>001</td>
  <td>T</td>
  <td>T</td>
  </tr>
  <tr>
  <td>19:45411941-T-C-F5</td>
  <td>001</td>
  <td>T</td>
  <td>T</td>
  </tr>
  <tr>
  <td>19:45411941-T-C-F6</td>
  <td>001</td>
  <td>T</td>
  <td>T</td>
  </tr>
  <tr>
  <td>19:45411941-T-C-F7</td>
  <td>001</td>
  <td>T</td>
  <td>T</td>
  </tr>
  <tr>
  <td>19:45411941-T-C-F8</td>
  <td>001</td>
  <td>T</td>
  <td>T</td>
  </tr>
  <tr>
  <td>19:45411941-T-C-F9</td>
  <td>001</td>
  <td>T</td>
  <td>T</td>
  </tr>
  <tr>
  <td>19:45411941-A-G</td>
  <td>002</td>
  <td>T</td>
  <td>T</td>
  </tr>
  <tr>
  <td>19:45411941-A-G-R1</td>
  <td>002</td>
  <td>T</td>
  <td>T</td>
  </tr>
  <tr>
  <td>19:45411941-A-G-R2</td>
  <td>002</td>
  <td>T</td>
  <td>T</td>
  </tr>
  <tr>
  <td>19:45411941-A-G-R3</td>
  <td>002</td>
  <td>T</td>
  <td>T</td>
  </tr>
  <tr>
  <td>19:45411941-A-G-R4</td>
  <td>002</td>
  <td>T</td>
  <td>T</td>
  </tr>
  <tr>
  <td>19:45411941-A-G-R5</td>
  <td>002</td>
  <td>T</td>
  <td>T</td>
  </tr>
  <tr>
  <td>19:45411941-T-C</td>
  <td>002</td>
  <td>T</td>
  <td>T</td>
  </tr>
  <tr>
  <td>19:45411941-T-C-F1</td>
  <td>002</td>
  <td>T</td>
  <td>T</td>
  </tr>
  <tr>
  <td>19:45411941-T-C-F10</td>
  <td>002</td>
  <td>T</td>
  <td>T</td>
  </tr>
  <tr>
  <td>19:45411941-T-C-F11</td>
  <td>002</td>
  <td>T</td>
  <td>T</td>
  </tr>
  <tr>
  <td>19:45411941-T-C-F12</td>
  <td>002</td>
  <td>T</td>
  <td>T</td>
  </tr>
  <tr>
  <td>19:45411941-T-C-F13</td>
  <td>002</td>
  <td>T</td>
  <td>T</td>
  </tr>
  <tr>
  <td>19:45411941-T-C-F15</td>
  <td>002</td>
  <td>T</td>
  <td>T</td>
  </tr>
  <tr>
  <td>19:45411941-T-C-F2</td>
  <td>002</td>
  <td>T</td>
  <td>T</td>
  </tr>
  <tr>
  <td>19:45411941-T-C-F3</td>
  <td>002</td>
  <td>T</td>
  <td>T</td>
  </tr>
  <tr>
  <td>19:45411941-T-C-F5</td>
  <td>002</td>
  <td>T</td>
  <td>T</td>
  </tr>
  <tr>
  <td>19:45411941-T-C-F6</td>
  <td>002</td>
  <td>T</td>
  <td>T</td>
  </tr>
  <tr>
  <td>19:45411941-T-C-F7</td>
  <td>002</td>
  <td>T</td>
  <td>T</td>
  </tr>
  <tr>
  <td>19:45411941-T-C-F8</td>
  <td>002</td>
  <td>T</td>
  <td>T</td>
  </tr>
  <tr>
  <td>19:45411941-T-C-F9</td>
  <td>002</td>
  <td>T</td>
  <td>T</td>
  </tr>
  </tbody>
  </table></div>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-02-16T12:41:59.180Z
Comments.Text: Isn't this simply a list of forward and reverse reads that do not support the variant? Can you explain where this table is coming from? How was it generated? What is it supposed to show?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-03-07T15:55:36.450Z
Comments.Text: @terdon Thank you, essentially, yes, that did end up being the case. After some reaching out, Illumina explained that with this particular genotyping process they were using at the time (this was done in 2017 I believe) they were attempting to circumvent a common issue with two particular SNPs that are difficult to genotype. They explained that the reason these reads are strange is due to their staff trying new strategies to do the read, but that they strategies did not prove to be successful. So indeed, it was basically an unsupported variant. Thanks!
Comments.UserDisplayName: KLN-RDN
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-03-07T15:56:47.767Z
Comments.Text: Oh great, and thanks for reporting back! I will close the question as non-reproducible then since you've figured it out.
Comments.UserDisplayName: terdon
Tags: <illumina><genotyping>
Title: Illumina Final Report seemingly giving impossible genotypes; how do I make sense of this file?
ThreadText: # Illumina Final Report seemingly giving impossible genotypes; how do I make sense of this file?
  
  (Asked by: username_0 on 2024-02-15)
  
  I am working with an Illumina-generated final report file from human genotyping; the MEGA chip I believe. It's in a massive .csv file I've been 'exploring' via unix commands on a compute cluster, something I'm fairly new to.
  
  For a particular SNP (an APOE variant, rs429358, ancestral allele T with the C MAF presumed to be ~15% in this population of ~160 genotyped persons), though, I'm seeing seemingly non-sensical reads. (Table of first two sample IDs' results at bottom.)
  
  I've been trying to make sense of this, and I think the R 1-5 indicates 5 reverse reads and F1-15 indicate 15 forward reads. This also makes sense as to why the R reads would be A-G in the name since that would be the opposing strand of the T-C of the forward reads.
  
  But, as you can see, literally everything on both reads is T-T. This is true for every single person in the sample, everyone is T-T, which even if not for the forward/back mismatch, would still be mathematically virtually impossible.
  
  This is my first time working with raw final report files large enough that I can't simply open them and look at them, and so I'm having trouble determining if there's something wrong with the file, or something wrong with how I'm reading it. Is there any explanation that more experienced people know of for what I'm seeing here? (I will turn to the organization that did the genotyping soon, but I wanted to see if I could figure it out on my own or get as much info as possible to help *them* troubleshoot first!)
  
  ---
  
  | SNP Name | Sample ID | Allele 1 - Forward | Allele 2 - Forward |
  | --- | --- | --- | --- |
  | 19:45411941-A-G | 001 | T | T |
  | 19:45411941-A-G-R1 | 001 | T | T |
  | 19:45411941-A-G-R2 | 001 | T | T |
  | 19:45411941-A-G-R3 | 001 | T | T |
  | 19:45411941-A-G-R4 | 001 | T | T |
  | 19:45411941-A-G-R5 | 001 | T | T |
  | 19:45411941-T-C | 001 | T | T |
  | 19:45411941-T-C-F1 | 001 | T | T |
  | 19:45411941-T-C-F10 | 001 | T | T |
  | 19:45411941-T-C-F11 | 001 | T | T |
  | 19:45411941-T-C-F12 | 001 | T | T |
  | 19:45411941-T-C-F13 | 001 | T | T |
  | 19:45411941-T-C-F15 | 001 | T | T |
  | 19:45411941-T-C-F2 | 001 | T | T |
  | 19:45411941-T-C-F3 | 001 | T | T |
  | 19:45411941-T-C-F5 | 001 | T | T |
  | 19:45411941-T-C-F6 | 001 | T | T |
  | 19:45411941-T-C-F7 | 001 | T | T |
  | 19:45411941-T-C-F8 | 001 | T | T |
  | 19:45411941-T-C-F9 | 001 | T | T |
  | 19:45411941-A-G | 002 | T | T |
  | 19:45411941-A-G-R1 | 002 | T | T |
  | 19:45411941-A-G-R2 | 002 | T | T |
  | 19:45411941-A-G-R3 | 002 | T | T |
  | 19:45411941-A-G-R4 | 002 | T | T |
  | 19:45411941-A-G-R5 | 002 | T | T |
  | 19:45411941-T-C | 002 | T | T |
  | 19:45411941-T-C-F1 | 002 | T | T |
  | 19:45411941-T-C-F10 | 002 | T | T |
  | 19:45411941-T-C-F11 | 002 | T | T |
  | 19:45411941-T-C-F12 | 002 | T | T |
  | 19:45411941-T-C-F13 | 002 | T | T |
  | 19:45411941-T-C-F15 | 002 | T | T |
  | 19:45411941-T-C-F2 | 002 | T | T |
  | 19:45411941-T-C-F3 | 002 | T | T |
  | 19:45411941-T-C-F5 | 002 | T | T |
  | 19:45411941-T-C-F6 | 002 | T | T |
  | 19:45411941-T-C-F7 | 002 | T | T |
  | 19:45411941-T-C-F8 | 002 | T | T |
  | 19:45411941-T-C-F9 | 002 | T | T |
  
  **Tags:** illumina, genotyping
  
  > **Comments:**
  > **username_1**: Isn't this simply a list of forward and reverse reads that do not support the variant? Can you explain where this table is coming from? How was it generated? What is it supposed to show?  
  > **username_0**: @username_1 Thank you, essentially, yes, that did end up being the case. After some reaching out, Illumina explained that with this particular genotyping process they were using at the time (this was done in 2017 I believe) they were attempting to circumvent a common issue with two particular SNPs that are difficult to genotype. They explained that the reason these reads are strange is due to their staff trying new strategies to do the read, but that they strategies did not prove to be successful. So indeed, it was basically an unsupported variant. Thanks!  
  > **username_1**: Oh great, and thanks for reporting back! I will close the question as non-reproducible then since you've figured it out.  
  
  ---
  
  ## 0 answers
  
  