Answers.Body: <blockquote>
    <p>Why is 't': 2' in there?</p>
  </blockquote>
  
  <p>How else do you think the pileup should show you that two reads (in the reverse direction) have a T in that position?</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-02-27T17:06:43.807Z
Answers.Text: Hey.. the reference is T, so if there are two bases with T on the reverse strand, it should be 2 ","
Answers.UserDisplayName: StupidWolf
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-02-28T00:56:55.350Z
Answers.Text: Yeah, that was the main point.
Answers.UserDisplayName: Liam McIntyre
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-02-27T16:47:40.930Z
Answers.LastActivityDate: 2020-02-27T16:47:40.930Z
Answers.UserDisplayName: swbarnes2
Body: <p>This is my first post here. I can think of no way of giving an easily reproducible example, as per the stack ethos. SO apologies in advance and any feedback on question format appreciated.</p>
  
  <p>I have called samtools mpileup (Version: 1.9 (using htslib 1.9)) on some oxford nanopore data (mapped to GRCh38).</p>
  
  <p>I am seeing some instances like below (grouped with pythons Counter), here reference is T at this position:</p>
  
  <pre><code> Counter({',': 34, '.': 33, 'c': 9, 'g': 6, 'a': 4, 't': 2, '-:ACTC': 1, '-:ACTCGG': 1, '-:5': 1, '$': 1, '*': 1})
  </code></pre>
  
  <p>Why is 't': 2' in there?</p>
  
  <p>flags used: -A -B -Q 1 -R -x</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-02-27T14:10:09.020Z
Comments.Text: Hi Liam, can you show the exact mpileup for this position? Because I see that you tried to parse this into python and also converted the cases (no upper cases).
Comments.UserDisplayName: StupidWolf
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-02-27T14:12:49.963Z
Comments.Text: This way it's easier to see exactly was called.
Comments.UserDisplayName: StupidWolf
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-02-28T01:37:16.157Z
Comments.Text: Thanks @StupidWolf . I stupidly didn't keep the position of the above and it was just one example of a big list. So I'll edit above and give more examples and more details. I appreciate the help. At this point I'm thinking mpileup is a bit buggy, hoping that its resolvable.
Comments.UserDisplayName: Liam McIntyre
Tags: <python><samtools><long-reads><mpileup>
Title: Why does samtools mpileup sometimes include ref bases (other than ',' or '.')?
ThreadText: # Why does samtools mpileup sometimes include ref bases (other than ',' or '.')?
  
  (Asked by: username_0 on 2020-02-27)
  
  This is my first post here. I can think of no way of giving an easily reproducible example, as per the stack ethos. SO apologies in advance and any feedback on question format appreciated.
  
  I have called samtools mpileup (Version: 1.9 (using htslib 1.9)) on some oxford nanopore data (mapped to GRCh38).
  
  I am seeing some instances like below (grouped with pythons Counter), here reference is T at this position:
  
  ```
   Counter({',': 34, '.': 33, 'c': 9, 'g': 6, 'a': 4, 't': 2, '-:ACTC': 1, '-:ACTCGG': 1, '-:5': 1, '$': 1, '*': 1})
  
  ```
  
  Why is 't': 2' in there?
  
  flags used: -A -B -Q 1 -R -x
  
  **Tags:** python, samtools, long-reads, mpileup
  
  > **Comments:**
  > **username_1**: Hi username_0, can you show the exact mpileup for this position? Because I see that you tried to parse this into python and also converted the cases (no upper cases).  
  > **username_1**: This way it's easier to see exactly was called.  
  > **username_0**: Thanks @username_1 . I stupidly didn't keep the position of the above and it was just one example of a big list. So I'll edit above and give more examples and more details. I appreciate the help. At this point I'm thinking mpileup is a bit buggy, hoping that its resolvable.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2020-02-27. Score: -1
  
  > Why is 't': 2' in there?
  
  How else do you think the pileup should show you that two reads (in the reverse direction) have a T in that position?
  
  > **Comments:**
  > **username_1**: Hey.. the reference is T, so if there are two bases with T on the reverse strand, it should be 2 ","  
  > **username_0**: Yeah, that was the main point.  
  
  ---
  
  