<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>

CC BY-SA 4.0
2020-02-27T17:06:43.807Z
Hey.. the reference is T, so if there are two bases with T on the reverse strand, it should be 2 ","
StupidWolf
CC BY-SA 4.0
2020-02-28T00:56:55.350Z
Yeah, that was the main point.
Liam McIntyre
CC BY-SA 4.0
2020-02-27T16:47:40.930Z
2020-02-27T16:47:40.930Z
swbarnes2
<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>

CC BY-SA 4.0
2020-02-27T14:10:09.020Z
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).
StupidWolf
CC BY-SA 4.0
2020-02-27T14:12:49.963Z
This way it's easier to see exactly was called.
StupidWolf
CC BY-SA 4.0
2020-02-28T01:37:16.157Z
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.
Liam McIntyre
<python><samtools><long-reads><mpileup>
Why does samtools mpileup sometimes include ref bases (other than ',' or '.')?
# 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 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).  
> **username_1**: This way it's easier to see exactly was called.  
> **username_0**: 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.  

---

## 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.  

---

