Answers.Body: <p>It is recommended you learn the degenerate nucleotide code. In sequencing it can signify poor quality sequence data, but in primer design it is useful. R (mutation within purines) and Y (mutation within pyrimidines) are common. K, a purine to pyrimadine or pyrimadine to purine mutation is, in my opinion, rare. I would treat a K mutation with caution and consider the triplet codon around it, i.e. if it is part of a protein gene.</p>
  
  <p>Most phylogeneitcs programs will work with the degenerate nucleotide code, so in theory you can still obtain useful information with it.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-12-28T04:12:47.557Z
Answers.LastActivityDate: 2019-12-28T15:04:40.540Z
Answers.LastEditDate: 2019-12-28T15:04:40.540Z
Answers.UserDisplayName: M__
Answers.Body: <p>See <a href="https://www.bioinformatics.org/sms/iupac.html" rel="noreferrer">IUPAC codes</a>:</p>
  
  <p><a href="https://i.sstatic.net/5uFOM.png" rel="noreferrer"><img src="https://i.sstatic.net/5uFOM.png" alt="IUPAC codes"></a></p>
  
  <p>So, as you can see above, <code>K</code> means "Either G or T".</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-12-28T01:52:09.000Z
Answers.LastActivityDate: 2019-12-28T15:57:38.753Z
Answers.LastEditDate: 2019-12-28T15:57:38.753Z
Answers.UserDisplayName: user6690
Body: <p>When a DNA sequence is sequenced, I've only ever dealt with A,T,C,G and N which indicates un-identifiable bases. However, I came across a 'k' recently and I had asked another researcher who gave me an answer for what 'k' represents but I don't quite recall. It can't just be an anomaly in that one sequence file. Any ideas?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-12-29T21:28:04.050Z
Comments.Text: K is also the lysine amino acid (and k-mers are something else of course)
Comments.UserDisplayName: Chris_Rands
Tags: <phylogenetics><ngs><phylogeny>
Title: What is 'k' in sequencing?
ThreadText: # What is 'k' in sequencing?
  
  (Asked by: username_0 on 2019-12-28)
  
  When a DNA sequence is sequenced, I've only ever dealt with A,T,C,G and N which indicates un-identifiable bases. However, I came across a 'k' recently and I had asked another researcher who gave me an answer for what 'k' represents but I don't quite recall. It can't just be an anomaly in that one sequence file. Any ideas?
  
  **Tags:** phylogenetics, ngs, phylogeny
  
  > **Comments:**
  > **username_1**: K is also the lysine amino acid (and k-mers are something else of course)  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_3 on 2019-12-28. Score: 16 | Accepted answer
  
  See [IUPAC codes](https://www.bioinformatics.org/sms/iupac.html):
  
  [![IUPAC codes](https://i.sstatic.net/5uFOM.png)](https://i.sstatic.net/5uFOM.png)
  
  So, as you can see above, `K` means "Either G or T".
  
  
  ---
  
  ### Answer by username_2 on 2019-12-28. Score: 4
  
  It is recommended you learn the degenerate nucleotide code. In sequencing it can signify poor quality sequence data, but in primer design it is useful. R (mutation within purines) and Y (mutation within pyrimidines) are common. K, a purine to pyrimadine or pyrimadine to purine mutation is, in my opinion, rare. I would treat a K mutation with caution and consider the triplet codon around it, i.e. if it is part of a protein gene.
  
  Most phylogeneitcs programs will work with the degenerate nucleotide code, so in theory you can still obtain useful information with it.
  
  
  ---
  
  