text: user2519: 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?
  
  user3848: 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.
  
  user6690: See IUPAC codes:
  
  So, as you can see above, K means "Either G or T".
  
original_text: 2519: <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>
   3848: <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>
   6690: <p>See <a href="https://www.bioinformatics.org/sms/iupac.html" rel="noreferrer">IUPAC codes</a>:</p>
  
  <p><a href="https://i.stack.imgur.com/5uFOM.png" rel="noreferrer"><img src="https://i.stack.imgur.com/5uFOM.png" alt="IUPAC codes"></a></p>
  
  <p>So, as you can see above, <code>K</code> means "Either G or T".</p>
  