<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>

CC BY-SA 4.0
2019-12-28T04:12:47.557Z
2019-12-28T15:04:40.540Z
2019-12-28T15:04:40.540Z
M__
<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>

CC BY-SA 4.0
2019-12-28T01:52:09.000Z
2019-12-28T15:57:38.753Z
2019-12-28T15:57:38.753Z
user6690
<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>

CC BY-SA 4.0
2019-12-29T21:28:04.050Z
K is also the lysine amino acid (and k-mers are something else of course)
Chris_Rands
<phylogenetics><ngs><phylogeny>
What is 'k' in sequencing?
# 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)  

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## 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".


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### 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.


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