Synonymous nucleotide mutation

It follows that the technique is useful to identify (1) point mutation (a single different nucleotide) that may be a silent mutation (also known as a synonymous mutation due to degenerate coding), resulting in a codon that codes for the same amino acid or a missense mutation (type of non-synonymous mutation) producing a codon that codes for a different amino acid the resulting protein may be non-functional but certain missense mutations can be quiet since the protein may stiU function polymorphisms, (3) insertions, and deletions. 

Gonzales, M. J., Dugan, J. M., and Shafer, R. W. (2002) Synonymous-non-synonymous mutation rates between sequences containing ambiguous nucleotides (Syn-SCAN). Bioinformatics 18, 886-887. 

Fig. 2. Sequence content of spa repeats at nucleotide and amino acid levels. Repeats differing at the nucleotide level may be identical at the amino acid level. Identical codons are depicted using the same colors equivalent codons corresponding to synonymous mutations are colored with similar hues. The translated sequence reveals a conserved octapeptide motif comprised almost exclusively of charged amino acids and is suggestive of a surface-exposed loop region with repeating turns. Repeats Tl-Zl bear a single codon insertion between positions 1 and 2 most common spa types begin with one of these repeats, such that the initial repeat is usually 27-bp in length (vs. 24-bp).

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