SNPs in Alignments

An example of a Single Nucleotide Polymorphism (SNP).

The image, as in the previous slide, shows two sequences, A C A G A C dash G A and A C A T A C A G A, placed one above the other. They have identical nucleotides at seven of the nine positions, which are indicated by asterisks. At the fourth position, where the top sequence has a G compared to a T in the lower sequence, the label above this mismatch indicates it’s a SNP.

A SNP in an alignment is a position where the letters in a column do not match.