Definition SNP and SNP-site as used in PanGEA

The term 'SNP' is widely used in the current literature but only vaguely defined. In the software PanGEA we use the term SNP-site and SNP. A SNP-site is the position of a SNP with respect to a reference sequence. A SNP is merely the nucleotide base found at a certain SNP-site in an EST mapping to the SNP-site. For example, imagine a SNP-site with 10 ESTs mapping to the site. Five of which have the character 'A' and the other five the character 'T'. According to our terminology this SNP-site has five SNPs with an 'A' and five SNPs with an 'T'. For this reason it should not be surprising if , for example, PanGEA reports 50 000 SNPs and only 500 SNP-sites.

SNP-Site

A SNP-site is an unambiguous position of SNPs with respect to a reference sequence. Which information is required to unambiguously define the position of SNPs:

• The identity of the reference sequence (gene ID), eg.: FBG00001
• The position within the reference sequence. The counting always starts at the first nucleotide of the reference sequence with a 1. (programmers know that arrays usually start with a 0).
• Due to indels a third piece of information is required: the indel shift. If no indel occured, a SNP-site has an indel-shift of 0. Alternatively a SNP being located at the second indel after the 6 nucleotide, has a position of 6 and an indel shift of 2 (6-2).