Fig. 3.

The representation problem. A A local graph with sequence explicitly shown. B, C The same graph with black reference path and alternate alleles in different colors, and the corresponding VCF records. In B, the black reference path is distinct from both alleles. The blue/red SNP then requires flanking sequence in order to allow it to have a coordinate. The SNP is thus represented as two ALT alleles, each 3 bases long, and the user is forced to notice they only differ in one base. C The reference follows the blue path, thus enabling a more succinct and natural representation of the SNP