The creation of a variant graph. Four alignments (left) are successively used to create a variant graph (right). (a) An alignment of a read that matches the reference. The associated variant graph consists of nodes that represent each base of the read. (b) An alignment of a read with a base difference at the second position. The base difference adds a new node that is connected to the existing first and third node. (c) An alignment of a read that has a base difference and a deletion relative to the reference. A new edge connecting the sixth and ninth nodes is added to the graph. (d) An alignment of a read that has a base difference, a deletion, and an insertion relative to the reference. Two new nodes are added creating a path from the previously existing SNP at the second position to the reference base at the second position. (e) The resulting variant graph with each edge labeled with the number of alignment paths containing this edge.