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. 2012 Nov;22(11):2270–2277. doi: 10.1101/gr.141515.112

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© 2012, Published by Cold Spring Harbor Laboratory Press

This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 3.0 Unported License), as described at http://creativecommons.org/licenses/by-nc/3.0/.

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Figure 2. — ALLPATHS-LG assemblies of three finished genomes. Vertices in the graph represent completely determined sequences, whereas an edge labeled n represents n possibilities for the sequence lying between its vertex sequences. For n > 1, these are local ambiguities. (1) E. coli. The assembly represents a circular chromosome that is completely determined except for a single local ambiguity for which there are two alternatives, as denoted by the edge labeled 2. This ambiguity represents either a T or a G. (2) R. sphaeroides. Each component of the graph is circular and corresponds to either a chromosome or plasmid, except for plasmids 4 and 5, which are highly similar and joined together in the assembly, resulting in two global ambiguities. The nine edges with labels exceeding 1 represent local ambiguities. (3) S. pneumoniae. The assembly is a circle. There are six local ambiguities.