Comparative Analysis of Functional Metagenomic Annotation and the Mappability of Short Reads
The phylogenetic tree was obtained from Ref. . Colored rings represent the recall for identifying reads originating from a KO gene using the top gene protocol. The 4 rings correspond to varying levels of database coverage. Specifically, the innermost ring illustrates the recall obtained when the strain from which the reads originated is included in the database, while the other 3 rings, respectively, correspond to cases where only genomes from the same species, genus, or more remote taxonomic relationships are present in the database. Entries where no data were available (for example, when the strain from which the reads originated was the only member of its species) are shaded gray. For one genome in each phylum, denoted by a black dot at the branch tip, every possible 101-bp read was generated for this analysis. For the remaining genomes, every 10th possible read was used. Blue bars represent the fraction of the genome's peptide genes associated with a KO; for reference, the values are shown for E. coli, B. thetaiotaomicron, and S. pneumoniae.