FIG. 3.

Illustrating variable regions within the 16S rRNA gene and location of chimeric breakpoints. (A) The frequency of occurrence of the most common nucleotide residue at each base position within the 16S rRNA gene, as determined from RDP-listed 4,383 type strains, with E. coli U00096 as a reference. These frequencies are measures of variability within the gene. (B) Smoothing the data, by taking the mean frequency within a window of 50 bases, moving one base at a time along the gene, creates the plot shown in panel B. The locations of the hypervariable regions are labeled, with gray bars on the x axis defining these regions as V1 to V9 (the Comparative RNA Web Site [http://www.rna.icmb.utexas.edu/]). (C) Histogram of all chimera breakpoints identified in this study and that of Hugenholtz and Huber (8).