Fig 3.

Limited genome-wide nucleotide variation at 4 weeks after SIVmac239 infection. The percent variation at each nucleotide position (from site 1300 to site 10200) is shown for the inoculum, six M1/M1 MCM (CY0320 to CY0325; black), six M1/M3 MCM (CY0326 to CY0331; orange), and six M3/M3 MCM (CY0332 to CY0337; blue). Each symbol shape represents a different animal. Nonsynonymous mutations are shown as filled characters, and synonymous mutations are shown as open characters. The nucleotide positions corresponding to the N and C termini of Gag_386-394GW9, Rev_59-68SP10, and Nef_103-111RM9 are shown as dashed vertical lines. Only variants present at a frequency of 1% or greater are shown. For an alternate visualization of these data with the Layercake visualization tool (12), please go to http://goo.gl/6uaDY.