Pairwise comparison of EAC02 and EAC03.

<p>A set of 23,755 SNVs confidently genotyped (20 or more reads) in EAC02, EAC03 and Brazil I and which are different from SalI are presented across 14 chromosomes. SNVs shared between the two strains are shown in lavender and positions where the two strains differ are shown in dark purple, revealing large regions of identity. The positions of the eight-microsatellite markers (<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0002882#pntd-0002882-t003" target="_blank">Table 3</a>) are indicated by arrows, including the region on chromosome 4 where the <i>msp4</i> and <i>msp5</i> markers are in a region of homozygosity surrounded by regions of heterozygosity (inset). Despite the two samples being identical at the eight microsatellite markers, they differ at many positions in the genome. A comparison between EAC02 and a Brazil I control strain (in red and blue) shows that the two strains are highly diverged and do not share blocks of contiguous DNA sequence.