Additional file 6.

Mann-Whitney analysis of genome-wide LGS. Scan showing allele frequencies (proportion of AJ allele) from pyrosequencing after untreated infection (control, black triangles) and treated infection (artemisinin 100 mg/kg/day, 3 days, red diamonds) (n.b Figure 3A in main text uses Comparative Index (y-axis, defined in legend Figure 3) rather than allele proportion used here). Treatment is expected to bias AJ allele frequencies downward by removing the sensitive parent, AJ and recombinants free from resistance mutations. To correct for this and other factors (Text S1), control allele frequencies were reduced before testing potential selection valleys. Significant valleys are highlighted by blue circles (P < 0.001 in Mann-Whitney U-tests comparing a sliding window of 3-5 markers on the same chromosome (treated) with all untreated markers reduced by the percentage (R) indicated (AF-reduction); grey triangles show untreated frequencies resulting from a -25% shift). Positions of this strain's new mutations found by genome comparisons are indicated at the bottom (x = SNP; circle = indel). Chromosome numbers are given at the top. Genome position indicates physical mapping (Kbp) of 92 markers in the genome of P. chabaudi (Additional File 1). Data points are each the mean of 3 independent determinations.

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Hunt et al. BMC Genomics 2010 11:499   doi:10.1186/1471-2164-11-499