Figure 2.

SNPs in Dd2. (a) Plot of -log10 P values for z-test (blue line) performed with Dd2 versus the 3D7 reference; detected are all of the reported single nucleotide polymorphisms (SNPs) in the pfcrt gene that were represented in the microarray (red triangles). Two SNPs were not detected (black triangles) because of the lack of unique probes to these positions. The thin and thick black arrows correspond to SNPs indicated in panel b. The P-value cutoff was 1 × 10-8 (black line). (b) Visualization of probe intensity log ratios in Dd2 versus 3D7. Each probe is shown as a single pixel and is colored based on its log ratio. Continuous strips of dimmer pixels correspond to SNPs that map to multiple unique probes, as indicated by the thin and thick white arrows. (c) Probes were tiled through the genome with an offset of two to three base pairs of alternating strands. The position marked in red is the position of the SNP marked by the thick arrows in panels a and b. The base pair positions on the left indicate the start of the probe with respect to the plus strand of chromosome 5 and its orientation.

Dharia et al. Genome Biology 2009 10:R21   doi:10.1186/gb-2009-10-2-r21
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