LGS-Illumina reveals selection by chloroquine on chr11. Allele proportions (sensitive strain, AJ) in uncloned progeny of genetic crosses using high-stringency quantitative AS/AJ SNPs. The position of aat1 point mutation is indicated at bottom of each panel, x. A. In the absence of CQ, each dark blue cross denotes AJ SNP frequency at each AS/AJ SNP. The upper and lower binomial 95% confidence intervals for this proportion are given in cyan and red, respectively. The black line averages the focal SNP with 50 SNPs on each side (95% confidence interval (CI) = red, blue line). The frequent small changes of mean allele frequencies on a local scale are more likely to reflect stochastic effects rather than 'real' effects of selection. B. As "A" but after growth in the presence of 3 mg CQ kg-1 day-1. C As "B" without CI of individual SNPs. Colour coding denotes probability that the observed allele frequency in the selected sample is significantly different from that in the unselected sample in "A"; red P < 10-12, yellow P < 10-10, cyan P < 10-8, blue P < 10-6, and grey represents other points. D As C, but with 25% AF-reduction (statistics performed with AJ frequencies (unselected population in "A") are reduced by 25%, see Methods). For A - D, corresponding high-resolution pdf files enable detailed inspection of individual SNPs, sliding-window means and standard errors, available from corresponding author on request.