Additional file 9.
Alleles assessed in assay are unlinked. Analysis of linkage disequilibrium among the bar code SNP markers for 52 parasites using data from a 3K Affymetrix Array (Neafsey, submitted). The plot shows a histogram of the pairwise correlation (R2) of 26 bar code SNP markers. The red line indicates the mean of the background distribution of R2, which is calculated from all pairs of SNP markers located on different chromosomes that were included on the Affymetrix 3k array, for the same group of samples shown in the corresponding histogram. The dotted and dash-dotted lines show one and two standard deviations away from the mean of the background distribution. The two outliers in a) are attributed to the SNP marker pairs Pf_07_000657939 and Pf_07_000671839 (R2 = 0.4137) and Pf_000488164 and Pf_000490877 (R2 = 0.5167). These SNP pairs are approximately 14 kb and 2.7 kb apart, respectively. As a result of this analysis, these two outlier assays were dropped from the final set of assays.
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Daniels et al. Malaria Journal 2008 7:223 doi:10.1186/1475-2875-7-223