Figure 1

JLIN screenshot. Figure 1 shows the JLIN visualisation for the pairwise LD comparison of six SNP markers, labelled SNP1 to SNP6, within a single gene. The top left triangle of the display (red triangle area) shows the pairwise D' LD statistics, while the bottom right triangle (blue) shows the pairwise r² statistics. Below this is a display measure to indicate relative physical distance between the markers. By selecting a particular comparison square, all available statistics for the particular comparison are displayed in the information area on the right of the graphical display. In Figure 1, the D' comparison between SNP2 and SNP4 was selected, with full statistics of the comparison between the two SNPs, including each possible haplotype and their associated calculated frequency, allele counts and frequencies for each SNP and genotype counts and frequencies for each SNP.