Figure 1

The graphical user interface of Gs2 makes it easy to analyse whole projects by arranging data in a hierarchical structure and by providing interactive plots and tables for summarising data. In this example data have been loaded by importing multiple genotype files, one for each chromosome. For the selected node, rare markers with minor allele frequency below 5% have been selected and a new cleaned dataset has been created in the tree. The table and the plots show the information for the selected dataset. The bars in the table show calculated values for cases and controls respectively. The plots on the right side of the window shows, in the order of vertical appearance with the first two showing marker information and the second two sample information, distribution of minor allele frequency with average Hardy Weinberg exact test probabilities, minor allele frequency plotted against failure rate, covariate distribution by regional origin and finally failure rate plotted against sample heterozygosity.