If we have access to the genome sequence of an individual there are a very large number of questions to be posed regarding that genome. For instance, what genetic markers are present that are of a predictive value in medical terms? What trait and disease alleles are present? What genetic properties are present that make the individual sensitive or resistant to a certain drug treatment? We may also want to know about the relationship of the individual to other individuals and whether there are markers characteristic of a certain human population. These are all questions that may be addressed using bioinformatics tools. In the previous chapter we examined SNPs and used them to get an idea about the genetic differences between individuals in general. Here, we will again use SNP data to analyse genomes, but we will see how we may identify SNPs that are shared between a group of individuals. We will also illustrate how SNP data may be mapped to information regarding exons, thus identifying SNPs that are likely to be in coding regions. In this way we are able to learn about the consequences of different SNPs at the level of protein products. The genomes that we are to examine are those of a few South African individuals. These genomes also highlight interesting questions regarding the early history of man.