The contributions of different data types to population genetic inferences. Exomes, SNP arrays, and genomes are likely to capture different combinations of these four basic site types: common variants, rare variants, invariant sites, and noncoding sites. Each site type offers unique information relevant to analyses of demography and natural selection. Rare variants and invariant sites captured in exomes are important for numerous evolutionary questions, from estimating the effective population size to detecting positive selective sweeps, and they may be missed by other methods. However, phenotypically causal noncoding variants and truly neutral regions far from genes and free from the effects of selection are absent from exomes.
Tennessen et al. Genome Biology 2011 12:127 doi:10.1186/gb-2011-12-9-127