Figure 2
From: Ranking insertion, deletion and nonsense mutations based on their effect on genetic information
Computation of the LLR score for indels in the non-coding DNA. Once the indel is detected in population (here 39 S. cerevisiae yeast strains depicted in the top panel), an alignment of width W = 21 of orthologous sequences (referred to as the DNA site) from 5 closely related yeast species (including the reference S. cer, S. paradoxus, S. mikatae, S. kudriavzevii, and S. bayanus) is made centred around the position of the indel (bottom panel). The conservation of the DNA site is measured through the LLR score by measuring the relative rate of evolution of the site compared to the synonymous rate of evolution of the protein's coding region. (a) shows an insertion that falls into a highly conserved DNA site whereas (b) shows a deletion that falls into a region that is not conserved.