Mutations in a genotype encoding a fit phenotype are often deleterious, and occasionally advantageous. There is a third possibility, that a mutation is neutral and leaves the fitness unchanged.
Neutral mutations can in turn be subdivided into two kinds, with a rather grey area between them. They can be in parts of `junk DNA', such that the decoding of the genotype ignores the values in that part. In this case it is only the functional part of the genotype (the part which is capable of causing some difference in the fitness) that counts towards effective genotype length when deciding upon mutation rates. For example, if a genotype of length 1000 is 90% junk, then a mutation rate set at the rate of one per effective genotype length should be implemented at the rate of 1/100 per locus, rather than 1/1000. It is often difficult to estimate what proportion of a genotype is junk, however, as this shades into the second class of neutral mutation.
This second type of mutation may leave the phenotype unchanged, yet open the possibility of a further mutation making some difference. As a simple example, a binary genotype with two loci, whose fitness is given by the logical AND of the alleles at each locus, retains a fitness of 0 during mutation from 00 to 01; yet this opens up the possibility of a further single point mutation reaching 11, with a fitness of 1 which was not achievable from the starting point. Such neutral mutations can in a high-dimensional space allow extended neutral paths which can percolate through vast areas of sequence space. Neutral drift of a population through such pathways means that it is much more difficult to get stuck on a local optimum than one's intuition based on 3-D landscapes might lead one to think. In addition, the percolation of such paths through sequence space tends to mean that it does not matter too much where in sequence space a converged population starts; under many circumstances it is possible to reach all possible fit regions from most starting points.
The SAGA selection and mutation rates encourage just such exploration through neutral drift in sequence space.