Every category of mutation was represented among VWS families, whereas PPS mutations were limited to missense, nonsense, and splicing mutations.
Thus, each mutation is represented as a signature vector that is used to train and test predictive machine learning methods in regression and classification tasks.
Moreover, we observed that when using "mutation" as a structure, students typically would construct propositions like "mutation changes the nucleotide sequence" or "mutation creates a new allele," wherein mutation was represented as an abstract agent causing a change.
Each feature associated with a mutation is represented in the form: p(ModeType, ModeType, …), where the ModeType is one of: (1) +ModeType specifying the input, (2) −ModeType specifying the output and (3) #ModeType specifying a constant.
Each mutation is represented by an arrow where the base (marked by a dot) indicates the estimated genetic map positions, and the arrowhead indicates the actual physical map positions.
As previously noted by others (Tajima 1983; Felsenstein 1992; Sherry et al. 1997), if a mutation has occurred when all but two members of a sample of size n have coalesced, it is equally likely that the mutation is represented in 1 to n − 1 copies in the sample.
We identified only a very small number of instances in which mutation was represented neither as a structure nor as a behavior; rather, it was used as an adjective to qualify a structure (e.g., "mutated gene" or "mutant allele"), or it was left "floating," meaning that the student placed it in the model but did not connect it to any other concept.
The mutations are represented by arrows and the corresponding mutation rates are marked.
Effectively neutral mutations are represented by 0 < Nes < 1, mildly deleterious by 1 < Nes < 10, deleterious by 10 < Nes < 100, and strongly deleterious by Nes > 100 (where Ne is the effective population size and s is the selection coefficient).
Until now, more than 40 different subsets of mutations have been identified and about 90% of NPM1 mutations are represented by subtype A and B (78% versus 12%, respectively).
