The height of the stack is especially sensitive to minor changes in the frequency of a very frequent base (e.g. if the frequency of the most common base falls from 1.0 to 0.9 the height falls from 2.0 to 1.6).
The most frequent base at a position was chosen for the consensus sequence.
All accessions of T. urartu had a specific restriction pattern with the frequent base cutting enzyme, Msp I, allowing us to distinguish T. urartu from the other diploid species.
In the Seq control sample, by far the most frequent base miscall was G to T (a G miscalled as a T) which represented approximately 23% of all Illumina base miscalls, followed by T to C, C to T, G to A and A to G which varied between approximately 12% and 15% (Additional file 1).
The most frequent base changes were C → T and G → A, each in 17 cases, mainly at hotspot sites.
Finally, starting from the AVA multi-alignments, we generated consensus sequences using a home-made Python script, which assigned the most frequent base at each position.
Henceforth, we transform the problem of ensemble pruning to the mining of frequent base classifiers on the classification matrix.
These families need a strong support network in order to deal successfully with everyday strains and sacrifices -- frequent base rotations, long deployments of spouses and parents, and the ever-present anxiety over a family member's safety.
The military families initiative highlights issues of special importance to military families across the country: unemployment, underachievement in school (military kids often fall behind with frequent base rotations), and other physical and emotional problems.
Subsequently, variance of the most frequent base in that position is calculated from the base composition.
