Consensus sequences and logos for individual subtypes were generated also using Geneious (version 6.1.7) based on the majority nucleotide present at each site.
In contrast, positions 89, 91, and 93 displayed an interdependent pattern of selection, such that the base present at one position influenced base pair selection at the other two.
A single nucleotide polymorphism (SNP) is defined as the difference between chromosomes in the base present at a particular site in the DNA sequence that naturally occurs within a population, and presents the most common type (90%) of genetic variation in humans [ 12].
We then show that the trinucleotide preferences, the preference-occurrence correlations, and the trinucleotide occurrences themselves, as well as the correlation between GC content and the GCvsAT balance must be to a great extent the product of mutation rates that depend strongly on the bases present at the site preceding and the site following each mutating site.
The results of both basic and advanced searches includes a table of genomic co-ordinates, bases present at the SNP position in reference genome sequence and corresponding variant base call.
The appropriate vector position is mapped considering whether each nucleotide within the window and with respect to the minimum free energy (MFE) structure is the left/right-hand side of a base-pair, an unpaired nucleotide on the stem, or part of the terminal loop, and, additionally, which base is present at the midpoint of the window.
If k is set to 50, for example, then the 50-base sequence present at the 5' end of each seed is used as a key in a hash table, and the hash value is a pointer to the seed in the list of seeds.
Extensive optimization of this platform allows unbiased detection of single base changes present at 0.3 1% frequency.
This could mean that selection is acting on all analyzed sequences, no matter which base is present at the editing site.
The general pattern seen was that if a wild type base was present at one position, the other two positions also tended towards wild type.
