The "noLRall2" subset of nt1 contributes 150 more sites to the non-synonymous category than does the similarly-motivated "noLR1" subset of Regier et al. [ 14], which excluded all sites at which even one leucine or arginine occurs.
We focused on LoF variants – frameshift, stop-gain, stop-loss and splicing – as they are currently of most interest in disease studies, and we saw better than 90% agreement between ANNOVAR and VEP annotations for nonsynonymous and synonymous variant categories (Table 2).
Categories are loosely ordered by the severity of effect, with LoF annotations listed before nonsynonymous, synonymous, non-exonic categories and so on.
An alternative approach is to employ idioms of distress that are locally salient, but these are not synonymous with psychiatric categories.
As Liszka (1990, 20) notes, "the received view in Peirce scholarship suggests that the divisions of interpretant into immediate, dynamic, and final are archetypal, all other divisions being relatively synonymous with these categories".
Still others have built brands that in just a few short years have become synonymous with new categories -- Robin Chase's zipcar and Angie's list and luminaries like Faye Wattleton.
Point mutations in coding regions of genes can be classified into two categories: synonymous and nonsynonymous.
4. Exonic variants: variants that fall anywhere in exons or splicing regions, so this includes all variants in the LoF, nonsynonymous and synonymous high-level categories above.
By aligning the reads of each species to the T. alpinus in-target assemblies, we found numerous SNPs between and within species, across all locations (intronic, UTR, and coding regions), and across both functional categories (non-synonymous, synonymous) (Table 1).
The SNPs were classified into four categories: non-synonymous (nsSNP), synonymous (sSNP), intergenic (IG) and single base indels.
