In order to support this variant role as a progression marker in knee OA, we meta-analyzed our results with those previously published by Valdes and colleagues [ 49].
For G68D-GCK, there was no evidence of protein instability, and the very mild degree of kinetic activation was not predicted to cause hypoglycemia (Supplementary Table 1), supporting this as a rare neutral variant.
The results support that this variant is a potential risk factor for IBD.
Given the weak clade support, this variant is probably an outlier that is not as homogenized as the other A. argentata variants.
If there were at least two reads supporting the variant, at least one of them must have had 10+ nt of flanking sequence.
Another common issue is strand bias, where the only evidence supporting the variant are reads aligning in just one direction.
Variant detection was performed using VarScan 2 (Koboldt et al., 2012) with thresholds of a minimum of 10 supporting variant reads and variant allele frequencies of at least 1%.
Additional quality filters were applied as follows: the reads supporting the variants were on both strands, the maximum coverage was 1000×, and the variants that were located in problematic regions47,48 and those detected in more than one individual were removed.
Classifying all evidence in a binary fashion ("supporting variant" versus "supporting non-variant") allows us to regard each piece of evidence as a Bernoulli trial, where a success is evidence for a specific change, and failures are everything else.
Genetic studies support the variant traits of Vibrio pathogens.
