Any behavior deemed ambiguous by one observer in the experimental mice was reviewed by both observers to assign a score.
An identification was deemed ambiguous if the pairwise distance of the sample was lower than the threshold value for multiple reference species, or if the distance from a query to all reference species was larger than the determined threshold value.
The ratio of these two distances was then assessed: if it was between 0.9 and 1.11, the patient-classification was deemed ambiguous.
The SNPs deemed ambiguous may indeed be under selection, but we failed to identify associations with the suite of environmental variables tested here.
In the first one, genes were classified as archaebacterial or eubacterial on the basis of the best hit retrieved, being only deemed ambiguous if there were hits of both domains sharing the best position (i.e., with the same E value).
This resulted in 939 genes (4.3%) being classified as archaebacterial, 7,884 (36.1%) as eubacterial, 204 (0.9%) deemed ambiguous (i.e., with genes of both domains sharing the lowest E value), and 12,685 genes (58.4%) without detectable prokaryotic homologs.
The median percent of survey questions answered correctly in this group was 90%, and based on their responses, a single question (Question # 2) was deemed ambiguous by the participating authors, and this question was omitted from the data analysis.
By reducing our stringency on which tags are deemed ambiguous we can successfully map an additional 3 genes of our top ten genes to the top 15 most abundant genes in the SAGE library.
