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We term these sequences pseudo-CNEs, as they are sequences that have high alignment scores, albeit below our conservation threshold, but lack orthology.
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If this number is below the conservation threshold, trimAl will add more columns to the trimmed alignment in a decreasing order of scores until the conservation threshold is reached.
Indeed, the proportion of sequence falling below a conservation threshold of 2.5 was even greater than in the reference gene set (56% vs. 31%) indicating that at a genomic level non-globular domains may be responsible for an even higher proportion of non-synonymous polymorphism than in our reference genes.
Consistent with this, amino acid variants in genes not involved in drug resistance fell almost exclusively in less conserved regions with 150 of 153 such amino acid variants below the 2.5 conservation threshold.
The Conservation threshold parameter is responsible for the elimination of TFBSs with conservation scores lower than the selected threshold.
The conservation threshold was also determined.
The conservation threshold removed 43 of these, leaving 56 total.
By contrast, conservation scores for PHAX are either low, or below our detection threshold for all eukaryotes in this study other than members of Metazoa, in agreement with a previous study [ 36].
This is well below our threshold of 1.18E-10, but above the threshold to be applied when considering all associations between SNPs and metabolite ratios.
That gets us below our toxic threshold.
This is well below our lower threshold of 40, although for reasons discussed below the absolute values of these thresholds should be interpreted with caution.
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