The alignments of these proteins were concatenated into a single alignment, which was then trimmed to remove positions with gaps in more than 50% of the organisms.
Aligned sequences were filtered to remove positions with gaps as well as positions directly adjacent to gaps.
Further, additional filtering used to remove positions with low number of alternate alleles (Section 2.4) is likely to remove such false SNPs.
For both analyses, we filtered data to remove positions where less than 75%% of individuals were genotyped for each of the two taxa being compared.
The paired alignment is then filtered to reduce redundancy to 90% sequence identity and to remove positions that have more than 75% gaps.
Phylogenetic trees were constructed by neighbor-joining analysis of nucleotide alignments using Jukes Cantor distance correction and a column filter to remove positions of uncertain homology.
NJ tree was based on the distance calculation with JTT matrix [ 46] after removing position containing gaps (complete deletion option) for genes other than Zic genes, or after removing only in pairwise sequence comparisons (Pairwise deletion option) for Zic genes.
We found that in the resulting profile, even upon removing position specific heterogeneity for each individual mRNA, we still observed a sharp decrease in average ribosome density with codon position.
The lower AUC for SuRFR, however, is likely to represent the lowest estimate of SuRFR's performance, as by comparing regulatory variants with control variants matched by distance to TSS, we are effectively removing position from consideration.
When all of the bolts are removed, position a large oil drain pan underneath differential cover, then pry the cover off slowly and carefully.
