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In all three datasets, the biggest change in GC content was observed in the third codon position where most nucleotide changes do not change the amino acid sequence of the encoded proteins due to the redundancy of the genetic code.
After the genetic shift in 2001 2002, most nucleotide changes observed were silent transitions (T ↔ C and A ↔ G).
Most nucleotide changes, except for disease-associated changes, might then be expected to distribute randomly throughout a protein.
Most nucleotide changes are silent, as can be appreciated by the shorter branch lengths in the phylogenetic tree constructed from deduced amino acid sequence data.
Most nucleotide changes reported in our study have been previously described and some of them are of particular interest and may have considerable biological impact [ 10, 46].
The predicted region of pairing overlaps the ribosome binding site of luxO, so most nucleotide changes in this region alter the basal level of luxO expression (data not shown).
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However, in 2/14 cases the most frequent nucleotide changes were A T → T A transitions (Fig. S8), suggesting that there might be other pollutants that caused this signature in the genomes.
Since most of the nucleotide changes in the HA1 and NA genes were silent, the rate of amino acid changes was clearly lower than the changes at nucleotide level.
As shown above, most of the nucleotide changes identified in the sequence of the relBE2Spn locus were located within the relE2Spn gene, two of them being missense mutations that affected the RelE2Spn toxin: change D39G was found in three strains (Polish 7153, and the NCBI genome project P1031 and JJA), whereas change T34I was relatively frequent (around 35% of the sequenced isolates).
Most of the nucleotide changes were G to A or C to T, as expected for EMS-induced transitions.
Within each of the PHYA1 and PHYA2 clades, the level of nucleotide diversity was very low, with at most four parsimonious nucleotide changes separating each contig.
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