Table 2. Detailed statistics on the polymorphisms in the whole core genome alignment, at synonymous positions (third positions in fourfold degenerate codons) and at second codon positions (where all substitutions are non-synonymous).

First, for each set of positions the table lists the total number of positions, and the number of positions at which 1, 2, 3 or 4 different nucleotides appear. Second, for the subset of positions where two nucleotides appear, the table lists the total number of transitions and transversions, and the number of positions with each of the six possible two-nucleotide subsets.

Statistic	All columns	Synom. codon pos.	Sec. codon pos.
Total columns	2,880,516	349,311	960,172
1-letter columns	2,484,831	299,536	936,588
2-letter columns	363,164	46,807	22,505
3-letter columns	30,611	2838	1029
4-letter columns	1910	130	50
Transitions	275,134	36,866	13,420
Transversions	88,030	9941	9085
A ↔ G	138,728	21,767	6676
C ↔ T	136,406	15,099	6744
G ↔ T	23,679	2198	963
A ↔ C	23,636	3294	3510
A ↔ T	21,036	2416	2549
C ↔ G	19,679	2033	2063