Table 2. Nature of genetic variation identified at generation 504 in all 12 populations.

	“No-DNA,” “Bacteria,” “Archaea”	“other-Bacillus”
	Mutations	Mutations	HGT
# of mismatches and indels	71	16	6,006
% of mismatches and indels in CDS	82%	87%	92%
% of nonsynonymous substitutions or indels	96%	64%	20%
% of substitutions in flagella CDS	28%	36%	0%
% of flagella mutations that are nonsynonymous	100%	100%	—

Table showing the summed number of mismatches and indels identified in the three other-Bacillus populations and that of the nine other populations (No-DNA, Bacteria, and Archaea) at generation 504. In the other-Bacillus populations, HGT-acquired fragments and mutations are considered separately. The percentage of mismatches and indels located in coding regions is calculated out of the total number of mismatches and indels observed. Out of those, the percentage of mismatches resulting in nonsynonymous substitution and indels (that are likely to change the protein sequence) is shown. Also presented is the percentage of mismatches and indels affecting the coding sequence of flagellar proteins and the percentage of nonsynonymous changes for this group of mismatches and indels.