Table 4.

Potential compensatory mutations identified in the genomes of the clones evolved in the competition between resistances H526Y and S531F.

Background	Genome Position	Gene(s)	Mutation	Annotation	Frequency	(%) Function
H526Y	3,438,465	rpoA	C→T	T196I	51.5	RNA polymerase, alpha subunit
	4,184,828	rpoC	T→C	S486P	25.5
	4,187,042	rpoC	C→T	R1224C	6.1	RNA polymerase, beta prime subunit
	4,184,721	rpoC	A→C	H450P	2.9
	3,797,382	waaZ	T→C	S280P	19.7	Lipopolysaccharide core biosynthesis protein
	3,946,224	yifE	G→A	G39D	12.0	Conserved protein, UPF0438 family, unknown function
	4,292,389	nrfG/gltP	A→T	Intergenic	5.0	[nrfG] Heme lyase (NrfEFG) for insertion of heme into c552, subunit NrfG/[gltP] glutamate/aspartate: proton symporte
	3,637,091	pitA	C→T	A476V	2.6	Phosphate transporter, low- affinity; tellurite importer
	374,196	mhpE/mhpT	T→C	Intergenic	2.4	4- hyroxy- 2- oxovalerate/4- hydroxy- 2- oxopentanoic acid aldolase, class I/putative 3- hydroxyphenylpropionic transporter
	3,464,375	bfr	C→T	R125C	2.0	Bacterioferritin, iron storage and detoxification protein
	1,743,180	ydhQ	T→C	S324S	3.1	Hypothetical protein
	3,898,043	yieL	C→A	T186T	2.5	Putative xylanase
S531F	4,183,521	rpoC	A→C	K50T	14.8	RNA polymerase, beta prime subunit
	4,292,389	nrfG/gltP	A→T	Intergenic	19.6	[nrfG] Heme lyase (NrfEFG) for insertion of heme into c552, subunit NrfG/[gltP] Glutamate/aspartate:proton symporte
	2,749,808	nadK/recN	δ1 bp	Intergenic	18.1	[nadK] NAD kinase/ [recN] Recombination and repair protein
	1,940,499	znuA	T→C	F37L	17.7	Zinc transporter subunit: periplasmic- binding component of ABC superfamily
	3,374,976	sspA	T→C	L156P	12.2	Stringent starvation protein A
	300,420	paoB	T→A	V231E	11.8	PaoABC aldehyde oxidoreductase, FAD- containing subunit
	2,036,728	yedW	IS1 Ins	Coding	9.9	Putative DNA- binding response regulator in two- component system with
	1,877,853	yeaR	IS186 Ins	Coding	8.4	Hypothetical protein
	3,410,893	envR	IS5 Ins	Coding	6.8	DNA-binding transcriptional regulator
	2,361,326	yfaY	A→G	V110V	9.4	Hypothetical protein

Mutations were identified in the genomes of the evolved clones in comparison with a reference genome. Shown are the single nucleotide polymorphisms or IS events identified in either of the backgrounds, and the frequencies at which they were detected. Mutations that occurred between genes (intergenic) are identified as such, otherwise all remaining mutations occurred within the gene indicated. The mutations previously identified to be compensatory are identified with a gray shaded cell.

IS: Insertion sequence.