Table 2.

Mutations significantly correlating with quinolone resistance. The dotted line separates synonymous and nonsynonymous variants. Freq. is the relative frequency among isolates, beta is the effect size, and SE is the standard error of the fit on beta. Effect size is similar for all, and p-values differ.

Quinolone	Position	Allele	Gene	Effect	Freq.	Beta	SE	Call Rate	p-Value
	3165735	A	parC	S80I	0.08	−1.56	0.20	100%	2.43 × 10−12
	2339162	T	gyrA	D87N	0.08	−1.56	0.20	100%	2.43 × 10−12
	2339173	A	gyrA	S83L	0.15	−1.20	0.16	99%	4.47 × 10−12
	4473651	T	bdcA	G135S	0.05	−1.58	0.29	90%	1.35 × 10−7
Levofloxacin	4481639	A	valS	R733	0.07	−1.15	0.24	100%	4.09 × 10−9
	4481393	A	valS	N815	0.12	−1.11	0.20	100%	6.79 × 10−8
	4481216	T	valS	E874	0.16	−1.61	0.29	100%	7.09 × 10−8
	4482482	A	valS	D452	0.05	−1.58	0.29	100%	1.35 × 10−7
	4482443	A	valS	V465	0.05	−1.58	0.29	100%	1.35 × 10−7
	4482440	T	valS	L466	0.05	−1.58	0.29	100%	1.35 × 10−7
	4486808	A	lptF	Q197	0.05	−1.58	0.29	100%	1.35 × 10−7
	4487635	A	lptG	V106	0.05	−1.58	0.29	100%	1.35 × 10−7
	3165735	A	parC	S80I	0.08	−2.29	0.22	100%	1.10 × 10−18
	2339162	T	gyrA	D87N	0.08	−2.29	0.22	100%	1.10 × 10−18
	2339173	A	gyrA	S83L	0.15	−1.59	0.19	99%	9.25 × 10−14
	4473651	T	bdcA	G135S	0.05	−2.01	0.36	90%	7.56 × 10−8
Norfloxacin	4481639	A	valS	R733	0.07	−1.85	0.30	100%	5.24 × 10−9
	4481216	T	valS	E874	0.16	−2.03	0.35	100%	4.36 × 10−8
	4481393	A	valS	N815	0.12	−1.39	0.25	100%	5.40 × 10−8
	4482482	A	valS	D452	0.05	−2.01	0.36	100%	7.56 × 10−8
	4482443	A	valS	V465	0.05	−2.01	0.36	100%	7.56 × 10−8
	4482440	T	valS	L466	0.05	−2.01	0.36	100%	7.56 × 10−8
	4486808	A	lptF	Q197	0.05	−2.01	0.36	100%	7.56 × 10−8
	4487635	A	lptG	V106	0.05	−2.01	0.36	100%	7.56 × 10−8
	240711	T	ivy	T123	0.05	−2.00	0.36	100%	1.04 × 10−7
	3165735	A	parC	S80I	0.08	−1.90	0.25	100%	7.37 × 10−12
Ciprofloxacin	2339162	T	gyrA	D87N	0.08	−1.90	0.25	100%	7.37 × 10−12
	2339173	A	gyrA	S83L	0.15	−1.22	0.22	99%	7.13 × 10−8
Nalidixic acid	2339173	A	gyrA	S83L	0.15	−1.57	0.24	99%	1.32 × 10−9