Table 3.

Haplotype analysis of number of days of infection treated as a binary variable or a quantitative trait.

Gene	Haplotypesa	Haplotype frequency in subjects with S. aureus bacteremia			P value comparing haplotype frequency between persistent and short-term bacteremia	P value from quantitative trait analysis
		All subjects (n = 202)	Persistent bacteremia (n = 44)	Short-term bacteremia (n = 158)
CISH	Major: TG	0.837	0.818	0.842	0.84	Ref
	Minor: CG	0.166	0.207	0.154	0.78	0.073
	All others (2 haplotypes)	0.00269	0	0.00344	NA	0.80
NOD2	Major: GCAGG-	0.398	0.375	0.408	0.81	Ref
	Minor: CCAGG-	0.0126	0.0114	0.0129	0.97	0.87
	CCATG-	0.291	0.295	0.290	0.92	0.68
	CTATGC	0.0367	0.0341	0.0373	0.94	0.44
	CTATG-	0.236	0.273	0.222	0.53	0.47
	All others (11 haplotypes)	0.0254	0.0114	0.0294	NA	0.30
TIRAP	Major: TCTGGACGCGTCA	0.371	0.294	0.391	0.020	Ref
	Minor: CCGGGACGCGGCA	0.230	0.307	0.212	0.037	0.052
	TCTGGACGCGTTA	0.226	0.273	0.212	0.27	0.61
	TCTGGGCGCGTCA	0.0860	0.0470	0.0968	0.29	0.032
	TCTGGGCGTGTCA	0.0272	0.0341	0.0253	0.54	0.43
	TGTGTACGCATCG	0.0322	0	0.0411	0.045	0.14
	All others (10 haplotypes):
	CCGAGATGCGGCA	0.00248	0	0.00316	NA	0.035
	CCTAGACGCGGCA	1.80E−04	0	0.00226	NA
	CCTAGACGCGTCA	0.00270	0	0.00188	NA
	CCTGGACGCGGCA	0.00311	2.00E−05	0.00407	NA
	CCTGGACGCGGTA	0.00285	0.0113	0	NA
	CCTGGACGCGTCA	0.00472	0.0114	0.00128	NA
	CGGGTACGCAGCA	0.00248	0	0.00316	NA
	TCGGGACGCGTTA	0.00248	0.0114	0	NA
	TCTGGACGCGGCA	5.20E−04	0	0.00158	NA
	TCTGGGCGCGGCA	0.00196	0	0.00158	NA
TLR2	Major: TC	0.901	0.875	0.908	0.22	Ref
	Minor: CC	0.0743	0.0909	0.0696	0.54	0.18
	TA	0.0248	0.0341	0.0222	0.14	0.39
TLR4	Major: CGG	0.987	1.000	0.984	0.22	Ref
	Minor: All 3 minor haplotypes	0.0146	0.0109	0.0157	NA	0.42

NA a P value was not available because P values were not calculated when a haplotype was very rare in both subject groups.

^aThe order of alleles in each haplotype is according to the order of the SNPs listed for each gene in Table 2.