Table 3. Genes, gene ontologies and expression pathways exhibiting the most significant enrichments or depletions of protein-altering B-class variants separating nose and infection site bacteria.

Enrichments below one represent depletions. The total number of variants and genes available for analysis differed by database. A -log₁₀ p-value above 5.2, 4.5 or 4.2 was considered genome-wide significant for loci, gene ontologies or expression pathways respectively (in bold).

Gene group	No. protein-altering B-class variants		Cumulative lengthof genes (kb)		Enrichment		Significance (-log10 p value)
Locus
agrA	5		0.7		58.27		7.53
clfB	5		2.6		15.87		4.70
Total	289		2363.8
BioCyc Gene Ontology (Caspi et al., 2016)
Cell wall	18		30.9		5.02		7.03
Cell adhesion	13		17.2		6.44		6.47
Pathogenesis	31		112.5		2.41		4.44
Total	288		2359.3
SAMMD Expression Pathway	Down-regulated	Up-regulated	Down-regulated	Up-regulated	Down-regulated	Up-regulated
Ovispirin-1 (Pietiäinen et al., 2009)	40	7	121.2	142.9	2.65	0.39	7.80
Temporin L (Pietiäinen et al., 2009)	42	14	125.1	156.1	2.78	0.74	6.86
rsp (Lei et al., 2011)	27	1	61.1	13.7	3.61	0.60	6.35
agrA (RN27) (Dunman et al., 2001)	9	30	41.0	85.0	1.83	2.94	5.57
VISA-vs-VSSA (Mu50 vs N315) (Cui et al., 2005)	0	17	0	34.4	0	3.95	5.27
VISA-vs-VSSA (Mu50 vs Mu50-P) (Cui et al., 2005)	0	17	0	36.7	0	3.70	4.90
VISA-vs-VSSA (isolate pair 2) (Howden et al., 2008)	14	3	26.9	59.7	4.06	0.39	4.71
sarA (RN27) (Dunman et al., 2001)	6	23	49.9	57.7	0.97	3.22	4.59
agrA (UAMS-1 OD 1.0) (Cassat et al., 2006)	0	5	0	2.7	0	14.57	4.52
Pine-Oil Disinfectant-Reduced-Susceptibility (Lamichhane-Khadka et al., 2008)	17	5	36.4	23.6	3.76	1.70	4.44
Total	275		2093.5