TABLE 3.

Genes disrupted by PMSCs overrepresented among isolates in NHA or HA SNP clusters

Gene	Odds ratioa	P valueb	Length of intact gene (bp)	Length of disrupted gene (bp)	Gene product annotation
Genes disrupted by PMSCsc overrepresented among NHA isolates
bglA	Inf	0.003	1,434	75	6-Phospho-beta-glucosidase
ygcH	Inf	0.003	651	369	Type I-E CRISPR-associated protein
bepF	Inf	0.003	1,227	1,170	Periplasmic multidrug efflux RND transporter
stfC	Inf	0.003	2,658	75	Fimbrial biogenesis outer membrane usher
yggR	4.5	0.003	981	153	Type IV pilus twitching motility protein
ydiV	16.33	0.003	714	369	Anti-FlhC2FlhD4 factor
orf319	Inf	0.022	960	333	DUF523 and DUF1722 domain-containing protein
Genes disrupted by PMSCs overrepresented among HA isolates
malX	0.22	0.003	237	144	PTS maltose transporter subunit IIBC
STM14_0610	0	0.003	1,248	321	MFS transporter; putative sulfoacetate transporter SauU
avrA	0	0.003	867	48	SPI-1 encoded acetyltransferase

^aThe odds ratio refers to the ratio of the odds that the gene is intact among the HA isolates to the odds that the gene is intact among the NHA isolates.

^bBH-corrected P value of the Fisher’s exact tests.

^cPMSCs, premature stop codons.