Table 1.

Mutations in genes involved in lipopolysaccharide synthesis and type VI secretion system of the S. Agona bacteriophage-insensitive mutants (BIMs). Mutations presented possess a minimum quality score of 20 and a minimum mapping coverage of 8.

Affected Gene	Putative Function	Strand	nt Position a	Strain	Mutation	Sequence b	Impact on Polypeptide Synthesis
rfaL	O-antigen ligase	+	425	WT	3 bp insertion	G------A	Insertion
				Δ95		GGATA
				Δ96		GGATA
		+	429	WT	Substitution	G	None
				Δ95		G>A
				Δ96		G>A
		+	442	WT	4 bp insertion	T-------A	Frameshift
				Δ95		TGGGA
				Δ96		TGGGA
rfaY	Lipopolysaccharide core heptose (II) kinase	-	514	WT	23 bp insertion	A---------------------------------------------- A	Frameshift
				Δ95		AGCGAAGCCCTAAACTTGTTAAAAA
				Δ96		AGCGAAGCCCTAAACTTGTTAAAAA
		-	538	WT	Substitution	T	Asn --> Lys
				Δ95		T>G
				Δ96		T>G
vgrG1_2	Actin cross-linking toxin, structural tip protein, involved in type VI secretion	+	792	WT	6 bp insertion	T-------------	Frameshift
				Δ87		TCAAGGA
				Δ95		TCAAGGA
				Δ96		TCAAGGA
				Δ99		TCAAGGA
				Δ102		TCAAGGA
		+	798	WT	Multi-nucleotide substitution	ATTTT	Leu --> Phe Phe --> Gly Tyr --> His
				Δ87		ATTT>CGGCC
				Δ95		ATTT>CGGCC
				Δ96		ATTT>CGGCC
				Δ99		ATTT>CGGCC
				Δ102		ATTT>CGGCC
		+	810	WT	4 bp insertion	A---------T	Frameshift
				Δ95		AGAACT
				Δ96		AGAACT
		+	816	WT	2 bp insertion	T----C	Frameshift
				Δ95		TCAC
				Δ96		TCAC
		+	820	WT	Substitution	G	Gly --> Arg
				Δ95		G>C
				Δ96		G>C
		+	823	WT	Substitution	G	Gly --> Stop codon
				Δ95		G>T
				Δ96		G>T
		+	825	WT	Substitution	A	None
				Δ95		A>G
				Δ96		A>G
		+	828	WT	3 bp deletion	AGGA	Deletion
				Δ95		A------
				Δ96		A------
		+	831	WT	Substitution	C	Asp --> Glu
				Δ95		C>G
				Δ96		C>G
		+	836	WT	Substitution	C	Ala --> Glu
				Δ95		C>A
				Δ96		C>A

^a relative to wild-type strain. nt: nucleotide. ^b presented in 5′ to 3′ direction. In substitutions, alternate sequences are preceded by the original sequence and separated with a “>” symbol.