Table 3. SNP/INDEL confirmed in Y. pestis KIM10+.

Type of substitution	Coordinate	Ref	Var	Nearest gene	Annotation	Coding	Result	Homopolymer or repetivite region
SNP (pCD1)	65595	A	G	y0087.1N	putative transposase	N		repetitive region
SNP	121683	A	G	y0111	transposase	Y	No amino acid change
SNP	142073	C	G	y0129	gltD; glutamate synthase beta subunit	Y	P to A at residue 223	4 C
INDEL	276834	−	G	y0258	hypothetical protein	Y	Extends N-term of ORF	3 G
INDEL	327388	G	−	y0305	transposase	N	Possibly extends ORF
INDEL	655265	−	C	y0579	tyrB; tyrosine biosynthesis	N
INDEL	887688	−	G	y0795	mrcB; murein sacculus	N		3 G
INDEL	897819	A	−	y0800	chloride channel protein	Y	Moves stop 2 aa up	4 A
SNP	988057	G	T	y0879	putative sugar transport	N
SNP	1086724	T	C	y0962	hypothetical protein	Y	No amino acid change
INDEL	1176674	G	−	y1043	tes; acyl-CoA thioesterase II	N		5 G
SNP	1184200	A	G	y1049	acrB; multidrug efflux pump	Y	No amino acid change	6 A
INDEL	1375636	−	C	y1224	NrdE truncation	N	Extends N-term of ORF	7 C
INDEL/SNP	1415467	A	−	y1265	kdpA; potassium transporter	Y	Changes balance out	repetitive region
INDEL/SNP	1415469	−	G	y1265	kdpA; potassium transporter	Y	Changes balance out	repetitive region
SNP*	1505634	C	T	y1354	hisS	Y	A to V at residue 88
INDEL	1544038	−	A	y1389	Transcriptional regulator	N		3 A
INDEL	1616527	−	G	y1457	hypothetical protein, putative peroxidase	N
SNP	1758361	G	T	y1590	fabB	N	May change promoter
INDEL	1830493	C	−	y1655	hypothetical protein	N
INDEL	2006614	−	C	y1821	mgtA; magnesium transporter	N		repetitive region
INDEL	2006622	A	−	y1821	mgtA; magnesium transporter	N		repetitive region
INDEL	2006743	−	T	y1821	mgtA; magnesium transporter	N		repetitive region
INDEL	2006767	−	T	y1821	mgtA; magnesium transporter	N		repetitive region
INDEL	2006775	−	T	y1821	mgtA; magnesium transporter	N		repetitive region
INDEL	2006778	−	T	y1821	mgtA; magnesium transporter	N		repetitive region
INDEL	2006781	−	T	y1821	mgtA; magnesium transporter	N		repetitive region
INDEL	2006785	−	T	y1821	mgtA; magnesium transporter	N		repetitive region
INDEL	2006791	−	T	y1821	mgtA; magnesium transporter	N		repetitive region
INDEL	2006801	−	T	y1821	mgtA; magnesium transporter	N		repetitive region
SNP	2006807	C	A	y1821	mgtA; magnesium transporter	N		repetitive region
INDEL	2018833	A	−	y1834	hypothetical proteins	Y	Unites 2 ORFs	3 A
SNP	2021584	C	T	y1834	hypothetical protein	Y	No amino acid change
SNP	2078371	C	T	y1880	hypothetical protein	Y	K to N at residue 33
INDEL	2253705	G	−	y2047	Tryptophan synthase alpha subunit	Y	Shorter C-term of trpA
INDEL	2377088	A	−	y2150	purU	N	Extends N-term of ORF	3 A
INDEL	2377158	T	−	y2150	purU	Y	2nd aa, restores reading frame due to other purU change	4 T
SNP	2470103	A	C	y2242	chaperone	Y	No amino acid change
INDEL	2563999	−	A	y2328	hypothetical protein	Y	Another stop available	5 A
INDEL	2564024	−	G	y2328	hypothetical protein	Y	Another stop available	3 G
SNP	2786829	G	A	y2524	ftn	Y	No amino acid change	repetitive region
SNP	2786831	G	A	y2524	ftn	Y	S to F at residue 11	repetitive region
SNP	2786834	G	A	y2524	ftn	Y	A to G at residue 10	repetitive region
INDEL	2959407	G	−	y2681	hypothetical protein	Y	Joins both ORFs	3 G
SNP	2978605	A	G	y2697	hypothetical protein	Y	V to G at residue 289
SNP	2981487	C	T	y2698	hypothetical protein	Y	No amino acid change
SNP	2981565	C	G	y2698	hypothetical protein	Y	No amino acid change
INDEL	3231270	−	G	y2925	hypothetical protein	N
SNP	3533369	A	G	y3211	hypothetical protein	Y	N to S at residue 188
INDEL	3546848	−	A	y3221	PTS permease	Y	Extends ORFs at C-term
INDEL	3782193	−	C	y3410	Non-ribosomal peptide synthase	Y	Changes balance out	3 C
INDEL	3782201	−	G	y3410	Non-ribosomal peptide synthase	Y	Changes balance out	4 G
INDEL	3782212	A	−	y3410	Non-ribosomal peptide synthase	Y	Changes balance out
INDEL	3824911	C	−	y3437	hypothetical protein	Y	Joins both ORFs
INDEL	4154719	G	−	y3736	NadR disrupted	Y	Functional NadR	3 G
INDEL	4363489	G	−	y3907	hypothetical protein	Y	Joins both ORFs	5 G
INDEL	4470283	T	−	y4034	phosphoethanolamine transferase	Y	No amino acid change