Number	Start	End	Strand	Gene	Description	Lesion	Location	Homologue
SPA0006	5881	7395	minus	yaaJ	putative amino-acid transport protein pseudogene	frameshift	1350	emb|CAD01159.1| putative amino-acid transport protein [Salmonella enterica subsp. enterica serovar Typhi]
SPA0018	17860	19959	plus	-	putative chitinase pseudogene	stop	784	emb|CAD01171.1| putative chitinase [Salmonella enterica subsp. enterica serovar Typhi]
SPA0026	29987	30505	plus	bcfF	fimbrial subunit pseudogene	stop	415	emb|CAD01180.1| fimbrial subunit [Salmonella enterica subsp. enterica serovar Typhi]
SPA0036	40118	41590	plus	-	putative secreted sulfatase pseudogene	frameshift (multiple)	1257	emb|CAD01190.1| putative secreted sulfatase [Salmonella enterica subspenterica serovar Typhi]
SPA0066	74925	75177	plus	-	-	frameshift	93	gb|AAL19029.1| putative viral protein [Salmonella typhimurium LT2]
SPA0086	98150	98681	plus	yabF	putative NAD(P)H oxidoreductase pseudogene	frameshift	218	emb|CAD01241.1| putative NAD(P)H oxidoreductase [Salmonella enterica subsp.enterica serovar Typhi]
SPA0197	227965	230192	plus	fhuA	"outer membrane protein receptor / transporter for ferrichrome, colicin M, and phages T1, T5, and phi80 pseudogene"	frameshift (multiple)	360	"gb|AAL19155.1| outer membrane protein receptor / transporter for ferrichrome, colicin M, and phages T1, T5, and phi80 [Salmonella typhimurium LT2]"
SPA0202	235569	238226	plus	stfC	putative fimbrial outer membrane usher pseudogene	stop	1236	gb|AAL19160.1| putative fimbrial outer membrane usher [Salmonella typhimurium [LT2]
SPA0205	239524	240000	plus	stfF	putative minor fimbrial subunit pseudogene	stop	376	gb|AAL19163.1| putative minor fimbrial subunit [Salmonella typhimurium LT2]
SPA0269	306518	306690	plus	-	-	stop	54	emb|CAD01834.1| pyridine nucleotide transhydrogenase subunit-beta [Salmonellaenterica subsp. enterica serovar Typhi]
SPA0296	331462	332097	plus	yfhB	putative membrane protein pseudogene	stop	386	emb|CAD02771.1| putative membrane protein [Salmonella enterica subsp. enterica serovar Typhi]
SPA0309	348490	350033	minus	cadC	transcriptional activator cadC pseudogene	frameshift	1080	emb|CAD02760.1| transcriptional activator cadC [Salmonella enterica subsp. enterica serovar Typhi]
SPA0337	381173	383578	plus	-	putative anaerobic dimethylsulfoxide reductase pseudogene	frameshift (multiple)	675	gb|AAL21424.1| putative anaerobic dimethylsulfoxide reductase [Salmonellatyphimurium LT2]
SPA0350	395688	397843	plus	sinH	putative invasin pseudogene	frameshift	864	gb|AAL21411.1| Similar to E. coli intimin and Y. pestis invasin proteins [Salmonella typhimurium LT2]
SPA0353	405448	412754	plus	ratB	putative outer membrane protein pseudogene	frameshift	426	gb|AAL21408.1| putative outer membrane protein [Salmonella typhimurium LT2]
SPA0354	413512	418620	plus	shdA	similar to the C-terminal region of AIDA; IcsA; subspecies I specific; Peyer's patch colonization and shedding factor pseudogene	stop 	93	gb|AAL21407.1| similar to the C-terminal region of AIDA; IcsA; subspecies I specific; Peyer's patch colonization and shedding factor[Salmonella typhimurium LT2]
SPA0359	423728	424415	minus	-	conserved hypothetical protein pseudogene	frameshift	615	emb|CAD02710.1| conserved hypothetical protein [Salmonella enterica subsp.enterica serovar Typhi]
SPA0374	439596	440664	plus	perM	putative permease pseudogene	frameshift	990	emb|CAD02695.1| putative membrane protein [Salmonella enterica subsp. enterica serovar Typhi]
SPA0389	457303	459005	minus	narQ	nitrate/nitrite sensor protein NarQ pseudogene	frameshift	1488	emb|CAD07710.1| nitrate/nitrite sensor protein NarQ [Salmonella entericasubsp. enterica serovar Typhi]
SPA0451	516655	517679	minus	nupC	nucleoside permease NupC pseudogene	frameshift	897	emb|CAD07647.1| nucleoside permease NupC [Salmonella enterica subsp. entericaserovar Typhi]
SPA0463	532441	534448	plus	pgtB	phosphoglycerate transport system sensor protein PgtB pseudogene	frameshift	741	emb|CAD07634.1| phosphoglycerate transport system sensor protein PgtB[Salmonella enterica subsp. enterica serovar Typhi]
SPA0466	537755	538302	plus	-	-	stop 	273	gb|AAL20775.1| putative transposase [Salmonella typhimurium LT2]
SPA0655	737146	738579	plus	-	putative L-serine dehydratase pseudogene	stop	887	emb|CAD02578.1| putative L-serine dehydratase [Salmonella enterica subsp. enterica serovar Typhi]
SPA0662	744777	746297	plus	mglA	"ABC superfamily (atp_bind), galactose (methyl-galactoside) transport protein pseudogene"	stop	222	"gb|AAL21093.1| ABC superfamily (atp_bind), galactose (methyl-galactoside)transport protein [Salmonella typhimurium LT2]"
SPA0739	823266	824578	minus	-	-	frameshift	291	emb|CAD02489.1| putative efflux system protein [Salmonella enterica subsp.enterica serovar Typhi]
SPA0763	851789	853183	plus	wcaJ	putative extracellular polysaccharide biosynthesis protein pseudogene	stop	1231	STY2315 putative extracellular polysaccharide biosynthesis protein
SPA0765	854785	856065	plus	wcaK	putative galactokinase in colanic acid gene cluster pseudogene	stop	825	gb|AAL21005.1| putative galactokinase in colanic acid gene cluster [Salmonellatyphimurium LT2]
SPA0768	858664	859686	plus	galF	UTP-glucose-1-phosphate uridylyltransferase pseudogene	stop	612	emb|CAD02461.1| UTP-glucose-1-phosphate uridylyltransferase [Salmonellaenterica subsp. enterica serovar Typhi]
SPA0805	901726	904069	minus	sopA	Secreted effector protein of Salmonella dublin pseudogene	frameshift (multiple)	273	gb|AAL20970.1| Secreted effector protein of Salmonella dublin [Salmonella typhimurium LT2]
SPA0806	904688	906963	plus	phsA	thiosulfate reductase precursor pseudogene	frameshift	1092	emb|CAD02426.1| thiosulfate reductase precursor [Salmonella enterica subsp. enterica serovar Typhi]
SPA0809	908441	909612	plus	dacD	"DD-carboxypeptidase, penicillin-binding protein 6b pseudogene"	frameshift	870	STY2268
SPA0834	929187	930306	plus	pduF	propanediol diffusion facilitator pseudogene	frameshift	972	emb|CAD02398.1| propanediol diffusion facilitator [Salmonella enterica subsp.enterica serovar Typhi]
SPA0836	931916	933404	plus	cbiA	"cobyrinic acid A,C-diamide synthase pseudogene"	frameshift 	129	"emb|CAD02396.1| cobyrinic acid A,C-diamide synthase [Salmonella entericasubsp. enterica serovar Typhi]"
SPA0859	949988	951446	plus	yeeO	putative inner membrane protein pseudogene	frameshift	276	emb|CAD02374.1| putative inner membrane protein [Salmonella enterica subsp.enterica serovar Typhi]
SPA0876	962020	962331	plus	-	putative membrane protein pseudogene	stop	237	emb|CAD05741.1| putative membrane protein [Salmonella enterica subsp. enterica serovar Typhi]
SPA0912	991353	992557	plus	fliB	N-methylation of lysine residues in flagellin pseudogene	frameshift	720	gb|AAL20870.1| N-methylation of lysine residues in flagellin [Salmonellatyphimurium LT2]
SPA0949	1020948	1022312	plus	tar	methyl-accepting chemotaxis protein II pseudogene	deletion	1233	STY2128
SPA0987	1061571	1061861	plus	yebG	conserved hypothetical protein pseudogene	stop	123	emb|CAD05633.1| conserved hypothetical protein [Salmonella enterica subsp. enterica serovar Typhi]
SPA0998	1069194	1070035	minus	-	-	framesgift	531	emb|CAD05622.1| putative integrase [Salmonella enterica subsp. enterica serovar Typhi]
SPA1012	1084442	1085590	plus	-	-	frameshift	375	gb|AAL20775.1| putative transposase [Salmonella typhimurium LT2]
SPA1027	1098251	1098930	plus	proQ	ProP effector pseudogene	frameshift	333	emb|CAD05528.1| ProP effector [Salmonella enterica subsp. enterica serovar Typhi]
SPA1075	1144133	1144868	minus	ycgR	conserved hypothetical protein pseudogene	frameshift	34	STY1926
SPA1087	1156190	1157297	minus	hyaA	uptake hydrogenase small subunit pseudogene	frameshift	426	emb|CAD01777.1| uptake hydrogenase small subunit [Salmonella enterica subsp. enterica serovar Typhi]
SPA1103	1173139	1173369	plus	chaB	cation transport regulator ChaB pseudogene	stop	66	emb|CAD08365.1| cation transport regulator ChaB [Salmonella enterica subsp.enterica serovar Typhi]
SPA1178	1250811	1252192	plus	-	hypothetical protein pseudogene	frameshift	543	emb|CAD01622.1| hypothetical protein [Salmonella enterica subsp. entericaserovar Typhi]
SPA1184	1256562	1256711	minus	-	-	insertion relative to STY	overlapped completely by another STY_only pseudogene on the other strand (1702b) Remove 1702c?	
SPA1185	1256574	1256704	plus	-	-	stop	57	stop and insertion relative to STY; completely overlaps another STY_only pseudogene on the other strand (1702c)
SPA1189	1259879	1260270	plus	-	-	stops (multiple)	15	emb|CAD05881.1| putative DNA-invertase [Salmonella enterica subsp. enterica serovar Typhi]
SPA1206	1274872	1275800	minus	-	putative oxidoreductase pseudogene	frameshift	540	emb|CAD01652.1| putative oxidoreductase [Salmonella enterica subsp. enterica serovar Typhi]
SPA1212	1280019	1281317	minus	-	hypothetical protein pseudogene	stop 	172	emb|CAD01658.1| hypothetical protein [Salmonella enterica subsp. enterica serovar Typhi]
SPA1215	1283585	1285568	plus	-	-	frameshift	709	emb|CAD01661.1| invasin-like protein [Salmonella enterica subsp. entericaserovar Typhi]
SPA1227	1294348	1295502	plus	-	putative chemo-receptor protein pseudogene	stop	414	emb|CAD01673.1| putative chemo-receptor protein [Salmonella enterica subsp.enterica serovar Typhi]
SPA1263	1333481	1334311	minus	-	putative benzoate membrane transport protein pseudogene	deletion	134 aa missing	STY1458
SPA1266	1337106	1338055	minus	sifB	putative virulence effector protein pseudogene	frameshift	111	emb|CAD01723.1| putative virulence effector protein [Salmonella entericasubsp. enterica serovar Typhi]
SPA1289	1363562	1364243	minus	narW	respiratory nitrate reductase 2 delta chain pseudogene	frameshift	372	emb|CAD01745.1| respiratory nitrate reductase 2 delta chain [Salmonellaenterica subsp. enterica serovar Typhi]
SPA1307	1387154	1387859	minus	-	hypothetical protein	frameshift	46	STY1499 hypothetical protein
SPA1314	1397718	1399146	minus	-	putative transport protein (pseudogene) pseudogene	frameshift 	1140	gb|AAL20474.1| putative Na+/H+ antiporter [Salmonella typhimurium LT2]
SPA1321	1406226	1406525	plus	-	hydrogenase isoenzymes formation protein pseudogene	frameshift	98	emb|CAD01781.1| hydrogenase isoenzymes formation protein [Salmonella entericasubsp. enterica serovar Typhi]
SPA1364	1443893	1445178	plus	-	putative voltage gated chloride channel protein pseudogene	frameshift	768	emb|CAD01823.1| putative voltage gated chloride channel protein [Salmonellaenterica subsp. enterica serovar Typhi]
SPA1371	1451350	1451678	minus	ydgE	putative membrane transporter pseudogene	frameshift	204	emb|CAD01831.1| putative membrane protein [Salmonella enterica subsp. entericaserovar Typhi]
SPA1381	1461052	1461409	minus	-	-	frameshift	237	emb|CAD01893.1| hypothetical protein [Salmonella enterica subsp. entericaserovar Typhi]
SPA1390	1473800	1474801	plus	add	adenosine deaminase pseudogene	stop	405	emb|CAD01904.1| adenosine deaminase [Salmonella enterica subsp. enterica serovar Typhi]
SPA1468	1541111	1541864	plus	ttrB	tetrathionate reductase subunit B pseudogene	frameshift	339	emb|CAD01980.1| tetrathionate reductase subunit B [Salmonella enterica subsp.enterica serovar Typhi]
SPA1471	1546265	1547491	plus	orf408	"putative regulatory protein, deoR family pseudogene"	stop	360	"gb|AAL20306.1| putative regulatory protein, deoR family [Salmonellatyphimurium LT2]"
SPA1481	1555206	1556425	minus	sufS	putative amintransferase pseudogene	frameshift	759	emb|CAD01992.1| putative amintransferase [Salmonella enterica subsp. enterica serovar Typhi]
SPA1482	1556422	1557693	minus	sufD	pseudogene of conserved hypothetical protein required for stability of iron-sulfur component of FhuF	stop	637	emb|CAD01993.1| conserved hypothetical protein [Salmonella enterica subsp.enterica serovar Typhi]
SPA1559	1635070	1637003	plus	yeaG	putative Ser protein kinase pseudogene	frameshift	1773	emb|CAD02069.1| conserved hypothetical protein [Salmonella enterica subsp. enterica serovar Typhi]
SPA1595	1662431	1662628	plus	-	putative secreted protein pseudogene	frameshift	0	emb|CAD02109.1| putative secreted protein [Salmonella enterica subsp. enterica serovar Typhi]
SPA1598	1663676	1663832	plus	-	-	frameshift	59	emb|CAD02111.1| hypothetical protein [Salmonella enterica subsp. enterica serovar Typhi]
SPA1647	1710130	1712304	plus	fhuE	"outer membrane receptor for Fe(III)-coprogen, Fe(III)-ferrioxamine B and Fe(III)-rhodotrulic acid uptake pseudogene"	stop	852	"gb|AAL20133.1| outer membrane receptor for Fe(III)-coprogen,Fe(III)-ferrioxamine B and Fe(III)-rhodotrulic acid uptake [Salmonella typhimurium LT2]"
SPA1687	1748583	1749210	plus	yceB	conserved hypothetical protein	frameshift	84	STY1202 conserved hypothetical protein
SPA1711	1769575	1769991	plus	csgF	assembly/transport component in curli production pseudogene	stop	54	emb|CAD08264.1| assembly/transport component in curli production [Salmonella enterica subsp. enterica serovar Typhi]
SPA1721	1777704	1778851	minus	-	-	frameshift	309	emb|CAD08255.1| conserved hypothetical protein [Salmonella enterica subsp. enterica serovar Typhi]
SPA1736	1795872	1797758	minus	scsB	"membrane protein, suppressor for copper-sensitivity B precursor pseudogene"	stop	240	"emb|CAD08239.1| membrane protein, suppressor for copper-sensitivity Bprecursor [Salmonella enterica subsp. enterica serovar Typhi]"
SPA1749	1808815	1810103	minus	hpaG	"4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase [includes: 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase pseudogene"	frameshift	423	"emb|CAD08227.1| 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase [includes:2-hydroxyhepta-2,4-diene-1,7-dioate isomerase [Salmonella entericasubsp. enterica serovar Typhi]"
SPA1756	1816217	1817686	plus	pipD	putative secreted peptidase pseudogene	stop	219	emb|CAD08220.1| putative secreted peptidase [Salmonella enterica subsp.enterica serovar Typhi]
SPA1769	1825604	1826151	minus	-	-	frameshift	240	gb|AAL20014.1| putative outer membrane protein [Salmonella typhimurium LT2]
SPA1815	1882092	1884356	minus	ycaI	putative competence-related protein pseudogene	stop (multiple) 	1332	emb|CAD05383.1| putative competence-related protein [Salmonella enterica subsp. enterica serovar Typhi]
SPA1826	1897471	1898429	minus	sopD2	possible secreted protein pseudogene	frameshift 	150	gb|AAL19906.1| homologous to secreted protein sopD [Salmonella typhimurium LT2]
SPA1832	1903232	1904095	minus	dmsC	anaerobic dimethyl sulfoxide reductase chain C pseudogene	stop	24	emb|CAD05366.1| anaerobic dimethyl sulfoxide reductase chain C [Salmonella enterica subsp. enterica serovar Typhi]
SPA1853	1926461	1927349	plus	-	-	frameshift	504	gb|AAL20775.1| putative transposase [Salmonella typhimurium LT2]
SPA1921	2001690	2002577	plus	ybiF	putative membrane protein pseudogene	stop	609	emb|CAD05279.1| putative membrane protein [Salmonella enterica subsp. enterica serovar Typhi]
SPA1952	2030862	2033127	minus	slrP	leucine-rich repeat protein pseudogene	frameshift	1554	gb|AAL19737.1| leucine-rich repeat protein [Salmonella typhimurium LT2]
SPA1962	2043417	2045102	minus	hutU	urocanate hydratase pseudogene	stop	239	emb|CAD05238.1| urocanate hydratase [Salmonella enterica subsp. entericaserovar Typhi]
SPA2024	2107564	2107890	minus	-	-	frameshift	198	emb|CAD05179.1| putative membrane protein [Salmonella enterica subsp. enterica serovar Typhi]
SPA2061	2150156	2151819	plus	asnB	asparagine synthetase B pseudogene	frameshift	1221	emb|CAD05143.1| asparagine synthetase B [Salmonella enterica subsp. entericaserovar Typhi]
SPA2109	2192762	2194423	minus	dpiB	sensor kinase DpiB pseudogene	stop	1426	emb|CAD05102.1| sensor kinase DpiB [Salmonella enterica subsp. entericaserovar Typhi]
SPA2119	2203231	2204468	minus	ybdR	hypothetical zinc-dependant alcohol dehydrogenase pseudogene	frameshift	349	emb|CAD05092.1| hypothetical zinc-dependant alcohol dehydrogenase [Salmonella enterica subsp. enterica serovar Typhi]
SPA2169	2258112	2259764	plus	-	putative membrane protein pseudogene	stop	349	emb|CAD05039.1| putative membrane protein [Salmonella enterica subsp. enterica serovar Typhi]
SPA2171	2260403	2260817	plus	-	-	frameshift (multiple) 	96	gb|AAL21403.1| putative IS3-like transposase [Salmonella typhimurium LT2]
SPA2194	2280328	2281901	minus	fdrA	FdrA protein pseudogene	frameshift	324	emb|CAD05013.1| FdrA protein [Salmonella enterica subsp. enterica serovar Typhi]
SPA2201	2289367	2290821	minus	-	-	stop	357	"gb|AAL19476.1| putative NCS1 family, allantoin transport protein [Salmonella typhimurium LT2]"
SPA2221	2310879	2311643	plus	ybbK	putative membrane protein pseudogene	deletion	missing first 50 aa	STY0547
SPA2343	2438409	2439497	plus	ddlA	D-alanine:D-alanine ligase A pseudogene	stop	856	emb|CAD08835.1| D-alanine:D-alanine ligase A [Salmonella enterica subsp.enterica serovar Typhi]
SPA2361	2461572	2461859	minus	-	hypothetical protein pseudogene	fs	124	emb|CAD08817.1| hypothetical protein [Salmonella enterica subsp. enterica serovar Typhi]
SPA2368	2471256	2471411	plus	-	hypothetical protein pseudogene	stop	93	emb|CAD08810.1| hypothetical protein [Salmonella enterica subsp. enterica serovar Typhi]
SPA2374	2474707	2475256	minus	-	hypothetical protein pseudogene	frameshift	442	emb|CAD08803.1| hypothetical protein [Salmonella enterica subsp. enterica serovar Typhi]
SPA2450	2547495	2548112	minus	-	hypothetical protein pseudogene	frameshift	409	emb|CAD08775.1| hypothetical protein [Salmonella enterica subsp. enterica serovar Typhi]
SPA2461	2559205	2559669	minus	safD	putative fimbrial structural subunit pseudogene	stop	433	emb|CAD08763.1| putative fimbrial structural subunit [Salmonella enterica subsp. enterica serovar Typhi]
SPA2468	2566054	2566362	minus	-	-	stop	277	gb|AAL19252.1| putative cytoplasmic protein [Salmonella typhimurium LT2]
SPA2477	2579410	2579879	minus	-	hypothetical protein pseudogene	frameshift	183	emb|CAD08742.1| hypothetical protein [Salmonella enterica subsp. enterica serovar Typhi]
SPA2498	2598213	2599115	plus	-	hypothetical protein pseudogene	stop	496	emb|CAD08725.1| hypothetical protein [Salmonella enterica subsp. enterica serovar Typhi]
SPA2606	2702888	2703922	minus	-	-	frameshift	0	emb|CAD05465.1| hypothetical prophage protein [Salmonella enterica subsp.enterica serovar Typhi]
SPA2628	2730665	2731236	plus	hin	H inversion: regulation of flagellar gene expression by site-specific inversion of DNA pseudogene			
SPA2634	2741935	2742177	plus	-	hypothetical protein pseudogene	frameshift	49	emb|CAD05887.1| hypothetical protein [Salmonella enterica subsp. enterica serovar Typhi]
SPA2666	2770464	2771423	plus	nrdF	ribonucleoside-diphosphate reductase 2 beta chain pseudogene	stop	373	emb|CAD05919.1| ribonucleoside-diphosphate reductase 2 beta chain [Salmonellaenterica subsp. enterica serovar Typhi]
SPA2674	2780381	2781751	minus	-	putative glycoporin pseudogene	stop	1087	emb|CAD05927.1| putative glycoporin [Salmonella enterica subsp. enterica serovar Typhi]
SPA2762	2861128	2861555	minus	-	-	frameshift	0	gb|AAL21786.1| putative cytoplasmic protein [Salmonella typhimurium LT2]
SPA2763	2861782	2862438	plus	pphB	possible serine/threonine protein phosphatase pseudogene	stop	54	emb|CAD06012.1| possible serine/threonine protein phosphatase [Salmonella enterica subsp. enterica serovar Typhi]
SPA2792	2888508	2889554	plus	iap	alkaline phosphatase isozyme conversion protein pseudogene	frameshift	277	emb|CAD06042.1| alkaline phosphatase isozyme conversion protein [Salmonella enterica subsp. enterica serovar Typhi]
SPA2799	2894339	2895874	minus	-	hypothetical protein pseudogene	stop	1057	emb|CAD06049.1| hypothetical protein [Salmonella enterica subsp. enterica serovar Typhi]
SPA2800	2896232	2898438	plus	-	conserved hypothetical protein pseudogene	frameshift	2078	emb|CAD06050.1| conserved hypothetical protein [Salmonella enterica subsp. enterica serovar Typhi]
SPA2806	2905559	2906355	minus	-	conserved hypothetical protein pseudogene	frameshift	651	 emb|CAD06056.1| STY3078 [Salmonella enterica subsp. enterica serovar Typhi]
SPA2826	2930875	2932232	minus	gudT	"putative MFS superfamily, D-glucarate permease pseudogene"	frameshift	192	emb|CAD06076.1| probable glucarate transporter [Salmonella enterica subsp. enterica serovar Typhi]
SPA2899	3010690	3011227	minus	-	outer membrane protein (associated with virulence) pseudogene	frameshift	468	emb|CAD02858.1| outer membrane protein (associated with virulence) [Salmonella enterica subsp. enterica serovar Typhi]
SPA3010	3114896	3115948	minus	-	"possible ABC-transport protein, periplasmic-binding component pseudogene"	stop	598	"emb|CAD02974.1| possible ABC-transport protein, periplasmic-binding component [Salmonella enterica subsp. enterica serovar Typhi]"
SPA3040	3144116	3144807	minus	-	-	frameshift	117	emb|CAD03003.1| putative membrane protein [Salmonella enterica subsp. enterica serovar Typhi]
SPA3106	3212192	3212348	plus	yhaL	putative cytoplasmic protein pseudogene	frameshift	72	emb|CAD07761.1| conserved hypothetical protein [Salmonella enterica subsp. enterica serovar Typhi]
SPA3108	3213797	3215128	minus	yhaO	putative HAAAP family transport protein pseudogene	stop	331	gb|AAL22112.1| putative HAAAP family transport protein [Salmonella typhimurium LT2]
SPA3119	3228776	3230343	plus	garD	D-galactarate dehydratase pseudogene	frameshift	393	emb|CAD07773.1| D-galactarate dehydratase [Salmonella enterica subsp. enterica serovar Typhi]
SPA3145	3252445	3253451	plus	yhbW	possible monooxygenase pseudogene	frameshift	882	emb|CAD07798.1| possible monooxygenase [Salmonella enterica subsp. enterica serovar Typhi]
SPA3223	3330315	3331667	minus	-	possible membrane transport protein pseudogene	stop	753	emb|CAD07871.1| possible membrane transport protein [Salmonella enterica subsp. enterica serovar Typhi]
SPA3253	3363167	3364050	plus	ccrM	DNA adenine methyltransferase pseudogene	frameshift	630	emb|CAD07901.1| putative adenine-specific DNA-modification methylase [Salmonella enterica subsp. enterica serovar Typhi]
SPA3326	3418190	3418432	minus	-	hypothetical protein pseudogene	stop	132	emb|CAD08153.1| hypothetical protein [Salmonella enterica subsp. entericaserovar Typhi]
SPA3345	3441646	3441815	plus	yhfL	conserved hypothetical protein pseudogene	frameshift	84	emb|CAD08134.1| conserved hypothetical protein [Salmonella enterica subsp. enterica serovar Typhi]
SPA3357	3451464	3452242	minus	yrfD	conserved hypothetical protein pseudogene	frameshift	351	emb|CAD08122.1| conserved hypothetical protein [Salmonella enterica subsp. enterica serovar Typhi]
SPA3396	3505231	3506268	minus	yhhX	putative oxidoreductase pseudogene	stop	196	emb|CAD08084.1| putative oxidoreductase [Salmonella enterica subsp. enterica serovar Typhi]
SPA3463	3574123	3575023	plus	yhjC	hypothetical lysR-family transcriptional regulator pseudogene	frameshift	478	emb|CAD08018.1| hypothetical lysR-family transcriptional regulator [Salmonella enterica subsp. enterica serovar Typhi]
SPA3466	3577968	3579895	minus	yhjG	putative inner membrane protein pseudogene	frameshift	123	emb|CAD08015.1| putative membrane protein [Salmonella enterica subsp. enterica serovar Typhi]
SPA3475	3594263	3596887	minus	yhjO	putative polysaccharide biosynthesis protein catalytic subunit pseudogene	stop	769	emb|CAD08006.1| putative polysaccharide biosynthesis protein catalytic subunit [Salmonella enterica subsp. enterica serovar Typhi]
SPA3492	3614196	3615887	minus	yhjW	putative membrane protein pseudogene	frameshift	831	emb|CAD07988.1| putative membrane protein [Salmonella enterica subsp. enterica serovar Typhi]
SPA3500	3623433	3623840	plus	yiaG	putative DNA-binding protein pseudogene	stop	334	emb|CAD07980.1| putative DNA-binding protein [Salmonella enterica subsp. enterica serovar Typhi]
SPA3521	3645043	3645975	plus	-	hypothetical protein pseudogene	stop	652	emb|CAD07958.1| hypothetical protein [Salmonella enterica subsp. enterica serovar Typhi]
SPA3537	3665219	3665322	plus	-	-	stop (multiple)	45	emb|CAD05943.1| hypothetical protein [Salmonella enterica subsp. enterica serovar Typhi]
SPA3539	3666556	3667145	plus	mtlR	mannitol operon repressor pseudogene	frameshift	60	emb|CAD03307.1| mannitol operon repressor (mannitol repressor protein) [Salmonella enterica subsp. enterica serovar Typhi]
SPA3543	3669231	3673558	plus	sapB	putative inner membrane protein pseudogene	frameshift	460	STM3691
SPA3600	3732414	3734732	minus	yicI	putative glycosyl hydrolase pseudogene	stop	138	emb|CAD03245.1| putative glycosyl hydrolase [Salmonella enterica subsp. enterica serovar Typhi]
SPA3605	3738363	3739406	plus	-	-	stop 	652	gb|AAL22612.1| putative cytoplasmic protein [Salmonella typhimurium LT2]
SPA3627	3766881	3767285	plus	-	-	stop	265	gb|AAL22635.1| putative cytoplasmic protein [Salmonella typhimurium LT2]
SPA3637	3774312	3775703	minus	uhpT	hexosephosphate transport protein pseudogene	stop	952	emb|CAD03207.1| hexosephosphate transport protein [Salmonella enterica subsp. enterica serovar Typhi]
SPA3638	3775846	3777174	minus	uhpC	regulatory protein pseudogene	stop	376	emb|CAD03206.1| regulatory protein [Salmonella enterica subsp. enterica serovar Typhi]
SPA3639	3777184	3778674	minus	uhpB	two-component system sensor histidine kinase pseudogene	stop	553	emb|CAD03205.1| two-component system sensor histidine kinase [Salmonella enterica subsp. enterica serovar Typhi]
SPA3662	3800479	3801427	minus	ccmH	cytochrome c-type biogenesis protein H1 pseudogene	frameshift	201	emb|CAD07479.1| cytochrome c-type biogenesis protein H1 [Salmonella enterica subsp. enterica serovar Typhi]
SPA3678	3818698	3820460	minus	dgoA	2-oxo-3-deoxygalactonate 6-phosphate aldolase and galactonate dehydratase pseudogene	frameshift	435	ref|NP_418147.1| 2-oxo-3-deoxygalactonate 6-phosphate aldolase and galactonate dehydratase [Escherichia coli K12]
SPA3722	3868618	3869584	plus	rbsC	high affinity ribose transport protein pseudogene	frameshift	366	emb|CAD03112.1| high affinity ribose transport protein [Salmonella enterica subsp. enterica serovar Typhi]
SPA3725	3871565	3872564	plus	rbsR	ribose operon repressor pseudogene	frameshift	219	emb|CAD03109.1| ribose operon repressor [Salmonella enterica subsp. enterica serovar Typhi]
SPA3755	3900982	3902249	minus	rhlB	putative ATP-dependent RNA helicase pseudogene	frameshift	261	emb|CAD09401.1| putative ATP-dependent RNA helicase [Salmonella enterica subsp. enterica serovar Typhi]
SPA3786	3929528	3930051	minus	-	-	frameshift (multiple)	246	emb|CAD09375.1| possible exported protein [Salmonella enterica subsp. enterica serovar Typhi]
SPA3821	3964336	3966169	plus	-	-	frameshift	183	emb|CAD07912.1| possible transferase [Salmonella enterica subsp. enterica serovar Typhi]
SPA3868	4015397	4016265	plus	rbn	ribonuclease BN pseudogene	frameshift	207	emb|CAD09599.1| ribonuclease BN [Salmonella enterica subsp. enterica serovar Typhi]
SPA3879	4022800	4025845	minus	fdoG	"formate dehydrogenase-O, major subunit pseudogene"	frameshift	2302	"emb|CAD09588.1| formate dehydrogenase-O, major subunit [Salmonella enterica subsp. enterica serovar Typhi]"
SPA3908	4053643	4054977	plus	-	putative membrane protein pseudogene	stop	850	emb|CAD09559.1| putative membrane protein [Salmonella enterica subsp. enterica serovar Typhi]
SPA3926	4069888	4070315	plus	yiiR	putative membrane protein pseudogene	frameshift	42	emb|CAD09540.1| putative membrane protein [Salmonella enterica subsp. enterica serovar Typhi]
SPA3948	4096620	4097880	plus	-	putative serine hydroxymethyltransferase pseudogene	frameshift	642	emb|CAD09519.1| putative serine hydroxymethyltransferase [Salmonella enterica subsp. enterica serovar Typhi]
SPA4023	4177160	4178911	plus	aceK	isocitrate dehydrogenase kinase/phosphatase pseudogene	stop	96	emb|CAD09191.1| isocitrate dehydrogenase kinase/phosphatase [Salmonella enterica subsp. enterica serovar Typhi]
SPA4091	4265078	4265388	minus	yjcH	putative membrane protein pseudogene	frameshift	150	emb|CAD09258.1| putative membrane protein [Salmonella enterica subsp. enterica serovar Typhi]
SPA4122	4301826	4303440	minus	dcuS	two-component sensor kinase pseudogene	frameshift	804	emb|CAD09289.1| two-component sensor kinase [Salmonella enterica subsp.enterica serovar Typhi]
SPA4123	4303796	4306225	plus	dmsA	"putative anaerobic dimethyl sulfoxide reductase, subunit A pseudogene"	stop	723	"gb|AAL23129.1| putative anaerobic dimethyl sulfoxide reductase, subunit A [Salmonella typhimurium LT2]"
SPA4164	4339061	4342363	minus	yjeP	putative membrane protein pseudogene	stop	1609	emb|CAD06827.1| putative membrane protein [Salmonella enterica subsp. enterica serovar Typhi]
SPA4217	4386773	4388161	plus	-	putative exported protein pseudogene	stop	1023	emb|CAD06877.1| putative exported protein [Salmonella enterica subsp. enterica serovar Typhi]
SPA4236	4409247	4411050	plus	mpl	murein peptide ligase pseudogene	frameshift	1389	emb|CAD06896.1| murein peptide ligase [Salmonella enterica subsp. enterica serovar Typhi]
SPA4257	4429762	4432470	plus	mgtA	"Mg(2+) transport ATPase, P-type pseudogene"	stop	640	"emb|CAD06917.1| Mg(2+) transport ATPase, P-type [Salmonella enterica subsp.enterica serovar Typhi]"
SPA4294	4465495	4466229	minus	-	-	frameshift	137	emb|CAD06949.1| putative phage capsid protein [Salmonella enterica subsp. enterica serovar Typhi]
SPA4295	4466771	4467101	plus	-	phage DNA binding protein pseudogene	frameshift	240	emb|CAD06950.1| phage DNA binding protein [Salmonella enterica subsp. enterica serovar Typhi]
SPA4302	4471199	4472053	minus	-	-	frameshift (multiple)	180	gb|AAL21655.1| putative transposase [Salmonella typhimurium LT2]
SPA4303	4472050	4472348	minus	-	-	frameshift	93	ref|NP_414832.1| putative factor [Escherichia coli K12]
SPA4308	4478392	4478601	plus	pefI	pefI protein pseudogene	stop	117	emb|CAD06963.1| probable regulatory protein [Salmonella enterica subsp. enterica serovar Typhi]
SPA4318	4493583	4493792	plus	-	hypothetical protein pseudogene	stop (multiple)	87	emb|CAD06973.1| hypothetical protein [Salmonella enterica subsp. enterica serovar Typhi]
SPA4338	4511992	4513232	minus	yjiO	putative MFS family transport protein pseudogene	frameshift	516	emb|CAD03363.1| putative sugar transport protein [Salmonella enterica subsp.enterica serovar Typhi]
SPA4407	4582401	4582900	minus	-	putative secreted protein pseudogene	frameshift	180	emb|CAD03428.1| putative secreted protein [Salmonella enterica subsp. enterica serovar Typhi] 
SPA3512	3634418	3635695	minus	xylA	D-xylose isomerase			
SPA3525	3648869	3650335	plus	lyxK	putative L-xylulose kinase			
SPA3751	3895795	3896490	plus	-	probable uridine phosphorylase			
Deleted				sseJ				
Deleted				trg