breseq  version 0.33.1  revision 8505477f25b3 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence	position	mutation	freq	annotation	gene	description
RA	204,556	A→G	100%	intergenic (+156/‑28)	alaV → / → rrlH	tRNA‑Ala/23S ribosomal RNA
RA	1,036,505	G→A	100%	A632A (GCG→GCA)	rsxC →	fused predicted 4Fe‑4S ferredoxin‑type protein
RA	1,892,019:1	+GC	100%	intergenic (‑437/+54)	gudP ← / ← ygdL	predicted D‑glucarate transporter/conserved hypothetical protein
RA	2,359,867	G→A	35.0%	noncoding (1228/2905 nt)	rrlA ←	23S ribosomal RNA
RA	2,359,876	C→T	31.8%	noncoding (1219/2905 nt)	rrlA ←	23S ribosomal RNA

Unassigned missing coverage evidence
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	Exported	5448	5475	28	2 [1]	[1] 2	yaaX	hypothetical protein
*	*	÷	Exported	16632	16647	16	2 [1]	[1] 3	nhaA	sodium‑proton antiporter
*	*	÷	Exported	23439	23455	17	2 [1]	[1] 2	lspA/fkpB	prolipoprotein signal peptidase/FKBP‑type peptidyl‑prolyl cis‑trans isomerase
*	*	÷	Exported	64281	64297	17	2 [0]	[1] 2	leuC	3‑isopropylmalate isomerase subunit, dehydratase component
*	*	÷	Exported	64498	64515	18	2 [1]	[1] 2	leuC	3‑isopropylmalate isomerase subunit, dehydratase component
*	*	÷	Exported	85225	85265	41	2 [1]	[1] 2	murG	N‑acetylglucosaminyl transferase
*	*	÷	Exported	111012	111042	31	2 [1]	[1] 2	aceF	pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2
*	*	÷	Exported	149304	149345	42	2 [1]	[1] 2	hrpB/mrcB	predicted ATP‑dependent helicase/fused glycosyl transferase and transpeptidase
*	*	÷	Exported	167491	167518	28	2 [1]	[1] 2	glnD/map	uridylyltransferase/methionine aminopeptidase
*	*	÷	Exported	170548	170577	30	2 [1]	[1] 2	tsf/pyrH	protein chain elongation factor EF‑Ts/uridylate kinase
*	*	÷	Exported	193418	193449	32	3 [1]	[1] 2	yaeQ	conserved hypothetical protein
*	*	÷	Exported	193914	193942	29	2 [1]	[1] 2	yaeJ	conserved hypothetical protein
*	*	÷	Exported	222593	222628	36	2 [1]	[1] 2	lpcA	D‑sedoheptulose 7‑phosphate isomerase
*	*	÷	Exported	252010	252043	34	2 [1]	[1] 2	malZ	maltodextrin glucosidase
*	*	÷	Exported	288431	288444	14	2 [1]	[1] 2	lon	DNA‑binding ATP‑dependent protease La
*	*	÷	Exported	304423	304453	31	2 [0]	[0] 2	[ybaZ]	[ybaZ]
*	*	÷	Exported	321883	321967	85	2 [1]	[1] 2	dnaX	DNA polymerase III/DNA elongation factor III, tau and gamma subunits
*	*	÷	Exported	329937	329960	24	2 [1]	[1] 2	gsk/ybaL	inosine/guanosine kinase/predicted transporter with NAD(P)‑binding Rossmann‑fold domain
*	*	÷	Exported	339144	339181	38	2 [1]	[1] 2	copA	copper transporter
*	*	÷	Exported	341116	341157	42	2 [1]	[1] 2	ybaT	predicted transporter
*	*	÷	Exported	343160	343178	19	2 [1]	[1] 2	ybbJ	conserved inner membrane protein
*	*	÷	Exported	377736	377765	30	2 [1]	[1] 2	ybdA	predicted transporter
*	*	÷	Exported	394542	394553	12	2 [1]	[1] 2	ahpC/ahpF	alkyl hydroperoxide reductase, C22 subunit/alkyl hydroperoxide reductase, F52a subunit, FAD/NAD(P)‑binding
*	*	÷	Exported	396315	396339	25	2 [1]	[1] 2	ahpF/ybeM	alkyl hydroperoxide reductase, F52a subunit, FAD/NAD(P)‑binding/predicted C‑N hydrolase superfamily, NAD(P)‑binding amidase/nitrilase
*	*	÷	Exported	409120	409155	36	2 [1]	[1] 3	holA	DNA polymerase III, delta subunit
*	*	÷	Exported	417116	417142	27	2 [1]	[1] 2	miaB	isopentenyl‑adenosine A37 tRNA methylthiolase
*	*	÷	Exported	431230	431277	48	2 [1]	[0] 2	glnS/ybfM	glutamyl‑tRNA synthetase/predicted outer membrane porin
*	*	÷	Exported	432316	432334	19	3 [1]	[1] 2	ybfM	predicted outer membrane porin
*	*	÷	Exported	444353	444445	93	3 [1]	[1] 2	[kdpE]	[kdpE]
*	*	÷	Exported	447388	447444	57	2 [1]	[1] 2	kdpD	fused sensory histidine kinase in two‑component regulatory system with KdpE
*	*	÷	Exported	480816	480828	13	2 [1]	[1] 2	ybgE	conserved inner membrane protein
*	*	÷	Exported	483540	483712	173	2 [1]	[1] 2	tolA	membrane anchored protein in TolA‑TolQ‑TolR complex
*	*	÷	Exported	497399	497456	58	2 [1]	[1] 2	galT	galactose‑1‑phosphate uridylyltransferase
*	*	÷	Exported	514529	514565	37	2 [1]	[1] 2	bioA	7,8‑diaminopelargonic acid synthase, PLP‑dependent
*	*	÷	Exported	525521	525545	25	2 [1]	[1] 2	moaD	molybdopterin synthase, small subunit
*	*	÷	Exported	538706	538720	15	2 [1]	[1] 3	rhlE/dps	RNA helicase/Fe‑binding and storage protein
*	*	÷	Exported	546116	546163	48	2 [1]	[1] 2	ybiS	conserved hypothetical protein
*	*	÷	Exported	562930	562942	13	2 [1]	[1] 2	ybjK	predicted DNA‑binding transcriptional regulator
*	*	÷	Exported	566703	566721	19	2 [1]	[1] 2	poxB	pyruvate dehydrogenase (pyruvate oxidase), thiamin‑dependent, FAD‑binding
*	*	÷	Exported	571862	571921	60	2 [1]	[1] 2	ybjE/aqpZ	predicted transporter/aquaporin
*	*	÷	Exported	577266	577289	24	2 [1]	[1] 2	macB	fused macrolide transporter subunits and ATP‑binding component and membrane component of ABC superfamily
*	*	÷	Exported	597447	597474	28	2 [1]	[1] 3	serS/dmsA	seryl‑tRNA synthetase, also charges selenocysteinyl‑tRNA with serine/dimethyl sulfoxide reductase, anaerobic, subunit A
*	*	÷	Exported	647577	647605	29	2 [1]	[1] 2	pepN	aminopeptidase N
*	*	÷	Exported	658288	658335	48	2 [1]	[1] 3	ycbS	predicted outer membrane usher protein
*	*	÷	Exported	698176	698199	24	2 [1]	[1] 2	appA	phosphoanhydride phosphorylase
*	*	÷	Exported	705619–705730	705740	11–122	2 [1]	[1] 2	ymcC/serX	predicted outer membrane lipoprotein/tRNA‑Ser
*	*	÷	Exported	712005	712048	44	2 [0]	[1] 2	yceP/dinI	hypothetical protein/DNA damage‑inducible protein I
*	*	÷	Exported	725195	725214	20	2 [1]	[0] 2	rluC/yceF	23S rRNA pseudouridylate synthase/hypothetical protein
*	*	÷	Exported	750863	750893	31	2 [1]	[1] 2	mfd	transcription‑repair coupling factor
*	*	÷	Exported	752122	752154	33	2 [1]	[1] 2	mfd	transcription‑repair coupling factor
*	*	÷	Exported	752225	752266	42	2 [0]	[1] 2	mfd	transcription‑repair coupling factor
*	*	÷	Exported	833586	833608	23	3 [1]	[1] 2	narG	nitrate reductase 1, alpha subunit
*	*	÷	Exported	850795	850809	15	2 [1]	[1] 3	[yciA]	[yciA]
*	*	÷	Exported	865558	865585	28	2 [1]	[1] 2	yciQ	predicted inner membrane protein
*	*	÷	Exported	875447	875461	15	2 [1]	[0] 2	acnA	aconitate hydratase 1
*	*	÷	Exported	899406	899451	46	2 [1]	[1] 3	pspD	peripheral inner membrane phage‑shock protein
*	*	÷	Exported	911156	911194	39	2 [1]	[1] 2	ycjV	predicted sugar transporter subunit
*	*	÷	Exported	914817	914842	26	3 [1]	[1] 2	ycjX	conserved hypothetical protein with nucleoside triphosphate hydrolase domain
*	*	÷	Exported	924005	924016	12	2 [1]	[1] 3	mppA	murein tripeptide (L‑ala‑gamma‑D‑glutamyl‑meso‑DAP) transporter subunit
*	*	÷	Exported	1030820	1030838	19	2 [1]	[1] 2	add	adenosine deaminase
*	*	÷	Exported	1033877	1033895	19	3 [1]	[1] 2	rsxA	predicted inner membrane subunit
*	*	÷	Exported	1034694	1034733	40	2 [1]	[1] 2	rsxC	fused predicted 4Fe‑4S ferredoxin‑type protein
*	*	÷	Exported	1037737	1037743	7	2 [1]	[0] 2	rsxD	predicted inner membrane oxidoreductase
*	*	÷	Exported	1046307	1046317	11	3 [1]	[1] 3	ydhH	conserved hypothetical protein
*	*	÷	Exported	1048053	1048061	9	2 [1]	[1] 2	slyB/slyA	outer membrane lipoprotein/DNA‑binding transcriptional activator
*	*	÷	Exported	1056849	1056895	47	2 [1]	[1] 3	lhr	predicted ATP‑dependent helicase
*	*	÷	Exported	1056967	1057000	34	2 [0]	[1] 2	lhr	predicted ATP‑dependent helicase
*	*	÷	Exported	1092390	1092431	42	2 [1]	[1] 2	sufA/ydiH	Fe‑S cluster assembly protein/hypothetical protein
*	*	÷	Exported	1103147	1103153	7	2 [1]	[1] 2	aroD/ydiF	3‑dehydroquinate dehydratase/fused predicted acetyl‑CoA:acetoacetyl‑CoA transferase: alpha subunit and beta subunit
*	*	÷	Exported	1154060	1154102	43	2 [1]	[1] 2	astE	succinylglutamate desuccinylase
*	*	÷	Exported	1157036	1157056	21	2 [1]	[1] 3	astD	succinylglutamic semialdehyde dehydrogenase
*	*	÷	Exported	1208802	1208804	3	2 [1]	[0] 2	yobD	conserved inner membrane protein
*	*	÷	Exported	1231134	1231164	31	2 [1]	[1] 2	ptrB	protease II
*	*	÷	Exported	1249836	1249855	20	3 [1]	[0] 2	ruvA	component of RuvABC resolvasome, regulatory subunit
*	*	÷	Exported	1279183	1279198	16	2 [1]	[1] 2	yeeJ	adhesin
*	*	÷	Exported	1292330	1292381	52	2 [1]	[1] 2	yeeO	predicted multidrug efflux system
*	*	÷	Exported	1309183	1309209	27	2 [1]	[1] 2	yeeZ	predicted epimerase, with NAD(P)‑binding Rossmann‑fold domain
*	*	÷	Exported	1320080	1320102	23	2 [1]	[1] 2	ugd/gnd	UDP‑glucose 6‑dehydrogenase/gluconate‑6‑phosphate dehydrogenase, decarboxylating
*	*	÷	Exported	1368198	1368281	84	2 [1]	[1] 2	yohH/dusC	conserved hypothetical protein/tRNA‑dihydrouridine synthase C
*	*	÷	Exported	1374845	1374875	31	3 [1]	[1] 2	yeiA	predicted oxidoreductase
*	*	÷	Exported	1391544	1391564	21	2 [1]	[1] 3	fruA	fused fructose‑specific PTS enzyme IIB'BC components
*	*	÷	Exported	1414249	1414282	34	2 [1]	[1] 2	rplY/yejK	50S ribosomal subunit protein L25/nucleotide associated protein
*	*	÷	Exported	1420600	1420649	50	2 [1]	[1] 2	ccmF	heme lyase, CcmF subunit
*	*	÷	Exported	1427679	1427700	22	2 [1]	[1] 2	napG	ferredoxin‑type protein essential for electron transfer from ubiquinol to periplasmic nitrate reductase (NapAB)
*	*	÷	Exported	1432594	1432635	42	2 [1]	[1] 2	eco/mqo	ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
*	*	÷	Exported	1433461	1433480	20	2 [1]	[1] 2	mqo	malate dehydrogenase, FAD/NAD(P)‑binding domain
*	*	÷	Exported	1527549	1527567	19	3 [1]	[1] 2	trmC	fused 5‑methylaminomethyl‑2‑thiouridine forming enzyme methyltransferase and FAD‑dependent demodification enzyme
*	*	÷	Exported	1527875	1527919	45	2 [1]	[1] 2	trmC	fused 5‑methylaminomethyl‑2‑thiouridine forming enzyme methyltransferase and FAD‑dependent demodification enzyme
*	*	÷	Exported	1593429	1593446	18	2 [1]	[1] 3	cysA	sulfate/thiosulfate transporter subunit
*	*	÷	Exported	1608244	1608270	27	2 [1]	[1] 2	yfeG/yffI	predicted DNA‑binding transcriptional regulator/predicted carboxysome structural protein with predicted role in ethanolamine utilization
*	*	÷	Exported	1616720	1616744	25	2 [1]	[1] 2	eutE	predicted aldehyde dehydrogenase, ethanolamine utilization protein
*	*	÷	Exported	1658268	1658306	39	3 [1]	[1] 2	ppx	exopolyphosphatase
*	*	÷	Exported	1703980	1703991	12	2 [1]	[0] 2	hcaB	2,3‑dihydroxy‑2,3‑dihydrophenylpropionate dehydrogenase
*	*	÷	Exported	1718372	1718377	6	2 [0]	[1] 2	glyA/hmp	serine hydroxymethyltransferase/fused nitric oxide dioxygenase and dihydropteridine reductase 2
*	*	÷	Exported	1727267	1727320	54	2 [1]	[1] 3	purL	phosphoribosylformyl‑glycineamide synthetase
*	*	÷	Exported	1736985	1736992	8	2 [1]	[1] 2	rnc/lepB	RNase III/leader peptidase
*	*	÷	Exported	1751269	1751281	13	2 [1]	[1] 3	yfiF/trxC	predicted methyltransferase/thioredoxin 2
*	*	÷	Exported	1766135	1766165	31	2 [1]	[1] 2	clpB	protein disaggregation chaperone
*	*	÷	Exported	1788677	1788712	36	2 [1]	[1] 2	smpB/ygaF	trans‑translation protein/hypothetical protein
*	*	÷	Exported	1789863	1789878	16	2 [1]	[1] 2	ygaF	hypothetical protein
*	*	÷	Exported	1790615	1790675	61	2 [1]	[1] 2	gabD	succinate‑semialdehyde dehydrogenase I, NADP‑dependent
*	*	÷	Exported	1791851	1791855	5	2 [1]	[0] 2	gabT	4‑aminobutyrate aminotransferase, PLP‑dependent
*	*	÷	Exported	1792922	1792967	46	2 [1]	[1] 2	gabT/gabP	4‑aminobutyrate aminotransferase, PLP‑dependent/gamma‑aminobutyrate transporter
*	*	÷	Exported	1808044	1808079	36	2 [1]	[1] 2	[gshA]	[gshA]
*	*	÷	Exported	1825827	1825840	14	2 [1]	[0] 2	hydN	formate dehydrogenase‑H, [4Fe‑4S] ferredoxin subunit
*	*	÷	Exported	1847469	1847503	35	2 [1]	[1] 2	iap/ygbF	aminopeptidase in alkaline phosphatase isozyme conversion/hypothetical protein
*	*	÷	Exported	1847573	1847653	81	2 [1]	[1] 2	iap/ygbF	aminopeptidase in alkaline phosphatase isozyme conversion/hypothetical protein
*	*	÷	Exported	1847743	1847947	205	2 [1]	[1] 2	iap/ygbF	aminopeptidase in alkaline phosphatase isozyme conversion/hypothetical protein
*	*	÷	Exported	1864676	1864772	97	2 [0]	[1] 2	ygcQ	predicted flavoprotein
*	*	÷	Exported	1873551	1873587	37	2 [1]	[1] 2	ygcE/ygcF	predicted kinase/conserved hypothetical protein
*	*	÷	Exported	1873637	1873705	69	2 [1]	[1] 2	ygcE/ygcF	predicted kinase/conserved hypothetical protein
*	*	÷	Exported	1873744	1873829	86	2 [1]	[1] 2	ygcE/ygcF	predicted kinase/conserved hypothetical protein
*	*	÷	Exported	1876016	1876104	89	2 [1]	[1] 2	[ygcG]	[ygcG]
*	*	÷	Exported	1898891	1898927	37	2 [1]	[1] 2	recD	exonuclease V (RecBCD complex), alpha chain
*	*	÷	Exported	1899058	1899063	6	3 [1]	[1] 2	recD	exonuclease V (RecBCD complex), alpha chain
*	*	÷	Exported	1945277	1945325	49	2 [1]	[1] 2	ygfF/gcvP	predicted NAD(P)‑binding oxidoreductase with NAD(P)‑binding Rossmann‑fold domain/glycine decarboxylase, PLP‑dependent, subunit (protein P) of glycine cleavage complex
*	*	÷	Exported	1988024	1988043	20	2 [1]	[1] 2	yggN	hypothetical protein
*	*	÷	Exported	2056679	2056693	15	2 [1]	[1] 2	ygiP	predicted DNA‑binding transcriptional regulator
*	*	÷	Exported	2056867	2056884	18	2 [1]	[1] 2	ygiP	predicted DNA‑binding transcriptional regulator
*	*	÷	Exported	2060626	2060657	32	2 [1]	[1] 2	ygjD	predicted peptidase
*	*	÷	Exported	2095558	2095600	43	2 [1]	[1] 3	rnpB	RNase P
*	*	÷	Exported	2142054	2142081	28	2 [1]	[0] 2	nusA	transcription termination/antitermination L factor
*	*	÷	Exported	2156403	2156413	11	2 [1]	[1] 2	obgE	GTPase involved in cell partioning and DNA repair
*	*	÷	Exported	2183099	2183118	20	2 [1]	[1] 2	gltB	glutamate synthase, large subunit
*	*	÷	Exported	2221675	2221711	37	2 [1]	[1] 2	accC	acetyl‑CoA carboxylase, biotin carboxylase subunit
*	*	÷	Exported	2228829	2228951	123	2 [1]	[1] 2	yhdZ/rrfF	predicted amino‑acid transporter subunit/5S ribosomal RNA
*	*	÷	Exported	2270442	2270576–2270449	8–135	4 [1]	[1] 2	murB/rrfB	UDP‑N‑acetylenolpyruvoylglucosamine reductase, FAD‑binding/5S ribosomal RNA
*	*	÷	Exported	2280223	2280236	14	2 [1]	[0] 3	trmA/yijD	tRNA (uracil‑5‑)‑methyltransferase/conserved inner membrane protein
*	*	÷	Exported	2342558	2342582	25	3 [1]	[1] 2	glnL	sensory kinase in two‑component regulatory system with GlnG
*	*	÷	Exported	2345031	2345064	34	2 [1]	[1] 2	glnG/hemN	fused DNA‑binding response regulator in two‑component regulatory system with GlnL, nitrogen regulator I (NRI)/coproporphyrinogen III oxidase, SAM and NAD(P)H dependent, oxygen‑independent
*	*	÷	Exported	2354509	2354521	13	2 [0]	[1] 2	yihF/dsbA	conserved hypothetical protein/periplasmic protein disulfide isomerase I
*	*	÷	Exported	2504513	2504535	23	2 [1]	[1] 2	uhpT/selC	hexose phosphate transporter/tRNA‑Sec
*	*	÷	Exported	2530228	2530265	38	2 [1]	[1] 2	rpmG/mutM	50S ribosomal subunit protein L33/formamidopyrimidine/5‑formyluracil/ 5‑hydroxymethyluracil DNA glycosylase
*	*	÷	Exported	2560327	2560361	35	2 [0]	[1] 2	yibK/lldD	predicted rRNA methylase/L‑lactate dehydrogenase, FMN‑linked
*	*	÷	Exported	2560396	2560420	25	2 [1]	[1] 2	yibK/lldD	predicted rRNA methylase/L‑lactate dehydrogenase, FMN‑linked
*	*	÷	Exported	2604939	2604960	22	2 [0]	[1] 4	yhiP/uspA	predicted transporter/universal stress global response regulator
*	*	÷	Exported	2607325	2607353	29	2 [1]	[1] 2	pitA	phosphate transporter, low‑affinity
*	*	÷	Exported	2608946	2608972	27	2 [0]	[1] 4	nikE	nickel transporter subunit
*	*	÷	Exported	2609209	2609258	50	2 [1]	[1] 2	nikE	nickel transporter subunit
*	*	÷	Exported	2610003	2610042	40	2 [1]	[1] 3	nikD	nickel transporter subunit
*	*	÷	Exported	2613619	2613631	13	2 [1]	[1] 2	nikA/acpT	nickel transporter subunit/holo‑(acyl carrier protein) synthase 2
*	*	÷	Exported	2618452	2618479	28	2 [1]	[1] 2	yhhP/zntA	conserved hypothetical protein required for cell growth/zinc, cobalt and lead efflux system
*	*	÷	Exported	2635360	2635420	61	2 [1]	[1] 2	ugpB	glycerol‑3‑phosphate transporter subunit
*	*	÷	Exported	2664452	2664472	21	2 [1]	[1] 2	rtcA	RNA 3'‑terminal phosphate cyclase
*	*	÷	Exported	2725751	2725805	55	2 [1]	[1] 2	yheS	fused predicted transporter subunits and ATP‑binding components of ABC superfamily
*	*	÷	Exported	2731782	2731823	42	3 [0]	[1] 2	fkpA/yheO	FKBP‑type peptidyl‑prolyl cis‑trans isomerase/predicted DNA‑binding transcriptional regulator
*	*	÷	Exported	2753665	2753682	18	3 [1]	[1] 2	mscL	mechanosensitive channel
*	*	÷	Exported	2840627	2840638	12	3 [1]	[0] 2	ampC/frdD	beta‑lactamase/D‑alanine carboxypeptidase/fumarate reductase (anaerobic), membrane anchor subunit
*	*	÷	Exported	2858097	2858126	30	2 [1]	[1] 2	amiB	N‑acetylmuramoyl‑l‑alanine amidase II
*	*	÷	Exported	2858655	2858688	34	2 [1]	[1] 2	amiB	N‑acetylmuramoyl‑l‑alanine amidase II
*	*	÷	Exported	2860489	2860508	20	4 [1]	[1] 2	mutL	methyl‑directed mismatch repair protein
*	*	÷	Exported	2913818	2913836	19	3 [1]	[1] 2	pyrL	pyrBI operon leader peptide
*	*	÷	Exported	2920401	2920443	43	2 [1]	[1] 5	[yjgM]	[yjgM]
*	*	÷	Exported	2973407	2973418	12	2 [0]	[1] 2	radA	predicted repair protein

Unassigned new junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	Exported	1611749 =	1 (0.100)	6 (0.680) +ATGCGGT	5/86	NT	69.9%	coding (1404/1404 nt)	eutA	reactivating factor for ethanolamine ammonia lyase
	?	Exported	= 2603083	5 (0.490)					coding (684/753 nt)	yhiQ	predicted SAM‑dependent methyltransferase