BRESEQ :: Mutation Predictions

Predicted mutations
evidence	position	mutation	annotation	gene	description
RA	12,086	C→T	intergenic (‑300/‑77)	yaaI ← / → dnaK	DUF2541 domain‑containing protein YaaI/chaperone protein DnaK
MC JC	15,389	Δ5,175 bp		insL‑1–insA‑1	insL‑1, hokC, mokC, sokC, nhaA, nhaR, insB‑1, insA‑1
MC JC	92,854	(GCG)_4→3	coding (1442‑1444/1767 nt)	ftsI →	peptidoglycan DD‑transpeptidase FtsI
RA	119,028	T→C	V99A (GTC→GCC)	ampD →	1,6‑anhydro‑N‑acetylmuramoyl‑L‑alanine amidase
MC JC	167,484	Δ5,964 bp		[fhuA]–fhuB	[fhuA], fhuC, fhuD, fhuB
RA	214,885	C→T	T18I (ACC→ATC)	arfB →	peptidyl‑tRNA hydrolase, ribosome rescue factor
RA	257,794	T→C	intergenic (+23/‑35)	frsA → / → crl	fermentation‑respiration switch protein/RNA polymerase holoenzyme assembly factor Crl
MC JC	257,908	Δ776 bp		insB9–[crl]	insB9, insA9, [crl]
MC JC	263,514	Δ61,897 bp		[ykfI]–ykgH	71 genes [ykfI], yafW, ykfH, ykfG, yafX, ykfF, ykfB, yafY, yafZ, ykfA, perR, insN, insI‑1, insN, eyeA, ykfC, insH‑1, mmuP, mmuM, afuC, afuB, insB‑2, insA‑2, yagB, yagA, yagE, yagF, yagG, yagH, xynR, argF, ykgS, insB‑3, insA‑3, yagJ, yagK, yagL, yagM, ykgV, yagN, intF, yagP, paoD, paoC, paoB, paoA, yagU, ykgJ, ecpE, ecpD, ecpC, ecpB, ecpA, ecpR, ykgL, ykgO, ykgM, ykgR, ykgP, eaeH, insE‑1, insF‑1, ykgA, rclC, rclB, rclA, rclR, ykgE, ykgF, ykgG, ykgH
MC JC	332,366	Δ44,951 bp		pdeL–yaiL	39 genes pdeL, yahB, yahC, yahD, yahE, yahF, yahG, yahH, yahI, yahJ, yahK, yahL, yahM, yahN, yahO, prpR, prpB, prpC, prpD, prpE, codB, codA, cynR, cynT, cynS, cynX, lacA, lacY, lacZ, lacI, mhpR, mhpA, mhpB, mhpC, mhpD, mhpF, mhpE, mhpT, yaiL
RA	380,022	(G)_10→9	intergenic (‑141/+47)	frmR ← / ← yaiO	DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO
MC JC	389,898	Δ9,908 bp		yaiT–[yaiZ]	yaiT, insF‑2, insE‑2, yaiT, iprA, ampH, sbmA, yaiW, yaiY, [yaiZ]
MC JC	508,873	Δ40,744 bp		copA–[ylbE]	37 genes copA, copA, copA, glsA, ybaT, cueR, ybbJ, qmcA, fetA, fetB, cnoX, ybbO, tesA, ybbA, ybbP, rhsD, ybbC, ylbH, ybbD, ylbI, ylbG, selU, allS, allA, allR, gcl, hyi, glxR, ybbW, allB, ybbY, glxK, allE, allC, allD, fdrA, [ylbE]
MC JC	565,055	Δ21,054 bp		[intD]–ompT	37 genes [intD], xisD, exoD, renD, insE‑3, insF‑3, renD, emrE, ylcJ, ybcK, ybcL, ybcM, ylcH, ybcN, ninE, ybcO, rusA, ylcG, ybcQ, nmpC, insH‑2, nmpC, essD, rrrD, rzpD, rzoD, borD, ybcV, ybcW, ylcI, nohD, aaaD, tfaD, ybcY, tfaX, appY, ompT
MC JC	603,467	Δ5,885 bp		[ybdG]–insL‑2	[ybdG], nfsB, ybdF, ybdJ, ybdK, sokE, hokE, insL‑2
MC JC	675,552	Δ7,819 bp		ybeQ–[hscC]	ybeQ, ybeR, djlB, ybeT, ybeU, djlC, [hscC]
MC JC	687,860	Δ1,185 bp	IS5‑mediated	insH‑3	insH‑3
MC JC	729,365	Δ9,598 bp		rhsC–ybfD	rhsC, ybfB, ybfO, ybfC, ybfQ, ybfL, ybfD
RA	765,191	Δ1 bp	coding (685/723 nt)	mngR ←	DNA‑binding transcriptional repressor MngR
MC JC	765,208	Δ5,405 bp		[mngR]–mngB	[mngR], mngA, mngB
MC JC	819,776	Δ62,977 bp		ybhL–deoR	57 genes ybhL, ybhM, ybhN, clsB, ybhP, ybhQ, ybhR, ybhS, ybhF, ybhG, cecR, rhlE, ybiA, dinG, ybiB, hcxB, ybiJ, ybiI, ybiX, fiu, mcbA, rlmF, ybiO, glnQ, glnP, glnH, dps, rhtA, yliM, ompX, opgE, rybA, mntS, mntR, ybiR, ldtB, ybiT, ybiU, ybiV, ybiW, ybiY, fsaA, moeB, moeA, iaaA, gsiA, gsiB, gsiC, gsiD, pdeI, dgcI, rimO, bssR, yliI, gstB, dacC, deoR
RA	972,866	Δ1 bp	coding (536/780 nt)	elyC ←	envelope biogenesis factor
RA	988,499	G→A	P163S (CCA→TCA)	asnS ←	asparagine‑‑tRNA ligase
MC JC	997,868	Δ6,818 bp		[elfA]–ycbF	[elfA], elfD, elfC, elfG, ycbU, ycbV, ycbF
MC JC	1,040,502	Δ73,763 bp		[appX]–[mdtG]	75 genes [appX], appA, etk, etp, gfcE, gfcD, gfcC, gfcB, gfcA, insA‑4, insB‑4, cspH, cspG, ymcF, ymcE, gnsA, yccM, torS, torT, torR, torC, torA, torD, cbpM, cbpA, yccE, agp, yccJ, wrbA, ymdF, rutG, rutF, rutE, rutD, rutC, rutB, rutA, rutR, putA, ymdG, putP, efeU, efeO, efeB, phoH, pgaD, pgaC, pgaB, pgaA, dgcT, insF‑4, insE‑4, ymdE, ycdU, serX, ghrA, ycdX, ycdY, ycdZ, csgG, csgF, csgE, csgD, csgB, csgA, csgC, ymdA, ymdB, clsC, opgC, opgG, opgH, yceK, msyB, [mdtG]
MC JC	1,129,397	Δ11,591 bp		flgN–flgL	flgN, flgM, flgA, flgB, flgC, flgD, flgE, flgF, flgG, flgH, flgI, flgJ, flgK, flgL
RA	1,154,362	C→T	A84V (GCC→GTC)	mltG →	endolytic murein transglycosylase
MC JC	1,197,137	25956 bp→12 bp		[ymfD]–[ymgI]	42 genes [ymfD], ymfE, lit, intE, xisE, ymfH, ymfI, ymfJ, ymfK, ymfT, ymfL, ymfM, oweE, ymfN, aaaE, ymfR, beeE, jayE, ymfQ, ycfK, tfaP, tfaE, stfE, pinE, mcrA, icdC, iraM, ymgK, ymgL, ycgX, bluR, bluF, ycgZ, ymgA, ariR, ymgC, pdeG, ymgF, ycgH, ymgD, ymgG, [ymgI]
RA	1,240,439	C→T	V60V (GTC→GTT) D545N (GAC→AAC)	ymgM → cvrA ←	protein YmgM putative K(+):H(+) antiporter
RA	1,270,811	C→T	V347M (GTG→ATG)	chaA ←	Na(+)/K(+):H(+) antiporter ChaA
MC JC	1,299,499	Δ1,199 bp		insH21	insH21
RA	1,382,555	C→T	S203S (AGC→AGT)	ompG →	outer membrane porin G
MC JC	1,388,889	Δ9,734 bp		ycjG–[uspE]	ycjG, mpaA, ymjC, ymjD, ycjY, pgrR, mppA, ynaI, insH‑4, ynaJ, [uspE]
RA	1,400,309	Δ1 bp	coding (1465/1527 nt)	abgT ←	p‑aminobenzoyl glutamate:H(+) symporter
RA	1,400,314	Δ1 bp	coding (1460/1527 nt)	abgT ←	p‑aminobenzoyl glutamate:H(+) symporter
MC JC	1,400,325	Δ81,931 bp		[abgT]–[azoR]	87 genes [abgT], abgB, abgA, abgR, mcaS, smrA, dgcM, zntB, fnrS, ynaL, dbpA, ttcA, intR, xisR, rcbA, ralA, ralR, recT, recE, racC, ydaE, kilR, sieB, ydaF, ydaG, racR, ydaS, ydaT, ydaU, ydaV, ydaW, rzpR, rzoR, trkG, ynaK, ydaY, ynaA, lomR, insH‑5, lomR, stfR, tfaR, pinR, ynaE, ynaM, ttcC, uspF, ompN, micC, ydbK, ydbJ, hslJ, ldhA, ydbH, ynbE, ydbL, feaR, feaB, tynA, paaZ, paaA, paaB, paaC, paaD, paaE, paaF, paaG, paaH, paaI, paaJ, paaK, paaX, paaY, ynbG, ydbA, insD‑2, insC‑2, ydbA, insI‑2, ydbA, pdxI, ydbD, ynbA, ynbB, ynbC, ynbD, [azoR]
MC JC	1,509,562	Δ46,201 bp		[hicB]–maeA	43 genes [hicB], ydcR, ydcS, ydcT, ydcU, ydcV, patD, yncL, ortT, ydcY, ydcZ, mnaT, curA, mcbR, yncD, yncE, ansP, yncG, yncH, rhsE, ydcD, yncO, yncI, ydcC, pptA, yddH, nhoA, yddE, narV, narW, narY, narZ, narU, yddJ, yddK, yddL, yddG, fdnG, fdnH, fdnI, yddM, adhP, maeA
RA	1,562,085	C→T	A133T (GCA→ACA)	ddpA ←	putative D,D‑dipeptide ABC transporter periplasmic binding protein
RA	1,626,996	C→T	D129N (GAT→AAT)	dcp ←	peptidyl‑dipeptidase Dcp
MC JC	1,627,518	Δ25,244 bp		[ydfG]–[ynfP]	48 genes [ydfG], ydfH, ydfZ, ydfI, ydfJ, ynfT, ydfK, pinQ, tfaQ, ydfN, nohA, ynfO, ydfO, gnsB, ynfN, ynfR, ynfQ, cspI, rzpQ, rzoQ, rrrQ, ydfR, essQ, cspB, cspF, ynfS, ydfT, ydfU, rem, hokD, relE, relB, ydfV, flxA, ydfW, ydfX, dicC, dicA, ydfA, ydfB, ydfC, dicF, dicB, ydfD, ydfE, insD‑7, intQ, [ynfP]
RA	1,662,872	C→T	R773W (CGG→TGG)	ynfF →	putative selenate reductase YnfF
RA	1,697,216	T→C	intergenic (‑164/+57)	uidR ← / ← hdhA	DNA‑binding transcriptional repressor UidR/7‑alpha‑hydroxysteroid dehydrogenase
RA	1,741,062	T→C	C384C (TGT→TGC)	ydhC →	putative transporter YdhC
RA	1,742,755	G→C	P163R (CCG→CGG)	ribC ←	riboflavin synthase
RA	1,776,533	G→A	G316D (GGC→GAC)	ydiF →	putative acetate‑CoA transferase
RA	1,811,208	T→C	V92A (GTT→GCT)	tcyP →	cystine/sulfocysteine:cation symporter
RA	1,847,724	(C)_6→7	coding (285/1044 nt)	selD ←	selenide, water dikinase
MC JC	1,872,030	Δ1,437 bp		[dgcJ]	[dgcJ]
RA	1,898,152	G→A	A407A (GCG→GCA)	sdaA →	L‑serine deaminase I
RA	1,907,399	C→T	E13K (GAG→AAG)	cspC ←	stress protein, member of the CspA family
RA	1,941,784	A→G	V267A (GTC→GCC)	znuA ←	Zn(2(+)) ABC transporter periplasmic binding protein
MC JC	1,962,566	Δ16,764 bp		flhE–insA‑5	17 genes flhE, flhA, flhB, cheZ, cheY, cheB, cheR, tap, tar, cheW, cheA, motB, motA, flhC, flhD, insB‑5, insA‑5
MC JC	1,997,112	Δ26,567 bp		[tcyN]–[fliR]	32 genes [tcyN], tcyL, dcyD, tcyJ, fliZ, fliA, fliC, fliD, fliS, fliT, amyA, yedD, yedE, yedF, yedK, yedL, yedN, intG, fliE, fliF, fliG, fliH, fliI, fliJ, fliK, fliL, fliM, fliN, fliO, fliP, fliQ, [fliR]
RA	2,040,801	T→C	L107L (TTA→CTA)	msrQ →	periplasmic protein‑L‑methionine sulfoxide reductase heme binding subunit
MC JC	2,101,397	Δ36,321 bp		[wbbL]–wza	34 genes [wbbL], insH‑7, wbbL, wbbK, wbbJ, wbbI, wbbH, glf, rfbX, rfbC, rfbA, rfbD, rfbB, galF, wcaM, wcaL, wcaK, wzxC, wcaJ, cpsG, cpsB, wcaI, gmm, fcl, gmd, wcaF, wcaE, wcaD, wcaC, wcaB, wcaA, wzc, wzb, wza
MC JC	2,165,151	Δ12,060 bp		yegP–gatY	17 genes yegP, yegQ, cyaR, ogrK, yegZ, yegR, yegS, gatR, insE‑5, insF‑5, gatR, gatD, gatC, gatB, gatA, gatZ, gatY
MC JC	2,204,350	Δ32,368 bp		yehL–preA	30 genes yehL, yehM, yehP, yehQ, yehR, yehS, btsR, btsS, mlrA, yohO, yehW, yehX, yehY, osmF, bglX, dld, pbpG, yohC, yohD, yohF, mdtQ, yohP, dusC, yohJ, yohK, cdd, sanA, yeiS, preT, preA
MC JC	2,286,401	Δ3,780 bp		[yejO]–[yejO]	[yejO], insH‑8, [yejO]
MC JC	2,320,144	Δ16,489 bp		[atoS]–[yfaA]	[atoS], atoC, atoD, atoA, atoE, atoB, yfaP, yfaQ, yfaS, yfaT, [yfaA]
RA	2,406,141	A→G	R167R (CGT→CGC)	lrhA ←	DNA‑binding transcriptional dual regulator LrhA
MC JC	2,416,380	(TGC)_3→2	coding (1634‑1636/2145 nt)	pta →	phosphate acetyltransferase
MC JC	2,466,545	Δ9,634 bp		[intS]–[ypdJ]	15 genes [intS], yfdG, yfdH, yfdI, yfdK, yfdL, yfdM, yfdN, yfdO, yfdP, yfdQ, yfdR, yfdS, [yfdT], [ypdJ]
MC JC	2,509,631	Δ8,319 bp		[yfeO]–pdeA	[yfeO], ypeC, mntH, nupC, insL‑3, pdeA
MC JC	2,558,699	Δ6,790 bp		intZ–[eutA]	intZ, yffL, yffM, yffN, yffO, yffP, yffQ, yffR, yffS, [eutA]
MC JC	2,601,201	Δ13,595 bp		[hyfA]–focB	[hyfA], hyfB, hyfC, hyfD, hyfE, hyfF, hyfG, hyfH, hyfI, hyfJ, hyfR, focB
RA	2,662,004	T→C	E43G (GAA→GGA)	iscR ←	DNA‑binding transcriptional dual regulator IscR
RA	2,756,138	Δ1 bp	intergenic (+183/‑21)	ssrA → / → intA	tmRNA/CP4‑57 prophage; integrase
MC JC	2,756,160	Δ35,091 bp		[intA]–[lhgO]	33 genes [intA], yfjH, alpA, yfjI, yfjJ, abpB, abpA, yfjM, rnlA, rnlB, yfjP, yfjQ, yfjR, ypjK, yfjS, yfjT, yfjU, yfjV, yfjW, ypjI, yfjX, yfjY, ypjJ, yfjZ, ypjF, ypjA, pinH, ypjB, ypjC, ileY, ygaQ, csiD, [lhgO]
RA	2,793,867	C→A	A378D (GCT→GAT)	gabT →	4‑aminobutyrate aminotransferase GabT
MC JC	2,798,370	(TTC)_4→3	coding (124‑126/405 nt)	stpA ←	DNA‑binding transcriptional repressor StpA with RNA chaperone activity
RA	2,813,364	T→C	V250A (GTC→GCC)	emrB →	multidrug efflux pump membrane subunit EmrB
RA	2,843,412	C→T	R12H (CGT→CAT)	hycH ←	formate hydrogenlyase assembly protein
MC JC	2,994,992	Δ3,877 bp		[ygeL]–ygeQ	[ygeL], ygeN, ygeO, insD‑4, insC‑4, ygeP, ygeQ
RA	3,052,352	C→A	W389C (TGG→TGT)	ubiH ←	2‑octaprenyl‑6‑methoxyphenol hydroxylase
RA	3,052,705	G→A	H272Y (CAC→TAC)	ubiH ←	2‑octaprenyl‑6‑methoxyphenol hydroxylase
RA	3,090,282	C→T	intergenic (+30/‑65)	yggI → / → endA	conserved protein YggI/DNA‑specific endonuclease I
RA	3,090,341	Δ1 bp	intergenic (+89/‑6)	yggI → / → endA	conserved protein YggI/DNA‑specific endonuclease I
MC JC	3,090,347	Δ708 bp	coding (1‑708/708 nt)	endA →	DNA‑specific endonuclease I
RA	3,091,305	A→G	S58G (AGC→GGC)	rsmE →	16S rRNA m(3)U1498 methyltransferase
MC JC	3,110,680	25702 bp→GA		[yghD]–pitB	20 genes [yghD], yghE, yghF, yghG, pppA, yghJ, glcA, glcB, glcG, glcF, glcE, glcD, glcC, yghO, insH‑9, yghQ, yghR, yghS, yghT, pitB
MC JC	3,184,782	Δ6,916 bp		ubiK–yqiI	ubiK, ygiL, yqiG, insC‑5, insD‑5, yqiG, yqiH, yqiI
RA	3,213,803	T→C	S253P (TCT→CCT)	rpoD →	RNA polymerase, sigma 70 (sigma D) factor
MC JC	3,362,162	Δ5,481 bp		[yhcA]–[yhcF]	[yhcA], yhcD, yhcE, insH‑10, yhcE, [yhcF]
MC JC	3,453,928	Δ15,926 bp		gspA–[chiA]	16 genes gspA, gspC, gspD, gspE, gspF, gspG, gspH, gspI, gspJ, gspK, gspL, gspM, gspO, bfr, bfd, [chiA]
RA	3,477,150	C→T	K90K (AAG→AAA)	fkpA ←	peptidyl‑prolyl cis‑trans isomerase FkpA
RA	3,495,261	A→G	K417K (AAA→AAG)	nirB →	nitrite reductase catalytic subunit NirB
RA	3,513,003	A→G	D212D (GAT→GAC)	trpS ←	tryptophan‑‑tRNA ligase
RA	3,527,760	A→G	N431S (AAC→AGC)	igaA →	inner membrane protein ‑ inhibits the Rcs signaling pathway
MC JC	3,581,139	3915 bp→6 bp		[yhhY]–yrhB	[yhhY], yhhZ, yrhA, insA‑6, insB‑6, yrhA, yrhD, yrhB
MC JC	3,618,992	Δ6,688 bp		rhsB–[yhhJ]	rhsB, yhhH, yhhI, [yhhJ]
MC JC	3,651,293	Δ2,422 bp		[yhiS]–yhiS	[yhiS], insH‑11, yhiS
RA	3,720,597	Δ1 bp	coding (4/153 nt)	hokA ←	small toxic polypeptide
MC JC	3,720,634	Δ1,442 bp	IS150‑mediated	insJ–insK	insJ, insK
MC JC	3,761,993	Δ8,250 bp		rhsA–yibV	rhsA, yibA, yibJ, yibG, yibS, yibV
RA	3,801,078	(T)_7→6	coding (922/1017 nt)	waaJ ←	UDP‑glucose:(glucosyl)LPS alpha‑1,2‑glucosyltransferase
RA	3,816,579	G→A	intergenic (‑30/‑97)	rph ← / → yicC	truncated RNase PH/UPF0701 family protein YicC
RA	3,829,233	C→A	L97M (CTG→ATG)	xanP →	xanthine:H(+) symporter XanP
RA	3,850,891	G→A	Q68* (CAA→TAA)	ilvN ←	acetohydroxy acid synthase I subunit IlvN
RA	3,871,692	C→T	R13R (CGG→CGA)	dgoT ←	putative D‑galactonate transporter
MC JC	3,888,432	Δ18,167 bp		tnaC–bglG	17 genes tnaC, tnaA, tnaB, mdtL, yidZ, yieE, yieF, adeP, yieH, cbrB, cbrC, yieK, yieL, bglH, bglB, bglF, bglG
RA	3,926,696	C→T	G103D (GGC→GAC)	asnC ←	DNA‑binding transcriptional dual regulator AsnC
RA	3,948,805	(G)_6→7	coding (1165/1521 nt)	yifB ←	putative magnesium chelatase YifB
RA	3,979,769	C→T	A390V (GCG→GTG)	wzyE →	enterobacterial common antigen polymerase
RA	3,980,957	(G)_6→7	coding (71/1386 nt)	yifK →	putative transporter YifK
RA	3,983,666	T→C	F237L (TTC→CTC)	aslB →	putative anaerobic sulfatase maturation enzyme AslB
RA	4,093,223	A→G	V72V (GTT→GTC)	rhaM ←	L‑rhamnose mutarotase
MC JC	4,299,628	Δ25,538 bp		[mdtP]–[phnC]	27 genes [mdtP], mdtO, mdtN, ytcA, yjcS, alsK, alsE, alsC, alsA, alsB, alsR, rpiB, yjdP, phnP, phnO, phnN, phnM, phnL, phnK, phnJ, phnI, phnH, phnG, phnF, phnE, phnD, [phnC]
RA	4,354,915	G→A	intergenic (‑198/+39)	lysU ← / ← dtpC	lysine‑‑tRNA ligase/Ap4A synthetase/Ap3A synthetase/dipeptide/tripeptide:H(+) symporter DtpC
RA	4,438,124	T→C	W140R (TGG→CGG)	ytfI →	protein YtfI
RA	4,485,906	C→A	A16S (GCC→TCC)	pepA ←	aminopeptidase A/I
MC JC	4,496,676	Δ53,036 bp		intB–fimH	54 genes intB, insC‑6, insD‑6, yjgX, yjgZ, insG, yjhB, yjhC, ythA, yjhD, yjhE, insO, insI‑3, insO, insO, yjhV, fecE, fecD, fecC, fecB, fecA, fecR, fecI, insA‑7, yjhU, yjhF, yjhG, yjhH, yjhI, sgcR, sgcE, sgcA, ryjB, sgcQ, sgcC, sgcB, sgcX, yjhP, yjhQ, topAI, yjhZ, yjhR, nanS, nanM, nanC, fimB, fimE, fimA, fimI, fimC, fimD, fimF, fimG, fimH
MC JC	4,555,491	Δ41,523 bp		[yjiC]–lgoD	37 genes [yjiC], ytiC, ytiD, idlP, iraD, hypT, iadA, yjiG, yjiH, kptA, yjiJ, yjiK, ytiA, yjiL, yjiM, yjiN, mdtM, rpnD, yjiR, yjiS, yjiT, yjiV, mcrC, mcrB, symE, symR, hsdS, hsdM, hsdR, mrr, yjiA, yjiX, btsT, tsr, lgoT, lgoR, lgoD
MC JC	4,626,183	(GCG)_3→2	coding (272‑274/1383 nt)	radA →	DNA recombination protein

Predicted mutations

evidence

position

mutation

annotation

gene

description

12,086

C→T

intergenic (‑300/‑77)

yaaI ← / → dnaK

DUF2541 domain‑containing protein YaaI/chaperone protein DnaK

MC JC

15,389

Δ5,175 bp

insL‑1–insA‑1

insL‑1, hokC, mokC, sokC, nhaA, nhaR, insB‑1, insA‑1

MC JC

92,854

(GCG)_4→3

coding (1442‑1444/1767 nt)

ftsI →

peptidoglycan DD‑transpeptidase FtsI

119,028

T→C

V99A (GTC→GCC)

ampD →

1,6‑anhydro‑N‑acetylmuramoyl‑L‑alanine amidase

MC JC

167,484

Δ5,964 bp

[fhuA]–fhuB

[fhuA], fhuC, fhuD, fhuB

214,885

C→T

T18I (ACC→ATC)

arfB →

peptidyl‑tRNA hydrolase, ribosome rescue factor

257,794

T→C

intergenic (+23/‑35)

frsA → / → crl

fermentation‑respiration switch protein/RNA polymerase holoenzyme assembly factor Crl

MC JC

257,908

Δ776 bp

insB9–[crl]

insB9, insA9, [crl]

MC JC

263,514

Δ61,897 bp

[ykfI]–ykgH

71 genes

[ykfI]yafWykfHykfGyafXykfFykfByafYyafZykfAperRinsNinsI‑1insNeyeAykfCinsH‑1mmuPmmuMafuCafuBinsB‑2insA‑2yagByagAyagEyagFyagGyagHxynRargFykgSinsB‑3insA‑3yagJyagKyagLyagMykgVyagNintFyagPpaoDpaoCpaoBpaoAyagUykgJecpEecpDecpCecpBecpAecpRykgLykgOykgMykgRykgPeaeHinsE‑1insF‑1ykgArclCrclBrclArclRykgEykgFykgGykgH

MC JC

332,366

Δ44,951 bp

pdeL–yaiL

39 genes

pdeLyahByahCyahDyahEyahFyahGyahHyahIyahJyahKyahLyahMyahNyahOprpRprpBprpCprpDprpEcodBcodAcynRcynTcynScynXlacAlacYlacZlacImhpRmhpAmhpBmhpCmhpDmhpFmhpEmhpTyaiL

380,022

(G)_10→9

intergenic (‑141/+47)

frmR ← / ← yaiO

DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO

MC JC

389,898

Δ9,908 bp

yaiT–[yaiZ]

yaiT, insF‑2, insE‑2, yaiT, iprA, ampH, sbmA, yaiW, yaiY, [yaiZ]

MC JC

508,873

Δ40,744 bp

copA–[ylbE]

37 genes

copAcopAcopAglsAybaTcueRybbJqmcAfetAfetBcnoXybbOtesAybbAybbPrhsDybbCylbHybbDylbIylbGselUallSallAallRgclhyiglxRybbWallBybbYglxKallEallCallDfdrA[ylbE]

MC JC

565,055

Δ21,054 bp

[intD]–ompT

37 genes

[intD]xisDexoDrenDinsE‑3insF‑3renDemrEylcJybcKybcLybcMylcHybcNninEybcOrusAylcGybcQnmpCinsH‑2nmpCessDrrrDrzpDrzoDborDybcVybcWylcInohDaaaDtfaDybcYtfaXappYompT

MC JC

603,467

Δ5,885 bp

[ybdG]–insL‑2

[ybdG], nfsB, ybdF, ybdJ, ybdK, sokE, hokE, insL‑2

MC JC

675,552

Δ7,819 bp

ybeQ–[hscC]

ybeQ, ybeR, djlB, ybeT, ybeU, djlC, [hscC]

MC JC

687,860

Δ1,185 bp

IS5‑mediated

insH‑3

insH‑3

MC JC

729,365

Δ9,598 bp

rhsC–ybfD

rhsC, ybfB, ybfO, ybfC, ybfQ, ybfL, ybfD

765,191

Δ1 bp

coding (685/723 nt)

mngR ←

DNA‑binding transcriptional repressor MngR

MC JC

765,208

Δ5,405 bp

[mngR]–mngB

[mngR], mngA, mngB

MC JC

819,776

Δ62,977 bp

ybhL–deoR

57 genes

ybhLybhMybhNclsBybhPybhQybhRybhSybhFybhGcecRrhlEybiAdinGybiBhcxBybiJybiIybiXfiumcbArlmFybiOglnQglnPglnHdpsrhtAyliMompXopgErybAmntSmntRybiRldtBybiTybiUybiVybiWybiYfsaAmoeBmoeAiaaAgsiAgsiBgsiCgsiDpdeIdgcIrimObssRyliIgstBdacCdeoR

972,866

Δ1 bp

coding (536/780 nt)

elyC ←

envelope biogenesis factor

988,499

G→A

P163S (CCA→TCA)

asnS ←

asparagine‑‑tRNA ligase

MC JC

997,868

Δ6,818 bp

[elfA]–ycbF

[elfA], elfD, elfC, elfG, ycbU, ycbV, ycbF

MC JC

1,040,502

Δ73,763 bp

[appX]–[mdtG]

75 genes

[appX]appAetketpgfcEgfcDgfcCgfcBgfcAinsA‑4insB‑4cspHcspGymcFymcEgnsAyccMtorStorTtorRtorCtorAtorDcbpMcbpAyccEagpyccJwrbAymdFrutGrutFrutErutDrutCrutBrutArutRputAymdGputPefeUefeOefeBphoHpgaDpgaCpgaBpgaAdgcTinsF‑4insE‑4ymdEycdUserXghrAycdXycdYycdZcsgGcsgFcsgEcsgDcsgBcsgAcsgCymdAymdBclsCopgCopgGopgHyceKmsyB[mdtG]

MC JC

1,129,397

Δ11,591 bp

flgN–flgL

flgN, flgM, flgA, flgB, flgC, flgD, flgE, flgF, flgG, flgH, flgI, flgJ, flgK, flgL

1,154,362

C→T

A84V (GCC→GTC)

mltG →

endolytic murein transglycosylase

MC JC

1,197,137

25956 bp→12 bp

[ymfD]–[ymgI]

42 genes

[ymfD]ymfElitintExisEymfHymfIymfJymfKymfTymfLymfMoweEymfNaaaEymfRbeeEjayEymfQycfKtfaPtfaEstfEpinEmcrAicdCiraMymgKymgLycgXbluRbluFycgZymgAariRymgCpdeGymgFycgHymgDymgG[ymgI]

1,240,439

C→T

V60V (GTC→GTT)
D545N (GAC→AAC)

ymgM →
cvrA ←

protein YmgM
putative K(+):H(+) antiporter

1,270,811

C→T

V347M (GTG→ATG)

chaA ←

Na(+)/K(+):H(+) antiporter ChaA

MC JC

1,299,499

Δ1,199 bp

insH21

insH21

1,382,555

C→T

S203S (AGC→AGT)

ompG →

outer membrane porin G

MC JC

1,388,889

Δ9,734 bp

ycjG–[uspE]

ycjG, mpaA, ymjC, ymjD, ycjY, pgrR, mppA, ynaI, insH‑4, ynaJ, [uspE]

1,400,309

Δ1 bp

coding (1465/1527 nt)

abgT ←

p‑aminobenzoyl glutamate:H(+) symporter

1,400,314

Δ1 bp

coding (1460/1527 nt)

abgT ←

p‑aminobenzoyl glutamate:H(+) symporter

MC JC

1,400,325

Δ81,931 bp

[abgT]–[azoR]

87 genes

[abgT]abgBabgAabgRmcaSsmrAdgcMzntBfnrSynaLdbpAttcAintRxisRrcbAralAralRrecTrecEracCydaEkilRsieBydaFydaGracRydaSydaTydaUydaVydaWrzpRrzoRtrkGynaKydaYynaAlomRinsH‑5lomRstfRtfaRpinRynaEynaMttcCuspFompNmicCydbKydbJhslJldhAydbHynbEydbLfeaRfeaBtynApaaZpaaApaaBpaaCpaaDpaaEpaaFpaaGpaaHpaaIpaaJpaaKpaaXpaaYynbGydbAinsD‑2insC‑2ydbAinsI‑2ydbApdxIydbDynbAynbBynbCynbD[azoR]

MC JC

1,509,562

Δ46,201 bp

[hicB]–maeA

43 genes

[hicB]ydcRydcSydcTydcUydcVpatDyncLortTydcYydcZmnaTcurAmcbRyncDyncEansPyncGyncHrhsEydcDyncOyncIydcCpptAyddHnhoAyddEnarVnarWnarYnarZnarUyddJyddKyddLyddGfdnGfdnHfdnIyddMadhPmaeA

1,562,085

C→T

A133T (GCA→ACA)

ddpA ←

putative D,D‑dipeptide ABC transporter periplasmic binding protein

1,626,996

C→T

D129N (GAT→AAT)

dcp ←

peptidyl‑dipeptidase Dcp

MC JC

1,627,518

Δ25,244 bp

[ydfG]–[ynfP]

48 genes

[ydfG]ydfHydfZydfIydfJynfTydfKpinQtfaQydfNnohAynfOydfOgnsBynfNynfRynfQcspIrzpQrzoQrrrQydfRessQcspBcspFynfSydfTydfUremhokDrelErelBydfVflxAydfWydfXdicCdicAydfAydfBydfCdicFdicBydfDydfEinsD‑7intQ[ynfP]

1,662,872

C→T

R773W (CGG→TGG)

ynfF →

putative selenate reductase YnfF

1,697,216

T→C

intergenic (‑164/+57)

uidR ← / ← hdhA

DNA‑binding transcriptional repressor UidR/7‑alpha‑hydroxysteroid dehydrogenase

1,741,062

T→C

C384C (TGT→TGC)

ydhC →

putative transporter YdhC

1,742,755

G→C

P163R (CCG→CGG)

ribC ←

riboflavin synthase

1,776,533

G→A

G316D (GGC→GAC)

ydiF →

putative acetate‑CoA transferase

1,811,208

T→C

V92A (GTT→GCT)

tcyP →

cystine/sulfocysteine:cation symporter

1,847,724

(C)_6→7

coding (285/1044 nt)

selD ←

selenide, water dikinase

MC JC

1,872,030

Δ1,437 bp

[dgcJ]

1,898,152

G→A

A407A (GCG→GCA)

sdaA →

L‑serine deaminase I

1,907,399

C→T

E13K (GAG→AAG)

cspC ←

stress protein, member of the CspA family

1,941,784

A→G

V267A (GTC→GCC)

znuA ←

Zn(2(+)) ABC transporter periplasmic binding protein

MC JC

1,962,566

Δ16,764 bp

flhE–insA‑5

17 genes

flhEflhAflhBcheZcheYcheBcheRtaptarcheWcheAmotBmotAflhCflhDinsB‑5insA‑5

MC JC

1,997,112

Δ26,567 bp

[tcyN]–[fliR]

32 genes

[tcyN]tcyLdcyDtcyJfliZfliAfliCfliDfliSfliTamyAyedDyedEyedFyedKyedLyedNintGfliEfliFfliGfliHfliIfliJfliKfliLfliMfliNfliOfliPfliQ[fliR]

2,040,801

T→C

L107L (TTA→CTA)

msrQ →

periplasmic protein‑L‑methionine sulfoxide reductase heme binding subunit

MC JC

2,101,397

Δ36,321 bp

[wbbL]–wza

34 genes

[wbbL]insH‑7wbbLwbbKwbbJwbbIwbbHglfrfbXrfbCrfbArfbDrfbBgalFwcaMwcaLwcaKwzxCwcaJcpsGcpsBwcaIgmmfclgmdwcaFwcaEwcaDwcaCwcaBwcaAwzcwzbwza

MC JC

2,165,151

Δ12,060 bp

yegP–gatY

17 genes

yegPyegQcyaRogrKyegZyegRyegSgatRinsE‑5insF‑5gatRgatDgatCgatBgatAgatZgatY

MC JC

2,204,350

Δ32,368 bp

yehL–preA

30 genes

yehLyehMyehPyehQyehRyehSbtsRbtsSmlrAyohOyehWyehXyehYosmFbglXdldpbpGyohCyohDyohFmdtQyohPdusCyohJyohKcddsanAyeiSpreTpreA

MC JC

2,286,401

Δ3,780 bp

[yejO]–[yejO]

[yejO], insH‑8, [yejO]

MC JC

2,320,144

Δ16,489 bp

[atoS]–[yfaA]

[atoS], atoC, atoD, atoA, atoE, atoB, yfaP, yfaQ, yfaS, yfaT, [yfaA]

2,406,141

A→G

R167R (CGT→CGC)

lrhA ←

DNA‑binding transcriptional dual regulator LrhA

MC JC

2,416,380

(TGC)_3→2

coding (1634‑1636/2145 nt)

pta →

phosphate acetyltransferase

MC JC

2,466,545

Δ9,634 bp

[intS]–[ypdJ]

15 genes

MC JC

2,509,631

Δ8,319 bp

[yfeO]–pdeA

[yfeO], ypeC, mntH, nupC, insL‑3, pdeA

MC JC

2,558,699

Δ6,790 bp

intZ–[eutA]

intZ, yffL, yffM, yffN, yffO, yffP, yffQ, yffR, yffS, [eutA]

MC JC

2,601,201

Δ13,595 bp

[hyfA]–focB

[hyfA], hyfB, hyfC, hyfD, hyfE, hyfF, hyfG, hyfH, hyfI, hyfJ, hyfR, focB

2,662,004

T→C

E43G (GAA→GGA)

iscR ←

DNA‑binding transcriptional dual regulator IscR

2,756,138

Δ1 bp

intergenic (+183/‑21)

ssrA → / → intA

tmRNA/CP4‑57 prophage; integrase

MC JC

2,756,160

Δ35,091 bp

[intA]–[lhgO]

33 genes

[intA]yfjHalpAyfjIyfjJabpBabpAyfjMrnlArnlByfjPyfjQyfjRypjKyfjSyfjTyfjUyfjVyfjWypjIyfjXyfjYypjJyfjZypjFypjApinHypjBypjCileYygaQcsiD[lhgO]

2,793,867

C→A

A378D (GCT→GAT)

gabT →

4‑aminobutyrate aminotransferase GabT

MC JC

2,798,370

(TTC)_4→3

coding (124‑126/405 nt)

stpA ←

DNA‑binding transcriptional repressor StpA with RNA chaperone activity

2,813,364

T→C

V250A (GTC→GCC)

emrB →

multidrug efflux pump membrane subunit EmrB

2,843,412

C→T

R12H (CGT→CAT)

hycH ←

formate hydrogenlyase assembly protein

MC JC

2,994,992

Δ3,877 bp

[ygeL]–ygeQ

[ygeL], ygeN, ygeO, insD‑4, insC‑4, ygeP, ygeQ

3,052,352

C→A

W389C (TGG→TGT)

ubiH ←

2‑octaprenyl‑6‑methoxyphenol hydroxylase

3,052,705

G→A

H272Y (CAC→TAC)

ubiH ←

2‑octaprenyl‑6‑methoxyphenol hydroxylase

3,090,282

C→T

intergenic (+30/‑65)

yggI → / → endA

conserved protein YggI/DNA‑specific endonuclease I

3,090,341

Δ1 bp

intergenic (+89/‑6)

yggI → / → endA

conserved protein YggI/DNA‑specific endonuclease I

MC JC

3,090,347

Δ708 bp

coding (1‑708/708 nt)

endA →

DNA‑specific endonuclease I

3,091,305

A→G

S58G (AGC→GGC)

rsmE →

16S rRNA m(3)U1498 methyltransferase

MC JC

3,110,680

25702 bp→GA

[yghD]–pitB

20 genes

[yghD]yghEyghFyghGpppAyghJglcAglcBglcGglcFglcEglcDglcCyghOinsH‑9yghQyghRyghSyghTpitB

MC JC

3,184,782

Δ6,916 bp

ubiK–yqiI

ubiK, ygiL, yqiG, insC‑5, insD‑5, yqiG, yqiH, yqiI

3,213,803

T→C

S253P (TCT→CCT)

rpoD →

RNA polymerase, sigma 70 (sigma D) factor

MC JC

3,362,162

Δ5,481 bp

[yhcA]–[yhcF]

[yhcA], yhcD, yhcE, insH‑10, yhcE, [yhcF]

MC JC

3,453,928

Δ15,926 bp

gspA–[chiA]

16 genes

gspAgspCgspDgspEgspFgspGgspHgspIgspJgspKgspLgspMgspObfrbfd[chiA]

3,477,150

C→T

K90K (AAG→AAA)

fkpA ←

peptidyl‑prolyl cis‑trans isomerase FkpA

3,495,261

A→G

K417K (AAA→AAG)

nirB →

nitrite reductase catalytic subunit NirB

3,513,003

A→G

D212D (GAT→GAC)

trpS ←

tryptophan‑‑tRNA ligase

3,527,760

A→G

N431S (AAC→AGC)

igaA →

inner membrane protein ‑ inhibits the Rcs signaling pathway

MC JC

3,581,139

3915 bp→6 bp

[yhhY]–yrhB

[yhhY], yhhZ, yrhA, insA‑6, insB‑6, yrhA, yrhD, yrhB

MC JC

3,618,992

Δ6,688 bp

rhsB–[yhhJ]

rhsB, yhhH, yhhI, [yhhJ]

MC JC

3,651,293

Δ2,422 bp

[yhiS]–yhiS

[yhiS], insH‑11, yhiS

3,720,597

Δ1 bp

coding (4/153 nt)

hokA ←

small toxic polypeptide

MC JC

3,720,634

Δ1,442 bp

IS150‑mediated

insJ–insK

insJ, insK

MC JC

3,761,993

Δ8,250 bp

rhsA–yibV

rhsA, yibA, yibJ, yibG, yibS, yibV

3,801,078

(T)_7→6

coding (922/1017 nt)

waaJ ←

UDP‑glucose:(glucosyl)LPS alpha‑1,2‑glucosyltransferase

3,816,579

G→A

intergenic (‑30/‑97)

rph ← / → yicC

truncated RNase PH/UPF0701 family protein YicC

3,829,233

C→A

L97M (CTG→ATG)

xanP →

xanthine:H(+) symporter XanP

3,850,891

G→A

Q68* (CAA→TAA)

ilvN ←

acetohydroxy acid synthase I subunit IlvN

3,871,692

C→T

R13R (CGG→CGA)

dgoT ←

putative D‑galactonate transporter

MC JC

3,888,432

Δ18,167 bp

tnaC–bglG

17 genes

tnaCtnaAtnaBmdtLyidZyieEyieFadePyieHcbrBcbrCyieKyieLbglHbglBbglFbglG

3,926,696

C→T

G103D (GGC→GAC)

asnC ←

DNA‑binding transcriptional dual regulator AsnC

3,948,805

(G)_6→7

coding (1165/1521 nt)

yifB ←

putative magnesium chelatase YifB

3,979,769

C→T

A390V (GCG→GTG)

wzyE →

enterobacterial common antigen polymerase

3,980,957

(G)_6→7

coding (71/1386 nt)

yifK →

putative transporter YifK

3,983,666

T→C

F237L (TTC→CTC)

aslB →

putative anaerobic sulfatase maturation enzyme AslB

4,093,223

A→G

V72V (GTT→GTC)

rhaM ←

L‑rhamnose mutarotase

MC JC

4,299,628

Δ25,538 bp

[mdtP]–[phnC]

27 genes

[mdtP]mdtOmdtNytcAyjcSalsKalsEalsCalsAalsBalsRrpiByjdPphnPphnOphnNphnMphnLphnKphnJphnIphnHphnGphnFphnEphnD[phnC]

4,354,915

G→A

intergenic (‑198/+39)

lysU ← / ← dtpC

lysine‑‑tRNA ligase/Ap4A synthetase/Ap3A synthetase/dipeptide/tripeptide:H(+) symporter DtpC

4,438,124

T→C

W140R (TGG→CGG)

ytfI →

protein YtfI

4,485,906

C→A

A16S (GCC→TCC)

pepA ←

aminopeptidase A/I

MC JC

4,496,676

Δ53,036 bp

intB–fimH

54 genes

intBinsC‑6insD‑6yjgXyjgZinsGyjhByjhCythAyjhDyjhEinsOinsI‑3insOinsOyjhVfecEfecDfecCfecBfecAfecRfecIinsA‑7yjhUyjhFyjhGyjhHyjhIsgcRsgcEsgcAryjBsgcQsgcCsgcBsgcXyjhPyjhQtopAIyjhZyjhRnanSnanMnanCfimBfimEfimAfimIfimCfimDfimFfimGfimH

MC JC

4,555,491

Δ41,523 bp

[yjiC]–lgoD

37 genes

[yjiC]ytiCytiDidlPiraDhypTiadAyjiGyjiHkptAyjiJyjiKytiAyjiLyjiMyjiNmdtMrpnDyjiRyjiSyjiTyjiVmcrCmcrBsymEsymRhsdShsdMhsdRmrryjiAyjiXbtsTtsrlgoTlgoRlgoD

MC JC

4,626,183

(GCG)_3→2

coding (272‑274/1383 nt)

radA →

DNA recombination protein

Unassigned missing coverage evidence
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913	167390	167398	9	6 [5]	[5] 8	mrcB/fhuA	peptidoglycan glycosyltransferase/peptidoglycan DD‑transpeptidase MrcB/ferrichrome outer membrane transporter/phage receptor
*	*	÷	NC_000913	380112	388682	8571	21 [0]	[5] 7	[yaiO]–tauD	[yaiO],yaiX,insC‑1,insD‑1,yaiX,yaiP,ykiC,yaiS,tauA,tauB,tauC,tauD
*	*	÷	NC_000913	696467–696506	696578–696542	37–112	6 [5]	[4] 6	[glnX]–[glnV]	[glnX],[glnV]
*	*	÷	NC_000913	2066220–2066302	2080591	14290–14372	6 [5]	[0] 30	insH‑6–[yeeA]	insH‑6,yoeA,insD‑3,insC‑3,yoeA,yeeP,isrC,flu,yeeR,yeeS,yeeT,cbeA,cbtA,yeeW,yoeF,yeeX,[yeeA]
*	*	÷	NC_000913	2846301	2856889	10589	25 [0]	[5] 6	[hycE]–ygbA	[hycE],hycD,hycC,hycB,hycA,hypA,hypB,hypC,hypD,hypE,fhlA,ygbA
*	*	÷	NC_000913	2859655	2867268	7614	12 [0]	[0] 26	pphB–[rpoS]	pphB,ygbI,ygbJ,ygbK,ygbL,ygbM,ygbN,[rpoS]
*	*	÷	NC_000913	3423694–3424234	3428521–3424653	420–4828	7 [5]	[5] 7	[rrfD]–[rrsD]	[rrfD],rrlD,alaU,ileU,[rrsD]
*	*	÷	NC_000913	4296100–4296380	4296387	8–288	6 [3]	[5] 6	gltP/yjcO	glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO

Unassigned missing coverage evidence

seq id

start

end

size

←reads

reads→

gene

description

NC_000913

167390

167398

6 [5]

[5] 8

mrcB/fhuA

peptidoglycan glycosyltransferase/peptidoglycan DD‑transpeptidase MrcB/ferrichrome outer membrane transporter/phage receptor

NC_000913

380112

388682

8571

21 [0]

[5] 7

[yaiO]–tauD

[yaiO],yaiX,insC‑1,insD‑1,yaiX,yaiP,ykiC,yaiS,tauA,tauB,tauC,tauD

NC_000913

696467–696506

696578–696542

37–112

6 [5]

[4] 6

[glnX]–[glnV]

[glnX],[glnV]

NC_000913

2066220–2066302

2080591

14290–14372

6 [5]

[0] 30

insH‑6–[yeeA]

insH‑6,yoeA,insD‑3,insC‑3,yoeA,yeeP,isrC,flu,yeeR,yeeS,yeeT,cbeA,cbtA,yeeW,yoeF,yeeX,[yeeA]

NC_000913

2846301

2856889

10589

25 [0]

[5] 6

[hycE]–ygbA

[hycE],hycD,hycC,hycB,hycA,hypA,hypB,hypC,hypD,hypE,fhlA,ygbA

NC_000913

2859655

2867268

7614

12 [0]

[0] 26

pphB–[rpoS]

pphB,ygbI,ygbJ,ygbK,ygbL,ygbM,ygbN,[rpoS]

NC_000913

3423694–3424234

3428521–3424653

420–4828

7 [5]

[5] 7

[rrfD]–[rrsD]

[rrfD],rrlD,alaU,ileU,[rrsD]

NC_000913

4296100–4296380

4296387

8–288

6 [3]

[5] 6

gltP/yjcO

glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO

Unassigned new junction evidence
	seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 213730	17 (0.620)	43 (2.170) +AGGACTTCTTGAA	4/70	1.7	75.3%	coding (203/255 nt)	rof	modulator of Rho‑dependent transcription termination
?	NC_000913	3958648 =	22 (0.800)	coding (679/1476 nt)	ilvC	ketol‑acid reductoisomerase (NADP(+))
*	?	NC_000913	= 380111	0 (0.000)	15 (0.710) +CGAGATGGACG	14/74	0.2	59.2%	coding (732/774 nt)	yaiO	outer membrane protein YaiO
?	NC_000913	624576 =	27 (0.990)	intergenic (‑66/‑309)	fepB/entC	ferric enterobactin ABC transporter periplasmic binding protein/isochorismate synthase EntC
*	?	NC_000913	1994264 =	30 (1.090)	41 (2.130) +ATTTCTAATGTCGT	4/68	1.7	73.1%	coding (443/1833 nt)	uvrC	excision nuclease subunit C
?	NC_000913	3208976 =	13 (0.470)	coding (953/1464 nt)	ttdT	L‑tartrate:succinate antiporter
*	?	NC_000913	= 2066304	NA (NA)	30 (1.090)	24/96	0.0	100%	noncoding (1050/1195 nt)	IS5	repeat region
?	NC_000913	2080592 =	0 (0.000)	intergenic (‑1/+197)	yeeA/sbmC	putative transporter YeeA/DNA gyrase inhibitor
*	?	NC_000913	= 2088716	32 (1.170)	9 (0.420) +AGGGGATCTT	7/76	1.1	41.7%	coding (413/825 nt)	yeeZ	putative epimerase YeeZ
?	NC_000913	= 2859654	0 (0.000)	coding (2562/2562 nt)	mutS	DNA mismatch repair protein MutS
*	?	NC_000913	= 2846300	0 (0.000)	23 (0.900)	18/90	0.2	100%	coding (172/1710 nt)	hycE	formate hydrogenlyase subunit HycE
?	NC_000913	2867269 =	0 (0.000)	coding (283/993 nt)	rpoS	RNA polymerase, sigma S (sigma 38) factor

Unassigned new junction evidence

seq id

position

reads (cov)

score

skew

freq

annotation

gene

product

NC_000913

= 213730

17 (0.620)

43 (2.170)
+AGGACTTCTTGAA

4/70

1.7

75.3%

coding (203/255 nt)

rof

modulator of Rho‑dependent transcription termination

NC_000913

3958648 =

22 (0.800)

coding (679/1476 nt)

ilvC

ketol‑acid reductoisomerase (NADP(+))

NC_000913

= 380111

0 (0.000)

15 (0.710)
+CGAGATGGACG

14/74

0.2

59.2%

coding (732/774 nt)

yaiO

outer membrane protein YaiO

NC_000913

624576 =

27 (0.990)

intergenic (‑66/‑309)

fepB/entC

ferric enterobactin ABC transporter periplasmic binding protein/isochorismate synthase EntC

NC_000913

1994264 =

30 (1.090)

41 (2.130)
+ATTTCTAATGTCGT

4/68

1.7

73.1%

coding (443/1833 nt)

uvrC

excision nuclease subunit C

NC_000913

3208976 =

13 (0.470)

coding (953/1464 nt)

ttdT

L‑tartrate:succinate antiporter

NC_000913

= 2066304

NA (NA)

30 (1.090)

24/96

0.0

100%

noncoding (1050/1195 nt)

IS5

repeat region

NC_000913

2080592 =

0 (0.000)

intergenic (‑1/+197)

yeeA/sbmC

putative transporter YeeA/DNA gyrase inhibitor

NC_000913

= 2088716

32 (1.170)

9 (0.420)
+AGGGGATCTT

7/76

1.1

41.7%

coding (413/825 nt)

yeeZ

putative epimerase YeeZ

NC_000913

= 2859654

0 (0.000)

coding (2562/2562 nt)

mutS

DNA mismatch repair protein MutS

NC_000913

= 2846300

0 (0.000)

23 (0.900)

18/90

0.2

100%

coding (172/1710 nt)

hycE

formate hydrogenlyase subunit HycE

NC_000913

2867269 =

0 (0.000)

coding (283/993 nt)

rpoS

RNA polymerase, sigma S (sigma 38) factor