BRESEQ :: Mutation Predictions

Predicted mutations
evidence	position	mutation	annotation	gene	description
MC JC	15,389	Δ5,175 bp		insL‑1–insA‑1	insL‑1, hokC, mokC, sokC, nhaA, nhaR, insB‑1, insA‑1
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	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
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	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
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	1,270,811	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
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	1,742,755	G→C	P163R (CCG→CGG)	ribC ←	riboflavin synthase
MC JC	1,872,030	Δ1,437 bp		[dgcJ]	[dgcJ]
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]
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]
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	2,756,138	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	2,843,412	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	3,090,282	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
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	3,513,003	A→G	D212D (GAT→GAC)	trpS ←	tryptophan‑‑tRNA ligase
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
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	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

Predicted mutations

evidence

position

mutation

annotation

gene

description

MC JC

15,389

Δ5,175 bp

insL‑1–insA‑1

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

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

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

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

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

MC JC

1,197,137

25956 bp→12 bp

[ymfD]–[ymgI]

42 genes

[ymfD]ymfElitintExisEymfHymfIymfJymfKymfTymfLymfMoweEymfNaaaEymfRbeeEjayEymfQycfKtfaPtfaEstfEpinEmcrAicdCiraMymgKymgLycgXbluRbluFycgZymgAariRymgCpdeGymgFycgHymgDymgG[ymgI]

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

MC JC

1,627,518

Δ25,244 bp

[ydfG]–[ynfP]

48 genes

[ydfG]ydfHydfZydfIydfJynfTydfKpinQtfaQydfNnohAynfOydfOgnsBynfNynfRynfQcspIrzpQrzoQrrrQydfRessQcspBcspFynfSydfTydfUremhokDrelErelBydfVflxAydfWydfXdicCdicAydfAydfBydfCdicFdicBydfDydfEinsD‑7intQ[ynfP]

1,742,755

G→C

P163R (CCG→CGG)

ribC ←

riboflavin synthase

MC JC

1,872,030

Δ1,437 bp

[dgcJ]

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]

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]

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

2,756,138

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]

2,843,412

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

3,090,282

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

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

3,513,003

A→G

D212D (GAT→GAC)

trpS ←

tryptophan‑‑tRNA ligase

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

MC JC

3,888,432

Δ18,167 bp

tnaC–bglG

17 genes

tnaCtnaAtnaBmdtLyidZyieEyieFadePyieHcbrBcbrCyieKyieLbglHbglBbglFbglG

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

Unassigned missing coverage evidence
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913	380112	388668	8557	54 [0]	[18] 23	[yaiO]–tauD	[yaiO],yaiX,insC‑1,insD‑1,yaiX,yaiP,ykiC,yaiS,tauA,tauB,tauC,tauD
*	*	÷	NC_000913	2066209–2066303	2080591	14289–14383	23 [22]	[0] 66	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	3423690–3424234	3428523–3424653	420–4834	23 [21]	[22] 25	[rrfD]–[rrsD]	[rrfD],rrlD,alaU,ileU,[rrsD]

Unassigned new junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 380111	0 (0.000)	42 (0.940) +CGAGATGGACG	25/76	0.2	64.5%	coding (732/774 nt)	yaiO	outer membrane protein YaiO
*	?	NC_000913	624576 =	60 (1.040)	42 (0.940) +CGAGATGGACG	25/76	0.2	64.5%	intergenic (‑66/‑309)	fepB/entC	ferric enterobactin ABC transporter periplasmic binding protein/isochorismate synthase EntC
*	?	NC_000913	= 2066304	NA (NA)	66 (1.140)	45/98	0.0	100%	noncoding (1050/1195 nt)	IS5	repeat region
*	?	NC_000913	2080592 =	0 (0.000)	66 (1.140)	45/98	0.0	100%	intergenic (‑1/+197)	yeeA/sbmC	putative transporter YeeA/DNA gyrase inhibitor
*	?	NC_000913	2798364 =	29 (0.500)	20 (0.420)	19/80	0.8	44.7%	coding (132/405 nt)	stpA	DNA‑binding transcriptional repressor StpA with RNA chaperone activity
*	?	NC_000913	= 2798360	26 (0.550)	20 (0.420)	19/80	0.8	44.7%	coding (136/405 nt)	stpA	DNA‑binding transcriptional repressor StpA with RNA chaperone activity
*	?	NC_000913	= 2846300	33 (0.570)	28 (0.520)	24/92	0.6	48.7%	coding (172/1710 nt)	hycE	formate hydrogenlyase subunit HycE
*	?	NC_000913	2867269 =	28 (0.520)	28 (0.520)	24/92	0.6	48.7%	coding (283/993 nt)	rpoS	RNA polymerase, sigma S (sigma 38) factor
*	?	NC_000913	= 3593298	17 (0.290)	23 (0.400)	20/98	1.3	59.7%	coding (140/714 nt)	livF	branched chain amino acid/phenylalanine ABC transporter ATP binding subunit LivF
*	?	NC_000913	3593309 =	14 (0.240)	23 (0.400)	20/98	1.3	59.7%	coding (129/714 nt)	livF	branched chain amino acid/phenylalanine ABC transporter ATP binding subunit LivF
*	?	NC_000913	= 4400288	27 (0.470)	34 (0.610)	26/94	0.5	56.3%	coding (1/309 nt)	hfq	RNA‑binding protein Hfq
*	?	NC_000913	4400296 =	27 (0.490)	34 (0.610)	26/94	0.5	56.3%	coding (9/309 nt)	hfq	RNA‑binding protein Hfq