breseq  version 0.35.4  revision f352f80f4bc9 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence	position	mutation	freq	annotation	gene	description
RA	125,085	Δ1 bp	100%	coding (2069/2664 nt)	aceE →	pyruvate dehydrogenase E1 component
MC JC	257,908	Δ776 bp	100%		insB9–[crl]	insB9, insA9, [crl]
JC JC	568,268	IS1 (–) +9 bp	100%	intergenic (+21/‑39)	renD → / → emrE	DLP12 prophage; protein RenD/multidrug/betaine/choline efflux transporter EmrE
RA	710,489	G→C	100%	A53G (GCT→GGT)	fur ←	DNA‑binding transcriptional dual regulator Fur
RA	1,026,927	A→T	100%	V30E (GTG→GAG)	mgsA ←	methylglyoxal synthase
RA	1,196,220	C→T	100%	H366H (CAC→CAT)	icd →	isocitrate dehydrogenase
RA	1,196,232	C→T	100%	T370T (ACC→ACT)	icd →	isocitrate dehydrogenase
RA	1,196,245	T→C	100%	L375M (TTA→CTG)	icd →	isocitrate dehydrogenase
RA	1,196,247	A→G	100%	L375M (TTA→CTG)	icd →	isocitrate dehydrogenase
JC JC	1,293,032	IS1 (–) +8 bp	100%	intergenic (‑110/‑488)	hns ← / → tdk	DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase
MC JC	1,299,499	Δ1,199 bp	100%		insH21	insH21
RA	1,785,179	A→T	100%	I645N (ATC→AAC)	ppsA ←	phosphoenolpyruvate synthetase
RA	1,789,616	C→A	75.4%	R2S (CGT→AGT)	ydiE →	PF10636 family protein YdiE
RA	1,940,584	C→A	100%	R351L (CGT→CTT)	mepM ←	peptidoglycan DD‑endopeptidase MepM
RA	1,941,326	C→T	100%	D104N (GAT→AAT)	mepM ←	peptidoglycan DD‑endopeptidase MepM
RA	1,956,975	G→T	100%	H11Q (CAC→CAA)	torZ ←	trimethylamine N‑oxide reductase 2
MC JC	1,978,503	Δ776 bp	100%		insB‑5–insA‑5	insB‑5, insA‑5
JC JC	1,979,486	IS5 (+) +4 bp	100%	intergenic (‑271/‑264)	insA‑5 ← / → uspC	IS1 protein InsA/universal stress protein C
RA	2,132,787	A→C	100%	I204S (ATC→AGC)	wcaA ←	putative colanic acid biosynthesis glycosyl transferase
RA	2,173,361	Δ2 bp	100%	pseudogene (917‑918/1358 nt)	gatC ←	galactitol‑specific PTS enzyme IIC component
RA	2,416,239	C→T	100%	T498M (ACG→ATG)	pta →	phosphate acetyltransferase
RA	2,661,872	A→G	82.8%	V87A (GTA→GCA)	iscR ←	DNA‑binding transcriptional dual regulator IscR
RA	3,041,398	T→G	100%	L29R (CTT→CGT)	ygfZ →	folate‑binding protein
RA	3,486,157	A→C	100%	E13A (GAA→GCA)	crp →	DNA‑binding transcriptional dual regulator CRP
RA	3,560,455:1	+G	100%	pseudogene (151/758 nt)	glpR ←	DNA‑binding transcriptional repressor GlpR
MC JC	3,815,859	Δ82 bp	100%		[rph]	[rph]
JC	4,001,645	Δ5 bp	100%	coding (220‑224/951 nt)	corA →	Ni(2(+))/Co(2(+))/Mg(2(+)) transporter
RA	4,184,543	C→A	100%	P1100Q (CCG→CAG)	rpoB →	RNA polymerase subunit beta
RA	4,296,060	C→T	40.1%	intergenic (+266/+376)	gltP → / ← yjcO	glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
RA	4,296,380:1	+CG	100%	intergenic (+586/+56)	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	366078	366435	358	6 [5]	[5] 6	[lacZ]–[lacI]	[lacZ],[lacI]
*	*	÷	NC_000913	1196262	1211456	15195	6 [4]	[5] 6	[icd]–[icdC]	[icd],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]
*	*	÷	NC_000913	3423755–3424515	3424515	1–761	6 [5]	[4] 7	[rrfD]–[rrlD]	[rrfD],[rrlD]
*	*	÷	NC_000913	3621218–3622313	3653108–3652031	29719–31891	6 [4]	[3] 7	[rhsB]–[insH‑11]	[rhsB],yhhH,yhhI,yhhJ,rbbA,yhiI,yhiJ,yhiL,yhiM,yhiN,pitA,uspB,uspA,dtpB,rsmJ,prlC,rlmJ,gor,dinQ,agrA,agrB,arsR,arsB,arsC,yhiS,[insH‑11]

Unassigned new junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	1465092 =	47 (1.890)	4 (0.180)	4/242	NT	8.8%	intergenic (+31/+73)	paaY/ynbG	2‑hydroxycyclohepta‑1,4,6‑triene‑1‑carboxyl‑CoA thioesterase/uncharacterized protein YnbG
	?	NC_000913	1465125 =	40 (1.760)					intergenic (+64/+40)	paaY/ynbG	2‑hydroxycyclohepta‑1,4,6‑triene‑1‑carboxyl‑CoA thioesterase/uncharacterized protein YnbG