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

Predicted mutations
evidence	position	mutation	annotation	gene	description
RA	123,050	A→T	I12F (ATC→TTC)	aceE →	pyruvate dehydrogenase E1 component
RA	125,085	2 bp→CA	coding (2069‑2070/2664 nt)	aceE →	pyruvate dehydrogenase E1 component
MC JC	257,908	Δ776 bp		insB9–[crl]	insB9, insA9, [crl]
JC JC	568,268	IS1 (–) +9 bp	intergenic (+21/‑39)	renD → / → emrE	DLP12 prophage; protein RenD/multidrug/betaine/choline efflux transporter EmrE
RA	1,196,220	C→T	H366H (CAC→CAT)	icd →	isocitrate dehydrogenase
RA	1,196,232	C→T	T370T (ACC→ACT)	icd →	isocitrate dehydrogenase
RA	1,196,245	T→C	L375M (TTA→CTG)	icd →	isocitrate dehydrogenase
RA	1,196,247	A→G	L375M (TTA→CTG)	icd →	isocitrate dehydrogenase
JC JC	1,293,032	IS1 (–) +8 bp	intergenic (‑110/‑488)	hns ← / → tdk	DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase
MC JC	1,299,499	Δ1,199 bp		insH21	insH21
MC JC	1,978,503	Δ776 bp		insB‑5–insA‑5	insB‑5, insA‑5
JC JC	1,979,486	IS5 (+) +4 bp	intergenic (‑271/‑264)	insA‑5 ← / → uspC	IS1 protein InsA/universal stress protein C
RA	2,132,787	A→C	I204S (ATC→AGC)	wcaA ←	putative colanic acid biosynthesis glycosyl transferase
RA	2,173,363	Δ2 bp	pseudogene (915‑916/1358 nt)	gatC ←	galactitol‑specific PTS enzyme IIC component
RA	2,448,508	G→A	intergenic (‑68/‑98)	prmB ← / → smrB	50S ribosomal subunit protein L3 N(5)‑glutamine methyltransferase/putative endonuclease SmrB
JC JC	2,601,785	Δ1 bp :: IS186 (–) +5 bp	coding (585‑589/618 nt)	hyfA →	hydrogenase 4 component A
RA	2,661,840	A→C	C98G (TGC→GGC)	iscR ←	DNA‑binding transcriptional dual regulator IscR
RA	2,917,603	T→G	V849V (GTT→GTG)	barA →	sensory histidine kinase BarA
RA	3,041,398	T→G	L29R (CTT→CGT)	ygfZ →	folate‑binding protein
RA	3,560,455	+G	pseudogene (151/758 nt)	glpR ←	DNA‑binding transcriptional repressor GlpR
MC JC	3,815,859	Δ82 bp		[rph]	[rph]
MC JC	4,001,645	Δ5 bp	coding (220‑224/951 nt)	corA →	Ni(2(+))/Co(2(+))/Mg(2(+)) transporter
RA	4,184,543	C→A	P1100Q (CCG→CAG)	rpoB →	RNA polymerase subunit beta
RA	4,296,381	+GC	intergenic (+587/+55)	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	1196269	1211445	15177	11 [10]	[10] 12	[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	3423744–3424537	3424537	1–794	11 [10]	[10] 11	[rrfD]–[rrlD]	[rrfD],[rrlD]
*	*	÷	NC_000913	3621166–3622325	3653141–3652030	29706–31976	11 [10]	[10] 11	[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]