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

Predicted mutations
evidence	position	mutation	annotation	gene	description
RA	1,124,062	Δ1 bp	coding (159/1536 nt)	mdoG →	glucan biosynthesis protein, periplasmic
RA	1,329,516	C→T	H33Y (CAC→TAC)	topA →	DNA topoisomerase I
RA	1,332,132	T→C	intergenic (+115/‑95)	topA → / → cysB	DNA topoisomerase I/DNA‑binding transcriptional dual regulator, O‑acetyl‑L‑serine‑binding
JC	1,733,297	(CGTATGAA)1→2	coding (333/1413 nt)	pykF →	pyruvate kinase
RA	2,193,779	G→T	L143I (CTT→ATT)	yeiB ←	conserved inner membrane protein
RA	3,388,714	G→T	M331I (ATG→ATT)	gspF →	general secretory pathway component, cryptic
RA	3,462,730	G→A	G410D (GGC→GAC)	pckA →	phosphoenolpyruvate carboxykinase
RA	3,465,186	C→T	G28D (GGC→GAC)	ompR ←	osmolarity response regulator
RA	3,762,741	A→T	K662I (AAA→ATA)	spoT →	bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase
RA	3,875,632	(T)7→8	intergenic (‑66/+287)	glmU ← / ← atpC	bifunctional N‑acetylglucosamine‑1‑phosphate uridyltransferase/glucosamine‑1‑phosphate acetyltransferase/F0F1 ATP synthase subunit epsilon
MC JC	3,894,997	Δ6,934 bp	IS150‑mediated	rbsD–[yieO]	rbsD, rbsA, rbsC, rbsB, rbsK, rbsR, [yieO]
MC JC	4,097,266	Δ13 bp	coding (295‑307/846 nt)	glpF ←	glycerol facilitator
RA	4,162,470	A→C	T539P (ACC→CCC)	rpoB →	DNA‑directed RNA polymerase subunit beta
RA	4,163,752	T→G	I966S (ATC→AGC)	rpoB →	DNA‑directed RNA polymerase subunit beta
JC JC	4,524,522	IS186 (+) +6 bp	coding (494‑499/549 nt)	fimA →	major type 1 subunit fimbrin (pilin)

Unassigned missing coverage evidence
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	REL606	546986–547700	593499	45800–46514	21 [19]	[19] 21	[insB‑6]–[fepA]	[insB‑6],insA‑6,nmpC,ybcR,ybcS,ybcT,ybcU,ECB_00510,nohB,ECB_00512,ECB_00513,ECB_00514,ECB_00515,ECB_00516,ECB_00517,appY,ompT,envY,ybcH,nfrA,nfrB,nfrB,ECB_00524,yhhI,ECB_00526,ECB_00527,ECB_00528,ECB_00529,ECB_00530,cusS,cusR,cusC,ylcC,cusB,cusA,pheP,ybdG,nfnB,ybdF,ybdJ,ybdK,insJ‑1,insK‑1,insB‑7,insA‑7,insK‑1,hokE,insL‑3,entD,[fepA]
*	*	÷	REL606	593519	619828–619116	25598–26310	21 [20]	[20] 21	[fepA]–[insA‑8]	[fepA],fes,ybdZ,entF,fepE,fepC,fepG,fepD,ybdA,fepB,entC,entE,entB,entA,ybdB,cstA,cstA,ybdD,ybdH,ybdL,ybdM,ybdN,insB‑8,[insA‑8]
*	*	÷	REL606	2031956–2032015	2055269–2055216	23202–23314	21 [20]	[18] 21	[manB]–[cpsG]	[manB],manC,insB‑14,insA‑14,wbbD,wbbC,wzy,wbbB,wbbA,vioB,vioA,wzx,rmlC,rfbA,rfbD,rfbB,galF,wcaM,wcaL,wcaK,wzxC,wcaJ,[cpsG]
*	*	÷	REL606	4146303–4148246	4151519–4150141	1896–5217	21 [20]	[20] 23	rrsB–[rrfB]	rrsB,gltT,rrlB,[rrfB]