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
MC JC	257,908	Δ776 bp		[crl]	[crl]
RA	1,261,474	C→A	Q134H (CAG→CAT)	prs ←	phosphoribosylpyrophosphate synthase
JC JC	1,293,015	IS1 (+) +8 bp	intergenic (‑93/‑505)	hns ← / → tdk	global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
MC JC	1,978,503	Δ776 bp		insB1–insA	insB1, insA
RA	2,019,460	G→A	V359I (GTC→ATC)	fliK →	flagellar hook‑length control protein
RA	2,173,363	Δ2 bp	intergenic (‑1/+1)	gatC ← / ← gatC	pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC
RA	2,317,667	T→G	E737A (GAA→GCA)	rcsC ←	hybrid sensory kinase in two‑component regulatory system with RcsB and YojN
RA	2,632,046	G→T	P164T (CCG→ACG)	guaA ←	GMP synthetase (glutamine aminotransferase)
RA	3,002,530	G→A	G729D (GGT→GAT)	xdhA →	xanthine dehydrogenase, molybdenum binding subunit
MC JC	3,366,751	Δ1,271 bp	IS5‑mediated	[yhcE]–[yhcG]	[yhcE], yhcF, [yhcG]
RA	3,560,455	+G	intergenic (‑2/+1)	glpR ← / ← glpR	pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon
JC JC	3,890,075	IS5 (–) +4 bp	coding (1346‑1349/1416 nt)	tnaA →	tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent
JC JC	3,922,629	IS5 (–) +4 bp	intergenic (‑189/+425)	atpI ← / ← rsmG	ATP synthase, membrane‑bound accessory factor/16S rRNA m(7)G527 methyltransferase, SAM‑dependent; glucose‑inhibited cell‑division protein
RA	3,991,579	T→A	W143R (TGG→AGG)	cyaA →	adenylate cyclase
RA	4,044,390	(T)6→5	coding (192/1431 nt)	yihF →	DUF945 family protein
RA	4,296,381	+GC	intergenic (+587/+55)	gltP → / ← yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein

Unassigned missing coverage evidence
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913	3423743–3424234	3424561–3424238	5–819	51 [50]	[50] 52	[rrfD]–[rrlD]	[rrfD],[rrlD]
*	*	÷	NC_000913	3514354	3515102	749	53 [50]	[50] 53	[gph]–[dam]	[gph],rpe,[dam]

Unassigned new junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	1207790 =	32 (0.240)	91 (0.790)	69/228	0.6	75.5%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	31 (0.270)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1207805	32 (0.240)	74 (0.640)	57/228	1.3	71.5%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	31 (0.270)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1299498	0 (0.000)	163 (1.270)	108/252	0.0	100%	intergenic (+253/‑1684)	ychE/oppA	UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
	?	NC_000913	1300698 =	0 (0.000)					intergenic (+1453/‑484)	ychE/oppA	UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein