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
MC JC	257,908	Δ776 bp		[crl]	[crl]
RA	699,471	Δ1 bp	intergenic (‑294/+103)	asnB ← / ← umpH	asparagine synthetase B/UMP phosphatase
JC JC	1,293,032	IS1 (–) +8 bp	intergenic (‑110/‑488)	hns ← / → tdk	global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
RA	1,678,024	C→T	intergenic (‑121/‑403)	pntA ← / → ydgH	pyridine nucleotide transhydrogenase, alpha subunit/DUF1471 family periplasmic protein
RA	1,697,375	T→C	Q222Q (CAA→CAG)	hdhA ←	7‑alpha‑hydroxysteroid dehydrogenase, NAD‑dependent
MC JC	1,978,503	Δ776 bp		insB1–insA	insB1, insA
JC JC	1,979,486	IS5 (+) +4 bp	intergenic (‑271/‑264)	insA ← / → uspC	IS1 repressor TnpA/universal stress protein
RA	2,132,787	A→C	I204S (ATC→AGC)	wcaA ←	putative glycosyl transferase
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	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
MC JC	3,815,859	Δ82 bp		[rph]–[rph]	[rph], [rph]
MC JC	3,951,735	Δ326 bp	pseudogene (194‑519/663 nt)	ilvG →	pseudogene, acetolactate synthase 2 large subunit, valine‑insensitive; acetolactate synthase II, large subunit, cryptic, interrupted
MC JC	4,001,645	Δ5 bp	coding (220‑224/951 nt)	corA →	magnesium/nickel/cobalt transporter
RA	4,184,543	C→A	P1100Q (CCG→CAG)	rpoB →	RNA polymerase, beta subunit
RA	4,242,636	Δ1 bp	coding (881/891 nt)	malG ←	maltose transporter subunit
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	365887	366443	557	16 [13]	[14] 15	[lacZ]–[lacI]	[lacZ],[lacI]
*	*	÷	NC_000913	2099847	2101283	1437	15 [14]	[14] 15	gnd	gnd
*	*	÷	NC_000913	3423744–3424523	3424523	1–780	15 [14]	[14] 15	[rrfD]–[rrlD]	[rrfD],[rrlD]

Unassigned new junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	1207790 =	7 (0.170)	28 (0.790)	26/252	0.4	87.2%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	2 (0.060)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1207805	7 (0.170)	41 (1.150)	37/252	0.0	90.9%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	2 (0.060)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1299498	0 (0.000)	56 (1.440)	53/276	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