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	755,790	G→A	W77* (TGG→TGA)	sdhD →	succinate dehydrogenase, membrane subunit, binds cytochrome b556
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
MC JC	1,299,499	Δ1,199 bp	intergenic (+254/‑485)	ychE → / → oppA	UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
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
JC	3,815,859	Δ82 bp		[rph]–[rph]	[rph], [rph]
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	4,296,381	+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	761505	762752	1248	7 [5]	[5] 7	[sucA]–sucB	[sucA],sucB
*	*	÷	NC_000913	2066276–2066581	2066581	1–306	6 [5]	[5] 7	[insH1]	[insH1]
*	*	÷	NC_000913	3423762–3424234	3424520–3424240	7–759	6 [3]	[5] 6	[rrfD]–[rrlD]	[rrfD],[rrlD]

Unassigned new junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 224374	NA (NA)	6 (0.190)	6/246	2.7	NA	noncoding (604/1542 nt)	rrsH	16S ribosomal RNA of rrnH operon
	?	NC_000913	= 224403	NA (NA)					noncoding (633/1542 nt)	rrsH	16S ribosomal RNA of rrnH operon
*	?	NC_000913	= 381669	NA (NA)	8 (0.250)	7/246	2.5	NA	noncoding (410/1331 nt)	IS2	repeat region
	?	NC_000913	= 381695	NA (NA)					noncoding (436/1331 nt)	IS2	repeat region
*	?	NC_000913	= 409055	NA (NA)	8 (0.250)	8/246	2.2	NA	noncoding (4/37 nt)	REP34 (repetitive extragenic palindromic) element; contains 1 REP sequences	REP34 (repetitive extragenic palindromic) element; contains 1 REP sequences
	?	NC_000913	= 409088	NA (NA)					noncoding (37/37 nt)	REP34 (repetitive extragenic palindromic) element; contains 1 REP sequences	REP34 (repetitive extragenic palindromic) element; contains 1 REP sequences
*	?	NC_000913	1207790 =	23 (0.680)	8 (0.270)	8/228	2.1	29.5%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	18 (0.600)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related