BRESEQ :: Mutation Predictions

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]
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
RA	1,806,340	C→T	intergenic (‑257/‑30)	ydiY ← / → pfkB	acid‑inducible putative outer membrane protein/6‑phosphofructokinase II
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	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	2066276–2066621	2066621	1–346	10 [8]	[9] 11	[insH1]	[insH1]
*	*	÷	NC_000913	3423738–3424234	3424535–3424238	5–798	12 [9]	[9] 11	[rrfD]–[rrlD]	[rrfD],[rrlD]
*	*	÷	NC_000913	4107541	4108513	973	10 [9]	[8] 11	[pfkA]	[pfkA]

Unassigned new junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	1207790 =	18 (0.420)	18 (0.480)	18/210	1.2	42.5%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
*	?	NC_000913	1209619 =	33 (0.880)	18 (0.480)	18/210	1.2	42.5%	pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 4171803	52 (1.210)	16 (0.380)	10/238	2.9	23.9%	intergenic (+47/‑254)	rrfB/murB	5S ribosomal RNA of rrnB operon/UDP‑N‑acetylenolpyruvoylglucosamine reductase, FAD‑binding
*	?	NC_000913	= 4213162	51 (1.210)	16 (0.380)	10/238	2.9	23.9%	intergenic (+3/‑72)	rrfE/yjaA	5S ribosomal RNA of rrnE operon/stress‑induced protein
*	?	NC_000913	= 4542690	41 (0.950)	16 (0.400)	14/224	2.0	30.5%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	= 4542986	35 (0.880)	16 (0.400)	14/224	2.0	30.5%	intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)