breseq  version 0.35.4  revision f352f80f4bc9 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence (highest frequency 20 of 266 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	2,319,929	0	T	G	50.0%	54.7 / 17.2	46	G114G (GGT→GGG)	atoB	acetyl‑CoA acetyltransferase
*	NZ_CP009273	1,598,494	0	C	T	47.4%	37.0 / 14.7	38	S64L (TCG→TTG)	lsrD	autoinducer 2 ABC transporter permease LsrD
*	NZ_CP009273	1,615,375	0	A	C	46.2%	73.3 / 12.8	52	V7G (GTG→GGG)	eamA	O‑acetylserine/cysteine exporter
*	NZ_CP009273	4,594,161	0	C	T	44.1%	66.7 / 43.7	69	S62F (TCT→TTT)	bglJ	DNA‑binding transcriptional activator BglJ
*	NZ_CP009273	3,659,062	0	C	A	43.8%	107.7 / 38.9	80	A37S (GCG→TCG)	gadX	acid resistance transcriptional activator GadX
*	NZ_CP009273	1,217,689	0	G	A	43.1%	65.9 / 18.3	51	pseudogene (2228/2243 nt)	BW25113_RS25990	autotransporter outer membrane beta‑barrel domain‑containing protein
*	NZ_CP009273	3,485,387	0	C	T	43.1%	64.4 / 28.3	53	Q90Q (CAG→CAA)	ppiA	peptidylprolyl isomerase A
*	NZ_CP009273	3,199,794	0	C	T	43.1%	60.3 / 37.2	65	intergenic (‑179/‑28)	ttdR/ttdA	DNA‑binding transcriptional activator TtdR/L(+)‑tartrate dehydratase subunit alpha
*	NZ_CP009273	4,594,167	0	C	T	42.0%	78.6 / 36.9	69	S64F (TCT→TTT)	bglJ	DNA‑binding transcriptional activator BglJ
*	NZ_CP009273	29,496	0	T	A	41.0%	95.3 / 25.6	61	intergenic (+301/‑155)	dapB/carA	4‑hydroxy‑tetrahydrodipicolinate reductase/glutamine‑hydrolyzing carbamoyl‑phosphate synthase small subunit
*	NZ_CP009273	3,344,212	0	A	C	40.8%	134.1 / 11.1	71	S725A (TCA→GCA)	arcB	aerobic respiration two‑component sensor histidine kinase ArcB
*	NZ_CP009273	4,419,801	0	T	G	40.6%	97.3 / 18.7	64	L41V (TTG→GTG)	cycA	D‑serine/D‑alanine/glycine transporter
*	NZ_CP009273	3,344,203	0	A	C	40.6%	126.2 / 14.4	69	L728V (TTA→GTA)	arcB	aerobic respiration two‑component sensor histidine kinase ArcB
*	NZ_CP009273	4,544,936	0	A	G	39.2%	69.8 / 18.7	51	I182V (ATC→GTC)	uxuR	Uxu operon transcriptional regulator
*	NZ_CP009273	29,486	0	C	A	39.1%	115.3 / 28.6	64	intergenic (+291/‑165)	dapB/carA	4‑hydroxy‑tetrahydrodipicolinate reductase/glutamine‑hydrolyzing carbamoyl‑phosphate synthase small subunit
*	NZ_CP009273	1,759,031	0	G	A	39.1%	100.6 / 19.2	64	intergenic (‑388/+160)	sufA/ydiH	Fe‑S cluster assembly scaffold SufA/YdiH family protein
*	NZ_CP009273	2,145,167	0	G	T	37.7%	67.6 / 13.1	53	intergenic (+40/+25)	yegJ/pphC	DUF2314 domain‑containing protein/protein‑serine/threonine phosphatase PphC
*	NZ_CP009273	3,659,017	0	C	A	37.7%	156.0 / 22.8	77	V52L (GTA→TTA)	gadX	acid resistance transcriptional activator GadX
*	NZ_CP009273	1,009,475	0	A	G	37.5%	111.3 / 21.9	66	E254G (GAA→GGA)	pqiB	intermembrane transport protein PqiB
*	NZ_CP009273	4,091,435	0	T	G	37.3%	126.8 / 11.4	67	intergenic (+77/‑183)	sodA/kdgT	superoxide dismutase [Mn]/2‑keto‑3‑deoxygluconate transporter

Marginal new junction evidence (sorted from low to high skew)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	= 4532507	85 (1.170)	17 (0.240)	17/476	6.3	18.6%	intergenic (+57/‑425)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
	?	NZ_CP009273	= 4532803	67 (0.960)					intergenic (+353/‑129)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
*	?	NZ_CP009273	= 2940826	43 (0.590)	3 (0.060)	3/328	10.1	8.3%	intergenic (+4/‑30)	BW25113_RS14635/BW25113_RS14640	tRNA‑Met/tRNA‑Met
	?	NZ_CP009273	2941047 =	38 (0.790)					intergenic (+5/+69)	BW25113_RS14645/amiC	tRNA‑Met/N‑acetylmuramoyl‑L‑alanine amidase AmiC
*	?	NZ_CP009273	4532499 =	86 (1.190)	6 (0.090)	6/476	11.2	7.4%	intergenic (+49/‑433)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
	?	NZ_CP009273	4532813 =	68 (0.970)					intergenic (+363/‑119)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA