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 140 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	4,277,647	0	T	A	46.7%	29.8 / 38.9	45	intergenic (‑348/‑45)	acs/nrfA	acetate‑‑CoA ligase/ammonia‑forming nitrite reductase cytochrome c552 subunit
*	NZ_CP009273	2,845,013	0	T	G	45.6%	73.5 / 24.6	57	G218G (GGT→GGG)	hypB	hydrogenase nickel incorporation protein HypB
*	NZ_CP009273	4,277,638	0	G	A	44.7%	44.3 / 26.0	47	intergenic (‑339/‑54)	acs/nrfA	acetate‑‑CoA ligase/ammonia‑forming nitrite reductase cytochrome c552 subunit
*	NZ_CP009273	4,336,492	0	T	G	42.6%	101.1 / 14.2	62	T218P (ACC→CCC)	fumB	class I fumarate hydratase
*	NZ_CP009273	595,032	0	T	G	41.7%	55.6 / 30.1	48	V288G (GTG→GGG)	cusA	Cu(+)/Ag(+) efflux RND transporter permease subunit CusA
*	NZ_CP009273	4,326,718	0	T	A	41.2%	49.6 / 25.1	51	Y44F (TAT→TTT)	adiC	arginine/agmatine antiporter
*	NZ_CP009273	339,155	0	A	G	40.9%	65.1 / 11.6	44	G187G (GGA→GGG)	yahK	NADPH‑dependent aldehyde reductase YahK
*	NZ_CP009273	4,091,435	0	T	G	40.6%	116.4 / 11.3	65	intergenic (+77/‑183)	sodA/kdgT	superoxide dismutase [Mn]/2‑keto‑3‑deoxygluconate transporter
*	NZ_CP009273	140,671	0	T	G	40.0%	81.2 / 20.9	50	G161G (GGT→GGG)	yadH	ABC transporter permease
*	NZ_CP009273	1,568,336	0	C	A	40.0%	71.2 / 13.1	40	G371V (GGT→GTT)	pqqL	insulinase family protein
*	NZ_CP009273	341,039	0	C	A	39.6%	92.1 / 23.7	53	intergenic (+337/‑76)	BW25113_RS01680/BW25113_RS01685	protein YahL/protein YahM
*	NZ_CP009273	15,395	0	G	A	39.5%	56.6 / 16.5	43	intergenic (+97/‑50)	dnaJ/BW25113_RS00080	molecular chaperone DnaJ/IS4‑like element IS421 family transposase
*	NZ_CP009273	3,806,632	0	C	T	39.5%	47.7 / 14.1	44	S181L (TCG→TTG)	coaBC	bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate‑‑cysteine ligase CoaBC
*	NZ_CP009273	4,594,161	0	C	T	39.3%	90.2 / 24.9	61	S62F (TCT→TTT)	bglJ	DNA‑binding transcriptional activator BglJ
*	NZ_CP009273	1,429,975	0	G	A	39.1%	80.5 / 14.0	47	intergenic (‑99/+42)	uspF/ompN	universal stress protein UspF/porin OmpN
*	NZ_CP009273	4,594,167	0	C	T	37.7%	87.7 / 23.1	61	S64F (TCT→TTT)	bglJ	DNA‑binding transcriptional activator BglJ
*	NZ_CP009273	140,647	0	C	T	37.5%	72.8 / 12.5	49	F153F (TTC→TTT)	yadH	ABC transporter permease
*	NZ_CP009273	4,526,014	0	A	T	37.1%	52.9 / 23.3	35	intergenic (+166/+102)	yjhR/BW25113_RS26295	helicase YjhR/HNH endonuclease
*	NZ_CP009273	2,380,341	0	G	A	36.8%	53.5 / 20.9	39	intergenic (+31/‑72)	yfbL/yfbM	M28 family metallopeptidase/YfbM family protein
*	NZ_CP009273	1,429,984	0	G	A	36.7%	84.1 / 20.2	49	intergenic (‑108/+33)	uspF/ompN	universal stress protein UspF/porin OmpN

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	4532499 =	64 (1.030)	11 (0.180)	11/478	7.1	15.4%	intergenic (+49/‑433)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
	?	NZ_CP009273	4532813 =	59 (0.980)					intergenic (+363/‑119)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
*	?	NZ_CP009273	= 4532507	60 (0.960)	8 (0.130)	8/478	8.5	12.1%	intergenic (+57/‑425)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
	?	NZ_CP009273	= 4532803	58 (0.960)					intergenic (+353/‑129)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA