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 193 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	4,245,997	0	G	C	44.3%	89.8 / 29.7	61	P133R (CCG→CGG)	plsB	glycerol‑3‑phosphate 1‑O‑acyltransferase PlsB
*	NZ_CP009273	4,570,451	0	C	T	42.9%	97.9 / 30.3	70	E277K (GAA→AAA)	hsdS	type I restriction‑modification system specificity subunit
*	NZ_CP009273	3,199,794	0	C	T	41.3%	39.3 / 57.5	75	intergenic (‑179/‑28)	ttdR/ttdA	DNA‑binding transcriptional activator TtdR/L(+)‑tartrate dehydratase subunit alpha
*	NZ_CP009273	2,221,757	0	G	C	39.0%	60.5 / 13.3	41	pseudogene (481/1436 nt)	mdtQ	multidrug resistance outer membrane protein MdtQ
*	NZ_CP009273	2,380,341	0	G	A	37.5%	73.1 / 35.9	56	intergenic (+31/‑72)	yfbL/yfbM	M28 family metallopeptidase/YfbM family protein
*	NZ_CP009273	2,221,768	0	T	C	36.6%	59.0 / 10.3	41	pseudogene (470/1436 nt)	mdtQ	multidrug resistance outer membrane protein MdtQ
*	NZ_CP009273	3,855,998	0	T	C	36.2%	68.9 / 17.1	48	pseudogene (966/1617 nt)	BW25113_RS19145	PTS sugar transporter subunit IIB
*	NZ_CP009273	595,032	0	T	G	36.1%	112.9 / 21.2	61	V288G (GTG→GGG)	cusA	Cu(+)/Ag(+) efflux RND transporter permease subunit CusA
*	NZ_CP009273	2,178,678	0	T	G	36.0%	131.9 / 22.2	75	T35P (ACC→CCC)	thiM	hydroxyethylthiazole kinase
*	NZ_CP009273	3,578,446	0	A	C	35.4%	150.7 / 26.3	79	Y580D (TAC→GAC)	ggt	gamma‑glutamyltransferase
*	NZ_CP009273	3,659,062	0	C	A	35.2%	149.6 / 33.4	88	A37S (GCG→TCG)	gadX	acid resistance transcriptional activator GadX
*	NZ_CP009273	3,524,799	0	A	C	34.7%	206.8 / 20.6	98	Y334D (TAT→GAT)	yhgE	DUF4153 domain‑containing protein
*	NZ_CP009273	328,711	0	A	G	34.4%	111.2 / 17.3	64	G210G (GGA→GGG)	pdeL	DNA‑binding transcriptional activator/c‑di‑GMP phosphodiesterase PdeL
*	NZ_CP009273	3,394,818	0	T	C	34.3%	136.8 / 13.8	70	D625G (GAT→GGT)	csrD	RNase E specificity factor CsrD
*	NZ_CP009273	748,581	0	T	A	34.2%	157.5 / 25.0	79	intergenic (‑330/+60)	ybgD/gltA	fimbrial protein/citrate synthase
*	NZ_CP009273	2,621,979	0	T	A	33.9%	97.8 / 19.4	62	T107S (ACT→TCT)	pdeF	cyclic‑guanylate‑specific phosphodiesterase PdeF
*	NZ_CP009273	4,612,067	0	A	G	33.9%	118.4 / 18.5	65	E161G (GAG→GGG)	yjjJ	type II toxin‑antitoxin system HipA family toxin YjjJ
*	NZ_CP009273	29,486	0	C	A	33.3%	139.6 / 23.9	66	intergenic (+291/‑165)	dapB/carA	4‑hydroxy‑tetrahydrodipicolinate reductase/glutamine‑hydrolyzing carbamoyl‑phosphate synthase small subunit
*	NZ_CP009273	1,240,690	0	G	T	33.3%	123.9 / 18.4	63	L25F (TTG→TTT)	BW25113_RS06225	protein YcgY
*	NZ_CP009273	1,652,424	0	G	T	33.3%	114.3 / 16.6	72	L33F (TTG→TTT)	ynfE	DmsA/YnfE/YnfF family dimethyl sulfoxide reductase

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	1203246 =	70 (0.900)	22 (0.300)	21/464	5.3	26.6%	coding (290/630 nt)	BW25113_RS05990	protein StfP
	?	NZ_CP009273	1205075 =	56 (0.770)					coding (40/540 nt)	BW25113_RS06005	phage tail protein
*	?	NZ_CP009273	= 1203261	66 (0.850)	20 (0.270)	20/464	5.5	25.5%	coding (305/630 nt)	BW25113_RS05990	protein StfP
	?	NZ_CP009273	= 1205058	55 (0.760)					coding (57/540 nt)	BW25113_RS06005	phage tail protein