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 210 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,906,007	0	T	G	63.3%	11.4 / 19.5	30	H276P (CAC→CCC)	htpX	protease HtpX
*	NZ_CP009273	595,032	0	T	G	61.9%	‑0.2 / 16.9	22	V288G (GTG→GGG)	cusA	Cu(+)/Ag(+) efflux RND transporter permease subunit CusA
*	NZ_CP009273	595,035	0	T	G	59.1%	1.9 / 17.2	22	V289G (GTG→GGG)	cusA	Cu(+)/Ag(+) efflux RND transporter permease subunit CusA
*	NZ_CP009273	642,203	0	T	G	59.1%	3.3 / 24.1	22	T255P (ACC→CCC)	citG	triphosphoribosyl‑dephospho‑CoA synthase CitG
*	NZ_CP009273	1,819,318	0	G	A	57.6%	‑2.7 / 32.4	33	intergenic (‑124/+79)	ves/spy	environmental stress‑induced protein Ves/ATP‑independent periplasmic protein‑refolding chaperone Spy
*	NZ_CP009273	4,594,161	0	C	T	57.3%	6.0 / 92.5	82	S62F (TCT→TTT)	bglJ	DNA‑binding transcriptional activator BglJ
*	NZ_CP009273	822,955	0	T	G	55.6%	32.1 / 45.5	37	T495P (ACC→CCC)	ybhF	ATP‑binding cassette domain‑containing protein
*	NZ_CP009273	822,963	0	T	G	55.6%	9.5 / 42.6	36	D492A (GAC→GCC)	ybhF	ATP‑binding cassette domain‑containing protein
*	NZ_CP009273	4,594,167	0	C	T	55.6%	19.6 / 94.7	82	S64F (TCT→TTT)	bglJ	DNA‑binding transcriptional activator BglJ
*	NZ_CP009273	1,819,313	0	G	A	54.5%	1.1 / 33.1	33	intergenic (‑119/+84)	ves/spy	environmental stress‑induced protein Ves/ATP‑independent periplasmic protein‑refolding chaperone Spy
*	NZ_CP009273	497,020	0	A	C	54.2%	8.4 / 31.1	24	*559E (TAA→GAA)	ybaL	Kef family K(+) transporter
*	NZ_CP009273	1,571,380	0	A	C	53.8%	46.5 / 65.8	52	V166G (GTA→GGA)	yddB	TonB‑dependent receptor plug domain‑containing protein
*	NZ_CP009273	353,601	0	C	A	52.7%	38.3 / 114.9	93	L267F (TTG→TTT)	cynR	transcriptional regulator CynR
*	NZ_CP009273	497,028	0	A	C	51.8%	27.1 / 38.4	27	V556G (GTG→GGG)	ybaL	Kef family K(+) transporter
*	NZ_CP009273	497,031	0	A	C	51.8%	30.6 / 38.5	27	V555G (GTG→GGG)	ybaL	Kef family K(+) transporter
*	NZ_CP009273	1,906,011	0	T	G	51.7%	21.6 / 29.7	30	T275P (ACC→CCC)	htpX	protease HtpX
*	NZ_CP009273	3,659,062	0	C	A	51.6%	78.0 / 129.7	62	A37S (GCG→TCG)	gadX	acid resistance transcriptional activator GadX
*	NZ_CP009273	1,548,257	0	T	G	51.1%	45.9 / 55.0	45	Y557S (TAC→TCC)	maeA	malate dehydrogenase
*	NZ_CP009273	997,447	0	T	G	48.9%	43.3 / 12.2	45	V62G (GTA→GGA)	elfG	fimbrial protein
*	NZ_CP009273	832,042	0	C	G	47.1%	60.9 / 17.5	51	A79G (GCG→GGG)	hcxB	hydroxycarboxylate dehydrogenase HcXB

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	3610600 =	98 (1.520)	4 (0.070)	4/150	3.2	4.5%	coding (226/765 nt)	nikD	nickel import ATP‑binding protein NikD
	?	NZ_CP009273	3610644 =	81 (1.390)					coding (270/765 nt)	nikD	nickel import ATP‑binding protein NikD
*	?	NZ_CP009273	= 4532507	1 (0.020)	3 (0.050)	3/148	3.5	15.8%	intergenic (+57/‑425)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
	?	NZ_CP009273	= 4532803	31 (0.540)					intergenic (+353/‑129)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
*	?	NZ_CP009273	142767 =	57 (0.890)	3 (0.050)	3/148	3.5	5.3%	coding (1200/1230 nt)	yadE	polysaccharide deacetylase family protein
	?	NZ_CP009273	142790 =	57 (0.990)					coding (1223/1230 nt)	yadE	polysaccharide deacetylase family protein