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 132 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,548,257	0	T	G	60.7%	11.0 / 18.4	28	Y557S (TAC→TCC)	maeA	malate dehydrogenase
*	NZ_CP009273	2,606,478	0	T	C	60.0%	8.0 / 16.5	15	I407T (ATC→ACC)	hyfR	DNA‑binding transcriptional regulator HyfR
*	NZ_CP009273	595,032	0	T	G	56.1%	‑1.4 / 44.4	41	V288G (GTG→GGG)	cusA	Cu(+)/Ag(+) efflux RND transporter permease subunit CusA
*	NZ_CP009273	595,035	0	T	G	56.1%	15.8 / 49.1	41	V289G (GTG→GGG)	cusA	Cu(+)/Ag(+) efflux RND transporter permease subunit CusA
*	NZ_CP009273	1,316,733	0	T	C	55.6%	11.7 / 20.7	18	G157G (GGA→GGG)	trpE	anthranilate synthase component I
*	NZ_CP009273	353,601	0	C	A	54.8%	25.9 / 77.8	62	L267F (TTG→TTT)	cynR	transcriptional regulator CynR
*	NZ_CP009273	3,941,183	0	T	G	54.8%	33.1 / 45.4	32	T49P (ACC→CCC)	hdfR	HTH‑type transcriptional regulator HdfR
*	NZ_CP009273	1,152,727	0	T	G	54.5%	21.1 / 28.7	22	G165G (GGT→GGG)	ycfH	metal‑dependent hydrolase
*	NZ_CP009273	3,090,826	0	T	G	53.8%	24.8 / 29.1	27	G67G (GGT→GGG)	hemW	radical SAM family heme chaperone HemW
*	NZ_CP009273	653,132	0	A	C	53.6%	32.8 / 41.9	28	V88G (GTG→GGG)	crcB	fluoride efflux transporter CrcB
*	NZ_CP009273	3,199,794	0	C	T	53.1%	10.9 / 47.4	32	intergenic (‑179/‑28)	ttdR/ttdA	DNA‑binding transcriptional activator TtdR/L(+)‑tartrate dehydratase subunit alpha
*	NZ_CP009273	3,837,579	0	T	G	52.4%	48.9 / 60.5	42	F86V (TTT→GTT)	adeD	adenine deaminase
*	NZ_CP009273	890,386	0	A	C	51.8%	29.7 / 36.0	27	intergenic (+34/‑61)	potF/potG	spermidine/putrescine ABC transporter substrate‑binding protein PotF/putrescine ABC transporter ATP‑binding subunit PotG
*	NZ_CP009273	510,080	0	A	C	51.7%	36.6 / 44.5	29	V79G (GTG→GGG)	ybbJ	NfeD family protein
*	NZ_CP009273	1,906,011	0	T	G	51.6%	40.4 / 48.4	31	T275P (ACC→CCC)	htpX	protease HtpX
*	NZ_CP009273	1,819,318	0	G	A	50.0%	8.7 / 14.4	20	intergenic (‑124/+79)	ves/spy	environmental stress‑induced protein Ves/ATP‑independent periplasmic protein‑refolding chaperone Spy
*	NZ_CP009273	3,012,931	0	A	C	50.0%	16.1 / 12.9	26	T138P (ACA→CCA)	ssnA	putative aminohydrolase SsnA
*	NZ_CP009273	353,591	0	T	C	49.1%	80.2 / 12.4	60	K271E (AAA→GAA)	cynR	transcriptional regulator CynR
*	NZ_CP009273	3,659,062	0	C	A	48.7%	38.7 / 26.4	39	A37S (GCG→TCG)	gadX	acid resistance transcriptional activator GadX
*	NZ_CP009273	2,380,341	0	G	A	48.0%	16.4 / 17.9	25	intergenic (+31/‑72)	yfbL/yfbM	M28 family metallopeptidase/YfbM family protein

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	2416060 =	37 (0.790)	3 (0.070)	3/146	3.1	7.9%	coding (874/894 nt)	yfcH	TIGR01777 family oxidoreductase
	?	NZ_CP009273	2416107 =	38 (0.940)					intergenic (+27/+21)	yfcH/rpnB	TIGR01777 family oxidoreductase/recombination‑promoting nuclease RpnB
*	?	NZ_CP009273	303067 =	95 (2.040)	4 (0.090)	3/152	3.2	4.4%	coding (1977/2526 nt)	ecpC	fimbrial usher EcpC
	?	NZ_CP009273	303096 =	87 (2.070)					coding (1948/2526 nt)	ecpC	fimbrial usher EcpC