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 39 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,634,777	0	G	A	60.0%	‑2.3 / 11.1	15	F22F (TTC→TTT)	essD	phage lysis protein EssD
*	NZ_CP009273	807,177	0	T	G	57.9%	4.6 / 16.8	19	V67G (GTG→GGG)	bioC	malonyl‑ACP O‑methyltransferase BioC
*	NZ_CP009273	71,561	0	T	G	57.1%	4.9 / 13.3	14	N136T (AAC→ACC)	thiB	thiamine ABC transporter substrate binding subunit
*	NZ_CP009273	3,300,628	0	T	G	57.1%	18.8 / 31.6	29	T198P (ACC→CCC)	deaD	ATP‑dependent RNA helicase DeaD
*	NZ_CP009273	832,042	0	C	G	56.5%	10.3 / 26.9	23	A79G (GCG→GGG)	hcxB	hydroxycarboxylate dehydrogenase HcXB
*	NZ_CP009273	976,689	0	A	G	56.5%	10.3 / 27.2	23	I63V (ATC→GTC)	ldtD	L,D‑transpeptidase
*	NZ_CP009273	4,558,321	0	T	G	56.4%	35.7 / 46.5	39	T6P (ACC→CCC)	mdtM	multidrug efflux MFS transporter MdtM
*	NZ_CP009273	1,598,180	0	T	G	56.2%	7.1 / 14.1	17	V302G (GTG→GGG)	lsrC	autoinducer 2 ABC transporter permease LsrC
*	NZ_CP009273	4,101,671	0	G	T	55.6%	1.7 / 10.4	9	R158S (CGT→AGT)	yiiQ	YiiQ family protein
*	NZ_CP009273	4,101,675	0	G	T	55.6%	0.4 / 13.1	9	N156K (AAC→AAA)	yiiQ	YiiQ family protein
*	NZ_CP009273	2,738,448	0	A	C	55.0%	13.7 / 21.7	20	V84G (GTG→GGG)	trmD	tRNA (guanosine(37)‑N1)‑methyltransferase TrmD
*	NZ_CP009273	2,259,116	0	A	C	54.5%	9.3 / 10.7	11	D63A (GAC→GCC)	yeiP	elongation factor P‑like protein YeiP
*	NZ_CP009273	2,259,118	0	A	C	54.5%	7.3 / 10.7	11	T64P (ACC→CCC)	yeiP	elongation factor P‑like protein YeiP
*	NZ_CP009273	3,729,190	0	T	C	54.5%	6.2 / 11.3	11	D284D (GAT→GAC)	xylR	DNA‑binding transcriptional regulator XylR
*	NZ_CP009273	4,142,237	0	T	G	54.2%	14.6 / 27.2	24	T264P (ACC→CCC)	ppc	phosphoenolpyruvate carboxylase
*	NZ_CP009273	546,689	0	T	G	53.8%	5.4 / 11.3	13	S265R (AGT→AGG)	ybcF	carbamate kinase
*	NZ_CP009273	497,031	0	A	C	53.3%	6.0 / 17.2	15	V555G (GTG→GGG)	ybaL	Kef family K(+) transporter
*	NZ_CP009273	2,221,735	0	A	C	53.3%	7.0 / 14.0	15	pseudogene (503/1436 nt)	mdtQ	multidrug resistance outer membrane protein MdtQ
*	NZ_CP009273	4,326,714	0	T	C	53.3%	7.6 / 11.3	15	G45G (GGA→GGG)	adiC	arginine/agmatine antiporter
*	NZ_CP009273	333,793	0	A	G	52.9%	9.3 / 17.8	17	G435G (GGA→GGG)	fdrA	acyl‑CoA synthetase FdrA

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	3861680 =	43 (1.750)	3 (0.130)	3/152	2.0	7.6%	coding (957/1215 nt)	yidR	DUF3748 domain‑containing protein
	?	NZ_CP009273	3861701 =	34 (1.510)					coding (936/1215 nt)	yidR	DUF3748 domain‑containing protein