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 50 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,458,386	0	A	G	73.7%	21.3 / 10.4	19	E369G (GAA→GGA)	gspL	type II secretion system protein GspL
*	NZ_CP009273	595,032	0	T	G	66.7%	‑0.9 / 10.9	15	V288G (GTG→GGG)	cusA	Cu(+)/Ag(+) efflux RND transporter permease subunit CusA
*	NZ_CP009273	595,035	0	T	G	66.7%	‑5.2 / 10.2	15	V289G (GTG→GGG)	cusA	Cu(+)/Ag(+) efflux RND transporter permease subunit CusA
*	NZ_CP009273	4,594,167	0	C	T	64.0%	‑4.3 / 17.2	25	S64F (TCT→TTT)	bglJ	DNA‑binding transcriptional activator BglJ
*	NZ_CP009273	40,515	0	G	T	62.5%	6.1 / 18.0	16	Q473K (CAA→AAA)	caiT	L‑carnitine/gamma‑butyrobetaine antiporter
*	NZ_CP009273	4,558,321	0	T	G	62.5%	8.5 / 14.0	16	T6P (ACC→CCC)	mdtM	multidrug efflux MFS transporter MdtM
*	NZ_CP009273	822,963	0	T	G	61.9%	‑5.7 / 18.9	21	D492A (GAC→GCC)	ybhF	ATP‑binding cassette domain‑containing protein
*	NZ_CP009273	4,058,958	0	G	A	61.9%	‑6.5 / 15.8	21	L57L (CTG→TTG)	yihO	MFS transporter
*	NZ_CP009273	349,999	0	T	G	61.5%	0.4 / 11.3	13	V528G (GTG→GGG)	prpE	propionate‑‑CoA ligase
*	NZ_CP009273	1,500,285	0	A	C	61.5%	5.1 / 11.0	13	V18G (GTA→GGA)	ydcO	BenE family transporter YdcO
*	NZ_CP009273	40,525	0	C	T	60.0%	‑2.3 / 11.5	15	L469L (CTG→CTA)	caiT	L‑carnitine/gamma‑butyrobetaine antiporter
*	NZ_CP009273	595,037	0	A	G	60.0%	6.2 / 12.4	15	I290V (ATC→GTC)	cusA	Cu(+)/Ag(+) efflux RND transporter permease subunit CusA
*	NZ_CP009273	2,630,518	0	A	C	60.0%	11.5 / 15.8	15	G66G (GGT→GGG)	der	ribosome biogenesis GTPase Der
*	NZ_CP009273	1,500,295	0	A	C	58.3%	6.5 / 10.7	12	F15V (TTT→GTT)	ydcO	BenE family transporter YdcO
*	NZ_CP009273	2,955,854	0	T	G	57.1%	14.5 / 20.2	21	S90S (TCA→TCC)	ppdC	prepilin‑type N‑terminal cleavage/methylation domain‑containing protein
*	NZ_CP009273	3,502,021	0	T	A	57.1%	‑2.2 / 16.1	14	E384D (GAA→GAT)	yhfW	phosphopentomutase
*	NZ_CP009273	4,142,237	0	T	G	57.1%	5.4 / 10.5	14	T264P (ACC→CCC)	ppc	phosphoenolpyruvate carboxylase
*	NZ_CP009273	4,558,329	0	C	A	57.1%	‑4.2 / 14.8	14	R3L (CGT→CTT)	mdtM	multidrug efflux MFS transporter MdtM
*	NZ_CP009273	2,088,380	0	A	C	56.2%	11.6 / 15.5	16	Y122S (TAC→TCC)	hisH	imidazole glycerol phosphate synthase subunit HisH
*	NZ_CP009273	3,774,215	0	T	G	56.2%	12.8 / 15.1	16	G343G (GGT→GGG)	lldD	quinone‑dependent L‑lactate dehydrogenase

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	= 2541282	17 (0.820)	3 (0.150)	3/168	1.9	16.8%	coding (1251/1425 nt)	murP	PTS N‑acetylmuramic acid transporter subunit IIBC
	?	NZ_CP009273	2541287 =	13 (0.630)					coding (1256/1425 nt)	murP	PTS N‑acetylmuramic acid transporter subunit IIBC