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 72 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	353,601	0	C	A	65.0%	‑4.5 / 16.7	20	L267F (TTG→TTT)	cynR	transcriptional regulator CynR
*	NZ_CP009273	2,380,331	0	T	G	61.9%	9.0 / 15.2	21	intergenic (+21/‑82)	yfbL/yfbM	M28 family metallopeptidase/YfbM family protein
*	NZ_CP009273	1,663,765	0	T	A	61.5%	0.7 / 12.3	13	I29F (ATT→TTT)	ynfL	LysR family transcriptional regulator
*	NZ_CP009273	832,048	0	T	G	61.1%	13.4 / 19.4	18	V81G (GTC→GGC)	hcxB	hydroxycarboxylate dehydrogenase HcXB
*	NZ_CP009273	1,548,257	0	T	G	60.9%	6.1 / 12.6	23	Y557S (TAC→TCC)	maeA	malate dehydrogenase
*	NZ_CP009273	228,181	0	C	T	60.6%	1.3 / 28.6	33	F191F (TTC→TTT)	yafD	endonuclease/exonuclease/phosphatase family protein
*	NZ_CP009273	2,380,341	0	G	A	60.0%	‑2.6 / 16.6	20	intergenic (+31/‑72)	yfbL/yfbM	M28 family metallopeptidase/YfbM family protein
*	NZ_CP009273	2,380,357	0	A	T	60.0%	7.0 / 21.6	20	intergenic (+47/‑56)	yfbL/yfbM	M28 family metallopeptidase/YfbM family protein
*	NZ_CP009273	4,419,801	0	T	G	58.8%	7.0 / 15.2	17	L41V (TTG→GTG)	cycA	D‑serine/D‑alanine/glycine transporter
*	NZ_CP009273	4,594,161	0	C	T	56.8%	‑4.5 / 31.0	44	S62F (TCT→TTT)	bglJ	DNA‑binding transcriptional activator BglJ
*	NZ_CP009273	4,594,167	0	C	T	56.8%	‑5.0 / 32.3	44	S64F (TCT→TTT)	bglJ	DNA‑binding transcriptional activator BglJ
*	NZ_CP009273	536,014	0	T	G	56.0%	17.9 / 32.7	25	intergenic (+50/‑7)	allB/ybbY	allantoinase AllB/uracil/xanthine transporter
*	NZ_CP009273	1,555,008	0	T	G	56.0%	3.5 / 15.2	25	D60A (GAC→GCC)	ddpB	ABC transporter permease
*	NZ_CP009273	799,325	0	G	T	55.6%	0.8 / 12.8	9	V123L (GTG→TTG)	ybhJ	hydratase
*	NZ_CP009273	2,089,571	0	A	G	55.6%	11.3 / 29.0	27	I83V (ATT→GTT)	hisF	imidazole glycerol phosphate synthase subunit HisF
*	NZ_CP009273	228,191	0	A	G	55.2%	11.8 / 28.2	29	S195G (AGC→GGC)	yafD	endonuclease/exonuclease/phosphatase family protein
*	NZ_CP009273	2,336,785	0	A	C	55.2%	29.9 / 40.1	29	G288G (GGT→GGG)	yfaL	AIDA‑I family autotransporter adhesin YfaL/EhaC
*	NZ_CP009273	3,055,679	0	A	C	55.2%	24.9 / 38.9	29	T491P (ACC→CCC)	scpA	methylmalonyl‑CoA mutase
*	NZ_CP009273	949,854	0	A	C	55.0%	7.1 / 17.9	20	G23G (GGT→GGG)	focA	formate transporter FocA
*	NZ_CP009273	2,360,813	0	C	T	55.0%	6.7 / 19.0	20	F88F (TTC→TTT)	arnC	undecaprenyl‑phosphate 4‑deoxy‑4‑formamido‑L‑arabinose transferase

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	= 4532507	8 (0.230)	3 (0.100)	3/152	2.6	15.3%	intergenic (+57/‑425)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
	?	NZ_CP009273	= 4532803	26 (0.850)					intergenic (+353/‑129)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
*	?	NZ_CP009273	= 4609809	43 (1.260)	3 (0.090)	3/158	2.7	6.9%	coding (390/1224 nt)	deoB	phosphopentomutase
	?	NZ_CP009273	4609882 =	41 (1.290)					coding (463/1224 nt)	deoB	phosphopentomutase