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 121 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	2,380,357	0	A	T	63.2%	1.4 / 20.1	19	intergenic (+47/‑56)	yfbL/yfbM	M28 family metallopeptidase/YfbM family protein
*	NZ_CP009273	822,963	0	T	G	62.1%	5.8 / 30.3	29	D492A (GAC→GCC)	ybhF	ATP‑binding cassette domain‑containing protein
*	NZ_CP009273	982,447	0	A	C	61.5%	8.9 / 11.9	13	intergenic (‑9/+594)	ompF/asnS	porin OmpF/asparagine‑‑tRNA ligase
*	NZ_CP009273	2,089,571	0	A	G	61.5%	‑5.0 / 19.9	27	I83V (ATT→GTT)	hisF	imidazole glycerol phosphate synthase subunit HisF
*	NZ_CP009273	4,594,161	0	C	T	58.3%	6.7 / 71.9	61	S62F (TCT→TTT)	bglJ	DNA‑binding transcriptional activator BglJ
*	NZ_CP009273	2,290,243	0	T	G	57.7%	21.4 / 30.1	26	L87F (TTA→TTC)	ccmB	heme exporter protein CcmB
*	NZ_CP009273	4,594,167	0	C	T	57.4%	8.5 / 70.5	61	S64F (TCT→TTT)	bglJ	DNA‑binding transcriptional activator BglJ
*	NZ_CP009273	1,663,765	0	T	A	57.1%	6.3 / 16.8	14	I29F (ATT→TTT)	ynfL	LysR family transcriptional regulator
*	NZ_CP009273	2,370,630	0	A	C	57.1%	5.5 / 10.8	14	Y148D (TAT→GAT)	menH	2‑succinyl‑6‑hydroxy‑2, 4‑cyclohexadiene‑1‑carboxylate synthase
*	NZ_CP009273	4,501,865	0	A	C	57.1%	37.0 / 56.3	42	L123V (TTG→GTG)	fecD	Fe(3+) dicitrate ABC transporter permease subunit FecD
*	NZ_CP009273	765,675	0	A	C	55.9%	34.0 / 41.3	34	T748P (ACC→CCC)	mngB	mannosylglycerate hydrolase
*	NZ_CP009273	822,955	0	T	G	55.6%	16.9 / 29.9	27	T495P (ACC→CCC)	ybhF	ATP‑binding cassette domain‑containing protein
*	NZ_CP009273	1,673,561	0	A	C	55.0%	12.9 / 18.6	20	Y293S (TAC→TCC)	ydgH	DUF1471 family protein YdgH
*	NZ_CP009273	2,380,362	0	C	T	55.0%	‑2.0 / 23.4	20	intergenic (+52/‑51)	yfbL/yfbM	M28 family metallopeptidase/YfbM family protein
*	NZ_CP009273	2,380,341	0	G	A	54.5%	3.5 / 29.2	22	intergenic (+31/‑72)	yfbL/yfbM	M28 family metallopeptidase/YfbM family protein
*	NZ_CP009273	1,571,380	0	A	C	54.0%	37.3 / 51.6	37	V166G (GTA→GGA)	yddB	TonB‑dependent receptor plug domain‑containing protein
*	NZ_CP009273	1,990,578	0	T	G	53.8%	7.0 / 12.0	13	T240P (ACC→CCC)	yecC	L‑cystine ABC transporter ATP‑binding protein YecC
*	NZ_CP009273	1,316,700	0	A	T	53.3%	9.1 / 20.7	15	N168K (AAT→AAA)	trpE	anthranilate synthase component I
*	NZ_CP009273	3,659,062	0	C	A	52.9%	52.0 / 99.9	51	A37S (GCG→TCG)	gadX	acid resistance transcriptional activator GadX
*	NZ_CP009273	1,213,870	0	A	C	52.6%	24.0 / 25.9	19	T363P (ACC→CCC)	pdeG	cyclic diguanylate phosphodiesterase

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	= 4047497	47 (0.990)	3 (0.070)	3/150	3.3	6.7%	coding (1142/1410 nt)	glnG	nitrogen regulation protein NR(I)
	?	NZ_CP009273	= 4047517	42 (1.000)					coding (1122/1410 nt)	glnG	nitrogen regulation protein NR(I)
*	?	NZ_CP009273	= 2869985	48 (1.010)	3 (0.060)	3/166	3.5	6.0%	coding (46/1038 nt)	iap	alkaline phosphatase isozyme conversion aminopeptidase
	?	NZ_CP009273	2869990 =	46 (0.980)					coding (51/1038 nt)	iap	alkaline phosphatase isozyme conversion aminopeptidase