breseq  version 0.29.0  revision 8f9c342918e4 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence (highest frequency 20 of 538 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	599,576	0	T	G	50.0%	35.9 / 45.8	62	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	2,151,689	0	G	T	48.9%	11.8 / 23.5	46	intergenic (+43/+22)	yegJ/yegK	uncharacterized protein/ser/thr phosphatase‑related protein
*	NC_000913	599,579	0	T	G	47.5%	57.9 / 17.0	62	V289G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	2,326,450	0	T	G	45.8%	62.4 / 13.2	48	G114G (GGT→GGG)	atoB	acetyl‑CoA acetyltransferase
*	NC_000913	523,326	0	T	G	44.1%	81.3 / 10.6	60	G22G (GGT→GGG)	rhsD	Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
*	NC_000913	1,487,155	0	T	A	42.2%	55.0 / 26.9	45	intergenic (+192/‑80)	hrpA/ydcF	putative ATP‑dependent helicase/DUF218 superfamily protein, SAM‑binding
*	NC_000913	2,151,686	0	G	T	41.3%	35.6 / 15.1	46	intergenic (+40/+25)	yegJ/yegK	uncharacterized protein/ser/thr phosphatase‑related protein
*	NC_000913	357,890	0	C	A	41.2%	17.5 / 17.2	34	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	753,125	0	T	A	41.0%	108.5 / 41.6	78	intergenic (‑330/+60)	ybgD/gltA	putative fimbrial‑like adhesin protein/citrate synthase
*	NC_000913	3,745,509	0	A	T	40.3%	74.9 / 35.7	67	T236S (ACC→TCC)	yiaN	2,3‑diketo‑L‑gulonate TRAP transporter large permease protein
*	NC_000913	2,096,090	0	A	G	40.3%	117.3 / 20.0	72	I83V (ATT→GTT)	hisF	imidazole glycerol phosphate synthase, catalytic subunit with HisH
*	NC_000913	3,751,537	0	A	C	40.2%	126.0 / 20.7	82	V111G (GTT→GGT)	yiaT	putative outer membrane protein
*	NC_000913	3,443,277	0	A	C	40.0%	109.4 / 26.0	71	V274G (GTA→GGA)	secY	preprotein translocase membrane subunit
*	NC_000913	4,604,344	0	C	T	40.0%	68.8 / 27.5	55	S62F (TCT→TTT)	bglJ	bgl operon transcriptional activator
*	NC_000913	1,292,458	0	T	A	39.8%	114.8 / 42.8	83	intergenic (+93/+51)	galU/hns	glucose‑1‑phosphate uridylyltransferase/global DNA‑binding transcriptional dual regulator H‑NS
*	NC_000913	1,376,349	0	A	C	39.2%	130.2 / 16.1	81	T106P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
*	NC_000913	1,574,051	0	G	T	38.9%	78.7 / 20.2	56	V384V (GTC→GTA)	pqqL	putative periplasmic M16 family zinc metalloendopeptidase
*	NC_000913	3,412,906	0	T	A	38.8%	138.9 / 44.7	80	Y187F (TAT→TTT)	acrS	acrAB operon transcriptional repressor
*	NC_000913	523,335	0	T	G	38.7%	96.0 / 11.4	64	G25G (GGT→GGG)	rhsD	Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
*	NC_000913	3,812,792	0	C	A	38.2%	119.9 / 28.0	68	T21N (ACC→AAC)	dfp	fused 4'‑phosphopantothenoylcysteine decarboxylase/phosphopantothenoylcysteine synthetase, FMN‑binding

Marginal new junction evidence (sorted from low to high skew)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	4542682 =	94 (1.170)	13 (0.170)	13/280	8.3	13.0%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	86 (1.140)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	= 4542690	99 (1.230)	12 (0.160)	11/280	9.2	11.9%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	84 (1.110)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)