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 762 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,261,055	0	A	C	53.9%	94.5 / 121.6	76	V455G (GTG→GGG)	tdcE	pyruvate formate‑lyase 4/2‑ketobutyrate formate‑lyase
*	NC_000913	357,890	0	C	A	49.1%	44.2 / 35.0	55	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	589,934	0	T	G	47.1%	98.7 / 28.4	71	T341P (ACC→CCC)	nfrA	bacteriophage N4 receptor, outer membrane subunit
*	NC_000913	357,880	0	T	C	47.1%	57.8 / 14.9	51	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	802,118	0	A	C	45.6%	103.1 / 24.1	79	T78P (ACC→CCC)	ybhI	putative DASS family tricarboxylate or dicarboxylate transporter
*	NC_000913	366,526	0	T	G	44.4%	119.5 / 55.0	99	T329P (ACC→CCC)	lacI	lactose‑inducible lac operon transcriptional repressor
*	NC_000913	357,875	0	A	T	43.1%	65.7 / 22.2	53	N272K (AAT→AAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	599,576	0	T	G	43.0%	137.5 / 16.6	79	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	2,001,918	0	A	C	42.1%	161.9 / 27.9	95	intergenic (‑129/+192)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein (flagellin)
*	NC_000913	1,376,505	0	A	C	41.6%	140.4 / 14.4	79	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
*	NC_000913	1,245,234	0	G	T	41.2%	143.9 / 49.6	97	L25F (TTG→TTT)	ycgY	uncharacterized protein
*	NC_000913	1,764,785	0	T	A	41.0%	147.8 / 52.1	95	intergenic (‑399/+149)	sufA/ydiH	Fe‑S cluster assembly protein/uncharacterized protein
*	NC_000913	3,585,086	0	A	C	41.0%	165.0 / 24.7	96	Y580D (TAC→GAC)	ggt	gamma‑glutamyltranspeptidase
*	NC_000913	4,332,791	0	A	C	41.0%	176.0 / 16.6	95	V161G (GTG→GGG)	basS	sensory histidine kinase in two‑component regulatory system with BasR
*	NC_000913	2,151,686	0	G	T	41.0%	31.6 / 24.3	61	intergenic (+40/+25)	yegJ/yegK	uncharacterized protein/ser/thr phosphatase‑related protein
*	NC_000913	2,619,230	0	T	C	40.9%	147.5 / 13.6	88	I311V (ATT→GTT)	uraA	uracil permease
*	NC_000913	2,578,143	0	A	C	40.8%	127.2 / 26.8	76	L79V (TTA→GTA)	maeB	malic enzyme: putative oxidoreductase/phosphotransacetylase
*	NC_000913	993,913	0	G	C	40.6%	115.0 / 18.4	64	G44G (GGC→GGG)	ssuB	aliphatic sulfonate ABC transporter ATPase
*	NC_000913	1,222,596	0	G	A	40.6%	85.0 / 34.7	71	F13F (TTC→TTT)	ymgD	uncharacterized protein
*	NC_000913	3,270,455	0	G	T	40.5%	115.2 / 38.0	79	intergenic (+853/+170)	yhaC/garK	pentapetide repeats‑related protein/glycerate kinase I

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 =	122 (1.210)	9 (0.100)	9/280	15.0	7.3%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	115 (1.210)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	925901 =	95 (0.940)	11 (0.110) +C	8/296	16.4	12.4%	noncoding (71/88 nt)	serW	tRNA‑Ser
	?	NC_000913	= 1097399	61 (0.610)					intergenic (+570/+166)	ycdU/serX	putative inner membrane protein/tRNA‑Ser