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 529 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,604,344	0	C	T	47.2%	54.5 / 49.8	72	S62F (TCT→TTT)	bglJ	bgl operon transcriptional activator
*	NC_000913	1,097,581	0	A	G	47.1%	90.4 / 30.9	71	noncoding (72/88 nt)	serX	tRNA‑Ser
*	NC_000913	357,890	0	C	A	46.8%	31.0 / 30.9	47	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	1,153,573	0	T	G	45.6%	63.8 / 19.4	46	Y92D (TAC→GAC)	pabC	4‑amino‑4‑deoxychorismate lyase component of para‑aminobenzoate synthase multienzyme complex
*	NC_000913	847,444	0	G	T	45.5%	73.8 / 34.0	55	I187I (ATC→ATA)	glnH	glutamine transporter subunit
*	NC_000913	1,376,505	0	A	C	45.3%	82.2 / 11.7	54	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
*	NC_000913	659,934	0	T	G	44.6%	122.1 / 11.9	74	T95P (ACC→CCC)	lipA	lipoate synthase
*	NC_000913	357,880	0	T	C	44.2%	58.9 / 20.4	52	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	1,397,830	0	T	C	44.2%	69.1 / 12.6	55	I265V (ATT→GTT)	uspE	stress‑induced protein
*	NC_000913	2,001,911	0	G	A	43.8%	52.0 / 27.5	48	intergenic (‑122/+199)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein (flagellin)
*	NC_000913	599,576	0	T	G	43.5%	99.6 / 18.4	63	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	4,604,350	0	C	T	43.1%	72.8 / 38.0	72	S64F (TCT→TTT)	bglJ	bgl operon transcriptional activator
*	NC_000913	1,157,271	0	T	G	42.6%	97.4 / 10.4	62	G165G (GGT→GGG)	ycfH	putative DNase
*	NC_000913	718,659	0	T	A	42.4%	102.3 / 34.6	66	D601V (GAT→GTT)	speF	ornithine decarboxylase isozyme, inducible
*	NC_000913	281,089	0	A	C	42.4%	97.2 / 11.2	61	Y299D (TAT→GAT)	yagA	CP4‑6 prophage; putative DNA‑binding transcriptional regulator
*	NC_000913	354,288	0	T	G	42.3%	84.7 / 12.2	52	V528G (GTG→GGG)	prpE	propionate‑‑CoA ligase
*	NC_000913	659,940	0	T	A	42.2%	114.0 / 29.9	71	I93F (ATT→TTT)	lipA	lipoate synthase
*	NC_000913	3,270,455	0	G	T	42.2%	92.9 / 29.5	64	intergenic (+853/+170)	yhaC/garK	pentapetide repeats‑related protein/glycerate kinase I
*	NC_000913	3,443,277	0	A	C	41.9%	114.9 / 13.2	62	V274G (GTA→GGA)	secY	preprotein translocase membrane subunit
*	NC_000913	1,969,794	0	A	C	41.3%	99.1 / 22.0	63	G397G (GGT→GGG)	tap	methyl‑accepting protein IV

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	= 4542690	86 (1.210)	10 (0.150)	9/280	9.4	11.0%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	81 (1.210)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	4542682 =	85 (1.190)	10 (0.150)	9/280	9.4	11.0%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	82 (1.220)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)