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 237 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,413,735	0	A	T	50.0%	23.7 / 23.5	33	Y2* (TAT→TAA)	ydaC	DUF1187 family protein, Rac prophage; putative double‑strand break reduction protein
*	NC_000913	357,890	0	C	A	48.8%	18.1 / 27.4	41	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	3,443,277	0	A	C	47.6%	85.9 / 21.6	64	V274G (GTA→GGA)	secY	preprotein translocase membrane subunit
*	NC_000913	357,880	0	T	C	46.3%	39.3 / 18.2	41	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	941,713	0	T	G	46.3%	61.8 / 23.6	54	V252G (GTG→GGG)	dmsA	dimethyl sulfoxide reductase, anaerobic, subunit A
*	NC_000913	2,001,918	0	A	C	45.8%	62.0 / 14.5	49	intergenic (‑129/+192)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein (flagellin)
*	NC_000913	2,483,254	0	G	A	44.9%	76.2 / 34.6	69	S29L (TCA→TTA)	emrK	multidrug resistance efflux pump membrane fusion protein
*	NC_000913	3,206,435	0	C	T	44.6%	50.2 / 36.4	58	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	2,603,342	0	A	C	44.4%	26.2 / 37.6	37	T509P (ACC→CCC)	hyfB	hydrogenase 4, membrane subunit
*	NC_000913	3,412,898	0	C	T	42.6%	55.3 / 50.1	62	A190T (GCC→ACC)	acrS	acrAB operon transcriptional repressor
*	NC_000913	1,701,310	0	A	C	41.7%	71.2 / 13.1	48	T118T (ACA→ACC)	malY	PLP‑dependent beta‑cystathionase and maltose regulon regulator
*	NC_000913	3,412,901	0	G	T	41.3%	113.0 / 26.5	63	Q189K (CAA→AAA)	acrS	acrAB operon transcriptional repressor
*	NC_000913	1,222,596	0	G	A	40.7%	20.4 / 14.7	27	F13F (TTC→TTT)	ymgD	uncharacterized protein
*	NC_000913	1,322,472	0	C	A	40.0%	60.9 / 11.7	40	E159* (GAA→TAA)	trpE	component I of anthranilate synthase
*	NC_000913	3,665,702	0	C	A	40.0%	141.5 / 42.8	90	A37S (GCG→TCG)	gadX	acid resistance regulon transcriptional activator; autoactivator
*	NC_000913	3,275,611	0	A	C	39.5%	137.5 / 13.8	77	E110D (GAA→GAC)	garD	D‑galactarate dehydrogenase
*	NC_000913	29,496	0	T	A	39.4%	107.0 / 39.3	71	intergenic (+301/‑155)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	4,538,109	0	A	C	39.4%	121.4 / 14.1	69	G219G (GGT→GGG)	nanM	N‑acetylneuraminic acid mutarotase
*	NC_000913	4,580,634	0	C	T	39.3%	99.2 / 20.0	62	E277K (GAA→AAA)	hsdS	specificity determinant for hsdM and hsdR
*	NC_000913	599,576	0	T	G	39.1%	74.9 / 12.2	46	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component

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 (1.300)	3 (0.050)	3/280	6.7	3.4%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	89 (1.430)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)