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 272 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,043,030	0	A	G	53.1%	27.3 / 43.1	32	N206D (AAT→GAT)	srkA	Cpx stress response Thr/Ser protein kinase; MazF antagonist protein
*	NC_000913	599,576	0	T	G	51.2%	31.5 / 71.2	43	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	4,042,993	0	C	T	50.0%	4.7 / 11.0	26	F193F (TTC→TTT)	srkA	Cpx stress response Thr/Ser protein kinase; MazF antagonist protein
*	NC_000913	29,496	0	T	A	49.0%	43.3 / 36.0	51	intergenic (+301/‑155)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	3,206,435	0	C	T	49.0%	24.5 / 47.1	51	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	753,125	0	T	A	47.8%	39.8 / 29.7	46	intergenic (‑330/+60)	ybgD/gltA	putative fimbrial‑like adhesin protein/citrate synthase
*	NC_000913	2,421,443	0	A	C	47.7%	59.7 / 12.7	44	Y40S (TAC→TCC)	folX	D‑erythro‑7,8‑dihydroneopterin triphosphate 2'‑epimerase and dihydroneopterin aldolase
*	NC_000913	1,755,871	0	T	A	46.8%	48.0 / 29.0	47	G58G (GGT→GGA)	pykF	pyruvate kinase I
*	NC_000913	1,825,056	0	G	A	46.5%	50.7 / 23.1	43	intergenic (‑119/+84)	ves/spy	cold‑ and stress‑inducible protein/periplasmic ATP‑independent protein refolding chaperone, stress‑induced
*	NC_000913	3,720	0	T	G	45.8%	71.2 / 12.4	48	V307G (GTA→GGA)	thrB	homoserine kinase
*	NC_000913	1,701,303	0	T	C	45.0%	74.9 / 18.2	61	I116T (ATC→ACC)	malY	PLP‑dependent beta‑cystathionase and maltose regulon regulator
*	NC_000913	907,602	0	A	C	44.8%	82.1 / 15.0	59	G227G (GGT→GGG)	ybjT	putative NAD‑dependent oxidoreductase
*	NC_000913	1,222,233	0	G	A	44.7%	42.9 / 24.8	47	pseudogene (60/75 nt)	ycgH	pseudogene; putative ATP‑binding component of a transport system
*	NC_000913	2,001,918	0	A	C	44.3%	99.8 / 14.5	61	intergenic (‑129/+192)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein (flagellin)
*	NC_000913	1,621,118	0	A	C	44.1%	96.7 / 14.4	60	V7G (GTG→GGG)	eamA	cysteine and O‑acetyl‑L‑serine efflux system
*	NC_000913	3,947,850	0	C	T	44.0%	64.1 / 25.9	50	E40K (GAA→AAA)	hdfR	flhDC operon transcriptional repressor
*	NC_000913	4,604,344	0	C	T	43.9%	40.8 / 19.0	41	S62F (TCT→TTT)	bglJ	bgl operon transcriptional activator
*	NC_000913	29,486	0	C	A	43.6%	84.3 / 33.8	55	intergenic (+291/‑165)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	1,825,061	0	G	A	43.2%	57.9 / 23.0	44	intergenic (‑124/+79)	ves/spy	cold‑ and stress‑inducible protein/periplasmic ATP‑independent protein refolding chaperone, stress‑induced
*	NC_000913	357,890	0	C	A	42.9%	16.6 / 14.2	28	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor

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	1207790 =	43 (0.760)	11 (0.220)	10/266	5.8	24.6%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	29 (0.580)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1207805	48 (0.850)	7 (0.140)	7/266	7.2	16.5%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	28 (0.560)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related