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 220 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,056,115	0	A	C	66.7%	7.2 / 31.9	36	G75G (GGT→GGG)	glnL	sensory histidine kinase in two‑component regulatory system with GlnG
*	NC_000913	4,042,993	0	C	T	60.0%	‑5.3 / 17.9	26	F193F (TTC→TTT)	srkA	Cpx stress response Thr/Ser protein kinase; MazF antagonist protein
*	NC_000913	599,576	0	T	G	54.2%	36.3 / 75.7	48	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	3,001,170	0	A	C	53.7%	35.9 / 57.2	41	T276P (ACC→CCC)	xdhA	xanthine dehydrogenase, molybdenum binding subunit
*	NC_000913	3,001,164	0	A	C	51.2%	32.2 / 66.9	41	T274P (ACC→CCC)	xdhA	xanthine dehydrogenase, molybdenum binding subunit
*	NC_000913	354,288	0	T	G	50.0%	31.1 / 24.5	42	V528G (GTG→GGG)	prpE	propionate‑‑CoA ligase
*	NC_000913	993,913	0	G	C	50.0%	47.5 / 13.2	34	G44G (GGC→GGG)	ssuB	aliphatic sulfonate ABC transporter ATPase
*	NC_000913	993,917	0	A	C	50.0%	39.5 / 10.4	32	V43G (GTG→GGG)	ssuB	aliphatic sulfonate ABC transporter ATPase
*	NC_000913	1,825,056	0	G	A	50.0%	50.5 / 36.8	58	intergenic (‑119/+84)	ves/spy	cold‑ and stress‑inducible protein/periplasmic ATP‑independent protein refolding chaperone, stress‑induced
*	NC_000913	370,888	0	A	C	48.6%	41.2 / 10.4	36	L204F (TTA→TTC)	mhpB	2,3‑dihydroxyphenylpropionate 1,2‑dioxygenase
*	NC_000913	1,825,061	0	G	A	48.3%	51.1 / 42.1	60	intergenic (‑124/+79)	ves/spy	cold‑ and stress‑inducible protein/periplasmic ATP‑independent protein refolding chaperone, stress‑induced
*	NC_000913	925,912	0	G	C	47.8%	63.4 / 24.8	47	noncoding (60/88 nt)	serW	tRNA‑Ser
*	NC_000913	3,206,435	0	C	T	47.7%	46.2 / 53.4	65	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	2,984,441	0	A	C	47.6%	60.0 / 12.9	42	G384G (GGT→GGG)	yqeF	short chain acyltransferase
*	NC_000913	1,222,233	0	G	A	46.2%	34.3 / 19.6	39	pseudogene (60/75 nt)	ycgH	pseudogene; putative ATP‑binding component of a transport system
*	NC_000913	343,444	0	A	G	45.0%	49.0 / 13.3	40	G187G (GGA→GGG)	yahK	broad specificity NADPH‑dependent aldehyde reductase, Zn‑containing
*	NC_000913	29,496	0	T	A	44.9%	57.0 / 30.1	49	intergenic (+301/‑155)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	3,508,657	0	A	G	44.7%	67.7 / 10.0	47	F386S (TTC→TCC)	yhfW	phosphopentomutase‑related metalloenzyme superfamily protein
*	NC_000913	1,222,242	0	G	T	44.1%	49.0 / 10.1	34	pseudogene (69/75 nt)	ycgH	pseudogene; putative ATP‑binding component of a transport system
*	NC_000913	3,423,290	0	A	C	44.0%	41.2 / 23.1	50	intergenic (+96/+133)	yhdZ/rrfF	putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon

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 =	52 (0.970)	8 (0.170)	8/266	6.1	15.9%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	38 (0.800)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1207805	53 (0.990)	7 (0.150)	7/266	6.6	14.4%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	36 (0.750)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related