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 277 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,376,505	0	A	C	51.1%	47.8 / 76.5	45	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
*	NC_000913	925,900	0	A	G	45.6%	66.5 / 10.5	46	noncoding (72/88 nt)	serW	tRNA‑Ser
*	NC_000913	29,496	0	T	A	45.6%	76.5 / 35.4	57	intergenic (+301/‑155)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	1,825,056	0	G	A	44.3%	75.0 / 33.3	61	intergenic (‑119/+84)	ves/spy	cold‑ and stress‑inducible protein/periplasmic ATP‑independent protein refolding chaperone, stress‑induced
*	NC_000913	213,341	0	A	G	44.1%	84.2 / 25.1	68	G337G (GGA→GGG)	tilS	tRNA(Ile)‑lysidine synthetase
*	NC_000913	718,690	0	T	G	43.8%	74.8 / 14.3	48	T591P (ACC→CCC)	speF	ornithine decarboxylase isozyme, inducible
*	NC_000913	1,435,727	0	G	A	43.6%	72.4 / 33.4	55	intergenic (‑108/+33)	uspF/ompN	stress‑induced protein, ATP‑binding protein/outer membrane pore protein N, non‑specific
*	NC_000913	599,576	0	T	G	43.1%	85.0 / 26.3	59	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	1,825,061	0	G	A	42.2%	88.7 / 30.5	64	intergenic (‑124/+79)	ves/spy	cold‑ and stress‑inducible protein/periplasmic ATP‑independent protein refolding chaperone, stress‑induced
*	NC_000913	2,228,222	0	T	G	41.8%	87.1 / 10.9	55	pseudogene (388/1287 nt)	mdtQ	pseudogene; putative channel/filament proteins
*	NC_000913	3,998,178	0	G	A	41.0%	43.3 / 21.5	39	A66T (GCG→ACG)	uvrD	DNA‑dependent ATPase I and helicase II
*	NC_000913	298,960	0	A	C	40.9%	115.5 / 22.9	66	Y659D (TAT→GAT)	paoC	PaoABC aldehyde oxidoreductase, Moco‑containing subunit
*	NC_000913	366,526	0	T	G	40.9%	122.5 / 16.6	66	T329P (ACC→CCC)	lacI	lactose‑inducible lac operon transcriptional repressor
*	NC_000913	357,890	0	C	A	40.6%	29.2 / 11.2	32	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	1,222,233	0	G	A	40.5%	52.3 / 19.8	42	pseudogene (60/75 nt)	ycgH	pseudogene; putative ATP‑binding component of a transport system
*	NC_000913	1,435,725	0	C	A	40.4%	90.5 / 22.5	53	intergenic (‑106/+35)	uspF/ompN	stress‑induced protein, ATP‑binding protein/outer membrane pore protein N, non‑specific
*	NC_000913	2,578,143	0	A	C	40.3%	110.6 / 21.7	62	L79V (TTA→GTA)	maeB	malic enzyme: putative oxidoreductase/phosphotransacetylase
*	NC_000913	29,486	0	C	A	40.0%	104.8 / 30.1	60	intergenic (+291/‑165)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	2,151,589	0	A	T	40.0%	69.7 / 29.6	50	L135F (TTA→TTT)	yegJ	uncharacterized protein
*	NC_000913	4,394,579	0	G	C	40.0%	91.9 / 21.8	50	G172R (GGC→CGC)	nnr	bifunctional NAD(P)H‑hydrate repair enzyme; C‑terminal domain ADP‑dependent (S)‑NAD(P)H‑hydrate dehydratase and N‑terminal domain NAD(P)H‑hydrate epimerase

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	= 1207805	49 (0.760)	13 (0.230)	13/266	6.2	22.5%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	46 (0.800)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	1207790 =	39 (0.610)	11 (0.190)	11/266	7.0	20.8%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	49 (0.860)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related