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 356 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	63.8%	‑3.4 / 44.2	47	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	357,880	0	T	C	52.1%	43.9 / 73.0	49	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	29,486	0	C	A	48.3%	67.8 / 33.7	60	intergenic (+291/‑165)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	2,434,882	0	T	G	48.2%	60.7 / 15.3	56	Y252S (TAC→TCC)	truA	tRNA pseudouridine(38‑40) synthase
*	NC_000913	357,875	0	A	T	48.0%	43.6 / 28.3	50	N272K (AAT→AAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	1,413,735	0	A	T	47.5%	30.7 / 31.1	40	Y2* (TAT→TAA)	ydaC	DUF1187 family protein, Rac prophage; putative double‑strand break reduction protein
*	NC_000913	4,486,580	0	A	G	45.6%	79.3 / 12.9	57	G121G (GGA→GGG)	lptF	lipopolysaccharide export ABC permease
*	NC_000913	29,496	0	T	A	45.3%	64.4 / 39.6	64	intergenic (+301/‑155)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	599,576	0	T	G	45.1%	115.8 / 25.3	71	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	289,251	0	T	C	44.1%	84.9 / 20.2	59	intergenic (‑89/+50)	yagI/argF	CP4‑6 prophage; putative DNA‑binding transcriptional regulator/ornithine carbamoyltransferase 2, chain F; CP4‑6 prophage
*	NC_000913	5,159	0	G	A	43.1%	69.3 / 40.9	65	intergenic (+139/‑75)	thrC/yaaX	L‑threonine synthase/DUF2502 family putative periplasmic protein
*	NC_000913	3,578,290	0	A	C	43.1%	112.4 / 14.4	65	V146G (GTG→GGG)	gntR	d‑gluconate inducible gluconate regulon transcriptional repressor
*	NC_000913	501,564	0	A	C	42.9%	129.5 / 12.7	70	*559E (TAA→GAA)	ybaL	inner membrane putative NAD(P)‑binding transporter
*	NC_000913	4,486,576	0	C	G	42.9%	87.6 / 19.4	56	A120G (GCG→GGG)	lptF	lipopolysaccharide export ABC permease
*	NC_000913	1,097,581	0	A	G	42.6%	90.3 / 16.8	55	noncoding (72/88 nt)	serX	tRNA‑Ser
*	NC_000913	1,622,816	0	G	A	42.6%	46.7 / 49.4	54	intergenic (+75/+144)	yneM/dgcZ	inner membrane‑associated protein/diguanylate cyclase, zinc‑sensing
*	NC_000913	4,196,089	0	G	T	42.4%	85.5 / 30.0	66	T4K (ACA→AAA)	thiC	phosphomethylpyrimidine synthase
*	NC_000913	357,887	0	C	A	42.2%	24.7 / 19.8	45	L268F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	3,508,662	0	T	A	42.2%	96.2 / 22.6	64	E384D (GAA→GAT)	yhfW	phosphopentomutase‑related metalloenzyme superfamily protein
*	NC_000913	3,578,287	0	T	C	41.9%	94.7 / 13.9	62	E147G (GAA→GGA)	gntR	d‑gluconate inducible gluconate regulon transcriptional repressor

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 (0.740)	9 (0.150)	9/266	8.0	17.7%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	40 (0.680)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	1207790 =	46 (0.700)	9 (0.150)	9/266	8.0	17.6%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	43 (0.730)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1209618	46 (0.700)	8 (0.130)	3/268	11.9	13.2%	pseudogene (2/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
	?	NC_000913	2471897 =	64 (1.080)					pseudogene (226/579 nt)	yfdL	pseudogene, CPS‑53 (KpLE1) prophage;Phage or Prophage Related