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 89 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,206,435	0	C	T	71.9%	10.6 / 19.0	32	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	3,206,452	0	C	A	53.1%	0.6 / 27.8	32	intergenic (‑196/‑11)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	925,900	0	A	G	52.3%	39.4 / 63.1	44	noncoding (72/88 nt)	serW	tRNA‑Ser
*	NC_000913	1,622,816	0	G	A	51.6%	3.6 / 45.5	31	intergenic (+75/+144)	yneM/dgcZ	inner membrane‑associated protein/diguanylate cyclase, zinc‑sensing
*	NC_000913	328,791	0	A	G	51.4%	17.9 / 44.6	35	S182P (TCC→CCC)	betI	choline‑inducible betIBA‑betT divergent operon transcriptional repressor
*	NC_000913	2,421,443	0	A	C	51.3%	43.2 / 57.7	39	Y40S (TAC→TCC)	folX	D‑erythro‑7,8‑dihydroneopterin triphosphate 2'‑epimerase and dihydroneopterin aldolase
*	NC_000913	328,803	0	T	G	50.0%	30.5 / 22.8	36	T178P (ACC→CCC)	betI	choline‑inducible betIBA‑betT divergent operon transcriptional repressor
*	NC_000913	599,576	0	T	G	50.0%	44.4 / 17.9	40	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	1,376,505	0	A	C	49.0%	46.7 / 30.8	51	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
*	NC_000913	3,508,662	0	T	A	48.7%	38.4 / 22.3	40	E384D (GAA→GAT)	yhfW	phosphopentomutase‑related metalloenzyme superfamily protein
*	NC_000913	2,624,508	0	A	T	48.5%	21.9 / 18.5	33	N489Y (AAC→TAC)	ppk	polyphosphate kinase, component of RNA degradosome
*	NC_000913	1,534,234	0	G	T	46.7%	33.3 / 14.0	30	E71* (GAG→TAG)	nhoA	N‑hydroxyarylamine O‑acetyltransferase
*	NC_000913	5,159	0	G	A	44.9%	47.5 / 25.2	49	intergenic (+139/‑75)	thrC/yaaX	L‑threonine synthase/DUF2502 family putative periplasmic protein
*	NC_000913	328,807	0	A	T	44.7%	36.1 / 15.7	38	D176E (GAT→GAA)	betI	choline‑inducible betIBA‑betT divergent operon transcriptional repressor
*	NC_000913	3,640,981	0	C	T	44.4%	33.4 / 17.2	36	F40F (TTC→TTT)	dtpB	dipeptide and tripeptide permease B
*	NC_000913	2,421,402	0	T	A	41.5%	62.2 / 17.2	41	I26I (ATT→ATA)	folX	D‑erythro‑7,8‑dihydroneopterin triphosphate 2'‑epimerase and dihydroneopterin aldolase
*	NC_000913	2,624,514	0	A	T	41.2%	38.1 / 13.3	34	I491F (ATT→TTT)	ppk	polyphosphate kinase, component of RNA degradosome
*	NC_000913	1,622,802	0	A	T	40.6%	46.3 / 13.2	32	intergenic (+61/+158)	yneM/dgcZ	inner membrane‑associated protein/diguanylate cyclase, zinc‑sensing
*	NC_000913	2,151,589	0	A	T	40.6%	32.6 / 20.3	33	L135F (TTA→TTT)	yegJ	uncharacterized protein
*	NC_000913	345,328	0	C	A	40.5%	50.7 / 18.0	37	intergenic (+337/‑76)	yahL/yahM	uncharacterized protein/uncharacterized protein

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 =	32 (0.700)	4 (0.100)	4/266	7.2	10.7%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	38 (0.940)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related