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 219 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	646,747	0	T	G	54.3%	38.2 / 57.0	35	T255P (ACC→CCC)	citG	2‑(5''‑triphosphoribosyl)‑3'‑dephosphocoenzyme‑A synthase
*	NC_000913	357,890	0	C	A	54.2%	6.9 / 36.7	24	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	354,288	0	T	G	51.3%	48.0 / 67.7	39	V528G (GTG→GGG)	prpE	propionate‑‑CoA ligase
*	NC_000913	501,564	0	A	C	51.1%	56.5 / 84.6	47	*559E (TAA→GAA)	ybaL	inner membrane putative NAD(P)‑binding transporter
*	NC_000913	504,616	0	T	A	48.6%	32.5 / 29.3	37	L27F (TTA→TTT)	fsr	putative fosmidomycin efflux system protein
*	NC_000913	1,506,028	0	A	C	48.1%	84.0 / 11.1	52	V18G (GTA→GGA)	ydcO	BenE family inner membrane putative transporter
*	NC_000913	3,864,099	0	C	A	47.7%	46.2 / 26.3	44	R67R (CGC→CGA)	yidP	UTRA domain‑containing GntR family putative transcriptional regulator
*	NC_000913	803,869	0	G	T	45.6%	72.9 / 25.2	46	V123L (GTG→TTG)	ybhJ	aconitase family protein
*	NC_000913	1,842,914	0	A	G	45.5%	40.3 / 17.3	46	M182V (ATG→GTG)	gdhA	glutamate dehydrogenase, NADP‑specific
*	NC_000913	1,376,505	0	A	C	45.2%	60.0 / 10.9	42	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
*	NC_000913	1,079,468	0	A	G	44.4%	46.5 / 10.2	36	D55G (GAT→GGT)	putP	proline:sodium symporter
*	NC_000913	616,564	0	A	T	43.8%	43.0 / 13.2	33	Y803F (TAT→TTT)	entF	enterobactin synthase multienzyme complex component, ATP‑dependent
*	NC_000913	3,508,657	0	A	G	42.9%	71.0 / 10.8	49	F386S (TTC→TCC)	yhfW	phosphopentomutase‑related metalloenzyme superfamily protein
*	NC_000913	646,765	0	G	T	42.4%	43.1 / 22.6	33	Q249K (CAA→AAA)	citG	2‑(5''‑triphosphoribosyl)‑3'‑dephosphocoenzyme‑A synthase
*	NC_000913	1,234,233	0	T	A	42.2%	62.2 / 18.0	45	Y162F (TAT→TTT)	nhaB	sodium:proton antiporter
*	NC_000913	3,364,396	0	A	T	42.1%	55.9 / 15.5	38	P530P (CCA→CCT)	yhcD	putative outer membrane fimbrial subunit usher protein
*	NC_000913	3,508,662	0	T	A	42.0%	71.9 / 22.3	50	E384D (GAA→GAT)	yhfW	phosphopentomutase‑related metalloenzyme superfamily protein
*	NC_000913	523,335	0	T	G	41.9%	68.0 / 12.0	44	G25G (GGT→GGG)	rhsD	Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
*	NC_000913	2,865,246	0	A	G	41.9%	66.2 / 12.0	44	E49G (GAA→GGA)	ygbN	putative transporter
*	NC_000913	357,875	0	A	T	41.7%	28.0 / 11.4	24	N272K (AAT→AAA)	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 =	35 (0.690)	7 (0.150)	7/266	6.5	18.4%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	31 (0.680)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1207805	35 (0.690)	6 (0.130)	6/266	7.0	16.2%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	31 (0.680)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related