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 296 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	599,576	0	T	G	50.7%	66.6 / 111.1	68	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	3,601,176	0	T	C	46.8%	43.7 / 24.6	47	E304G (GAA→GGA)	ftsX	putative ABC transporter permease
*	NC_000913	1,622,816	0	G	A	43.4%	36.5 / 51.2	53	intergenic (+75/+144)	yneM/dgcZ	inner membrane‑associated protein/diguanylate cyclase, zinc‑sensing
*	NC_000913	3,601,173	0	A	C	43.2%	55.9 / 13.0	47	V305G (GTG→GGG)	ftsX	putative ABC transporter permease
*	NC_000913	1,376,505	0	A	C	42.4%	113.5 / 13.8	66	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
*	NC_000913	4,287,719	0	T	A	42.4%	66.9 / 32.8	59	intergenic (‑348/‑45)	acs/nrfA	acetyl‑CoA synthetase/nitrite reductase, formate‑dependent, cytochrome
*	NC_000913	29,496	0	T	A	42.2%	98.6 / 37.9	71	intergenic (+301/‑155)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	993,913	0	G	C	42.2%	102.1 / 28.5	71	G44G (GGC→GGG)	ssuB	aliphatic sulfonate ABC transporter ATPase
*	NC_000913	354,288	0	T	G	42.1%	85.2 / 19.3	57	V528G (GTG→GGG)	prpE	propionate‑‑CoA ligase
*	NC_000913	2,252,646	0	T	G	41.8%	86.9 / 12.7	56	V316G (GTA→GGA)	yeiI	putative kinase
*	NC_000913	2,151,686	0	G	T	41.0%	8.2 / 16.0	39	intergenic (+40/+25)	yegJ/yegK	uncharacterized protein/ser/thr phosphatase‑related protein
*	NC_000913	1,969,794	0	A	C	40.8%	76.7 / 10.3	49	G397G (GGT→GGG)	tap	methyl‑accepting protein IV
*	NC_000913	3,601,170	0	G	C	40.8%	72.3 / 18.0	49	A306G (GCA→GGA)	ftsX	putative ABC transporter permease
*	NC_000913	40,525	0	C	T	40.7%	60.9 / 21.0	54	L469L (CTG→CTA)	caiT	putative transporter
*	NC_000913	2,984,441	0	A	C	40.7%	98.3 / 13.5	59	G384G (GGT→GGG)	yqeF	short chain acyltransferase
*	NC_000913	1,271,827	0	A	T	40.3%	95.0 / 31.2	68	V8E (GTA→GAA)	chaA	calcium/sodium:proton antiporter
*	NC_000913	357,890	0	C	A	40.0%	41.0 / 20.1	40	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	3,206,435	0	C	T	39.7%	79.1 / 26.8	65	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	3,333,776	0	G	T	39.6%	78.5 / 20.0	48	E23* (GAG→TAG)	ispB	octaprenyl diphosphate synthase
*	NC_000913	3,601,160	0	G	A	39.6%	59.0 / 24.1	51	F309F (TTC→TTT)	ftsX	putative ABC transporter permease

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	61 (0.870)	15 (0.240)	13/266	6.6	22.8%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	47 (0.750)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	1207790 =	59 (0.840)	10 (0.160)	9/266	8.3	16.0%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	52 (0.830)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1209618	54 (0.770)	13 (0.210)	3/268	12.3	19.0%	pseudogene (2/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
	?	NC_000913	2471897 =	62 (0.980)					pseudogene (226/579 nt)	yfdL	pseudogene, CPS‑53 (KpLE1) prophage;Phage or Prophage Related