breseq  version 0.35.4  revision f352f80f4bc9 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence (highest frequency 20 of 23 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,364,558	0	T	C	50.3%	25.1 / inf	296	S584S (AGT→AGC)	yhcD	putative fimbrial usher protein YhcD
*	NC_000913	4,604,344	0	C	T	46.4%	49.2 / 46.2	69	S62F (TCT→TTT)	bglJ	DNA‑binding transcriptional regulator BglJ
*	NC_000913	4,083,877	0	T	C	45.2%	12.1 / 130.2	93	D649G (GAC→GGC)	fdoG	formate dehydrogenase O subunit alpha
*	NC_000913	4,111,747	0	G	T	41.9%	62.3 / 38.7	43	N156K (AAC→AAA)	yiiQ	DUF1454 domain‑containing protein YiiQ
*	NC_000913	2,001,918	0	A	C	39.3%	30.0 / 15.9	28	intergenic (‑129/+192)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein
*	NC_000913	4,111,752	0	T	C	34.0%	76.1 / 10.6	50	K155E (AAA→GAA)	yiiQ	DUF1454 domain‑containing protein YiiQ
*	NC_000913	2,326,450	0	T	G	33.9%	97.1 / 38.9	62	G114G (GGT→GGG)	atoB	acetyl‑CoA acetyltransferase
*	NC_000913	3,206,435	0	C	T	32.5%	50.9 / 21.3	40	intergenic (‑179/‑28)	ttdR/ttdA	DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha
*	NC_000913	753,125	0	T	A	31.7%	74.9 / 16.2	41	intergenic (‑330/+60)	ybgD/gltA	putative fimbrial protein YbgD/citrate synthase
*	NC_000913	646,747	0	T	G	31.4%	61.6 / 13.4	35	T255P (ACC→CCC)	citG	triphosphoribosyl‑dephospho‑CoA synthase
*	NC_000913	3,206,444	0	T	A	30.8%	59.6 / 13.0	39	intergenic (‑188/‑19)	ttdR/ttdA	DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha
*	NC_000913	4,628,649	0	A	C	29.8%	138.9 / 16.6	67	intergenic (+102/+206)	nadR/ettA	DNA‑binding transcriptional repressor/NMN adenylyltransferase NadR/energy‑dependent translational throttle protein EttA
*	NC_000913	2,583,424	0	T	G	28.6%	98.3 / 11.3	49	T19P (ACC→CCC)	nudK	GDP‑mannose hydrolase
*	NC_000913	4,296,060	0	C	T	28.4%	139.2 / 58.9	81	intergenic (+266/+376)	gltP/yjcO	glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
*	NC_000913	646,760	0	T	C	27.8%	62.1 / 11.9	36	K250K (AAA→AAG)	citG	triphosphoribosyl‑dephospho‑CoA synthase
*	NC_000913	3,740,909	0	T	G	27.1%	113.5 / 13.4	59	V402G (GTG→GGG)	avtA	valine‑‑pyruvate aminotransferase
*	NC_000913	372,640	0	T	G	26.3%	113.7 / 18.6	57	L176V (TTA→GTA)	mhpD	2‑hydroxypentadienoate hydratase
*	NC_000913	3,531,440	0	A	C	25.3%	183.4 / 16.2	81	Y334D (TAT→GAT)	yhgE	putative transport protein YhgE
*	NC_000913	2,721,378	0	G	A	25.0%	142.1 / 45.4	76	E476K (GAA→AAA)	patZ	peptidyl‑lysine acetyltransferase
*	NC_000913	3,240,977	2	.	G	25.0%	52.5 / 28.3	28	coding (1034/1245 nt)	sstT	serine/threonine:Na(+) symporter

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	= 374963	NA (NA)	10 (0.190)	6/190	4.2	NA	noncoding (33/34 nt)	other	REP31a
	?	NC_000913	= 377487	NA (NA)					intergenic (+176/+48)	yaiL/frmB	DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB
*	?	NC_000913	374922 =	NA (NA)	3 (0.050)	3/202	5.9	NA	intergenic (+41/‑537)	mhpE/mhpT	4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter
	?	NC_000913	377430 =	NA (NA)					intergenic (+119/+105)	yaiL/frmB	DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB
*	?	NC_000913	1462089 =	64 (0.850)	4 (0.060)	3/252	6.9	5.3%	coding (1197/1206 nt)	paaJ	beta‑ketoadipyl‑CoA thiolase
	?	NC_000913	1462223 =	84 (1.230)					coding (99/1314 nt)	paaK	phenylacetate‑CoA ligase