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

Marginal read alignment evidence
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,604,344	0	C	T	40.4%	69.4 / 32.8	57	S62F (TCT→TTT)	bglJ	DNA‑binding transcriptional regulator BglJ
*	NC_000913	3,556,205	0	A	C	38.3%	67.8 / 17.2	47	S215R (AGT→AGG) ‡	rtcA	RNA 3'‑terminal phosphate cyclase
*	NC_000913	3,556,207	0	T	C	38.3%	53.0 / 26.7	47	S215G (AGT→GGT) ‡	rtcA	RNA 3'‑terminal phosphate cyclase
*	NC_000913	4,111,747	0	G	T	33.3%	77.4 / 16.2	33	N156K (AAC→AAA)	yiiQ	DUF1454 domain‑containing protein YiiQ
*	NC_000913	3,206,435	0	C	T	30.0%	80.8 / 27.6	50	intergenic (‑179/‑28)	ttdR/ttdA	DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha
*	NC_000913	2,326,450	0	T	G	29.0%	104.9 / 36.8	62	G114G (GGT→GGG)	atoB	acetyl‑CoA acetyltransferase
*	NC_000913	4,429,984	0	T	G	28.3%	118.2 / 20.8	60	L41V (TTG→GTG)	cycA	serine/alanine/glycine/cycloserine:H(+)symporter
*	NC_000913	4,032,731	0	T	G	26.8%	139.4 / 19.6	71	G80G (GGT→GGG)	yigZ	IMPACT family member YigZ
*	NC_000913	2,001,918	0	A	C	26.2%	82.4 / 12.7	42	intergenic (‑129/+192)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein
*	NC_000913	650,809	0	T	G	25.4%	129.2 / 16.4	63	T350P (ACC→CCC)	citC	citrate lyase synthetase
*	NC_000913	888,014	0	T	G	25.0%	106.9 / 10.2	52	noncoding (44/81 nt)	rybB	small regulatory RNA RybB
*	NC_000913	4,296,060	0	C	T	25.0%	162.5 / 48.7	80	intergenic (+266/+376)	gltP/yjcO	glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
*	NC_000913	445,558	0	A	C	22.6%	114.6 / 18.5	53	V370G (GTA→GGA)	yajR	putative major facilitator superfamily transport protein YajR
*	NC_000913	753,125	0	T	A	21.9%	165.0 / 17.9	64	intergenic (‑330/+60)	ybgD/gltA	putative fimbrial protein YbgD/citrate synthase
*	NC_000913	3,740,909	0	T	G	20.7%	180.5 / 18.5	82	V402G (GTG→GGG)	avtA	valine‑‑pyruvate aminotransferase
*	NC_000913	1,335,691	0	T	G	20.4%	203.2 / 12.7	88	intergenic (+24/‑140)	ymiC/acnA	protein YmiC/aconitate hydratase 1
*	NC_000913	1,577,123	0	A	C	20.0%	244.8 / 25.9	105	V166G (GTA→GGA)	yddB	putative TonB‑dependent receptor
*	NC_000913	3,206,444	0	T	A	20.0%	117.8 / 12.6	50	intergenic (‑188/‑19)	ttdR/ttdA	DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha

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	= 4542690	94 (1.040)	18 (0.210)	17/256	3.2	16.2%	intergenic (+57/‑425)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	= 4542986	99 (1.170)					intergenic (+353/‑129)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
*	?	NC_000913	4542682 =	98 (1.080)	13 (0.150)	9/256	5.2	12.0%	intergenic (+49/‑433)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	4542996 =	99 (1.170)					intergenic (+363/‑119)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
*	?	NC_000913	= 3954165	89 (0.980)	4 (0.050)	4/268	7.5	4.4%	coding (688/1851 nt)	ilvD	dihydroxy‑acid dehydratase
	?	NC_000913	3954169 =	86 (0.970)					coding (692/1851 nt)	ilvD	dihydroxy‑acid dehydratase
*	?	NC_000913	= 2384812	110 (1.220)	3 (0.030)	3/268	8.0	2.7%	coding (911/1728 nt)	yfbK	IPR002035/DUF3520 domain‑containing protein YfbK
	?	NC_000913	2384816 =	106 (1.200)					coding (907/1728 nt)	yfbK	IPR002035/DUF3520 domain‑containing protein YfbK