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	48.6%	38.5 / 59.2	74	S62F (TCT→TTT)	bglJ	DNA‑binding transcriptional regulator BglJ
*	NC_000913	1,825,061	0	G	A	33.3%	59.6 / 15.0	39	intergenic (‑124/+79)	ves/spy	HutD family protein Ves/ATP‑independent periplasmic chaperone
*	NC_000913	2,628,625	0	A	C	32.5%	71.7 / 13.9	40	V105G (GTC→GGC)	pdeF	cyclic di‑GMP phosphodiesterase PdeF
*	NC_000913	4,111,747	0	G	T	32.4%	72.7 / 17.4	34	N156K (AAC→AAA)	yiiQ	DUF1454 domain‑containing protein YiiQ
*	NC_000913	501,575	0	A	C	28.9%	75.7 / 11.6	38	V555G (GTG→GGG)	ybaL	putative transporter YbaL
*	NC_000913	1,068,173	0	T	G	26.9%	162.9 / 27.9	78	G31G (GGT→GGG)	ymdF	conserved protein YmdF
*	NC_000913	650,809	0	T	G	26.6%	132.1 / 17.7	64	T350P (ACC→CCC)	citC	citrate lyase synthetase
*	NC_000913	4,101,514	0	G	T	26.5%	125.2 / 19.0	49	intergenic (+84/‑176)	sodA/kdgT	superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter
*	NC_000913	4,296,060	0	C	T	25.9%	165.1 / 53.7	85	intergenic (+266/+376)	gltP/yjcO	glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
*	NC_000913	3,206,435	0	C	T	24.4%	80.3 / 14.7	41	intergenic (‑179/‑28)	ttdR/ttdA	DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha
*	NC_000913	2,001,918	0	A	C	24.4%	183.6 / 20.1	78	intergenic (‑129/+192)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein
*	NC_000913	445,558	0	A	C	23.4%	101.4 / 16.5	47	V370G (GTA→GGA)	yajR	putative major facilitator superfamily transport protein YajR
*	NC_000913	888,014	0	T	G	23.1%	141.0 / 11.6	65	noncoding (44/81 nt)	rybB	small regulatory RNA RybB
*	NC_000913	29,496	0	T	A	22.4%	120.4 / 11.8	49	intergenic (+301/‑155)	dapB/carA	4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha
*	NC_000913	2,326,450	0	T	G	21.9%	141.3 / 33.1	64	G114G (GGT→GGG)	atoB	acetyl‑CoA acetyltransferase
*	NC_000913	599,576	0	T	G	21.4%	97.2 / 12.5	42	V288G (GTG→GGG)	cusA	copper/silver export system RND permease
*	NC_000913	753,125	0	T	A	21.4%	181.8 / 16.7	70	intergenic (‑330/+60)	ybgD/gltA	putative fimbrial protein YbgD/citrate synthase

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 =	100 (1.140)	17 (0.220)	17/244	2.8	17.0%	coding (290/630 nt)	ycfK	e14 prophage; protein StfP
	?	NC_000913	1209619 =	78 (1.010)					pseudogene (37/537 nt)	stfE	e14 prophage; putative side tail fiber protein fragment
*	?	NC_000913	4542682 =	108 (1.230)	10 (0.120)	10/258	4.6	9.5%	intergenic (+49/‑433)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	4542996 =	89 (1.090)					intergenic (+363/‑119)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
*	?	NC_000913	= 1207805	90 (1.030)	9 (0.120)	9/244	4.6	10.4%	coding (305/630 nt)	ycfK	e14 prophage; protein StfP
	?	NC_000913	= 1209602	76 (0.980)					pseudogene (54/537 nt)	stfE	e14 prophage; putative side tail fiber protein fragment
*	?	NC_000913	= 4542690	98 (1.120)	7 (0.090)	6/258	5.9	7.2%	intergenic (+57/‑425)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	= 4542986	89 (1.090)					intergenic (+353/‑129)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
*	?	NC_000913	= 995677	66 (0.750)	4 (0.050)	3/270	7.6	5.8%	coding (312/1146 nt)	ssuD	FMNH2‑dependent alkanesulfonate monooxygenase
	?	NC_000913	995681 =	66 (0.770)					coding (308/1146 nt)	ssuD	FMNH2‑dependent alkanesulfonate monooxygenase
*	?	NC_000913	= 69455	58 (0.660)	3 (0.030)	3/270	7.6	5.1%	coding (594/1701 nt)	araB	ribulokinase
	?	NC_000913	69459 =	55 (0.640)					coding (590/1701 nt)	araB	ribulokinase