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 26 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,097,574	0	G	.	71.4%	47.4 / 20.5	21	noncoding (79/88 nt)	serX	tRNA‑Ser
*	NC_000913	1,097,392	1	.	G	50.0%	11.7 / 23.0	14	intergenic (+563/+173)	ycdU/serX	uncharacterized protein YcdU/tRNA‑Ser
*	NC_000913	4,074,913	0	A	.	48.9%	177.8 / 162.6	92	coding (245/786 nt)	yihW	putative DNA‑binding transcriptional regulator YihW
*	NC_000913	1,775,703	0	T	C	48.4%	‑1.7 / 83.5	62	G39G (GGT→GGC)	ydiF	putative acetate‑CoA transferase
*	NC_000913	1,097,357	0	A	G	47.1%	‑3.8 / 18.0	17	intergenic (+528/+208)	ycdU/serX	uncharacterized protein YcdU/tRNA‑Ser
*	NC_000913	1,507,935	0	T	C	46.3%	17.8 / 105.8	82	R385R (CGT→CGC)	rlhA	23S rRNA 5‑hydroxycytidine C2501 synthase
*	NC_000913	4,604,344	0	C	T	44.3%	49.5 / 60.6	79	S62F (TCT→TTT)	bglJ	DNA‑binding transcriptional regulator BglJ
*	NC_000913	4,207,185	0	A	G	42.6%	58.9 / 138.3	122	G116G (GGT→GGC)	purH	bifunctional AICAR transformylase/IMP cyclohydrolase
*	NC_000913	3,556,205	0	A	C	39.1%	63.2 / 20.5	46	S215R (AGT→AGG) ‡	rtcA	RNA 3'‑terminal phosphate cyclase
*	NC_000913	3,556,207	0	T	C	38.3%	64.5 / 16.8	47	S215G (AGT→GGT) ‡	rtcA	RNA 3'‑terminal phosphate cyclase
*	NC_000913	4,111,747	0	G	T	36.8%	74.7 / 19.2	38	N156K (AAC→AAA)	yiiQ	DUF1454 domain‑containing protein YiiQ
*	NC_000913	4,568,504	0	T	G	35.0%	136.8 / 16.3	80	T6P (ACC→CCC)	mdtM	multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter
*	NC_000913	3,192,592	0	G	A	34.3%	107.6 / 96.3	105	D129N (GAC→AAC)	yqiJ	putative inner membrane protein
*	NC_000913	3,943,488	0	T	G	30.8%	58.6 / 12.7	39	noncoding (54/76 nt)	gltU	tRNA‑Glu
*	NC_000913	2,326,450	0	T	G	28.1%	120.9 / 28.7	64	G114G (GGT→GGG)	atoB	acetyl‑CoA acetyltransferase
*	NC_000913	29,496	0	T	A	27.3%	66.8 / 12.3	33	intergenic (+301/‑155)	dapB/carA	4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha
*	NC_000913	753,114	0	G	T	26.2%	158.5 / 10.7	65	intergenic (‑319/+71)	ybgD/gltA	putative fimbrial protein YbgD/citrate synthase
*	NC_000913	3,404,218	0	T	G	25.7%	159.5 / 18.1	74	G245G (GGT→GGG)	yhdH	acrylyl‑CoA reductase
*	NC_000913	753,125	0	T	A	25.4%	150.1 / 17.8	63	intergenic (‑330/+60)	ybgD/gltA	putative fimbrial protein YbgD/citrate synthase
*	NC_000913	3,181,908	0	A	G	25.0%	178.7 / 59.5	104	V176A (GTG→GCG)	ygiD	4,5‑DOPA dioxygenase extradiol

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	59 (0.680)	11 (0.140)	10/256	4.6	16.4%	intergenic (+57/‑425)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	= 4542986	57 (0.710)					intergenic (+353/‑129)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
*	?	NC_000913	4542682 =	61 (0.710)	9 (0.110)	7/256	5.5	13.6%	intergenic (+49/‑433)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	4542996 =	57 (0.710)					intergenic (+363/‑119)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
*	?	NC_000913	374922 =	NA (NA)	4 (0.060)	3/200	6.3	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