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 80 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	4,036,390	0	A	G	48.6%	36.0 / 14.8	37	N206D (AAT→GAT)	srkA	stress response kinase SrkA
*	NZ_CP009273	1,819,313	0	G	A	41.5%	68.1 / 29.7	53	intergenic (‑119/+84)	ves/spy	environmental stress‑induced protein Ves/ATP‑independent periplasmic protein‑refolding chaperone Spy
*	NZ_CP009273	1,819,318	0	G	A	41.5%	78.0 / 24.6	54	intergenic (‑124/+79)	ves/spy	environmental stress‑induced protein Ves/ATP‑independent periplasmic protein‑refolding chaperone Spy
*	NZ_CP009273	2,380,357	0	A	T	38.9%	90.6 / 21.7	54	intergenic (+47/‑56)	yfbL/yfbM	M28 family metallopeptidase/YfbM family protein
*	NZ_CP009273	29,496	0	T	A	38.8%	87.8 / 19.0	49	intergenic (+301/‑155)	dapB/carA	4‑hydroxy‑tetrahydrodipicolinate reductase/glutamine‑hydrolyzing carbamoyl‑phosphate synthase small subunit
*	NZ_CP009273	2,380,341	0	G	A	38.2%	73.7 / 31.6	55	intergenic (+31/‑72)	yfbL/yfbM	M28 family metallopeptidase/YfbM family protein
*	NZ_CP009273	2,380,362	0	C	T	37.9%	76.0 / 40.6	58	intergenic (+52/‑51)	yfbL/yfbM	M28 family metallopeptidase/YfbM family protein
*	NZ_CP009273	1,819,288	0	C	T	37.5%	65.9 / 31.2	50	intergenic (‑94/+109)	ves/spy	environmental stress‑induced protein Ves/ATP‑independent periplasmic protein‑refolding chaperone Spy
*	NZ_CP009273	4,419,801	0	T	G	36.7%	118.2 / 11.6	60	L41V (TTG→GTG)	cycA	D‑serine/D‑alanine/glycine transporter
*	NZ_CP009273	4,594,167	0	C	T	36.7%	81.6 / 26.8	60	S64F (TCT→TTT)	bglJ	DNA‑binding transcriptional activator BglJ
*	NZ_CP009273	4,526,014	0	A	T	36.2%	61.8 / 29.1	48	intergenic (+166/+102)	yjhR/BW25113_RS26295	helicase YjhR/HNH endonuclease
*	NZ_CP009273	4,594,161	0	C	T	35.0%	88.7 / 25.1	60	S62F (TCT→TTT)	bglJ	DNA‑binding transcriptional activator BglJ
*	NZ_CP009273	71,566	0	C	T	34.8%	78.3 / 19.0	46	L134L (CTG→CTA)	thiB	thiamine ABC transporter substrate binding subunit
*	NZ_CP009273	2,178,678	0	T	G	34.7%	131.4 / 20.8	72	T35P (ACC→CCC)	thiM	hydroxyethylthiazole kinase
*	NZ_CP009273	2,819,597	0	A	C	34.7%	79.5 / 14.3	50	N136T (AAC→ACC)	srlA	PTS glucitol/sorbitol transporter subunit IIC
*	NZ_CP009273	4,049,475	0	A	C	34.5%	113.6 / 12.7	58	G75G (GGT→GGG)	glnL	nitrogen regulation protein NR(II)
*	NZ_CP009273	4,501,865	0	A	C	33.9%	113.8 / 13.1	59	L123V (TTG→GTG)	fecD	Fe(3+) dicitrate ABC transporter permease subunit FecD
*	NZ_CP009273	3,199,805	0	C	A	32.8%	84.8 / 14.7	58	intergenic (‑190/‑17)	ttdR/ttdA	DNA‑binding transcriptional activator TtdR/L(+)‑tartrate dehydratase subunit alpha
*	NZ_CP009273	3,725,073	0	G	A	32.8%	89.0 / 19.0	58	E195K (GAA→AAA)	xylF	D‑xylose ABC transporter substrate‑binding protein
*	NZ_CP009273	1,598,494	0	C	T	32.6%	67.3 / 15.4	44	S64L (TCG→TTG)	lsrD	autoinducer 2 ABC transporter permease LsrD

Marginal new junction evidence (sorted from low to high skew)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	= 4532507	84 (1.190)	4 (0.060)	4/478	11.1	5.1%	intergenic (+57/‑425)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
	?	NZ_CP009273	= 4532803	67 (0.990)					intergenic (+353/‑129)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
*	?	NZ_CP009273	= 280006	80 (1.130)	3 (0.040)	3/470	11.7	4.7%	coding (1095/1968 nt)	yagF	xylonate dehydratase YagF
	?	NZ_CP009273	3351942 =	45 (0.670)					coding (3859/4461 nt)	gltB	glutamate synthase large subunit
*	?	NZ_CP009273	4532499 =	85 (1.210)	3 (0.040)	3/478	11.9	3.9%	intergenic (+49/‑433)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
	?	NZ_CP009273	4532813 =	67 (0.990)					intergenic (+363/‑119)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA