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 74 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	748,581	0	T	A	40.8%	59.3 / 27.6	49	intergenic (‑330/+60)	ybgD/gltA	fimbrial protein/citrate synthase
*	NZ_CP009273	4,091,442	0	G	T	38.3%	79.6 / 18.4	47	intergenic (+84/‑176)	sodA/kdgT	superoxide dismutase [Mn]/2‑keto‑3‑deoxygluconate transporter
*	NZ_CP009273	748,577	0	C	A	34.7%	85.7 / 10.6	49	intergenic (‑326/+64)	ybgD/gltA	fimbrial protein/citrate synthase
*	NZ_CP009273	3,199,799	0	C	A	34.0%	70.4 / 18.6	54	intergenic (‑184/‑23)	ttdR/ttdA	DNA‑binding transcriptional activator TtdR/L(+)‑tartrate dehydratase subunit alpha
*	NZ_CP009273	4,555,655	0	T	G	33.3%	143.1 / 12.5	66	T5P (ACC→CCC)	yjiM	double‑cubane‑cluster‑containing anaerobic reductase
*	NZ_CP009273	5,159	0	G	A	32.6%	82.5 / 17.2	50	intergenic (+139/‑75)	thrC/yaaX	threonine synthase/DUF2502 domain‑containing protein
*	NZ_CP009273	3,907,913	0	A	G	32.1%	99.1 / 14.2	56	H216H (CAT→CAC)	glmU	bifunctional UDP‑N‑acetylglucosamine diphosphorylase/glucosamine‑1‑phosphate N‑acetyltransferase GlmU
*	NZ_CP009273	3,659,062	0	C	A	32.1%	109.3 / 17.3	53	A37S (GCG→TCG)	gadX	acid resistance transcriptional activator GadX
*	NZ_CP009273	3,184,462	0	C	T	31.2%	119.1 / 15.1	64	P158S (CCA→TCA)	yqiI	fimbrial protein
*	NZ_CP009273	4,277,647	0	T	A	30.9%	112.5 / 24.6	55	intergenic (‑348/‑45)	acs/nrfA	acetate‑‑CoA ligase/ammonia‑forming nitrite reductase cytochrome c552 subunit
*	NZ_CP009273	4,326,718	0	T	A	30.6%	80.7 / 17.0	49	Y44F (TAT→TTT)	adiC	arginine/agmatine antiporter
*	NZ_CP009273	1,870,272	0	A	G	30.4%	103.8 / 11.1	58	I115V (ATT→GTT)	nimT	2‑nitroimidazole transporter
*	NZ_CP009273	554,632	0	T	A	29.7%	120.8 / 15.2	65	V68E (GTA→GAA)	fimC	type 1 fimbria chaperone FimC
*	NZ_CP009273	554,616	0	G	A	29.4%	128.4 / 19.1	68	E63K (GAA→AAA)	fimC	type 1 fimbria chaperone FimC
*	NZ_CP009273	2,237,691	0	C	T	29.3%	49.8 / 10.4	41	G101G (GGC→GGT)	yeiG	S‑formylglutathione hydrolase
*	NZ_CP009273	4,594,161	0	C	T	29.2%	99.5 / 10.9	48	S62F (TCT→TTT)	bglJ	DNA‑binding transcriptional activator BglJ
*	NZ_CP009273	3,725,084	0	G	A	28.7%	170.7 / 13.8	80	L198L (TTG→TTA)	xylF	D‑xylose ABC transporter substrate‑binding protein
*	NZ_CP009273	2,001,854	0	G	T	28.3%	140.3 / 13.2	61	G33C (GGC→TGC)	yedE	selenium metabolism membrane protein YedE/FdhT
*	NZ_CP009273	2,621,979	0	T	A	28.3%	106.0 / 12.3	54	T107S (ACT→TCT)	pdeF	cyclic‑guanylate‑specific phosphodiesterase PdeF
*	NZ_CP009273	117,994	0	A	T	28.1%	157.7 / 12.0	64	L15L (CTT→CTA)	aroP	aromatic amino acid transporter AroP

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	1203246 =	55 (0.810)	21 (0.330)	20/464	4.1	29.1%	coding (290/630 nt)	BW25113_RS05990	protein StfP
	?	NZ_CP009273	1205075 =	51 (0.810)					coding (40/540 nt)	BW25113_RS06005	phage tail protein
*	?	NZ_CP009273	= 1203261	53 (0.780)	10 (0.160)	10/464	7.3	16.7%	coding (305/630 nt)	BW25113_RS05990	protein StfP
	?	NZ_CP009273	= 1205058	50 (0.790)					coding (57/540 nt)	BW25113_RS06005	phage tail protein
*	?	NZ_CP009273	4532499 =	72 (1.070)	7 (0.110)	7/478	8.9	8.4%	intergenic (+49/‑433)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
	?	NZ_CP009273	4532813 =	83 (1.270)					intergenic (+363/‑119)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
*	?	NZ_CP009273	= 4532507	73 (1.080)	6 (0.090)	6/478	9.4	7.3%	intergenic (+57/‑425)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
	?	NZ_CP009273	= 4532803	83 (1.270)					intergenic (+353/‑129)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA