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 188 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,217,689	0	G	A	40.0%	79.3 / 21.0	55	pseudogene (2228/2243 nt)	BW25113_RS25990	autotransporter outer membrane beta‑barrel domain‑containing protein
*	NZ_CP009273	1,750,128	0	T	A	35.3%	83.9 / 25.2	51	G58G (GGT→GGA)	pykF	pyruvate kinase PykF
*	NZ_CP009273	1,750,119	0	C	A	35.2%	108.5 / 19.9	54	S55R (AGC→AGA)	pykF	pyruvate kinase PykF
*	NZ_CP009273	1,340,902	0	G	A	34.9%	75.1 / 10.6	43	S33F (TCT→TTT)	pdeR	cyclic di‑GMP phosphodiesterase
*	NZ_CP009273	4,612,067	0	A	G	34.6%	140.0 / 25.1	78	E161G (GAG→GGG)	yjjJ	type II toxin‑antitoxin system HipA family toxin YjjJ
*	NZ_CP009273	1,820,636	0	T	C	34.2%	129.3 / 19.1	73	E182G (GAG→GGG)	astE	succinylglutamate desuccinylase
*	NZ_CP009273	748,581	0	T	A	34.2%	154.3 / 30.5	79	intergenic (‑330/+60)	ybgD/gltA	fimbrial protein/citrate synthase
*	NZ_CP009273	3,578,446	0	A	C	34.1%	189.5 / 17.7	88	Y580D (TAC→GAC)	ggt	gamma‑glutamyltransferase
*	NZ_CP009273	3,578,438	0	A	C	33.7%	191.9 / 18.0	92	intergenic (+35/+3)	yrhB/ggt	YrhB family protein/gamma‑glutamyltransferase
*	NZ_CP009273	2,977,800	0	A	C	32.8%	121.7 / 16.0	58	G384G (GGT→GGG)	yqeF	acetyl‑CoA C‑acetyltransferase
*	NZ_CP009273	4,245,989	0	C	T	32.7%	80.0 / 13.7	55	E136K (GAA→AAA)	plsB	glycerol‑3‑phosphate 1‑O‑acyltransferase PlsB
*	NZ_CP009273	2,826,892	0	T	G	32.6%	192.9 / 11.5	90	V353G (GTG→GGG)	norV	anaerobic nitric oxide reductase flavorubredoxin
*	NZ_CP009273	2,178,717	0	A	G	32.5%	159.2 / 15.9	83	S22P (TCC→CCC)	thiM	hydroxyethylthiazole kinase
*	NZ_CP009273	2,621,979	0	T	A	32.5%	119.0 / 37.9	80	T107S (ACT→TCT)	pdeF	cyclic‑guanylate‑specific phosphodiesterase PdeF
*	NZ_CP009273	4,058,958	0	G	A	32.5%	155.5 / 21.5	80	L57L (CTG→TTG)	yihO	MFS transporter
*	NZ_CP009273	1,155,293	0	A	G	32.2%	116.2 / 10.5	59	I572T (ATC→ACC)	fhuE	ferric‑rhodotorulic acid/ferric‑coprogen receptor FhuE
*	NZ_CP009273	2,178,678	0	T	G	32.1%	157.1 / 20.6	82	T35P (ACC→CCC)	thiM	hydroxyethylthiazole kinase
*	NZ_CP009273	4,544,936	0	A	G	32.0%	128.9 / 19.6	76	I182V (ATC→GTC)	uxuR	Uxu operon transcriptional regulator
*	NZ_CP009273	653,132	0	A	C	31.9%	135.8 / 11.5	69	V88G (GTG→GGG)	crcB	fluoride efflux transporter CrcB
*	NZ_CP009273	4,203,693	0	A	C	31.5%	182.7 / 18.1	92	V120G (GTG→GGG)	yjaB	acetyltransferase

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	= 3416707	43 (0.460)	3 (0.140) +191 bp	3/114	4.2	23.5%	intergenic (+154/+77)	yhdZ/rrf	amino acid ABC transporter ATP‑binding protein/5S ribosomal RNA
	?	NZ_CP009273	3416716 =	42 (0.450)					intergenic (+163/+68)	yhdZ/rrf	amino acid ABC transporter ATP‑binding protein/5S ribosomal RNA
*	?	NZ_CP009273	4532499 =	126 (1.340)	5 (0.060)	5/478	12.8	4.1%	intergenic (+49/‑433)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
	?	NZ_CP009273	4532813 =	113 (1.250)					intergenic (+363/‑119)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
*	?	NZ_CP009273	= 4532507	129 (1.370)	4 (0.040)	4/478	13.5	3.3%	intergenic (+57/‑425)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
	?	NZ_CP009273	= 4532803	113 (1.250)					intergenic (+353/‑129)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA