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 218 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	2,251,361	0	A	C	74.2%	55.9 / 21.9	31	C162W (TGT→TGG)	psuG	pseudouridine‑5'‑phosphate glycosidase
*	NZ_CP009273	1,510,306	0	A	G	72.7%	80.3 / 43.3	55	K158E (AAA→GAA)	patD	aminobutyraldehyde dehydrogenase
*	NZ_CP009273	957,621	0	G	T	71.4%	63.4 / 38.2	42	Q57H (CAG→CAT)	rpsA	30S ribosomal protein S1
*	NZ_CP009273	1,373,159	0	T	C	71.4%	26.9 / 14.4	21	L340S (TTA→TCA)	ycjT	kojibiose phosphorylase
*	NZ_CP009273	2,068,298	0	A	C	71.4%	101.3 / 56.7	63	A13A (GCA→GCC)	BW25113_RS10450	hypothetical protein
*	NZ_CP009273	1,008,230	0	G	A	69.7%	49.6 / 24.3	33	A258A (GCG→GCA)	pqiA	membrane integrity‑associated transporter subunit PqiA
*	NZ_CP009273	1,303,928	0	A	G	69.2%	32.6 / 20.6	26	L200S (TTG→TCG)	kch	voltage‑gated potassium channel protein
*	NZ_CP009273	186,707	0	A	T	67.7%	42.0 / 29.1	31	D116V (GAC→GTC)	rpsB	30S ribosomal protein S2
*	NZ_CP009273	185,064	0	A	C	67.4%	47.0 / 42.3	43	V25G (GTC→GGC)	glnD	bifunctional uridylyltransferase/uridylyl‑removing protein GlnD
*	NZ_CP009273	353,591	0	T	C	66.7%	‑4.5 / 15.3	18	K271E (AAA→GAA)	cynR	transcriptional regulator CynR
*	NZ_CP009273	2,525,546	0	T	C	66.7%	54.5 / 53.0	54	V242A (GTC→GCC)	cysZ	sulfate transporter CysZ
*	NZ_CP009273	1,662,814	0	G	A	65.8%	47.3 / 39.8	41	A3V (GCT→GTT)	mlc	DNA‑binding transcriptional repressor Mlc
*	NZ_CP009273	4,144,209	0	A	G	64.5%	26.3 / 30.9	31	I189I (ATT→ATC)	argE	acetylornithine deacetylase
*	NZ_CP009273	49,884	0	C	T	64.1%	35.6 / 36.5	39	P21L (CCG→CTG)	folA	type 3 dihydrofolate reductase
*	NZ_CP009273	4,435,379	0	A	G	63.9%	57.7 / 66.2	61	D484G (GAC→GGC)	tamB	autotransporter assembly complex protein TamB
*	NZ_CP009273	3,815,692	0	A	G	63.8%	37.3 / 67.5	58	E76G (GAA→GGA)	rpoZ	DNA‑directed RNA polymerase subunit omega
*	NZ_CP009273	1,436,853	0	T	C	63.3%	39.9 / 49.7	54	D83G (GAC→GGC)	ldhA	D‑lactate dehydrogenase
*	NZ_CP009273	2,363,413	0	G	A	63.0%	23.5 / 24.5	27	W632* (TGG→TGA)	arnA	bifunctional UDP‑4‑amino‑4‑deoxy‑L‑arabinose formyltransferase/UDP‑glucuronic acid oxidase ArnA
*	NZ_CP009273	146,045	0	T	C	62.5%	34.3 / 54.6	48	E15G (GAA→GGA)	panB	3‑methyl‑2‑oxobutanoate hydroxymethyltransferase
*	NZ_CP009273	4,525,950	0	T	A	62.2%	42.0 / 59.0	45	intergenic (+102/+166)	yjhR/BW25113_RS26295	helicase YjhR/HNH endonuclease

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	= 3633951	58 (1.390)	5 (0.150)	5/192	2.7	9.2%	intergenic (+46/+21)	uspA/BW25113_RS26225	universal stress protein UspA/hypothetical protein
	?	NZ_CP009273	= 3633929	51 (1.500)					intergenic (+24/+43)	uspA/BW25113_RS26225	universal stress protein UspA/hypothetical protein
*	?	NZ_CP009273	= 1980922	59 (1.410)	3 (0.080)	3/216	3.7	5.2%	intergenic (+13/+66)	ftnB/yecJ	non‑heme ferritin‑like protein/DUF2766 domain‑containing protein
	?	NZ_CP009273	= 1980931	56 (1.460)					intergenic (+22/+57)	ftnB/yecJ	non‑heme ferritin‑like protein/DUF2766 domain‑containing protein
*	?	NZ_CP009273	684757 =	56 (1.340)	3 (0.080)	3/222	3.8	5.5%	intergenic (‑324/+42)	BW25113_RS03405/lnt	IS5‑like element IS5 family transposase/apolipoprotein N‑acyltransferase
	?	NZ_CP009273	684788 =	51 (1.300)					intergenic (‑355/+11)	BW25113_RS03405/lnt	IS5‑like element IS5 family transposase/apolipoprotein N‑acyltransferase