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 290 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	4,526,014	0	A	T	45.7%	62.5 / 62.8	71	intergenic (+166/+102)	yjhR/BW25113_RS26295	helicase YjhR/HNH endonuclease
*	NZ_CP009273	4,036,390	0	A	G	41.5%	71.5 / 15.0	54	N206D (AAT→GAT)	srkA	stress response kinase SrkA
*	NZ_CP009273	2,360,878	0	T	C	41.1%	64.5 / 15.9	60	I110T (ATC→ACC)	arnC	undecaprenyl‑phosphate 4‑deoxy‑4‑formamido‑L‑arabinose transferase
*	NZ_CP009273	4,526,029	0	T	A	40.0%	94.9 / 32.5	71	intergenic (+181/+87)	yjhR/BW25113_RS26295	helicase YjhR/HNH endonuclease
*	NZ_CP009273	2,145,084	0	C	A	39.0%	74.7 / 15.9	41	P140Q (CCA→CAA)	yegJ	DUF2314 domain‑containing protein
*	NZ_CP009273	4,526,064	0	G	T	37.1%	107.7 / 34.0	71	intergenic (+216/+52)	yjhR/BW25113_RS26295	helicase YjhR/HNH endonuclease
*	NZ_CP009273	2,476,733	0	G	A	37.1%	198.9 / 47.4	116	S29L (TCA→TTA)	emrK	multidrug efflux MFS transporter periplasmic adaptor subunit EmrK
*	NZ_CP009273	368,096	0	T	G	36.9%	158.8 / 21.1	84	L176V (TTA→GTA)	mhpD	2‑keto‑4‑pentenoate hydratase
*	NZ_CP009273	762,172	0	G	T	35.9%	78.0 / 17.6	53	A225S (GCG→TCG)	mngA	PTS 2‑O‑a‑mannosyl‑D‑glycerate transporter subunit IIABC
*	NZ_CP009273	2,671,398	0	T	G	35.2%	136.2 / 21.3	71	N108T (AAC→ACC)	yphE	sugar ABC transporter ATP‑binding protein
*	NZ_CP009273	2,977,800	0	A	C	35.2%	144.6 / 26.5	71	G384G (GGT→GGG)	yqeF	acetyl‑CoA C‑acetyltransferase
*	NZ_CP009273	3,199,805	0	C	A	35.1%	89.4 / 23.2	78	intergenic (‑190/‑17)	ttdR/ttdA	DNA‑binding transcriptional activator TtdR/L(+)‑tartrate dehydratase subunit alpha
*	NZ_CP009273	3,725,084	0	G	A	35.0%	164.1 / 30.0	97	L198L (TTG→TTA)	xylF	D‑xylose ABC transporter substrate‑binding protein
*	NZ_CP009273	1,009,479	0	T	G	34.9%	166.2 / 24.3	83	G255G (GGT→GGG)	pqiB	intermembrane transport protein PqiB
*	NZ_CP009273	4,526,060	0	C	T	34.8%	102.4 / 21.4	66	intergenic (+212/+56)	yjhR/BW25113_RS26295	helicase YjhR/HNH endonuclease
*	NZ_CP009273	2,476,747	0	T	A	34.5%	200.2 / 37.7	113	L24F (TTA→TTT)	emrK	multidrug efflux MFS transporter periplasmic adaptor subunit EmrK
*	NZ_CP009273	2,089,571	0	A	G	34.4%	164.7 / 23.8	90	I83V (ATT→GTT)	hisF	imidazole glycerol phosphate synthase subunit HisF
*	NZ_CP009273	4,570,451	0	C	T	34.4%	151.5 / 34.5	91	E277K (GAA→AAA)	hsdS	type I restriction‑modification system specificity subunit
*	NZ_CP009273	1,429,984	0	G	A	34.1%	167.3 / 32.5	85	intergenic (‑108/+33)	uspF/ompN	universal stress protein UspF/porin OmpN
*	NZ_CP009273	2,145,167	0	G	T	34.0%	39.1 / 12.9	51	intergenic (+40/+25)	yegJ/pphC	DUF2314 domain‑containing protein/protein‑serine/threonine phosphatase PphC

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	= 2940826	61 (0.600)	4 (0.060)	4/330	13.3	9.2%	intergenic (+4/‑30)	BW25113_RS14635/BW25113_RS14640	tRNA‑Met/tRNA‑Met
	?	NZ_CP009273	2941047 =	38 (0.570)					intergenic (+5/+69)	BW25113_RS14645/amiC	tRNA‑Met/N‑acetylmuramoyl‑L‑alanine amidase AmiC
*	?	NZ_CP009273	= 692197	63 (0.620)	4 (0.060)	4/340	13.7	7.4%	intergenic (‑1/+15)	BW25113_RS03450/BW25113_RS03455	tRNA‑Met/tRNA‑Gln
	?	NZ_CP009273	692591 =	57 (0.820)					intergenic (‑2/+378)	BW25113_RS03470/asnB	tRNA‑Met/asparagine synthase B