breseq  version 0.35.4  revision f352f80f4bc9 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	KT2440	2,391,026	0	T	G	58.8%	3.4 / 11.9	19	Q561P (CAG→CCG)	bvgS	Virulence sensor protein BvgS
*	KT2440	3,440,367	0	T	G	57.9%	‑0.9 / 13.5	20	W26G (TGG→GGG)	CJ019_03266	hypothetical protein
*	KT2440	4,409,322	0	G	A	55.4%	18.9 / 86.3	65	intergenic (‑29/‑121)	CJ019_04171/CJ019_04172	hypothetical protein/hypothetical protein
*	KT2440	1,524,732	0	T	G	55.0%	5.9 / 16.7	20	Q67P (CAG→CCG)	CJ019_01439	hypothetical protein
*	KT2440	828,869	0	A	C	54.5%	6.6 / 18.6	22	L87R (CTG→CGG)	CJ019_00791	putative sulfate transporter
*	KT2440	2,432,605	0	T	G	52.2%	8.1 / 18.3	23	S97A (TCG→GCG)	fadA_2	3‑ketoacyl‑CoA thiolase
*	KT2440	3,138,367	0	T	G	52.0%	9.2 / 25.2	25	F240V (TTT→GTT)	rbsC_2	Ribose import permease protein RbsC
*	KT2440	5,334,688	0	T	G	40.0%	51.5 / 14.3	40	intergenic (+231/‑32)	folK/panB	2‑amino‑4‑hydroxy‑6‑hydroxymethyldihydropteridine pyrophosphokinase/3‑methyl‑2‑oxobutanoatehydroxymethyltransferase

Marginal new junction evidence (sorted from low to high skew)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	KT2440	= 4257352	28 (0.750)	3 (0.090) +GCGGCCGC	3/234	4.0	9.8%	intergenic (‑281/‑1)	CJ019_03991/tsaM1	putative ABC transporter ATP‑binding protein/Toluene‑4‑sulfonate monooxygenase systemiron‑sulfur subunit TsaM1
	?	KT2440	4259384 =	31 (0.830)					intergenic (+1/+6)	pht2/CJ019_03994	Phthalate 4,5‑dioxygenase oxygenase reductasesubunit/hypothetical protein
*	?	KT2440	= 3141374	38 (1.020)	4 (0.110)	3/236	4.1	11.1%	coding (111/561 nt)	msuE	FMN reductase (NADPH)
	?	KT2440	4345498 =	28 (0.790)					coding (331/360 nt)	CJ019_04083	hypothetical protein