breseq  version 0.39.0   mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence (highest frequency 20 of 45 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	377,402	0	G	A	49.0%	19.5 / 157.4	102	intergenic (+91/+133)	yaiL/frmB	DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB
*	NC_000913	377,407	0	C	T	48.5%	21.5 / 160.3	100	intergenic (+96/+128)	yaiL/frmB	DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB
*	NC_000913	377,423	0	G	T	42.7%	50.7 / 135.7	96	intergenic (+112/+112)	yaiL/frmB	DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB
*	NC_000913	377,425	0	C	T	42.5%	58.5 / 135.5	94	intergenic (+114/+110)	yaiL/frmB	DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB
*	NC_000913	377,431	1	.	T	38.9%	135.6 / 186.2	90	intergenic (+120/+104)	yaiL/frmB	DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB
*	NC_000913	377,432	0	C	G	38.5%	134.2 / 127.4	91	intergenic (+121/+103)	yaiL/frmB	DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB
*	NC_000913	2,434,882	0	T	G	34.5%	94.6 / 19.4	55	Y252S (TAC→TCC)	truA	tRNA pseudouridine(38‑40) synthase
*	NC_000913	4,361,508	0	C	G	34.2%	86.6 / 15.0	41	A143P (GCA→CCA)	cadC	DNA‑binding transcriptional activator CadC
*	NC_000913	354,288	0	T	G	34.0%	175.4 / 24.3	97	V528G (GTG→GGG)	prpE	propionyl‑CoA synthetase
*	NC_000913	4,256,061	0	C	T	34.0%	64.4 / 21.5	53	E136K (GAA→AAA)	plsB	glycerol‑3‑phosphate 1‑O‑acyltransferase
*	NC_000913	3,135,781	0	G	T	33.3%	62.7 / 17.7	51	R197R (CGC→CGA)	pitB	metal phosphate:H(+) symporter PitB
*	NC_000913	385,797	0	T	G	32.8%	129.4 / 14.7	69	V189G (GTG→GGG)	tauA	taurine ABC transporter periplasmic binding protein
*	NC_000913	1,435,727	0	G	A	32.5%	74.9 / 13.7	40	intergenic (‑108/+33)	uspF/ompN	universal stress protein F/outer membrane porin N
*	NC_000913	1,604,237	0	C	T	31.4%	52.8 / 12.9	35	S64L (TCG→TTG)	lsrD	Autoinducer‑2 ABC transporter membrane subunit LsrD
*	NC_000913	4,465,787	0	G	A	30.2%	72.1 / 11.9	43	R132C (CGC→TGC)	treB	trehalose‑specific PTS enzyme IIBC component
*	NC_000913	377,465	0	G	T	29.6%	162.2 / 50.2	71	intergenic (+154/+70)	yaiL/frmB	DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB
*	NC_000913	377,450	0	T	G	29.3%	142.3 / 70.5	76	intergenic (+139/+85)	yaiL/frmB	DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB
*	NC_000913	377,451	0	T	.	29.3%	198.0 / 85.1	76	intergenic (+140/+84)	yaiL/frmB	DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB
*	NC_000913	377,452	0	G	A	28.9%	145.1 / 62.3	76	intergenic (+141/+83)	yaiL/frmB	DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB
*	NC_000913	3,813,272	0	C	T	28.9%	70.3 / 12.9	45	S181L (TCG→TTG)	dfp	fused 4'‑phosphopantothenoylcysteine decarboxylase and phosphopantothenoylcysteine synthetase

Marginal new junction evidence (sorted from low to high skew)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 2290113	NA (NA)	7 (0.120)	7/484	3.0	19.4%	noncoding (1/1195 nt)	IS5	repeat region
	?	NC_000913	3890671 =	29 (0.490)					coding (436/1248 nt)	tnaB	tryptophan:H(+) symporter TnaB
*	?	NC_000913	2288919 =	NA (NA)	6 (0.100)	5/484	3.4	17.6%	noncoding (1195/1195 nt)	IS5	repeat region
	?	NC_000913	= 3890674	28 (0.480)					coding (439/1248 nt)	tnaB	tryptophan:H(+) symporter TnaB