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 70 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	707,981	0	C	G	62.1%	‑1.4 / 26.2	43	intergenic (+224/‑353)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	2,177,234	0	C	A	59.4%	‑6.1 / 16.7	47	intergenic (‑30/+278)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	2,177,245	0	G	T	58.7%	7.6 / 19.4	49	intergenic (‑41/+267)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	708,004	0	C	A	58.3%	4.5 / 28.6	43	intergenic (+247/‑330)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	2,177,255	0	G	T	54.7%	‑4.1 / 40.0	53	intergenic (‑51/+257)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	454,873	0	C	G	52.2%	0.9 / 17.1	25	intergenic (+84/‑260)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	454,919	0	G	T	51.8%	22.0 / 36.0	30	intergenic (+130/‑214)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	707,976	0	T	G	51.2%	‑2.2 / 26.8	43	intergenic (+219/‑358)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	4,007,825	0	C	G	48.5%	31.3 / 13.5	35	F23L (TTC→TTG)	rhtC	L‑threonine exporter
*	NC_000913	4,082,686	0	T	C	47.8%	3.9 / 14.3	27	D25G (GAC→GGC)	fdoH	formate dehydrogenase O subunit beta
*	NC_000913	2,177,221	0	T	G	47.1%	20.7 / 27.9	51	intergenic (‑17/+291)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	2,177,228	0	C	G	44.1%	29.5 / 18.2	50	intergenic (‑24/+284)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	454,926	0	G	A	42.1%	10.1 / 14.5	32	intergenic (+137/‑207)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	707,984	0	C	G	39.5%	19.3 / 13.0	43	intergenic (+227/‑350)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	4,220,016	0	A	T	39.5%	30.5 / 17.8	38	Y474F (TAT→TTT)	aceK	isocitrate dehydrogenase kinase/phosphatase
*	NC_000913	3,418,492	0	C	G	38.9%	53.9 / 16.2	59	H35D (CAC→GAC)	yhdV	lipoprotein YhdV
*	NC_000913	1,708,326	0	G	T	36.0%	65.9 / 11.6	52	E470* (GAA→TAA)	rsxC	SoxR [2Fe‑2S] reducing system protein RsxC
*	NC_000913	3,955,616	0	T	G	34.7%	62.3 / 14.2	49	F96V (TTT→GTT)	ilvA	threonine deaminase
*	NC_000913	4,220,018	0	G	T	34.2%	41.8 / 12.8	42	D475Y (GAT→TAT)	aceK	isocitrate dehydrogenase kinase/phosphatase
*	NC_000913	2,185,429	0	T	G	34.0%	69.7 / 12.7	53	intergenic (‑128/+95)	thiM/rcnR	hydroxyethylthiazole kinase/DNA‑binding transcriptional repressor RcnR

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	= 2070275	NA (NA)	9 (0.130)	5/248	5.4	NA	intergenic (‑95/‑2)	insC‑3/yoeA	CP4‑44 prophage; IS2 insertion element repressor InsA/CP4‑44 prophage; TonB‑dependent receptor plug domain‑containing protein YoeA
	?	NC_000913	2996364 =	NA (NA)					noncoding (1328/1331 nt)	IS2	repeat region