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 87 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	454,926	0	G	C	57.9%	0.1 / 21.1	32	intergenic (+137/‑207)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	454,934	0	A	C	57.6%	‑4.6 / 21.6	33	intergenic (+145/‑199)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	454,906	0	G	T	54.2%	3.1 / 18.1	29	intergenic (+117/‑227)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	454,919	0	G	T	53.3%	6.5 / 22.1	33	intergenic (+130/‑214)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	2,177,255	0	G	T	50.0%	‑6.2 / 28.9	40	intergenic (‑51/+257)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	707,981	0	C	G	48.4%	20.1 / 18.9	39	intergenic (+224/‑353)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	2,177,228	0	C	G	48.0%	13.7 / 13.7	34	intergenic (‑24/+284)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	707,976	0	T	G	47.4%	18.6 / 13.6	38	intergenic (+219/‑358)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	1,097,109	0	A	T	46.7%	5.5 / 11.0	31	intergenic (+280/+456)	ycdU/serX	uncharacterized protein YcdU/tRNA‑Ser
*	NC_000913	3,750,798	0	T	G	46.5%	5.2 / 15.2	44	intergenic (+17/+330)	sgbE/yiaT	L‑ribulose‑5‑phosphate 4‑epimerase SgbE/outer membrane protein YiaT
*	NC_000913	454,933	0	T	A	45.5%	5.2 / 17.2	33	intergenic (+144/‑200)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	1,636,440	0	T	G	42.2%	42.1 / 19.4	45	intergenic (‑73/‑316)	nohA/ynfO	Qin prophage; putative prophage DNA‑packaging protein NohA/Qin prophage; protein YnfO
*	NC_000913	1,636,442	0	C	G	41.5%	44.8 / 16.4	46	intergenic (‑75/‑314)	nohA/ynfO	Qin prophage; putative prophage DNA‑packaging protein NohA/Qin prophage; protein YnfO
*	NC_000913	580,759	0	G	C	40.0%	29.8 / 11.5	33	intergenic (‑314/‑75)	ylcI/nohD	DLP12 prophage; DUF3950 domain‑containing protein YlcI/DLP12 prophage; putative DNA‑packaging protein NohD
*	NC_000913	1,860,130	0	G	C	40.0%	59.1 / 13.6	45	L34V (CTT→GTT)	ydjK	putative transporter YdjK
*	NC_000913	1,879,848	0	C	G	40.0%	59.7 / 16.6	45	G34A (GGA→GCA)	yeaR	DUF1971 domain‑containing protein YeaR
*	NC_000913	3,454,069	0	G	T	39.2%	70.9 / 25.6	75	Q444K (CAA→AAA)	gspA	Type II secretion system protein GspA
*	NC_000913	3,750,793	0	G	C	39.1%	41.8 / 13.3	46	intergenic (+12/+335)	sgbE/yiaT	L‑ribulose‑5‑phosphate 4‑epimerase SgbE/outer membrane protein YiaT
*	NC_000913	298,557	0	A	C	37.7%	43.1 / 13.0	56	L57R (CTC→CGC)	paoD	molybdenum cofactor insertion chaperone for PaoABC
*	NC_000913	1,879,846	0	T	G	37.0%	50.2 / 18.0	46	T35P (ACG→CCG)	yeaR	DUF1971 domain‑containing protein YeaR

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)	11 (0.140)	7/254	5.1	15.7%	noncoding (1/1195 nt)	IS5	repeat region
	?	NC_000913	= 4327162	59 (0.760)					coding (28/2229 nt)	crfC	clamp‑binding sister replication fork colocalization protein
*	?	NC_000913	= 2067353	NA (NA)	4 (0.050)	4/254	6.5	6.3%	noncoding (1/1195 nt)	IS5	repeat region
	?	NC_000913	= 4327162	59 (0.760)					coding (28/2229 nt)	crfC	clamp‑binding sister replication fork colocalization protein
*	?	NC_000913	3652036 =	NA (NA)	7 (0.090)	3/256	7.1	12.3%	noncoding (1195/1195 nt)	IS5	repeat region
	?	NC_000913	4327159 =	50 (0.640)					coding (25/2229 nt)	crfC	clamp‑binding sister replication fork colocalization protein