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 69 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	454,906	0	G	T	60.0%	‑3.4 / 11.0	24	intergenic (+117/‑227)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	454,919	0	G	T	59.1%	0.6 / 12.9	25	intergenic (+130/‑214)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	2,177,234	0	C	A	58.3%	5.5 / 18.1	61	intergenic (‑30/+278)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	1,097,109	0	A	T	52.2%	‑0.3 / 18.9	23	intergenic (+280/+456)	ycdU/serX	uncharacterized protein YcdU/tRNA‑Ser
*	NC_000913	2,177,228	0	C	G	51.2%	12.6 / 49.2	62	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	50.0%	‑5.8 / 11.2	24	intergenic (+137/‑207)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	2,470,427	0	C	A	50.0%	32.0 / 10.9	39	Q433K (CAA→AAA)	yfdI	CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase
*	NC_000913	2,177,255	0	G	T	47.8%	2.3 / 42.3	68	intergenic (‑51/+257)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	3,537,327	0	G	T	47.6%	15.7 / 11.2	21	intergenic (+39/‑58)	greB/yhgF	transcription elongation factor GreB/putative RNA‑binding protein YhgF
*	NC_000913	707,976	0	T	G	47.2%	4.9 / 17.0	36	intergenic (+219/‑358)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	707,981	0	C	G	46.2%	15.8 / 16.0	38	intergenic (+224/‑353)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	3,004,946	0	G	T	45.8%	31.2 / 33.3	59	Q281K (CAA→AAA)	ygeV	putative sigma(54)‑dependent transcriptional regulator YgeV
*	NC_000913	3,455,671	0	A	T	43.4%	41.7 / 26.6	53	I32F (ATT→TTT)	gspC	Type II secretion system protein GspC
*	NC_000913	3,407,970	0	C	G	41.4%	36.5 / 17.8	29	L122V (CTT→GTT)	panF	pantothenate:Na(+) symporter
*	NC_000913	707,984	0	C	G	40.5%	24.8 / 11.4	38	intergenic (+227/‑350)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	4,220,007	0	T	G	39.0%	38.4 / 13.7	41	V471G (GTG→GGG)	aceK	isocitrate dehydrogenase kinase/phosphatase
*	NC_000913	1,879,846	0	T	G	38.5%	26.8 / 17.0	39	T35P (ACG→CCG)	yeaR	DUF1971 domain‑containing protein YeaR
*	NC_000913	2,177,221	0	T	G	38.3%	25.1 / 30.3	60	intergenic (‑17/+291)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	2,470,416	0	A	T	35.9%	41.2 / 12.7	40	Y429F (TAT→TTT)	yfdI	CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase
*	NC_000913	1,425,560	0	A	T	35.0%	111.7 / 32.1	80	M62L (ATG→TTG)	ynaK	Rac prophage; ParB‑like nuclease domain‑containing protein YnaK

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	2996360 =	NA (NA)	4 (0.060) +C	3/254	6.9	NA	pseudogene (1/399 nt)	ygeO	putative uncharacterized protein YgeO
	?	NC_000913	= 2997691	NA (NA)					noncoding (1/1331 nt)	IS2	repeat region
*	?	NC_000913	2068941 =	NA (NA)	7 (0.100)	3/256	7.0	NA	noncoding (1331/1331 nt)	IS2	repeat region
	?	NC_000913	= 2070273	NA (NA)					intergenic (‑93/‑4)	insC‑3/yoeA	CP4‑44 prophage; IS2 insertion element repressor InsA/CP4‑44 prophage; TonB‑dependent receptor plug domain‑containing protein YoeA