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 74 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,177,245	0	G	T	58.7%	‑6.0 / 28.3	51	intergenic (‑41/+267)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	454,919	0	G	T	53.8%	10.8 / 24.7	29	intergenic (+130/‑214)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	2,470,427	0	C	A	53.6%	21.5 / 37.6	28	Q433K (CAA→AAA)	yfdI	CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase
*	NC_000913	2,177,221	0	T	G	52.3%	8.6 / 37.5	44	intergenic (‑17/+291)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	2,177,234	0	C	A	51.6%	5.0 / 22.6	48	intergenic (‑30/+278)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	2,177,228	0	C	G	50.0%	17.9 / 28.1	51	intergenic (‑24/+284)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	931,029	0	G	C	48.9%	47.2 / 28.8	47	intergenic (‑67/+56)	cydD/trxB	glutathione/L‑cysteine ABC exporter subunit CydD/thioredoxin reductase
*	NC_000913	707,981	0	C	G	48.1%	15.8 / 16.8	38	intergenic (+224/‑353)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	1,097,092	0	T	C	47.6%	‑3.7 / 12.5	21	intergenic (+263/+473)	ycdU/serX	uncharacterized protein YcdU/tRNA‑Ser
*	NC_000913	454,933	0	T	A	46.2%	‑1.6 / 11.8	27	intergenic (+144/‑200)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	3,455,680	0	G	T	45.0%	21.6 / 17.1	41	V35L (GTG→TTG)	gspC	Type II secretion system protein GspC
*	NC_000913	2,177,255	0	G	T	44.2%	16.7 / 34.6	52	intergenic (‑51/+257)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	3,455,677	0	A	T	44.2%	24.5 / 22.4	43	N34Y (AAT→TAT)	gspC	Type II secretion system protein GspC
*	NC_000913	2,171,831	0	T	G	43.8%	23.5 / 10.6	32	intergenic (‑104/+2)	gatR/gatD	DNA‑binding transcriptional repressor GatR, N‑terminal fragment/galactitol‑1‑phosphate 5‑dehydrogenase
*	NC_000913	3,407,970	0	C	G	43.8%	44.2 / 10.2	32	L122V (CTT→GTT)	panF	pantothenate:Na(+) symporter
*	NC_000913	1,879,846	0	T	G	42.9%	21.4 / 14.9	35	T35P (ACG→CCG)	yeaR	DUF1971 domain‑containing protein YeaR
*	NC_000913	3,004,946	0	G	T	42.9%	41.3 / 22.5	49	Q281K (CAA→AAA)	ygeV	putative sigma(54)‑dependent transcriptional regulator YgeV
*	NC_000913	3,455,669	0	T	G	42.9%	28.8 / 21.1	43	I31S (ATT→AGT)	gspC	Type II secretion system protein GspC
*	NC_000913	1,879,848	0	C	G	42.4%	37.3 / 11.3	35	G34A (GGA→GCA)	yeaR	DUF1971 domain‑containing protein YeaR
*	NC_000913	707,976	0	T	G	42.1%	14.8 / 11.3	38	intergenic (+219/‑358)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel

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	= 1334196	84 (1.270)	3 (0.050)	3/250	6.4	3.4%	coding (342/975 nt)	cysB	DNA‑binding transcriptional dual regulator CysB
	?	NC_000913	1334207 =	87 (1.340)					coding (353/975 nt)	cysB	DNA‑binding transcriptional dual regulator CysB
*	?	NC_000913	= 382594	NA (NA)	4 (0.060)	3/248	6.4	NA	pseudogene (279/282 nt)	yaiX	putative acyltransferase, N‑terminal fragment
	?	NC_000913	= 1469238	NA (NA)					noncoding (3/1331 nt)	IS2	repeat region