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 47 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,177,221	0	T	G	56.2%	‑3.9 / 24.2	32	intergenic (‑17/+291)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	2,177,255	0	G	T	54.3%	8.3 / 13.6	35	intergenic (‑51/+257)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	454,906	0	G	T	54.2%	1.6 / 13.6	25	intergenic (+117/‑227)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	454,919	0	G	T	53.3%	9.9 / 15.9	20	intergenic (+130/‑214)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	4,220,016	0	A	T	52.0%	4.1 / 31.2	25	Y474F (TAT→TTT)	aceK	isocitrate dehydrogenase kinase/phosphatase
*	NC_000913	4,220,007	0	T	G	50.0%	5.4 / 12.4	24	V471G (GTG→GGG)	aceK	isocitrate dehydrogenase kinase/phosphatase
*	NC_000913	2,470,411	0	A	T	47.8%	3.0 / 16.3	23	L427F (TTA→TTT)	yfdI	CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase
*	NC_000913	707,984	0	C	G	45.8%	12.7 / 10.9	24	intergenic (+227/‑350)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	3,955,616	0	T	G	44.2%	37.7 / 15.5	43	F96V (TTT→GTT)	ilvA	threonine deaminase
*	NC_000913	1,879,846	0	T	G	37.1%	34.5 / 10.2	35	T35P (ACG→CCG)	yeaR	DUF1971 domain‑containing protein YeaR
*	NC_000913	3,455,680	0	G	T	36.7%	61.5 / 16.9	49	V35L (GTG→TTG)	gspC	Type II secretion system protein GspC
*	NC_000913	3,004,946	0	G	T	35.9%	37.0 / 11.9	39	Q281K (CAA→AAA)	ygeV	putative sigma(54)‑dependent transcriptional regulator YgeV
*	NC_000913	1,087,697	0	G	C	34.4%	38.6 / 13.6	32	V50V (GTC→GTG)	pgaC	poly‑N‑acetyl‑D‑glucosamine synthase subunit PgaC
*	NC_000913	18,124	0	C	G	34.2%	57.6 / 10.3	41	G212G (GGC→GGG)	nhaA	Na(+):H(+) antiporter NhaA
*	NC_000913	931,029	0	G	C	34.0%	80.9 / 23.2	50	intergenic (‑67/+56)	cydD/trxB	glutathione/L‑cysteine ABC exporter subunit CydD/thioredoxin reductase
*	NC_000913	4,296,060	0	C	T	32.6%	118.3 / 84.2	89	intergenic (+266/+376)	gltP/yjcO	glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
*	NC_000913	2,736,240	0	C	A	32.4%	54.1 / 16.0	37	P32Q (CCA→CAA)	bamD	outer membrane protein assembly factor BamD
*	NC_000913	18,110	0	T	G	32.4%	46.9 / 11.3	35	Y208D (TAT→GAT)	nhaA	Na(+):H(+) antiporter NhaA
*	NC_000913	1,425,558	0	T	G	32.1%	64.9 / 18.7	56	V61G (GTT→GGT)	ynaK	Rac prophage; ParB‑like nuclease domain‑containing protein YnaK
*	NC_000913	3,955,631	0	T	G	31.9%	69.1 / 11.3	47	L101V (TTA→GTA)	ilvA	threonine deaminase

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	4498181 =	NA (NA)	18 (0.330)	9/256	3.1	NA	noncoding (1/1331 nt)	IS2	repeat region
	?	NC_000913	= 4499512	NA (NA)					intergenic (+12/+81)	insD‑6/yjgX	KpLE2 phage‑like element; IS2 insertion element protein InsB/KpLE2 phage‑like element; putative phosphoethanolamine transferase YjgX, N‑terminal fragment
*	?	NC_000913	381258 =	NA (NA)	19 (0.350)	9/254	3.1	NA	pseudogene (3/417 nt)	yaiX	putative acyltransferase, N‑terminal fragment
	?	NC_000913	= 382589	NA (NA)					noncoding (1330/1331 nt)	IS2	repeat region
*	?	NC_000913	3594086 =	54 (0.990)	3 (0.060)	3/254	5.4	6.5%	coding (121/768 nt)	livG	branched chain amino acid/phenylalanine ABC transporter ATP binding subunit LivG
	?	NC_000913	= 3594265	33 (0.610)					coding (1216/1278 nt)	livM	branched chain amino acid/phenylalanine ABC transporter membrane subunit LivM