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	2,177,234	0	C	A	58.3%	3.9 / 19.8	32	intergenic (‑30/+278)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	2,177,221	0	T	G	58.1%	‑0.1 / 25.7	31	intergenic (‑17/+291)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	1,080,910	0	A	T	55.6%	0.3 / 10.1	22	intergenic (+97/‑446)	putP/efeU	proline:Na(+) symporter/inactive ferrous iron permease EfeU, N‑terminal fragment
*	NC_000913	454,919	0	G	T	55.2%	13.6 / 27.2	31	intergenic (+130/‑214)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	2,177,228	0	C	G	54.5%	6.9 / 28.8	32	intergenic (‑24/+284)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	2,470,427	0	C	A	54.5%	6.1 / 20.7	25	Q433K (CAA→AAA)	yfdI	CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase
*	NC_000913	708,004	0	C	A	53.3%	24.2 / 41.4	31	intergenic (+247/‑330)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	454,926	0	G	T	52.6%	‑0.3 / 19.1	30	intergenic (+137/‑207)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	2,470,436	0	C	A	52.2%	‑0.4 / 15.0	24	Q436K (CAA→AAA)	yfdI	CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase
*	NC_000913	2,470,405	0	T	G	51.8%	13.4 / 33.7	27	V425V (GTT→GTG)	yfdI	CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase
*	NC_000913	454,906	0	G	T	51.7%	7.1 / 21.9	31	intergenic (+117/‑227)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	2,177,245	0	G	T	51.5%	1.9 / 24.8	35	intergenic (‑41/+267)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	707,976	0	T	G	48.3%	5.2 / 17.3	29	intergenic (+219/‑358)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	2,177,255	0	G	T	47.6%	10.0 / 28.0	42	intergenic (‑51/+257)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	4,220,016	0	A	T	47.5%	19.3 / 28.7	40	Y474F (TAT→TTT)	aceK	isocitrate dehydrogenase kinase/phosphatase
*	NC_000913	454,877	0	A	T	47.1%	11.0 / 13.7	38	intergenic (+88/‑256)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	931,018	0	G	C	43.2%	55.2 / 13.5	46	intergenic (‑56/+67)	cydD/trxB	glutathione/L‑cysteine ABC exporter subunit CydD/thioredoxin reductase
*	NC_000913	454,873	0	C	G	42.9%	10.6 / 13.5	37	intergenic (+84/‑260)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	3,004,946	0	G	T	42.9%	25.9 / 27.5	56	Q281K (CAA→AAA)	ygeV	putative sigma(54)‑dependent transcriptional regulator YgeV
*	NC_000913	707,981	0	C	T	42.1%	10.1 / 14.8	30	intergenic (+224/‑353)	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	1467910 =	NA (NA)	4 (0.060)	4/256	5.5	NA	noncoding (1331/1331 nt)	IS2	repeat region
	?	NC_000913	= 1469241	NA (NA)					intergenic (‑92/‑5)	insC‑2/ydbA	IS2 insertion element repressor InsA/putative outer membrane protein, N‑terminal fragment
*	?	NC_000913	= 932612	70 (1.110)	3 (0.050)	3/254	6.1	3.6%	coding (18/495 nt)	lrp	DNA‑binding transcriptional dual regulator Lrp
	?	NC_000913	933072 =	93 (1.490)					coding (478/495 nt)	lrp	DNA‑binding transcriptional dual regulator Lrp
*	?	NC_000913	= 274695	NA (NA)	3 (0.050)	3/254	6.1	NA	noncoding (455/1195 nt)	IS5	repeat region
	?	NC_000913	274699 =	NA (NA)					noncoding (451/1195 nt)	IS5	repeat region