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 70 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	74.4%	17.5 / 18.6	45	intergenic (‑41/+267)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	2,177,234	0	C	A	63.9%	‑5.0 / 24.0	54	intergenic (‑30/+278)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	2,177,255	0	G	T	59.2%	13.3 / 33.1	49	intergenic (‑51/+257)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	707,992	0	C	G	57.9%	3.6 / 20.5	25	intergenic (+235/‑342)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	707,989	0	C	T	52.6%	‑0.2 / 24.7	25	intergenic (+232/‑345)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	707,981	0	C	T	50.0%	‑0.4 / 18.6	27	intergenic (+224/‑353)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	2,177,221	0	T	G	49.1%	16.5 / 32.9	53	intergenic (‑17/+291)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	707,976	0	T	G	46.2%	7.6 / 12.8	26	intergenic (+219/‑358)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	4,220,007	0	T	G	45.8%	4.9 / 12.3	24	V471G (GTG→GGG)	aceK	isocitrate dehydrogenase kinase/phosphatase
*	NC_000913	2,177,228	0	C	G	45.7%	22.3 / 25.0	54	intergenic (‑24/+284)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	1,636,442	0	C	G	43.9%	41.4 / 16.7	49	intergenic (‑75/‑314)	nohA/ynfO	Qin prophage; putative prophage DNA‑packaging protein NohA/Qin prophage; protein YnfO
*	NC_000913	2,470,411	0	A	T	42.4%	30.9 / 14.9	33	L427F (TTA→TTT)	yfdI	CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase
*	NC_000913	454,873	0	C	G	41.4%	7.2 / 12.1	34	intergenic (+84/‑260)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	3,004,946	0	G	T	41.4%	59.0 / 23.2	59	Q281K (CAA→AAA)	ygeV	putative sigma(54)‑dependent transcriptional regulator YgeV
*	NC_000913	3,455,671	0	A	T	38.9%	48.1 / 25.0	54	I32F (ATT→TTT)	gspC	Type II secretion system protein GspC
*	NC_000913	4,220,016	0	A	T	38.5%	15.5 / 14.2	27	Y474F (TAT→TTT)	aceK	isocitrate dehydrogenase kinase/phosphatase
*	NC_000913	2,185,429	0	T	G	37.8%	51.0 / 16.4	45	intergenic (‑128/+95)	thiM/rcnR	hydroxyethylthiazole kinase/DNA‑binding transcriptional repressor RcnR
*	NC_000913	454,883	0	C	G	37.5%	28.8 / 10.8	33	intergenic (+94/‑250)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	1,636,440	0	T	G	37.2%	48.0 / 26.5	51	intergenic (‑73/‑316)	nohA/ynfO	Qin prophage; putative prophage DNA‑packaging protein NohA/Qin prophage; protein YnfO
*	NC_000913	1,636,452	0	C	G	36.4%	68.8 / 14.0	55	intergenic (‑85/‑304)	nohA/ynfO	Qin prophage; putative prophage DNA‑packaging protein NohA/Qin prophage; protein YnfO

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	1207790 =	64 (1.060)	12 (0.230)	11/224	2.4	19.7%	coding (290/630 nt)	ycfK	e14 prophage; protein StfP
	?	NC_000913	1209619 =	42 (0.800)					pseudogene (37/537 nt)	stfE	e14 prophage; putative side tail fiber protein fragment
*	?	NC_000913	= 1207805	56 (0.930)	7 (0.130)	4/224	4.7	13.5%	coding (305/630 nt)	ycfK	e14 prophage; protein StfP
	?	NC_000913	= 1209602	41 (0.780)					pseudogene (54/537 nt)	stfE	e14 prophage; putative side tail fiber protein fragment