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 85 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	65.0%	9.0 / 14.0	44	intergenic (‑41/+267)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	4,378,973	0	G	C	56.0%	‑0.6 / 10.8	25	intergenic (‑29/+34)	ampC/frdD	beta‑lactamase/fumarate reductase membrane protein FrdD
*	NC_000913	2,177,221	0	T	G	54.2%	7.9 / 48.1	48	intergenic (‑17/+291)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	2,139,594	0	A	C	53.8%	3.1 / 17.5	26	intergenic (+109/+165)	yegH/asmA	inner membrane protein YegH/putative assembly protein AsmA
*	NC_000913	580,759	0	G	C	51.7%	20.9 / 42.8	29	intergenic (‑314/‑75)	ylcI/nohD	DLP12 prophage; DUF3950 domain‑containing protein YlcI/DLP12 prophage; putative DNA‑packaging protein NohD
*	NC_000913	4,220,016	0	A	T	51.7%	4.3 / 36.6	29	Y474F (TAT→TTT)	aceK	isocitrate dehydrogenase kinase/phosphatase
*	NC_000913	454,919	0	G	T	51.6%	30.6 / 43.2	34	intergenic (+130/‑214)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	4,220,007	0	T	G	51.6%	1.3 / 25.8	31	V471G (GTG→GGG)	aceK	isocitrate dehydrogenase kinase/phosphatase
*	NC_000913	2,177,234	0	C	G	50.0%	3.0 / 19.0	47	intergenic (‑30/+278)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	2,470,427	0	C	A	48.7%	35.1 / 12.3	40	Q433K (CAA→AAA)	yfdI	CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase
*	NC_000913	729,383	0	T	G	48.4%	‑4.0 / 12.1	31	intergenic (+43/‑200)	ybfA/rhsC	DUF2517 domain‑containing protein YbfA/rhs element protein RhsC
*	NC_000913	3,455,677	0	A	T	46.0%	32.9 / 27.0	50	N34Y (AAT→TAT)	gspC	Type II secretion system protein GspC
*	NC_000913	454,866	0	G	T	45.7%	4.7 / 14.5	35	intergenic (+77/‑267)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	2,177,228	0	C	G	45.2%	23.0 / 17.4	49	intergenic (‑24/+284)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	2,177,255	0	G	T	44.7%	3.6 / 26.9	47	intergenic (‑51/+257)	gatY/fbaB	tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I
*	NC_000913	3,720,433	0	T	C	44.4%	19.4 / 17.2	27	intergenic (+172/+15)	cspA/hokA	cold shock protein CspA/small toxic polypeptide
*	NC_000913	3,455,671	0	A	T	44.0%	38.1 / 29.0	50	I32F (ATT→TTT)	gspC	Type II secretion system protein GspC
*	NC_000913	454,933	0	T	A	43.3%	5.5 / 14.3	31	intergenic (+144/‑200)	bolA/tig	DNA‑binding transcriptional dual regulator BolA/trigger factor
*	NC_000913	707,981	0	C	G	42.9%	11.1 / 12.1	33	intergenic (+224/‑353)	glnS/chiP	glutamine‑‑tRNA ligase/chitobiose outer membrane channel
*	NC_000913	1,425,568	0	T	G	40.0%	75.9 / 15.7	67	A64A (GCT→GCG)	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	= 2497503	61 (0.900)	3 (0.040)	3/254	6.5	4.9%	coding (793/1239 nt)	alaC	glutamate‑‑pyruvate aminotransferase AlaC
	?	NC_000913	= 2957267	57 (0.850)					coding (1618/2889 nt)	ptrA	protease 3