breseq  version 0.29.0  revision 8f9c342918e4 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence (highest frequency 20 of 242 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	51.3%	25.2 / 61.6	39	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	1,510,395	0	C	A	48.8%	25.5 / 33.0	41	S131R (AGC→AGA)	ydcR	putative DNA‑binding transcriptional regulator and putative aminotransferase
*	NC_000913	941,713	0	T	G	47.8%	60.8 / 20.4	46	V252G (GTG→GGG)	dmsA	dimethyl sulfoxide reductase, anaerobic, subunit A
*	NC_000913	172,911	0	A	G	46.5%	56.4 / 13.7	43	M484V (ATG→GTG)	fhuB	iron(3+)‑hydroxamate import ABC transporter permease
*	NC_000913	1,376,505	0	A	C	46.0%	76.9 / 10.6	51	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
*	NC_000913	907,580	0	T	G	45.2%	53.3 / 15.6	43	I235L (ATC→CTC)	ybjT	putative NAD‑dependent oxidoreductase
*	NC_000913	599,576	0	T	G	45.1%	70.1 / 20.3	52	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	2,984,441	0	A	C	44.9%	69.6 / 18.0	49	G384G (GGT→GGG)	yqeF	short chain acyltransferase
*	NC_000913	2,511,772	0	A	C	44.6%	92.9 / 10.8	57	V312G (GTG→GGG)	mntH	manganese/divalent cation transporter
*	NC_000913	357,875	0	A	T	44.4%	51.3 / 12.2	36	N272K (AAT→AAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	366,526	0	T	G	43.8%	104.2 / 24.9	64	T329P (ACC→CCC)	lacI	lactose‑inducible lac operon transcriptional repressor
*	NC_000913	1,222,233	0	G	A	43.8%	53.1 / 20.1	48	pseudogene (60/75 nt)	ycgH	pseudogene; putative ATP‑binding component of a transport system
*	NC_000913	2,434,882	0	T	G	43.8%	76.0 / 19.0	50	Y252S (TAC→TCC)	truA	tRNA pseudouridine(38‑40) synthase
*	NC_000913	4,332,791	0	A	C	42.9%	87.0 / 13.8	49	V161G (GTG→GGG)	basS	sensory histidine kinase in two‑component regulatory system with BasR
*	NC_000913	3,206,435	0	C	T	42.4%	75.3 / 39.8	67	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	1,510,391	0	T	A	41.5%	48.1 / 16.8	41	V130E (GTA→GAA)	ydcR	putative DNA‑binding transcriptional regulator and putative aminotransferase
*	NC_000913	300,721	0	G	T	41.0%	58.7 / 16.2	39	Q72K (CAA→AAA)	paoC	PaoABC aldehyde oxidoreductase, Moco‑containing subunit
*	NC_000913	300,711	0	G	C	40.5%	68.1 / 20.2	42	P75R (CCG→CGG)	paoC	PaoABC aldehyde oxidoreductase, Moco‑containing subunit
*	NC_000913	3,364,396	0	A	T	40.0%	78.0 / 21.8	50	P530P (CCA→CCT)	yhcD	putative outer membrane fimbrial subunit usher protein
*	NC_000913	4,112,578	0	T	G	39.6%	87.3 / 10.2	49	G88G (GGT→GGG)	yiiR	DUF805 family putative inner membrane protein

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	= 4542690	69 (1.090)	4 (0.070)	4/280	10.9	5.4%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	75 (1.260)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)