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 543 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	59.5%	5.9 / 52.6	42	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	357,880	0	T	C	50.0%	34.6 / 16.4	40	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	2,678,039	0	T	G	44.7%	125.8 / 15.9	76	N108T (AAC→ACC)	yphE	putative sugar ABC transporter ATPase
*	NC_000913	357,875	0	A	T	44.4%	54.2 / 20.6	45	N272K (AAT→AAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	3,133,302	0	T	G	43.7%	112.2 / 11.5	72	H219P (CAC→CCC)	yghS	putative ATP‑binding protein
*	NC_000913	3,556,200	0	G	A	43.7%	82.7 / 34.8	71	S217F (TCC→TTC)	rtcA	RNA 3'‑terminal phosphate cyclase
*	NC_000913	2,984,718	0	G	C	43.3%	87.6 / 32.1	69	P292R (CCG→CGG)	yqeF	short chain acyltransferase
*	NC_000913	3,026,941	0	A	C	43.3%	103.0 / 16.5	67	E392D (GAA→GAC)	guaD	guanine deaminase
*	NC_000913	3,261,055	0	A	C	43.2%	151.7 / 15.8	90	V455G (GTG→GGG)	tdcE	pyruvate formate‑lyase 4/2‑ketobutyrate formate‑lyase
*	NC_000913	4,332,791	0	A	C	42.5%	163.5 / 21.9	87	V161G (GTG→GGG)	basS	sensory histidine kinase in two‑component regulatory system with BasR
*	NC_000913	941,713	0	T	G	41.9%	106.3 / 16.0	62	V252G (GTG→GGG)	dmsA	dimethyl sulfoxide reductase, anaerobic, subunit A
*	NC_000913	1,435,727	0	G	A	41.9%	90.1 / 46.5	74	intergenic (‑108/+33)	uspF/ompN	stress‑induced protein, ATP‑binding protein/outer membrane pore protein N, non‑specific
*	NC_000913	2,578,143	0	A	C	41.9%	125.8 / 25.3	74	L79V (TTA→GTA)	maeB	malic enzyme: putative oxidoreductase/phosphotransacetylase
*	NC_000913	1,222,233	0	G	A	41.7%	77.2 / 25.2	60	pseudogene (60/75 nt)	ycgH	pseudogene; putative ATP‑binding component of a transport system
*	NC_000913	4,378,802	0	A	C	41.3%	106.3 / 17.7	66	V48G (GTA→GGA)	ampC	penicillin‑binding protein; beta‑lactamase, intrinsically weak
*	NC_000913	2,001,918	0	A	C	40.9%	175.1 / 12.9	89	intergenic (‑129/+192)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein (flagellin)
*	NC_000913	1,080,856	0	T	G	40.3%	125.6 / 10.0	73	intergenic (+43/‑500)	putP/efeU	proline:sodium symporter/ferrous iron permease (pseudogene)
*	NC_000913	1,376,505	0	A	C	39.7%	106.4 / 20.8	63	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
*	NC_000913	29,496	0	T	A	39.4%	117.4 / 35.8	71	intergenic (+301/‑155)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	3,350,853	0	A	C	39.2%	144.6 / 12.7	79	S725A (TCA→GCA)	arcB	aerobic respiration control sensor histidine protein kinase, cognate to two‑component response regulators ArcA and RssB

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 =	54 (0.620)	14 (0.180)	14/266	9.0	20.3%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	62 (0.800)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1207805	57 (0.660)	12 (0.160)	12/266	10.0	17.8%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	60 (0.780)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related