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 331 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,206,435	0	C	T	63.6%	‑6.3 / 51.2	55	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	941,713	0	T	G	51.9%	87.4 / 127.1	77	V252G (GTG→GGG)	dmsA	dimethyl sulfoxide reductase, anaerobic, subunit A
*	NC_000913	589,934	0	T	G	51.3%	42.2 / 64.6	39	T341P (ACC→CCC)	nfrA	bacteriophage N4 receptor, outer membrane subunit
*	NC_000913	357,890	0	C	A	48.3%	39.4 / 34.9	58	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	993,913	0	G	C	47.8%	111.1 / 21.5	69	G44G (GGC→GGG)	ssuB	aliphatic sulfonate ABC transporter ATPase
*	NC_000913	29,496	0	T	A	47.0%	63.5 / 40.9	66	intergenic (+301/‑155)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	354,288	0	T	G	46.8%	105.4 / 10.5	62	V528G (GTG→GGG)	prpE	propionate‑‑CoA ligase
*	NC_000913	993,917	0	A	C	46.3%	96.9 / 23.6	67	V43G (GTG→GGG)	ssuB	aliphatic sulfonate ABC transporter ATPase
*	NC_000913	4,378,802	0	A	C	45.6%	91.0 / 10.6	58	V48G (GTA→GGA)	ampC	penicillin‑binding protein; beta‑lactamase, intrinsically weak
*	NC_000913	3,206,452	0	C	A	44.8%	56.6 / 32.2	58	intergenic (‑196/‑11)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	73,581	0	A	C	44.6%	115.0 / 11.4	65	V314G (GTA→GGA)	thiP	thiamine/thiamine pyrophosphate ABC transporter permease
*	NC_000913	1,842,914	0	A	G	44.3%	70.1 / 25.4	61	M182V (ATG→GTG)	gdhA	glutamate dehydrogenase, NADP‑specific
*	NC_000913	2,903,692	0	C	A	44.1%	78.2 / 45.6	59	intergenic (+318/+1055)	ygcE/queE	putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis
*	NC_000913	15,410	0	T	G	43.4%	91.0 / 11.7	53	intergenic (+112/‑35)	dnaJ/insL1	chaperone Hsp40, DnaK co‑chaperone/IS186 transposase
*	NC_000913	2,921,173	0	T	C	43.3%	89.8 / 14.1	60	I310V (ATT→GTT)	gudP	putative D‑glucarate transporter
*	NC_000913	3,443,277	0	A	C	43.3%	123.1 / 12.8	67	V274G (GTA→GGA)	secY	preprotein translocase membrane subunit
*	NC_000913	15,382	0	A	G	43.1%	81.5 / 14.8	58	intergenic (+84/‑63)	dnaJ/insL1	chaperone Hsp40, DnaK co‑chaperone/IS186 transposase
*	NC_000913	2,001,918	0	A	C	43.1%	94.8 / 11.5	58	intergenic (‑129/+192)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein (flagellin)
*	NC_000913	4,112,578	0	T	G	43.1%	93.0 / 10.5	58	G88G (GGT→GGG)	yiiR	DUF805 family putative inner membrane protein
*	NC_000913	3,333,757	0	T	G	42.9%	79.5 / 13.2	51	G16G (GGT→GGG)	ispB	octaprenyl diphosphate synthase

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	= 1207805	53 (0.810)	16 (0.270)	16/266	5.3	24.4%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	52 (0.890)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	1207790 =	59 (0.900)	11 (0.190)	11/266	7.2	17.2%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	53 (0.900)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 4542690	94 (1.430)	6 (0.100)	6/280	10.3	7.1%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	69 (1.120)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	4542682 =	92 (1.400)	4 (0.060)	4/280	11.7	4.9%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	69 (1.120)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)