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 440 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	46.9%	41.3 / 22.9	50	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	29,496	0	T	A	45.4%	108.5 / 58.7	98	intergenic (+301/‑155)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	599,576	0	T	G	44.0%	137.4 / 36.3	100	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	2,326,450	0	T	G	43.5%	150.6 / 13.4	86	G114G (GGT→GGG)	atoB	acetyl‑CoA acetyltransferase
*	NC_000913	29,486	0	C	A	41.8%	117.8 / 45.2	91	intergenic (+291/‑165)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	1,153,573	0	T	G	41.2%	105.1 / 28.0	68	Y92D (TAC→GAC)	pabC	4‑amino‑4‑deoxychorismate lyase component of para‑aminobenzoate synthase multienzyme complex
*	NC_000913	3,423,294	0	T	C	41.0%	135.3 / 25.1	95	intergenic (+100/+129)	yhdZ/rrfF	putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon
*	NC_000913	357,880	0	T	C	40.8%	68.9 / 11.8	49	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	2,984,441	0	A	C	40.2%	148.1 / 16.0	84	G384G (GGT→GGG)	yqeF	short chain acyltransferase
*	NC_000913	366,526	0	T	G	40.0%	130.7 / 29.2	86	T329P (ACC→CCC)	lacI	lactose‑inducible lac operon transcriptional repressor
*	NC_000913	3,423,297	0	G	C	39.8%	152.3 / 42.4	94	intergenic (+103/+126)	yhdZ/rrfF	putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon
*	NC_000913	3,717,014	0	T	G	39.3%	167.3 / 14.0	90	G156G (GGT→GGG)	yiaD	multicopy suppressor of bamB; outer membrane lipoprotein
*	NC_000913	689,514	0	A	C	39.1%	110.1 / 12.7	71	G456G (GGT→GGG)	lnt	apolipoprotein N‑acyltransferase
*	NC_000913	2,001,918	0	A	C	38.8%	146.0 / 13.7	84	intergenic (‑129/+192)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein (flagellin)
*	NC_000913	4,332,309	0	A	C	38.1%	136.2 / 35.1	84	L322V (TTA→GTA)	basS	sensory histidine kinase in two‑component regulatory system with BasR
*	NC_000913	3,423,287	0	G	C	37.9%	114.6 / 34.6	89	intergenic (+93/+136)	yhdZ/rrfF	putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon
*	NC_000913	1,415,786	0	A	C	37.8%	123.7 / 18.1	75	V534G (GTG→GGG)	recE	Rac prophage; exonuclease VIII, 5' to 3' specific dsDNA exonuclease
*	NC_000913	144,184	0	T	G	37.8%	145.2 / 24.0	92	G161G (GGT→GGG)	yadH	putative ABC transporter permease
*	NC_000913	1,356,201	0	T	G	37.7%	149.1 / 10.9	78	T304P (ACC→CCC)	sapA	antimicrobial peptide transport ABC transporter periplasmic binding protein
*	NC_000913	354,288	0	T	G	37.2%	132.8 / 15.7	79	V528G (GTG→GGG)	prpE	propionate‑‑CoA ligase

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 =	91 (0.890)	18 (0.200)	17/266	9.5	19.2%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	70 (0.760)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1207805	96 (0.930)	10 (0.110)	10/266	12.9	11.7%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	66 (0.720)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 4542690	144 (1.400)	6 (0.060)	6/280	16.2	4.8%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	105 (1.090)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)