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 1160 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	163,082	0	T	C	68.8%	191.6 / 128.3	138	R326R (CGT→CGC)	hrpB	putative ATP‑dependent helicase
*	NC_000913	4,593,890	0	G	A	63.5%	104.5 / 117.4	105	A278V (GCC→GTC)	lgoT	putative L‑galactonate:H+ symporter
*	NC_000913	599,576	0	T	G	56.7%	107.4 / 201.0	127	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	987,494	0	T	G	52.9%	114.4 / 148.1	85	intergenic (‑512/+91)	ompF/asnS	outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase
*	NC_000913	941,713	0	T	G	48.9%	174.5 / 57.6	135	V252G (GTG→GGG)	dmsA	dimethyl sulfoxide reductase, anaerobic, subunit A
*	NC_000913	3,350,853	0	A	C	47.5%	191.5 / 28.3	120	S725A (TCA→GCA)	arcB	aerobic respiration control sensor histidine protein kinase, cognate to two‑component response regulators ArcA and RssB
*	NC_000913	3,350,844	0	A	C	47.1%	209.8 / 25.1	119	L728V (TTA→GTA)	arcB	aerobic respiration control sensor histidine protein kinase, cognate to two‑component response regulators ArcA and RssB
*	NC_000913	599,579	0	T	G	46.5%	203.8 / 16.0	127	V289G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	2,434,882	0	T	G	45.9%	216.5 / 31.8	122	Y252S (TAC→TCC)	truA	tRNA pseudouridine(38‑40) synthase
*	NC_000913	354,288	0	T	G	44.8%	222.7 / 28.0	125	V528G (GTG→GGG)	prpE	propionate‑‑CoA ligase
*	NC_000913	3,640,981	0	C	T	43.6%	147.3 / 87.5	140	F40F (TTC→TTT)	dtpB	dipeptide and tripeptide permease B
*	NC_000913	987,501	0	T	A	43.2%	109.9 / 42.6	82	intergenic (‑519/+84)	ompF/asnS	outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase
*	NC_000913	987,503	0	G	A	43.2%	87.4 / 43.6	82	intergenic (‑521/+82)	ompF/asnS	outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase
*	NC_000913	993,913	0	G	C	43.1%	256.0 / 57.7	144	G44G (GGC→GGG)	ssuB	aliphatic sulfonate ABC transporter ATPase
*	NC_000913	3,177,748	0	C	A	43.0%	200.1 / 72.5	128	E55* (GAG→TAG)	nudF	ADP‑ribose pyrophosphatase
*	NC_000913	2,676,106	0	C	A	42.9%	174.2 / 51.0	105	L240F (TTG→TTT)	yphD	putative sugar ABC transporter permease
*	NC_000913	436,516	0	C	A	42.7%	190.7 / 55.6	110	Q295K (CAA→AAA)	thiL	thiamine monophosphate kinase
*	NC_000913	2,921,177	0	A	C	42.4%	198.5 / 17.6	99	G308G (GGT→GGG)	gudP	putative D‑glucarate transporter
*	NC_000913	1,222,596	0	G	A	42.2%	156.9 / 95.0	142	F13F (TTC→TTT)	ymgD	uncharacterized protein
*	NC_000913	2,349,145	0	A	C	41.5%	229.6 / 35.6	118	F110V (TTC→GTC)	inaA	acid‑inducible Kdo/WaaP family putative kinase

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	121 (0.870)	28 (0.230)	28/266	10.2	22.8%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	82 (0.660)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	1207790 =	124 (0.890)	26 (0.210)	26/266	10.9	20.8%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	87 (0.700)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1209618	102 (0.730)	23 (0.180)	4/268	23.8	18.0%	pseudogene (2/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
	?	NC_000913	2471897 =	118 (0.940)					pseudogene (226/579 nt)	yfdL	pseudogene, CPS‑53 (KpLE1) prophage;Phage or Prophage Related