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 506 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	52.9%	7.5 / 47.4	34	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	941,713	0	T	G	50.0%	53.5 / 29.8	54	V252G (GTG→GGG)	dmsA	dimethyl sulfoxide reductase, anaerobic, subunit A
*	NC_000913	2,001,911	0	G	A	47.9%	57.4 / 47.3	71	intergenic (‑122/+199)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein (flagellin)
*	NC_000913	3,751,537	0	A	C	47.8%	82.2 / 15.1	67	V111G (GTT→GGT)	yiaT	putative outer membrane protein
*	NC_000913	1,292,458	0	T	A	46.8%	96.2 / 52.9	77	intergenic (+93/+51)	galU/hns	glucose‑1‑phosphate uridylyltransferase/global DNA‑binding transcriptional dual regulator H‑NS
*	NC_000913	4,381,728	0	A	C	46.2%	70.8 / 10.1	52	G197G (GGT→GGG)	frdA	anaerobic fumarate reductase catalytic and NAD/flavoprotein subunit
*	NC_000913	3,847,971	0	A	C	46.0%	111.2 / 12.6	74	G218G (GGT→GGG)	uhpC	membrane protein regulates uhpT expression
*	NC_000913	2,326,450	0	T	G	43.8%	97.6 / 18.4	65	G114G (GGT→GGG)	atoB	acetyl‑CoA acetyltransferase
*	NC_000913	3,508,657	0	A	G	43.8%	113.7 / 25.0	81	F386S (TTC→TCC)	yhfW	phosphopentomutase‑related metalloenzyme superfamily protein
*	NC_000913	3,508,662	0	T	A	43.8%	116.0 / 37.7	81	E384D (GAA→GAT)	yhfW	phosphopentomutase‑related metalloenzyme superfamily protein
*	NC_000913	2,001,918	0	A	C	43.5%	99.4 / 12.8	71	intergenic (‑129/+192)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein (flagellin)
*	NC_000913	501,575	0	A	C	42.9%	97.9 / 14.4	63	V555G (GTG→GGG)	ybaL	inner membrane putative NAD(P)‑binding transporter
*	NC_000913	3,665,702	0	C	A	41.6%	112.2 / 48.4	91	A37S (GCG→TCG)	gadX	acid resistance regulon transcriptional activator; autoactivator
*	NC_000913	357,875	0	A	T	40.5%	43.9 / 13.8	37	N272K (AAT→AAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	1,245,247	0	G	T	40.3%	95.8 / 30.7	68	E30* (GAA→TAA)	ycgY	uncharacterized protein
*	NC_000913	3,253,775	0	T	C	40.0%	76.0 / 10.3	50	D147G (GAT→GGT)	yhaJ	LysR family putative transcriptional regulator
*	NC_000913	3,585,086	0	A	C	40.0%	123.5 / 12.1	70	Y580D (TAC→GAC)	ggt	gamma‑glutamyltranspeptidase
*	NC_000913	501,564	0	A	C	39.7%	114.7 / 16.6	68	*559E (TAA→GAA)	ybaL	inner membrane putative NAD(P)‑binding transporter
*	NC_000913	3,177,748	0	C	A	39.4%	60.2 / 44.3	66	E55* (GAG→TAG)	nudF	ADP‑ribose pyrophosphatase
*	NC_000913	3,443,277	0	A	C	39.3%	95.7 / 18.4	57	V274G (GTA→GGA)	secY	preprotein translocase membrane subunit

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	66 (0.830)	16 (0.230)	14/266	7.7	23.0%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	48 (0.680)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	1207790 =	68 (0.860)	11 (0.160)	11/266	9.0	16.6%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	50 (0.710)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related