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 241 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	599,576	0	T	G	53.2%	40.1 / 72.0	47	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	357,890	0	C	A	52.4%	10.8 / 58.1	42	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	213,341	0	A	G	50.0%	56.5 / 20.3	53	G337G (GGA→GGG)	tilS	tRNA(Ile)‑lysidine synthetase
*	NC_000913	357,875	0	A	T	50.0%	32.8 / 18.9	44	N272K (AAT→AAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	357,880	0	T	C	50.0%	24.1 / 20.1	44	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	4,604,344	0	C	T	48.1%	37.9 / 29.8	52	S62F (TCT→TTT)	bglJ	bgl operon transcriptional activator
*	NC_000913	3,508,662	0	T	A	46.8%	54.5 / 15.8	47	E384D (GAA→GAT)	yhfW	phosphopentomutase‑related metalloenzyme superfamily protein
*	NC_000913	354,288	0	T	G	46.2%	97.2 / 14.0	66	V528G (GTG→GGG)	prpE	propionate‑‑CoA ligase
*	NC_000913	3,508,681	0	A	C	45.2%	42.1 / 12.0	43	V378G (GTG→GGG)	yhfW	phosphopentomutase‑related metalloenzyme superfamily protein
*	NC_000913	925,900	0	A	G	44.4%	67.3 / 17.7	55	noncoding (72/88 nt)	serW	tRNA‑Ser
*	NC_000913	3,443,277	0	A	C	44.4%	89.3 / 13.6	54	V274G (GTA→GGA)	secY	preprotein translocase membrane subunit
*	NC_000913	364,526	0	C	A	43.8%	68.0 / 22.1	48	G594C (GGC→TGC)	lacZ	beta‑D‑galactosidase
*	NC_000913	298,960	0	A	C	43.2%	56.3 / 15.5	44	Y659D (TAT→GAT)	paoC	PaoABC aldehyde oxidoreductase, Moco‑containing subunit
*	NC_000913	3,508,657	0	A	G	43.2%	52.5 / 10.5	44	F386S (TTC→TCC)	yhfW	phosphopentomutase‑related metalloenzyme superfamily protein
*	NC_000913	3,133,302	0	T	G	42.9%	87.9 / 10.1	56	H219P (CAC→CCC)	yghS	putative ATP‑binding protein
*	NC_000913	3,578,287	0	T	C	42.9%	56.5 / 16.3	42	E147G (GAA→GGA)	gntR	d‑gluconate inducible gluconate regulon transcriptional repressor
*	NC_000913	4,042,993	0	C	T	42.3%	15.7 / 10.2	26	F193F (TTC→TTT)	srkA	Cpx stress response Thr/Ser protein kinase; MazF antagonist protein
*	NC_000913	3,740	0	C	A	41.3%	73.3 / 16.3	47	L3I (CTC→ATC)	thrC	L‑threonine synthase
*	NC_000913	3,862,664	0	C	G	40.9%	12.7 / 24.9	44	pseudogene (940/1617 nt)	glvC	pseudogene, arbutin specific enzyme IIC component of PTS;enzyme; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system, arbutin‑like IIB component; PTS system, arbutin‑like IIC component
*	NC_000913	2,001,911	0	G	A	40.7%	77.0 / 28.4	59	intergenic (‑122/+199)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein (flagellin)

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	50 (0.780)	12 (0.210)	12/266	6.0	21.3%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	44 (0.770)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	1207790 =	54 (0.840)	12 (0.210)	12/266	6.0	20.5%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	45 (0.790)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related