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 220 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	535,925	0	T	G	59.6%	53.7 / 65.3	47	G72G (GGT→GGG)	hyi	hydroxypyruvate isomerase
*	NC_000913	357,890	0	C	A	57.1%	4.4 / 33.1	28	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	535,918	0	A	G	55.6%	33.0 / 53.1	45	E70G (GAG→GGG)	hyi	hydroxypyruvate isomerase
*	NC_000913	523,335	0	T	G	54.3%	35.2 / 51.0	36	G25G (GGT→GGG)	rhsD	Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
*	NC_000913	357,880	0	T	C	53.6%	22.0 / 40.0	28	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	4,043,030	0	A	G	52.9%	13.4 / 22.0	17	N206D (AAT→GAT)	srkA	Cpx stress response Thr/Ser protein kinase; MazF antagonist protein
*	NC_000913	3,604,937	0	T	G	51.4%	39.2 / 59.1	35	V182G (GTG→GGG)	rsmD	16S rRNA m(2)G966 methyltransferase, SAM‑dependent
*	NC_000913	599,576	0	T	G	50.0%	56.4 / 19.6	48	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	1,764,774	0	G	A	48.8%	45.6 / 18.6	41	intergenic (‑388/+160)	sufA/ydiH	Fe‑S cluster assembly protein/uncharacterized protein
*	NC_000913	2,228,222	0	T	G	47.6%	38.4 / 10.1	43	pseudogene (388/1287 nt)	mdtQ	pseudogene; putative channel/filament proteins
*	NC_000913	3,947,829	0	G	A	46.8%	28.0 / 25.5	47	L47F (CTT→TTT)	hdfR	flhDC operon transcriptional repressor
*	NC_000913	2,001,918	0	A	C	46.4%	88.2 / 14.0	56	intergenic (‑129/+192)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein (flagellin)
*	NC_000913	4,457,105	0	A	G	46.4%	61.6 / 19.7	56	I441V (ATC→GTC)	mpl	UDP‑N‑acetylmuramate:L‑alanyl‑gamma‑D‑glutamyl‑ meso‑diaminopimelate ligase
*	NC_000913	1,825,056	0	G	A	45.6%	46.0 / 28.5	46	intergenic (‑119/+84)	ves/spy	cold‑ and stress‑inducible protein/periplasmic ATP‑independent protein refolding chaperone, stress‑induced
*	NC_000913	213,341	0	A	G	45.3%	65.4 / 19.8	53	G337G (GGA→GGG)	tilS	tRNA(Ile)‑lysidine synthetase
*	NC_000913	1,245,234	0	G	T	44.9%	57.9 / 23.1	49	L25F (TTG→TTT)	ycgY	uncharacterized protein
*	NC_000913	3,177,748	0	C	A	44.2%	37.1 / 29.9	43	E55* (GAG→TAG)	nudF	ADP‑ribose pyrophosphatase
*	NC_000913	3,947,850	0	C	T	44.0%	55.6 / 29.6	50	E40K (GAA→AAA)	hdfR	flhDC operon transcriptional repressor
*	NC_000913	3,995,457	0	T	G	44.0%	78.1 / 11.4	50	G232G (GGT→GGG)	dapF	diaminopimelate epimerase
*	NC_000913	718,659	0	T	A	43.9%	66.3 / 14.8	41	D601V (GAT→GTT)	speF	ornithine decarboxylase isozyme, inducible

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 =	29 (0.570)	10 (0.220)	10/266	5.0	25.0%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	34 (0.750)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1207805	36 (0.710)	9 (0.200)	9/266	5.4	21.6%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	33 (0.730)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related