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 262 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	436,516	0	C	A	53.4%	29.5 / 78.4	58	Q295K (CAA→AAA)	thiL	thiamine monophosphate kinase
*	NC_000913	501,564	0	A	C	52.0%	80.7 / 119.4	75	*559E (TAA→GAA)	ybaL	inner membrane putative NAD(P)‑binding transporter
*	NC_000913	1,376,505	0	A	C	51.1%	42.3 / 70.0	46	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
*	NC_000913	501,575	0	A	C	50.0%	89.9 / 17.9	70	V555G (GTG→GGG)	ybaL	inner membrane putative NAD(P)‑binding transporter
*	NC_000913	366,526	0	T	G	49.2%	79.0 / 19.5	61	T329P (ACC→CCC)	lacI	lactose‑inducible lac operon transcriptional repressor
*	NC_000913	1,478,324	0	T	G	48.1%	78.0 / 12.5	52	G33G (GGT→GGG)	ynbB	putative CDP‑diglyceride synthase
*	NC_000913	599,576	0	T	G	47.9%	59.9 / 18.2	48	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	2,578,143	0	A	C	47.8%	62.6 / 11.4	46	L79V (TTA→GTA)	maeB	malic enzyme: putative oxidoreductase/phosphotransacetylase
*	NC_000913	1,014,023	0	T	G	47.4%	56.1 / 10.3	39	G255G (GGT→GGG)	pqiB	paraquat‑inducible, SoxRS‑regulated MCE domain protein
*	NC_000913	1,222,233	0	G	A	47.4%	32.2 / 18.1	38	pseudogene (60/75 nt)	ycgH	pseudogene; putative ATP‑binding component of a transport system
*	NC_000913	1,649,295	0	T	G	46.5%	62.9 / 15.3	43	intergenic (+254/‑314)	ydfC/dicB	uncharacterized protein, Qin prophage/Qin prophage; cell division inhibition protein
*	NC_000913	3,556,207	0	T	C	46.3%	69.2 / 17.0	54	S215G (AGT→GGT)	rtcA	RNA 3'‑terminal phosphate cyclase
*	NC_000913	3,556,200	0	G	A	46.2%	51.2 / 27.3	52	S217F (TCC→TTC)	rtcA	RNA 3'‑terminal phosphate cyclase
*	NC_000913	4,332,791	0	A	C	44.3%	97.9 / 17.5	61	V161G (GTG→GGG)	basS	sensory histidine kinase in two‑component regulatory system with BasR
*	NC_000913	436,504	0	A	C	43.6%	70.0 / 18.6	55	T291P (ACC→CCC)	thiL	thiamine monophosphate kinase
*	NC_000913	3,206,435	0	C	T	43.1%	83.8 / 43.8	73	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	646,747	0	T	G	42.9%	58.7 / 15.6	44	T255P (ACC→CCC)	citG	2‑(5''‑triphosphoribosyl)‑3'‑dephosphocoenzyme‑A synthase
*	NC_000913	718,690	0	T	G	42.2%	104.3 / 35.8	72	T591P (ACC→CCC)	speF	ornithine decarboxylase isozyme, inducible
*	NC_000913	436,497	0	A	C	41.8%	68.4 / 17.7	56	V288V (GTA→GTC)	thiL	thiamine monophosphate kinase
*	NC_000913	266,358	0	T	G	41.0%	68.8 / 11.2	40	T66P (ACC→CCC)	yafY	lipoprotein, inner membrane; degP regulator; CP4‑6 prophage

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 =	52 (0.830)	14 (0.250)	14/266	5.6	25.6%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	35 (0.630)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	925901 =	64 (1.020)	21 (0.340) +C	15/296	6.1	26.4%	noncoding (71/88 nt)	serW	tRNA‑Ser
	?	NC_000913	= 1097399	54 (0.860)					intergenic (+570/+166)	ycdU/serX	putative inner membrane protein/tRNA‑Ser
*	?	NC_000913	= 1207805	52 (0.830)	10 (0.180)	9/266	7.7	20.1%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	33 (0.590)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related