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 87 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	65.5%	0.2 / 24.7	30	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	357,880	0	T	C	57.1%	7.9 / 32.9	28	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	3,443,277	0	A	C	51.1%	53.9 / 71.3	45	V274G (GTA→GGA)	secY	preprotein translocase membrane subunit
*	NC_000913	4,042,993	0	C	T	50.0%	3.2 / 11.2	24	F193F (TTC→TTT)	srkA	Cpx stress response Thr/Ser protein kinase; MazF antagonist protein
*	NC_000913	3,508,662	0	T	A	47.7%	36.4 / 23.1	44	E384D (GAA→GAT)	yhfW	phosphopentomutase‑related metalloenzyme superfamily protein
*	NC_000913	2,984,718	0	G	C	47.6%	30.2 / 24.9	46	P292R (CCG→CGG)	yqeF	short chain acyltransferase
*	NC_000913	2,378,968	0	C	T	47.5%	16.8 / 19.7	40	E98K (GAA→AAA)	menD	2‑succinyl‑5‑enolpyruvyl‑6‑hydroxy‑3‑ cyclohexene‑1‑carboxylate synthase; SEPHCHC synthase
*	NC_000913	4,227,407	0	C	A	46.0%	55.2 / 16.6	37	Q1194K (CAA→AAA)	metH	homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent
*	NC_000913	1,413,735	0	A	T	45.7%	33.5 / 21.6	35	Y2* (TAT→TAA)	ydaC	DUF1187 family protein, Rac prophage; putative double‑strand break reduction protein
*	NC_000913	1,369,516	0	T	A	44.8%	29.1 / 10.5	30	S42T (TCA→ACA)	pspD	peripheral inner membrane phage‑shock protein
*	NC_000913	2,483,254	0	G	A	43.6%	40.2 / 20.4	39	S29L (TCA→TTA)	emrK	multidrug resistance efflux pump membrane fusion protein
*	NC_000913	2,903,692	0	C	A	43.2%	62.9 / 17.4	37	intergenic (+318/+1055)	ygcE/queE	putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis
*	NC_000913	3,705,653	0	T	G	42.4%	35.0 / 11.9	33	P46P (CCA→CCC)	dppB	dipeptide/heme ABC transporter permease
*	NC_000913	3,705,661	0	T	C	42.4%	32.5 / 13.6	34	I44V (ATC→GTC)	dppB	dipeptide/heme ABC transporter permease
*	NC_000913	29,496	0	T	A	42.0%	72.7 / 25.6	50	intergenic (+301/‑155)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	1,222,596	0	G	A	41.2%	32.4 / 13.4	36	F13F (TTC→TTT)	ymgD	uncharacterized protein
*	NC_000913	3,270,489	0	A	C	41.0%	45.7 / 17.5	40	intergenic (+887/+136)	yhaC/garK	pentapetide repeats‑related protein/glycerate kinase I
*	NC_000913	357,842	0	C	A	40.6%	38.3 / 14.1	32	L283F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	395,286	0	G	A	39.0%	53.0 / 12.2	41	F334F (TTC→TTT)	ampH	D‑alanyl‑D‑alanine‑ carboxypeptidase/endopeptidase; penicillin‑binding protein; weak beta‑lactamase
*	NC_000913	1,622,816	0	G	A	39.0%	44.8 / 24.5	41	intergenic (+75/+144)	yneM/dgcZ	inner membrane‑associated protein/diguanylate cyclase, zinc‑sensing

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	35 (0.790)	11 (0.280)	11/266	3.8	23.3%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	41 (1.040)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	1207790 =	37 (0.830)	7 (0.180)	7/266	5.4	15.7%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	42 (1.060)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related