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 505 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,999,673	1	.	G	57.8%	130.6 / 110.7	64	coding (219/756 nt)	ygeR	LysM domain‑containing M23 family putative peptidase; septation lipoprotein
*	NC_000913	3,907,439	0	T	C	56.0%	15.5 / 117.0	84	D47G (GAC→GGC)	phoU	negative regulator of PhoR/PhoB two‑component regulator
*	NC_000913	1,826,188	0	T	C	51.2%	0.2 / 107.2	82	T246A (ACA→GCA)	astE	succinylglutamate desuccinylase
*	NC_000913	599,576	0	T	G	50.6%	99.1 / 142.5	77	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	357,890	0	C	A	48.4%	27.9 / 17.9	31	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	2,492,781	0	A	G	48.0%	22.9 / 99.8	76	G158G (GGT→GGC)	frc	formyl‑CoA transferase, NAD(P)‑binding
*	NC_000913	4,378,802	0	A	C	46.7%	97.8 / 12.8	62	V48G (GTA→GGA)	ampC	penicillin‑binding protein; beta‑lactamase, intrinsically weak
*	NC_000913	4,457,105	0	A	G	45.7%	84.2 / 28.2	71	I441V (ATC→GTC)	mpl	UDP‑N‑acetylmuramate:L‑alanyl‑gamma‑D‑glutamyl‑ meso‑diaminopimelate ligase
*	NC_000913	2,326,450	0	T	G	45.6%	116.9 / 19.5	68	G114G (GGT→GGG)	atoB	acetyl‑CoA acetyltransferase
*	NC_000913	4,359,827	0	C	T	45.3%	20.1 / 108.6	75	G69S (GGC→AGC)	cadB	putative lysine/cadaverine transporter
*	NC_000913	599,579	0	T	G	44.7%	127.0 / 14.0	77	V289G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	4,112,578	0	T	G	44.0%	132.2 / 17.5	76	G88G (GGT→GGG)	yiiR	DUF805 family putative inner membrane protein
*	NC_000913	2,162,120	0	T	G	42.6%	108.0 / 16.1	62	G219G (GGT→GGG)	iceT	putative citrate/iron‑citrate/zinc‑citrate efflux transporter
*	NC_000913	3,206,435	0	C	T	42.6%	62.0 / 42.4	61	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	4,604,344	0	C	T	42.2%	67.6 / 41.2	71	S62F (TCT→TTT)	bglJ	bgl operon transcriptional activator
*	NC_000913	1,489,174	0	G	T	41.8%	101.0 / 31.7	67	G315C (GGT→TGT)	aldA	aldehyde dehydrogenase A, NAD‑linked
*	NC_000913	501,564	0	A	C	41.3%	148.3 / 18.6	75	*559E (TAA→GAA)	ybaL	inner membrane putative NAD(P)‑binding transporter
*	NC_000913	802,118	0	A	C	40.3%	115.9 / 10.7	73	T78P (ACC→CCC)	ybhI	putative DASS family tricarboxylate or dicarboxylate transporter
*	NC_000913	501,575	0	A	C	40.0%	151.5 / 14.8	75	V555G (GTG→GGG)	ybaL	inner membrane putative NAD(P)‑binding transporter
*	NC_000913	2,903,692	0	C	A	40.0%	98.3 / 40.5	60	intergenic (+318/+1055)	ygcE/queE	putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis

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 =	69 (0.850)	15 (0.210)	14/266	7.9	19.7%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	61 (0.840)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1207805	69 (0.850)	11 (0.150)	11/266	9.2	15.4%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	59 (0.810)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	3515076 =	86 (1.060)	3 (0.040) +AAGCTTG	3/284	15.1	5.1%	intergenic (‑17/+1)	rpe/dam	D‑ribulose‑5‑phosphate 3‑epimerase/DNA adenine methyltransferase
	?	NC_000913	4171556 =	31 (0.380)					intergenic (+12/‑81)	rrlB/rrfB	23S ribosomal RNA of rrnB operon/5S ribosomal RNA of rrnB operon
*	?	NC_000913	= 3423868	NA (NA)	3 (0.040) +CAAGCTT	3/284	15.1	3.5%	intergenic (‑81/+12)	rrfD/rrlD	5S ribosomal RNA of rrnD operon/23S ribosomal RNA of rrnD operon
	?	NC_000913	3515076 =	86 (1.060)					intergenic (‑17/+1)	rpe/dam	D‑ribulose‑5‑phosphate 3‑epimerase/DNA adenine methyltransferase