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 687 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,296,160	0	A	C	73.9%	195.2 / 64.8	88	T118P (ACC→CCC)	diaA	DnaA initiator‑associating factor for replication initiation
*	NC_000913	357,890	0	C	A	55.1%	19.5 / 72.4	49	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	357,880	0	T	C	47.9%	55.3 / 15.5	48	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	599,576	0	T	G	47.6%	130.7 / 34.0	82	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	354,288	0	T	G	46.8%	116.4 / 22.9	77	V528G (GTG→GGG)	prpE	propionate‑‑CoA ligase
*	NC_000913	606,612	0	G	A	46.1%	94.7 / 34.8	76	Q258* (CAG→TAG)	ybdK	weak gamma‑glutamyl:cysteine ligase
*	NC_000913	941,713	0	T	G	45.8%	124.5 / 30.0	83	V252G (GTG→GGG)	dmsA	dimethyl sulfoxide reductase, anaerobic, subunit A
*	NC_000913	4,332,791	0	A	C	45.7%	127.1 / 13.8	70	V161G (GTG→GGG)	basS	sensory histidine kinase in two‑component regulatory system with BasR
*	NC_000913	689,514	0	A	C	44.8%	90.8 / 10.7	58	G456G (GGT→GGG)	lnt	apolipoprotein N‑acyltransferase
*	NC_000913	5,159	0	G	A	44.4%	85.6 / 52.9	81	intergenic (+139/‑75)	thrC/yaaX	L‑threonine synthase/DUF2502 family putative periplasmic protein
*	NC_000913	993,917	0	A	C	44.3%	110.5 / 26.0	70	V43G (GTG→GGG)	ssuB	aliphatic sulfonate ABC transporter ATPase
*	NC_000913	2,421,443	0	A	C	44.3%	106.7 / 11.2	61	Y40S (TAC→TCC)	folX	D‑erythro‑7,8‑dihydroneopterin triphosphate 2'‑epimerase and dihydroneopterin aldolase
*	NC_000913	3,404,215	0	T	G	44.3%	92.9 / 13.1	62	G244G (GGT→GGG)	acuI	putative acryloyl‑CoA reductase
*	NC_000913	32,653	0	T	C	43.4%	99.9 / 30.5	77	S613P (TCC→CCC)	carB	carbamoyl‑phosphate synthase large subunit
*	NC_000913	2,483,268	0	T	A	43.4%	88.3 / 40.6	76	L24F (TTA→TTT)	emrK	multidrug resistance efflux pump membrane fusion protein
*	NC_000913	354,282	0	T	G	42.5%	124.2 / 14.2	75	V526G (GTT→GGT)	prpE	propionate‑‑CoA ligase
*	NC_000913	345,328	0	C	A	42.1%	139.7 / 47.7	76	intergenic (+337/‑76)	yahL/yahM	uncharacterized protein/uncharacterized protein
*	NC_000913	3,585,086	0	A	C	42.1%	155.6 / 14.4	77	Y580D (TAC→GAC)	ggt	gamma‑glutamyltranspeptidase
*	NC_000913	4,457,105	0	A	G	42.0%	132.5 / 38.2	100	I441V (ATC→GTC)	mpl	UDP‑N‑acetylmuramate:L‑alanyl‑gamma‑D‑glutamyl‑ meso‑diaminopimelate ligase
*	NC_000913	3,460,777	0	A	C	41.7%	96.2 / 13.7	61	T321P (ACC→CCC)	gspF	general secretory pathway component, cryptic

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	72 (0.890)	21 (0.290)	21/266	5.8	28.5%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	41 (0.570)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	1207790 =	69 (0.850)	13 (0.180)	13/266	8.9	19.8%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	44 (0.610)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1209618	49 (0.600)	18 (0.250)	4/268	14.5	23.7%	pseudogene (2/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
	?	NC_000913	2471897 =	72 (0.990)					pseudogene (226/579 nt)	yfdL	pseudogene, CPS‑53 (KpLE1) prophage;Phage or Prophage Related