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 498 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	380,012	2	.	G	69.8%	104.6 / 47.7	43	intergenic (‑131/+57)	frmR/yaiO	regulator protein that represses frmRAB operon/outer membrane protein
*	NC_000913	3,943,488	0	T	G	51.7%	12.5 / 26.4	29	noncoding (54/76 nt)	gltU	tRNA‑Glu
*	NC_000913	357,890	0	C	A	45.7%	22.5 / 19.4	35	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	3,261,055	0	A	C	45.1%	100.8 / 33.0	82	V455G (GTG→GGG)	tdcE	pyruvate formate‑lyase 4/2‑ketobutyrate formate‑lyase
*	NC_000913	2,903,692	0	C	A	43.1%	101.7 / 45.7	72	intergenic (+318/+1055)	ygcE/queE	putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis
*	NC_000913	1,097,581	0	A	G	42.1%	94.5 / 21.1	59	noncoding (72/88 nt)	serX	tRNA‑Ser
*	NC_000913	599,576	0	T	G	42.0%	111.3 / 18.1	69	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	3,862,664	0	C	G	42.0%	27.3 / 22.0	50	pseudogene (940/1617 nt)	glvC	pseudogene, arbutin specific enzyme IIC component of PTS;enzyme; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system, arbutin‑like IIB component; PTS system, arbutin‑like IIC component
*	NC_000913	2,678,039	0	T	G	41.4%	90.7 / 12.3	58	N108T (AAC→ACC)	yphE	putative sugar ABC transporter ATPase
*	NC_000913	1,245,234	0	G	T	41.1%	116.2 / 37.9	73	L25F (TTG→TTT)	ycgY	uncharacterized protein
*	NC_000913	3,350,853	0	A	C	41.0%	95.5 / 15.9	61	S725A (TCA→GCA)	arcB	aerobic respiration control sensor histidine protein kinase, cognate to two‑component response regulators ArcA and RssB
*	NC_000913	2,483,268	0	T	A	40.4%	65.9 / 30.2	57	L24F (TTA→TTT)	emrK	multidrug resistance efflux pump membrane fusion protein
*	NC_000913	559,181	0	G	A	40.3%	90.0 / 25.6	68	E70K (GAA→AAA)	sfmC	putative periplasmic pilus chaperone
*	NC_000913	1,376,505	0	A	C	40.3%	101.6 / 31.9	67	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
*	NC_000913	3,864,599	0	A	C	40.0%	120.6 / 13.3	76	H234P (CAC→CCC)	yidP	UTRA domain‑containing GntR family putative transcriptional regulator
*	NC_000913	4,223,143	0	A	C	40.0%	96.9 / 12.8	63	G162G (GGT→GGG)	iclR	transcriptional repressor
*	NC_000913	4,604,344	0	C	T	40.0%	66.3 / 30.9	55	S62F (TCT→TTT)	bglJ	bgl operon transcriptional activator
*	NC_000913	5,159	0	G	A	39.5%	92.0 / 50.0	77	intergenic (+139/‑75)	thrC/yaaX	L‑threonine synthase/DUF2502 family putative periplasmic protein
*	NC_000913	2,781,626	0	G	T	39.3%	142.3 / 35.3	86	N367K (AAC→AAA)	ypjA	adhesin‑like autotransporter
*	NC_000913	2,236,901	0	T	C	39.2%	100.3 / 16.6	74	T285A (ACG→GCG)	mglC	methyl‑galactoside transporter subunit

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	67 (0.860)	19 (0.270)	17/266	6.2	26.6%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	45 (0.650)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	1207790 =	62 (0.800)	16 (0.230)	15/266	6.9	23.8%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	47 (0.680)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 4542690	107 (1.380)	11 (0.150)	11/280	9.0	10.3%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	91 (1.250)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	4542682 =	108 (1.390)	7 (0.100)	7/280	11.2	6.7%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	93 (1.270)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)