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 93 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,306,136	0	A	C	57.9%	12.4 / 18.2	19	G575G (GGT→GGG)	deaD	ATP‑dependent RNA helicase
*	NC_000913	3,306,139	0	A	C	57.9%	7.4 / 18.7	19	G574G (GGT→GGG)	deaD	ATP‑dependent RNA helicase
*	NC_000913	354,288	0	T	G	54.0%	35.5 / 52.0	38	V528G (GTG→GGG)	prpE	propionate‑‑CoA ligase
*	NC_000913	599,576	0	T	G	50.0%	39.5 / 10.5	32	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	2,943,869	0	A	G	50.0%	35.2 / 14.0	37	D178G (GAT→GGT)	csdA	cysteine sulfinate desulfinase
*	NC_000913	3,423,297	0	G	C	48.2%	64.1 / 34.0	56	intergenic (+103/+126)	yhdZ/rrfF	putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon
*	NC_000913	2,421,443	0	A	C	47.2%	46.4 / 12.8	36	Y40S (TAC→TCC)	folX	D‑erythro‑7,8‑dihydroneopterin triphosphate 2'‑epimerase and dihydroneopterin aldolase
*	NC_000913	345,328	0	C	A	46.7%	31.2 / 16.6	30	intergenic (+337/‑76)	yahL/yahM	uncharacterized protein/uncharacterized protein
*	NC_000913	3,412,898	0	C	T	46.3%	22.6 / 36.2	41	A190T (GCC→ACC)	acrS	acrAB operon transcriptional repressor
*	NC_000913	3,705,661	0	T	C	45.0%	52.6 / 10.6	40	I44V (ATC→GTC)	dppB	dipeptide/heme ABC transporter permease
*	NC_000913	718,669	0	C	T	43.9%	52.4 / 15.8	41	E598K (GAA→AAA)	speF	ornithine decarboxylase isozyme, inducible
*	NC_000913	3,601,160	0	G	A	43.9%	42.2 / 20.4	42	F309F (TTC→TTT)	ftsX	putative ABC transporter permease
*	NC_000913	4,457,105	0	A	G	43.6%	47.6 / 13.4	39	I441V (ATC→GTC)	mpl	UDP‑N‑acetylmuramate:L‑alanyl‑gamma‑D‑glutamyl‑ meso‑diaminopimelate ligase
*	NC_000913	1,622,816	0	G	A	43.5%	12.3 / 19.9	23	intergenic (+75/+144)	yneM/dgcZ	inner membrane‑associated protein/diguanylate cyclase, zinc‑sensing
*	NC_000913	2,984,441	0	A	C	43.2%	54.6 / 10.8	38	G384G (GGT→GGG)	yqeF	short chain acyltransferase
*	NC_000913	1,574,051	0	G	T	42.9%	45.1 / 11.8	35	V384V (GTC→GTA)	pqqL	putative periplasmic M16 family zinc metalloendopeptidase
*	NC_000913	3,601,164	0	A	C	42.9%	64.8 / 10.8	42	V308G (GTT→GGT)	ftsX	putative ABC transporter permease
*	NC_000913	3,601,176	0	T	C	42.9%	47.3 / 21.2	43	E304G (GAA→GGA)	ftsX	putative ABC transporter permease
*	NC_000913	3,585,058	0	T	C	41.3%	71.3 / 10.9	46	intergenic (+15/+23)	yrhB/ggt	stable heat shock chaperone/gamma‑glutamyltranspeptidase
*	NC_000913	2,185,199	0	T	G	41.0%	55.9 / 12.3	39	T35P (ACC→CCC)	thiM	hydoxyethylthiazole kinase

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 (0.830)	4 (0.110)	4/266	6.6	11.7%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	29 (0.770)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 4542690	49 (1.160)	3 (0.080)	3/280	7.6	5.7%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	54 (1.360)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)