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 403 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,222,233	0	G	A	55.9%	28.5 / 87.5	68	pseudogene (60/75 nt)	ycgH	pseudogene; putative ATP‑binding component of a transport system
*	NC_000913	2,248,431	0	A	C	48.5%	66.4 / 30.2	67	G34G (GGT→GGG)	lysP	lysine transporter
*	NC_000913	1,157,271	0	T	G	47.1%	76.7 / 14.1	52	G165G (GGT→GGG)	ycfH	putative DNase
*	NC_000913	4,536,197	0	A	T	46.9%	34.7 / 46.9	49	intergenic (+166/+417)	yjhR/nanS	pseudogene, helicase family; putative frameshift suppressor/9‑O‑acetyl N‑acetylneuraminic acid esterase
*	NC_000913	1,478,324	0	T	G	45.5%	137.8 / 18.3	77	G33G (GGT→GGG)	ynbB	putative CDP‑diglyceride synthase
*	NC_000913	2,678,039	0	T	G	45.0%	93.8 / 16.6	61	N108T (AAC→ACC)	yphE	putative sugar ABC transporter ATPase
*	NC_000913	2,421,443	0	A	C	44.9%	100.7 / 28.0	69	Y40S (TAC→TCC)	folX	D‑erythro‑7,8‑dihydroneopterin triphosphate 2'‑epimerase and dihydroneopterin aldolase
*	NC_000913	4,604,344	0	C	T	44.8%	57.3 / 29.1	58	S62F (TCT→TTT)	bglJ	bgl operon transcriptional activator
*	NC_000913	2,421,397	0	G	A	43.5%	76.3 / 43.0	62	E25K (GAA→AAA)	folX	D‑erythro‑7,8‑dihydroneopterin triphosphate 2'‑epimerase and dihydroneopterin aldolase
*	NC_000913	2,386,862	0	G	A	43.3%	63.4 / 50.8	60	intergenic (+31/‑72)	yfbL/yfbM	putative M28A family peptidase/DUF1877 family protein
*	NC_000913	599,576	0	T	G	42.9%	97.4 / 17.0	56	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	213,341	0	A	G	42.6%	72.1 / 15.6	54	G337G (GGA→GGG)	tilS	tRNA(Ile)‑lysidine synthetase
*	NC_000913	3,206,435	0	C	T	42.6%	59.7 / 36.5	54	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	4,287,719	0	T	A	42.2%	71.9 / 37.1	64	intergenic (‑348/‑45)	acs/nrfA	acetyl‑CoA synthetase/nitrite reductase, formate‑dependent, cytochrome
*	NC_000913	987,494	0	T	G	42.0%	127.7 / 11.5	70	intergenic (‑512/+91)	ompF/asnS	outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase
*	NC_000913	357,890	0	C	A	41.9%	30.8 / 17.2	31	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	2,248,424	0	C	A	41.9%	70.2 / 38.1	62	V37F (GTT→TTT)	lysP	lysine transporter
*	NC_000913	3,355,457	0	A	C	41.9%	110.3 / 14.5	62	T245P (ACC→CCC)	gltB	glutamate synthase, large subunit
*	NC_000913	2,421,437	0	T	C	41.5%	99.6 / 17.0	65	I38T (ATC→ACC)	folX	D‑erythro‑7,8‑dihydroneopterin triphosphate 2'‑epimerase and dihydroneopterin aldolase
*	NC_000913	15,410	0	T	G	41.5%	69.3 / 10.9	42	intergenic (+112/‑35)	dnaJ/insL1	chaperone Hsp40, DnaK co‑chaperone/IS186 transposase

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	56 (0.780)	9 (0.140)	9/266	8.9	16.1%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	44 (0.690)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	1207790 =	53 (0.740)	8 (0.130)	8/266	9.4	14.8%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	45 (0.710)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	4542682 =	77 (1.080)	6 (0.090)	6/280	11.1	8.9%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	51 (0.760)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	= 4542690	75 (1.050)	3 (0.040)	3/280	13.4	4.7%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	51 (0.760)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)