breseq  version 0.35.4  revision f352f80f4bc9 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,825,061	0	G	A	37.8%	43.1 / 22.2	37	intergenic (‑124/+79)	ves/spy	HutD family protein Ves/ATP‑independent periplasmic chaperone
*	NC_000913	4,111,747	0	G	T	35.4%	99.5 / 34.1	48	N156K (AAC→AAA)	yiiQ	DUF1454 domain‑containing protein YiiQ
*	NC_000913	4,604,344	0	C	T	32.8%	103.7 / 36.1	67	S62F (TCT→TTT)	bglJ	DNA‑binding transcriptional regulator BglJ
*	NC_000913	3,206,435	0	C	T	32.4%	50.2 / 20.7	37	intergenic (‑179/‑28)	ttdR/ttdA	DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha
*	NC_000913	2,001,918	0	A	C	32.4%	54.8 / 12.4	34	intergenic (‑129/+192)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein
*	NC_000913	3,745,397	0	A	C	30.2%	66.0 / 12.2	44	L198F (TTA→TTC)	yiaN	2,3‑diketo‑L‑gulonate:Na(+) symporter ‑ membrane subunit
*	NC_000913	2,326,450	0	T	G	27.5%	68.2 / 20.7	40	G114G (GGT→GGG)	atoB	acetyl‑CoA acetyltransferase
*	NC_000913	3,206,444	0	T	A	27.0%	67.8 / 15.5	37	intergenic (‑188/‑19)	ttdR/ttdA	DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha
*	NC_000913	4,296,060	0	C	T	26.4%	139.1 / 45.2	72	intergenic (+266/+376)	gltP/yjcO	glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
*	NC_000913	4,161,148	0	G	A	23.5%	171.6 / 23.9	81	E28K (GAA→AAA)	fabR	DNA‑binding transcriptional repressor FabR
*	NC_000913	3,926,366	0	A	C	22.2%	192.7 / 28.2	91	G30G (GGT→GGG)	mioC	flavoprotein MioC
*	NC_000913	646,747	0	T	G	21.9%	84.4 / 15.4	41	T255P (ACC→CCC)	citG	triphosphoribosyl‑dephospho‑CoA synthase
*	NC_000913	4,287,719	0	T	A	20.8%	127.1 / 17.8	53	intergenic (‑348/‑45)	acs/nrfA	acetyl‑CoA synthetase (AMP‑forming)/cytochrome c552 nitrite reductase
*	NC_000913	1,335,691	0	T	G	20.7%	187.9 / 12.1	82	intergenic (+24/‑140)	ymiC/acnA	protein YmiC/aconitate hydratase 1
*	NC_000913	1,377,140	0	A	C	20.6%	144.5 / 11.3	63	K103N (AAA→AAC)	ycjS	putative oxidoreductase YcjS
*	NC_000913	3,531,440	0	A	C	20.2%	192.6 / 10.2	79	Y334D (TAT→GAT)	yhgE	putative transport protein YhgE
*	NC_000913	650,809	0	T	G	20.0%	128.4 / 12.3	55	T350P (ACC→CCC)	citC	citrate lyase synthetase
*	NC_000913	3,401,459	0	T	C	20.0%	151.9 / 10.9	70	D625G (GAT→GGT)	csrD	regulator of CsrB and CsrC decay

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	4542682 =	80 (0.960)	7 (0.090)	6/256	6.0	8.5%	intergenic (+49/‑433)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	4542996 =	76 (0.970)					intergenic (+363/‑119)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
*	?	NC_000913	= 4542690	74 (0.880)	6 (0.080)	3/256	7.5	7.6%	intergenic (+57/‑425)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	= 4542986	76 (0.970)					intergenic (+353/‑129)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
*	?	NC_000913	= 2737263	88 (1.050)	3 (0.040)	3/272	7.7	3.4%	coding (110/342 nt)	raiA	stationary phase translation inhibitor and ribosome stability factor
	?	NC_000913	2737275 =	81 (0.970)					coding (122/342 nt)	raiA	stationary phase translation inhibitor and ribosome stability factor
*	?	NC_000913	704724 =	92 (1.100)	3 (0.040)	3/270	7.7	3.0%	coding (781/1947 nt)	nagE	N‑acetylglucosamine specific PTS enzyme IIABC component
	?	NC_000913	2035599 =	104 (1.260)					intergenic (+356/‑236)	yedS/hchA	putative outer membrane protein YedS, N‑terminal fragment/protein/nucleic acid deglycase 1