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

Marginal read alignment evidence (highest frequency 20 of 42 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	746,706	0	T	C	54.8%	34.1 / 103.2	84	C258R (TGC→CGC)	nei	endonuclease VIII
*	NC_000913	3,364,787	0	G	A	48.0%	81.6 / inf	254	A661T (GCC→ACC)	yhcD	putative fimbrial usher protein YhcD
*	NC_000913	4,604,344	0	C	T	40.9%	56.6 / 39.9	66	S62F (TCT→TTT)	bglJ	DNA‑binding transcriptional regulator BglJ
*	NC_000913	4,568,504	0	T	G	36.1%	203.6 / 33.0	122	T6P (ACC→CCC)	mdtM	multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter
*	NC_000913	4,101,507	0	T	G	35.7%	97.9 / 14.9	56	intergenic (+77/‑183)	sodA/kdgT	superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter
*	NC_000913	4,098,155	0	A	C	35.1%	167.6 / 24.2	94	L140F (TTA→TTC)	rhaS	DNA‑binding transcriptional activator RhaS
*	NC_000913	3,745,397	0	A	C	34.0%	79.9 / 12.7	47	L198F (TTA→TTC)	yiaN	2,3‑diketo‑L‑gulonate:Na(+) symporter ‑ membrane subunit
*	NC_000913	888,014	0	T	G	32.8%	130.2 / 22.8	67	noncoding (44/81 nt)	rybB	small regulatory RNA RybB
*	NC_000913	4,168,425	0	T	G	32.6%	85.9 / 11.7	46	noncoding (54/76 nt)	gltT	tRNA‑Glu
*	NC_000913	4,213,778	0	A	C	32.3%	167.1 / 27.6	93	F116V (TTC→GTC)	yjaB	putative N‑acetyltransferase YjaB
*	NC_000913	1,491,103	0	A	C	32.1%	171.3 / 17.1	81	T68P (ACC→CCC)	cybB	cytochrome b561
*	NC_000913	1,491,098	0	A	C	30.3%	164.0 / 15.6	76	Y66S (TAC→TCC)	cybB	cytochrome b561
*	NC_000913	3,755,363	0	A	C	30.3%	169.5 / 10.6	76	G383G (GGT→GGG)	aldB	aldehyde dehydrogenase B
*	NC_000913	4,111,747	0	G	T	30.0%	91.2 / 18.2	40	N156K (AAC→AAA)	yiiQ	DUF1454 domain‑containing protein YiiQ
*	NC_000913	2,001,918	0	A	C	29.7%	162.0 / 32.6	74	intergenic (‑129/+192)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein
*	NC_000913	2,168,966	0	A	C	28.9%	212.7 / 23.4	90	I85I (ATA→ATC)	yegS	lipid kinase
*	NC_000913	3,206,435	0	C	T	28.6%	49.4 / 16.4	35	intergenic (‑179/‑28)	ttdR/ttdA	DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha
*	NC_000913	3,206,444	0	T	A	28.6%	59.9 / 11.1	35	intergenic (‑188/‑19)	ttdR/ttdA	DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha
*	NC_000913	1,335,691	0	T	G	28.2%	195.0 / 21.5	85	intergenic (+24/‑140)	ymiC/acnA	protein YmiC/aconitate hydratase 1
*	NC_000913	1,068,173	0	T	G	28.1%	141.5 / 22.8	65	G31G (GGT→GGG)	ymdF	conserved protein YmdF

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 =	16 (0.170)	16 (0.180)	14/260	4.2	35.6%	intergenic (+49/‑433)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	4542996 =	43 (0.480)					intergenic (+363/‑119)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
*	?	NC_000913	= 374963	NA (NA)	9 (0.140)	7/192	5.0	NA	noncoding (33/34 nt)	other	REP31a
	?	NC_000913	= 377487	NA (NA)					intergenic (+176/+48)	yaiL/frmB	DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB
*	?	NC_000913	= 4542690	12 (0.130)	8 (0.090)	8/260	6.0	23.1%	intergenic (+57/‑425)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
	?	NC_000913	= 4542986	42 (0.470)					intergenic (+353/‑129)	fimE/fimA	regulator for fimA/type 1 fimbriae major subunit
*	?	NC_000913	= 374963	NA (NA)	3 (0.030)	3/270	8.7	NA	noncoding (33/34 nt)	other	REP31a
	?	NC_000913	= 377387	NA (NA)					intergenic (+76/+148)	yaiL/frmB	DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB