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 23 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,825,061	0	G	A	37.2%	51.4 / 27.1	43	intergenic (‑124/+79)	ves/spy	HutD family protein Ves/ATP‑independent periplasmic chaperone
*	NC_000913	4,604,344	0	C	T	34.9%	143.5 / 61.2	103	S62F (TCT→TTT)	bglJ	DNA‑binding transcriptional regulator BglJ
*	NC_000913	2,326,450	0	T	G	34.5%	76.2 / 40.2	55	G114G (GGT→GGG)	atoB	acetyl‑CoA acetyltransferase
*	NC_000913	4,296,060	0	C	T	33.7%	151.0 / 93.9	104	intergenic (+266/+376)	gltP/yjcO	glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
*	NC_000913	3,556,207	0	T	C	31.8%	69.5 / 14.8	44	S215G (AGT→GGT)	rtcA	RNA 3'‑terminal phosphate cyclase
*	NC_000913	4,568,504	0	T	G	31.7%	230.9 / 26.1	123	T6P (ACC→CCC)	mdtM	multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter
*	NC_000913	4,111,752	0	T	C	30.4%	120.3 / 20.2	70	K155E (AAA→GAA)	yiiQ	DUF1454 domain‑containing protein YiiQ
*	NC_000913	650,809	0	T	G	28.4%	169.4 / 22.0	81	T350P (ACC→CCC)	citC	citrate lyase synthetase
*	NC_000913	4,101,514	0	G	T	28.1%	161.6 / 27.9	64	intergenic (+84/‑176)	sodA/kdgT	superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter
*	NC_000913	4,111,747	0	G	T	27.5%	128.4 / 25.1	51	N156K (AAC→AAA)	yiiQ	DUF1454 domain‑containing protein YiiQ
*	NC_000913	2,001,918	0	A	C	26.3%	125.7 / 10.4	57	intergenic (‑129/+192)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein
*	NC_000913	29,496	0	T	A	25.0%	140.6 / 26.3	64	intergenic (+301/‑155)	dapB/carA	4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha
*	NC_000913	4,101,507	0	T	G	25.0%	147.4 / 10.6	68	intergenic (+77/‑183)	sodA/kdgT	superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter
*	NC_000913	3,404,215	0	T	G	24.7%	155.4 / 23.1	73	G244G (GGT→GGG)	yhdH	acrylyl‑CoA reductase
*	NC_000913	445,558	0	A	C	23.8%	81.4 / 17.3	42	V370G (GTA→GGA)	yajR	putative major facilitator superfamily transport protein YajR
*	NC_000913	4,429,984	0	T	G	23.5%	154.9 / 17.4	68	L41V (TTG→GTG)	cycA	serine/alanine/glycine/cycloserine:H(+)symporter
*	NC_000913	3,404,218	0	T	G	23.3%	162.8 / 20.8	73	G245G (GGT→GGG)	yhdH	acrylyl‑CoA reductase
*	NC_000913	3,206,435	0	C	T	23.3%	81.7 / 15.9	43	intergenic (‑179/‑28)	ttdR/ttdA	DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha
*	NC_000913	1,550,663	0	A	C	23.2%	117.5 / 16.5	56	N68T (AAC→ACC)	fdnH	formate dehydrogenase N subunit beta
*	NC_000913	646,747	0	T	G	22.0%	135.0 / 21.9	59	T255P (ACC→CCC)	citG	triphosphoribosyl‑dephospho‑CoA synthase

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	= 374963	NA (NA)	5 (0.070)	5/188	6.0	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	= 1650975	0 (0.000)	18 (0.170) +ACAT	3/252	8.4	100%	noncoding (133/706 nt)	IS2	repeat region
	?	NC_000913	1650976 =	NA (NA)					noncoding (134/706 nt)	IS2	repeat region
*	?	NC_000913	= 382017	NA (NA)	41 (0.400) +ACAT	3/252	8.4	NA	noncoding (758/1331 nt)	IS2	repeat region
	?	NC_000913	382018 =	NA (NA)					noncoding (759/1331 nt)	IS2	repeat region
*	?	NC_000913	2999394 =	90 (0.850)	3 (0.030)	3/266	8.6	3.3%	coding (498/756 nt)	ygeR	LysM domain‑containing putative peptidase lipoprotein YgeR
	?	NC_000913	= 2999390	89 (0.860)					coding (502/756 nt)	ygeR	LysM domain‑containing putative peptidase lipoprotein YgeR
*	?	NC_000913	1468476 =	NA (NA)	3 (0.030)	3/268	8.7	NA	noncoding (765/1331 nt)	IS2	repeat region
	?	NC_000913	1650979 =	NA (NA)					noncoding (137/706 nt)	IS2	repeat region