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	4,082,290	0	A	G	62.2%	33.4 / 43.6	45	V157A (GTC→GCC)	fdoH	formate dehydrogenase O subunit beta
*	NC_000913	3,237,421	0	A	G	48.2%	‑2.0 / 77.6	56	E37E (GAA→GAG)	ygjR	putative oxidoreductase YgjR
*	NC_000913	1,099,390	0	A	G	47.5%	3.9 / 83.3	61	D171G (GAC→GGC)	ycdX	zinc‑binding phosphatase
*	NC_000913	2,001,918	0	A	C	44.8%	21.6 / 17.1	29	intergenic (‑129/+192)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein
*	NC_000913	2,130,453	0	G	A	44.3%	19.9 / 72.3	61	S142S (AGC→AGT)	wcaD	putative colanic acid polymerase
*	NC_000913	1,825,061	0	G	A	42.9%	21.5 / 17.8	28	intergenic (‑124/+79)	ves/spy	HutD family protein Ves/ATP‑independent periplasmic chaperone
*	NC_000913	4,604,344	0	C	T	40.0%	65.6 / 35.3	60	S62F (TCT→TTT)	bglJ	DNA‑binding transcriptional regulator BglJ
*	NC_000913	380,012	1	.	G	38.2%	36.7 / 126.1	68	intergenic (‑131/+57)	frmR/yaiO	DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO
*	NC_000913	650,809	0	T	G	34.4%	38.7 / 13.3	32	T350P (ACC→CCC)	citC	citrate lyase synthetase
*	NC_000913	4,296,060	0	C	T	29.6%	113.3 / 52.8	71	intergenic (+266/+376)	gltP/yjcO	glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
*	NC_000913	3,401,459	0	T	C	29.2%	76.7 / 10.5	48	D625G (GAT→GGT)	csrD	regulator of CsrB and CsrC decay
*	NC_000913	372,640	0	T	G	28.8%	92.5 / 15.3	52	L176V (TTA→GTA)	mhpD	2‑hydroxypentadienoate hydratase
*	NC_000913	3,404,218	0	T	G	26.5%	95.8 / 11.3	49	G245G (GGT→GGG)	yhdH	acrylyl‑CoA reductase
*	NC_000913	3,404,215	0	T	G	26.0%	97.0 / 11.9	50	G244G (GGT→GGG)	yhdH	acrylyl‑CoA reductase

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	375023 =	NA (NA)	15 (0.370)	5/192	4.0	NA	intergenic (+142/‑436)	mhpE/mhpT	4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter
	?	NC_000913	377530 =	NA (NA)					intergenic (+219/+5)	yaiL/frmB	DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB
*	?	NC_000913	375248 =	NA (NA)	16 (0.320)	6/238	4.4	NA	noncoding (15/34 nt)	other	REP31g
	?	NC_000913	377507 =	NA (NA)					noncoding (16/34 nt)	other	REP32d
*	?	NC_000913	375124 =	NA (NA)	3 (0.070)	3/192	4.9	NA	intergenic (+243/‑335)	mhpE/mhpT	4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter
	?	NC_000913	377530 =	NA (NA)					intergenic (+219/+5)	yaiL/frmB	DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB
*	?	NC_000913	374922 =	NA (NA)	4 (0.090)	3/202	5.1	NA	intergenic (+41/‑537)	mhpE/mhpT	4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter
	?	NC_000913	377430 =	NA (NA)					intergenic (+119/+105)	yaiL/frmB	DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB
*	?	NC_000913	4373301 =	NA (NA)	7 (0.120)	4/268	5.6	NA	intergenic (+139/+64)	yjeI/yjeJ	DUF4156 domain‑containing lipoprotein YjeI/protein YjeJ
	?	NC_000913	4374493 =	NA (NA)					intergenic (‑259/+136)	yjeJ/epmB	protein YjeJ/lysine 2,3‑aminomutase
*	?	NC_000913	2898102 =	65 (1.100)	4 (0.070)	4/264	5.6	6.2%	coding (1317/1455 nt)	ygcU	putative FAD‑containing dehydrogenase
	?	NC_000913	= 2898098	59 (1.050)					coding (1321/1455 nt)	ygcU	putative FAD‑containing dehydrogenase
*	?	NC_000913	= 3220246	48 (0.810)	3 (0.050)	3/256	6.0	5.3%	coding (753/1380 nt)	patA	putrescine aminotransferase
	?	NC_000913	= 3220398	63 (1.150)					coding (905/1380 nt)	patA	putrescine aminotransferase
*	?	NC_000913	= 54507	66 (1.120)	3 (0.050)	3/258	6.0	4.3%	coding (196/1287 nt)	surA	peptidyl‑prolyl cis‑trans isomerase SurA
	?	NC_000913	4200787 =	72 (1.310)					coding (222/696 nt)	yjaH	DUF1481 domain‑containing protein YjaH