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	4,296,060	0	C	T	41.7%	66.3 / 145.6	129	intergenic (+266/+376)	gltP/yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
*	NC_000913	1,552,191	0	C	A	27.6%	170.0 / 20.0	98	intergenic (+200/+207)	fdnI/yddM	formate dehydrogenase‑N, cytochrome B556 (gamma) subunit, nitrate‑inducible/putative DNA‑binding transcriptional regulator
*	NC_000913	422,429	0	T	G	26.4%	112.6 / 14.2	73	intergenic (+70/‑89)	proY/malZ	proline‑specific permease/maltodextrin glucosidase
*	NC_000913	1,286,965	0	A	G	23.1%	56.9 / 12.4	45	intergenic (+439/+101)	narI/rttR	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript

Marginal new junction evidence (lowest skew 10 of 295 shown)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	781577 =	63 (0.500)	43 (0.350) +GAAG	13/290	8.0	44.8%	noncoding (1/76 nt)	lysQ	tRNA‑Lys
	?	NC_000913	= 2521006	46 (0.360)					noncoding (76/76 nt)	valU	tRNA‑Val
*	?	NC_000913	377321 =	NA (NA)	7 (0.090) +54 bp	6/190	8.2	NA	intergenic (+10/+214)	yaiL/frmB	DUF2058 family protein/S‑formylglutathione hydrolase
	?	NC_000913	377335 =	NA (NA)					noncoding (1/187 nt)	REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences	REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences
*	?	NC_000913	2726064 =	149 (1.170)	10 (0.080) +AAAACG	8/286	9.8	6.0%	intergenic (‑318/+5)	kgtP/rrfG	alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon
	?	NC_000913	3423384 =	178 (1.400)					intergenic (+190/+39)	yhdZ/rrfF	putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon
*	?	NC_000913	= 1428264	NA (NA)	34 (0.280)	8/286	9.8	94.7%	noncoding (531/1196 nt)	IS5	repeat region
	?	NC_000913	= 2066866	2 (0.020)					noncoding (488/1195 nt)	IS5	repeat region
*	?	NC_000913	1396537 =	NA (NA)	34 (0.280)	8/286	9.8	24.7%	noncoding (494/1195 nt)	IS5	repeat region
	?	NC_000913	= 1428270	108 (0.850)					noncoding (525/1196 nt)	IS5	repeat region
*	?	NC_000913	315563 =	NA (NA)	8 (0.070)	7/278	10.0	NA	noncoding (335/1255 nt)	IS3	repeat region
	?	NC_000913	315599 =	NA (NA)					noncoding (371/1255 nt)	IS3	repeat region
*	?	NC_000913	= 3559768	162 (1.280)	8 (0.070)	7/280	10.1	4.9%	coding (1501/1599 nt)	rtcR	sigma 54‑dependent transcriptional regulator of rtcBA expression
	?	NC_000913	= 3559808	159 (1.330)					coding (1541/1599 nt)	rtcR	sigma 54‑dependent transcriptional regulator of rtcBA expression
*	?	NC_000913	= 2964326	145 (1.140)	7 (0.060)	7/284	10.2	4.9%	intergenic (‑149/+35)	ppdA/thyA	putative prepilin peptidase‑dependent protein/thymidylate synthetase
	?	NC_000913	= 2964332	136 (1.120)					intergenic (‑155/+29)	ppdA/thyA	putative prepilin peptidase‑dependent protein/thymidylate synthetase
*	?	NC_000913	3203112 =	NA (NA)	3 (0.040) +50 bp	3/198	10.3	NA	coding (1222/1239 nt)	cca	fused tRNA nucleotidyl transferase/2'3'‑cyclic phosphodiesterase/2'nucleotidase and phosphatase
	?	NC_000913	= 4285380	NA (NA)					intergenic (‑167/+33)	yjcH/acs	DUF485 family inner membrane protein/acetyl‑CoA synthetase
*	?	NC_000913	4096861 =	169 (1.330)	7 (0.060)	6/284	10.6	4.0%	coding (588/1470 nt)	rhaB	rhamnulokinase
	?	NC_000913	4096886 =	173 (1.430)					coding (563/1470 nt)	rhaB	rhamnulokinase