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 29 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	AP012306	1,091,992	0	T	G	43.4%	403.9 / 89.5	281	intergenic (+38/‑145)	narI/ychS	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/predicted protein
*	AP012306	1,944,288	0	A	C	36.6%	378.6 / 58.5	216	G361G (GGT→GGG)	menE	o‑succinylbenzoate‑CoA ligase
*	AP012306	644,417	0	G	A	32.1%	791.4 / inf	537	intergenic (+32/‑401)	lysQ/nadA	tRNA‑Lys/quinolinate synthase, subunit A
*	AP012306	341,377	0	T	G	31.6%	226.5 / 28.1	139	G60G (GGT→GGG)	ribD	fused diaminohydroxyphosphoribosylaminopyrimidin e deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase
*	AP012306	3,527,368	0	A	C	31.5%	560.7 / 60.4	260	L140F (TTA→TTC)	rhaS	DNA‑binding transcriptional activator, L‑rhamnose‑binding
*	AP012306	3,938,887	0	C	T	28.8%	491.2 / 157.9	257	S44F (TCT→TTT)	bglJ	DNA‑binding transcriptional regulator
*	AP012306	800,675	0	A	C	27.7%	651.4 / 38.0	289	T192P (ACC→CCC)	lolA	chaperone for lipoproteins
*	AP012306	1,226,557	0	A	G	27.6%	404.2 / 86.6	196	G55G (GGA→GGG)	ydcU	predicted spermidine/putrescine transporter subunit
*	AP012306	935,054	0	G	T	27.1%	266.7 / 49.3	96	intergenic (+24/‑1406)	putP/ycdO	proline:sodium symporter/conserved protein
*	AP012306	3,182,861	0	A	C	26.4%	309.3 / 17.0	129	L198F (TTA→TTC)	yiaN	predicted transporter
*	AP012306	2,558,071	0	A	C	26.3%	452.3 / 40.6	209	V302G (GTA→GGA)	visC	predicted oxidoreductase, FAD/NAD(P)‑binding domain
*	AP012306	202,417	0	T	G	25.9%	609.4 / 29.3	263	V409G (GTA→GGA)	tilS	tRNA(Ile)‑lysidine synthetase
*	AP012306	3,282,076	0	T	G	24.8%	619.1 / 21.7	274	intergenic (‑79/+27)	ilvB/ivbL	acetolactate synthase I, large subunit/ilvB operon leader peptide
*	AP012306	1,128,412	0	T	G	24.5%	696.6 / 40.4	286	V29G (GTG→GGG)	yciO	conserved protein
*	AP012306	1,854,851	0	A	C	23.5%	724.8 / 55.2	289	T25P (ACC→CCC)	yejH	predicted ATP‑dependet helicase
*	AP012306	1,421,147	0	T	G	23.4%	571.2 / 10.7	259	T79P (ACC→CCC)	ydhB	predicted DNA‑binding transcriptional regulator
*	AP012306	1,270,226	0	A	G	23.1%	625.8 / 48.2	229	S779P (TCC→CCC)	dos	cAMP phosphodiesterase, heme‑regulated
*	AP012306	3,372,701	0	T	G	22.9%	183.1 / 12.9	83	noncoding (54/76 nt)	gltU	tRNA‑Glu
*	AP012306	3,324,433	0	T	A	22.7%	604.3 / 82.3	238	intergenic (+2/+52)	yieF/yieG	chromate reductase, Class I, flavoprotein/predicted inner membrane protein
*	AP012306	1,066,323	0	A	C	22.4%	687.4 / 15.3	264	intergenic (‑92/+33)	ychM/prsA	predicted transporter/phosphoribosylpyrophosphate synthase

Marginal new junction evidence (lowest skew 10 of 146 shown)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	AP012306	= 997497	303 (0.940)	14 (0.050)	12/268	15.3	5.1%	coding (41/1305 nt)	ndh	respiratory NADH dehydrogenase 2/cupric reductase
	?	AP012306	997993 =	251 (0.870)					coding (537/1305 nt)	ndh	respiratory NADH dehydrogenase 2/cupric reductase
*	?	AP012306	= 1092512	416 (1.290)	11 (0.040)	9/258	16.3	3.3%	intergenic (+100/+3)	ychS/tpr	predicted protein/predicted protamine‑like protein
	?	AP012306	1092985 =	286 (1.030)					noncoding (66/85 nt)	tyrT	tRNA‑Tyr
*	?	AP012306	= 1092334	329 (1.020)	11 (0.040)	8/258	16.7	3.7%	coding (198/276 nt)	ychS	predicted protein
	?	AP012306	1092985 =	286 (1.030)					noncoding (66/85 nt)	tyrT	tRNA‑Tyr
*	?	AP012306	= 3608580	392 (1.220)	8 (0.030)	8/284	17.4	2.1%	coding (489/705 nt)	rplA	50S ribosomal subunit protein L1
	?	AP012306	= 3608581	365 (1.190)					coding (490/705 nt)	rplA	50S ribosomal subunit protein L1
*	?	AP012306	153092 =	260 (0.810)	7 (0.020)	7/288	18.0	2.7%	coding (860/1398 nt)	pcnB	poly(A) polymerase I
	?	AP012306	153120 =	254 (0.820)					coding (832/1398 nt)	pcnB	poly(A) polymerase I
*	?	AP012306	3371114 =	61 (0.190)	7 (0.020) +A	7/296	18.2	13.9%	noncoding (94/1542 nt)	rrsC	16S ribosomal RNA (rrnC)
	?	AP012306	3464820 =	26 (0.080)					noncoding (77/1542 nt)	rrsA	16S ribosomal RNA (rrnA)
*	?	AP012306	= 1628011	377 (1.170)	6 (0.020)	6/274	18.2	1.7%	coding (287/741 nt)	yebC	conserved protein
	?	AP012306	= 1627999	347 (1.170)					coding (299/741 nt)	yebC	conserved protein
*	?	AP012306	1740016 =	396 (1.230)	6 (0.020)	6/290	18.6	1.5%	intergenic (‑681/‑207)	yegL/mdtA	conserved protein/multidrug efflux system, subunit A
	?	AP012306	1740041 =	402 (1.280)					intergenic (‑706/‑182)	yegL/mdtA	conserved protein/multidrug efflux system, subunit A
*	?	AP012306	3371114 =	61 (0.190)	6 (0.020) +A	6/296	18.7	9.0%	noncoding (94/1542 nt)	rrsC	16S ribosomal RNA (rrnC)
	?	AP012306	3595948 =	NA (NA)					noncoding (77/1542 nt)	rrsB	16S ribosomal RNA (rrnB)
*	?	AP012306	= 2153239	299 (0.930)	5 (0.020)	5/274	18.8	1.8%	coding (696/1581 nt)	hyfF	hydrogenase 4, membrane subunit
	?	AP012306	= 2153227	269 (0.910)					coding (684/1581 nt)	hyfF	hydrogenase 4, membrane subunit