BRESEQ :: Marginal Predictions

breseq version 0.27.1 revision 87c22d663cc3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence (highest frequency 20 of 34 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,606,197	0	G	T	37.0%	114.4 / 15.2	80	intergenic (‑32/+3)	leuV/leuP	tRNA‑Leu/tRNA‑Leu
*	NC_000913	422,429	0	T	G	33.3%	616.2 / 132.2	402	intergenic (+70/‑89)	proY/malZ	proline‑specific permease/maltodextrin glucosidase
*	NC_000913	1,708,930	0	C	A	30.1%	376.0 / 84.1	238	P671Q (CCG→CAG)	rsxC	SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
*	NC_000913	3,269,994	0	G	T	28.8%	191.3 / 24.3	176	intergenic (+392/+631)	yhaC/garK	pentapetide repeats‑related protein/glycerate kinase I
*	NC_000913	4,296,060	0	C	T	28.2%	725.8 / inf	612	intergenic (+266/+376)	gltP/yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
*	NC_000913	1,708,880	0	C	A	27.7%	277.7 / 35.6	184	A654A (GCC→GCA)	rsxC	SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
*	NC_000913	3,270,167	0	C	G	27.5%	304.0 / 57.2	243	intergenic (+565/+458)	yhaC/garK	pentapetide repeats‑related protein/glycerate kinase I
*	NC_000913	1,708,758	0	G	C	27.3%	137.7 / 40.4	136	E614Q (GAA→CAA)	rsxC	SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
*	NC_000913	2,947,591	0	A	.	26.9%	279.3 / 101.8	105	intergenic (+18/‑16)	metW/metV	tRNA‑Met/tRNA‑Met
*	NC_000913	3,270,163	0	C	A	26.4%	320.3 / 16.1	231	intergenic (+561/+462)	yhaC/garK	pentapetide repeats‑related protein/glycerate kinase I
*	NC_000913	2,560,996	0	G	T	26.3%	587.2 / 70.0	343	intergenic (+98/‑372)	yffL/yffM	CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein
*	NC_000913	1,552,191	0	C	A	26.0%	1011.9 / 112.9	490	intergenic (+200/+207)	fdnI/yddM	formate dehydrogenase‑N, cytochrome B556 (gamma) subunit, nitrate‑inducible/putative DNA‑binding transcriptional regulator
*	NC_000913	3,270,151	0	A	C	25.5%	205.1 / 40.6	212	intergenic (+549/+474)	yhaC/garK	pentapetide repeats‑related protein/glycerate kinase I
*	NC_000913	1,286,965	0	A	C	25.4%	190.9 / 32.7	216	intergenic (+439/+122)	narI/tpr	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/protamine‑like protein
*	NC_000913	1,708,901	0	A	C	25.4%	256.3 / 41.4	220	R661R (CGA→CGC)	rsxC	SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
*	NC_000913	2,947,467	0	A	C	24.8%	278.5 / 112.8	129	intergenic (+4/‑30)	metZ/metW	tRNA‑Met/tRNA‑Met
*	NC_000913	422,432	0	T	G	24.7%	838.1 / 75.8	402	intergenic (+73/‑86)	proY/malZ	proline‑specific permease/maltodextrin glucosidase
*	NC_000913	1,708,862	0	C	A	24.5%	225.4 / 12.8	163	V648V (GTC→GTA)	rsxC	SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
*	NC_000913	2,947,465	0	T	.	24.5%	391.3 / 131.9	152	intergenic (+2/‑32)	metZ/metW	tRNA‑Met/tRNA‑Met
*	NC_000913	2,818,158	0	T	A	24.3%	339.9 / 105.0	203	intergenic (‑23/+40)	argZ/argY	tRNA‑Arg/tRNA‑Arg

Marginal new junction evidence (lowest skew 10 of 33 shown)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	1207790 =	365 (0.800)	89 (0.220)	74/268	16.7	21.4%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
*	?	NC_000913	1209619 =	329 (0.800)	89 (0.220)	74/268	16.7	21.4%	pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1207805	345 (0.750)	90 (0.220)	72/268	17.3	22.5%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
*	?	NC_000913	= 1209602	313 (0.770)	90 (0.220)	72/268	17.3	22.5%	pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	696863 =	146 (0.320)	109 (0.260) +GAAGAAACAATC	44/276	28.4	27.9%	intergenic (‑33/+2)	glnW/glnU	tRNA‑Gln/tRNA‑Gln
*	?	NC_000913	= 697134	466 (1.020)	109 (0.260) +GAAGAAACAATC	44/276	28.4	27.9%	intergenic (‑1/+379)	metT/asnB	tRNA‑Met/asparagine synthetase B
*	?	NC_000913	= 781446	344 (0.750)	48 (0.120)	34/260	31.3	12.7%	intergenic (+2/‑131)	lysZ/lysQ	tRNA‑Lys/tRNA‑Lys
*	?	NC_000913	2521487 =	361 (0.910)	48 (0.120)	34/260	31.3	12.7%	intergenic (+159/+106)	lysV/xapR	tRNA‑Lys/transcriptional activator of xapAB
*	?	NC_000913	781369 =	339 (0.740)	128 (0.280) +G	32/298	36.5	36.7%	noncoding (1/76 nt)	lysZ	tRNA‑Lys
*	?	NC_000913	= 2521129	106 (0.230)	128 (0.280) +G	32/298	36.5	36.7%	intergenic (+3/‑44)	valX/valY	tRNA‑Val/tRNA‑Val
*	?	NC_000913	781577 =	342 (0.750)	199 (0.440) +G	31/298	37.0	47.2%	noncoding (1/76 nt)	lysQ	tRNA‑Lys
*	?	NC_000913	= 2521129	106 (0.230)	199 (0.440) +G	31/298	37.0	47.2%	intergenic (+3/‑44)	valX/valY	tRNA‑Val/tRNA‑Val
*	?	NC_000913	780554 =	485 (1.060)	96 (0.210) +G	31/298	37.0	24.6%	noncoding (1/76 nt)	lysT	tRNA‑Lys
*	?	NC_000913	= 2521129	106 (0.230)	96 (0.210) +G	31/298	37.0	24.6%	intergenic (+3/‑44)	valX/valY	tRNA‑Val/tRNA‑Val
*	?	NC_000913	= 1287084	149 (0.330)	41 (0.100)	20/260	39.6	16.1%	intergenic (+558/+3)	narI/tpr	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/protamine‑like protein
*	?	NC_000913	1287557 =	300 (0.760)	41 (0.100)	20/260	39.6	16.1%	noncoding (66/85 nt)	tyrT	tRNA‑Tyr
*	?	NC_000913	781369 =	339 (0.740)	93 (0.210) +GAG	25/294	40.0	26.2%	noncoding (1/76 nt)	lysZ	tRNA‑Lys
*	?	NC_000913	= 2521006	195 (0.430)	93 (0.210) +GAG	25/294	40.0	26.2%	noncoding (76/76 nt)	valU	tRNA‑Val
*	?	NC_000913	781369 =	339 (0.740)	108 (0.240) +G	25/298	40.4	32.7%	noncoding (1/76 nt)	lysZ	tRNA‑Lys
*	?	NC_000913	= 2521128	109 (0.240)	108 (0.240) +G	25/298	40.4	32.7%	intergenic (+2/‑45)	valX/valY	tRNA‑Val/tRNA‑Val