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 36 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,947,591	0	A	.	35.9%	218.8 / 126.1	92	intergenic (+18/‑16)	metW/metV	tRNA‑Met/tRNA‑Met
*	NC_000913	2,947,467	0	A	C	30.9%	242.8 / 146.7	136	intergenic (+4/‑30)	metZ/metW	tRNA‑Met/tRNA‑Met
*	NC_000913	1,708,901	0	A	C	29.8%	280.6 / 71.6	251	R661R (CGA→CGC)	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%	317.9 / 32.2	222	intergenic (+392/+631)	yhaC/garK	pentapetide repeats‑related protein/glycerate kinase I
*	NC_000913	4,296,060	0	C	T	28.4%	687.9 / inf	619	intergenic (+266/+376)	gltP/yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
*	NC_000913	1,552,191	0	C	A	28.0%	968.6 / 136.6	509	intergenic (+200/+207)	fdnI/yddM	formate dehydrogenase‑N, cytochrome B556 (gamma) subunit, nitrate‑inducible/putative DNA‑binding transcriptional regulator
*	NC_000913	1,708,930	0	C	A	27.9%	499.2 / 76.4	267	P671Q (CCG→CAG)	rsxC	SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
*	NC_000913	1,286,965	0	A	C	27.6%	203.9 / 43.8	228	intergenic (+439/+122)	narI/tpr	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/protamine‑like protein
*	NC_000913	915,213	0	A	C	26.4%	263.2 / 36.7	215	intergenic (‑356/+139)	ybjE/aqpZ	putative transporter/aquaporin Z
*	NC_000913	4,392,457	0	G	T	26.2%	379.8 / 24.4	245	intergenic (+22/‑15)	glyV/glyX	tRNA‑Gly/tRNA‑Gly
*	NC_000913	1,308,745	0	T	G	26.0%	703.6 / 72.7	377	intergenic (‑100/‑43)	clsA/yciY	cardiolipin synthase 1/uncharacterized protein
*	NC_000913	1,287,217	0	G	T	25.6%	801.9 / 165.0	413	intergenic (‑41/+27)	tpr/tyrV	protamine‑like protein/tRNA‑Tyr
*	NC_000913	1,708,758	0	G	C	25.5%	166.4 / 41.3	154	E614Q (GAA→CAA)	rsxC	SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
*	NC_000913	2,818,158	0	T	A	24.4%	342.5 / 113.9	225	intergenic (‑23/+40)	argZ/argY	tRNA‑Arg/tRNA‑Arg
*	NC_000913	2,560,996	0	G	T	24.4%	753.1 / 89.6	412	intergenic (+98/‑372)	yffL/yffM	CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein
*	NC_000913	2,947,465	0	T	.	24.2%	479.7 / 162.1	189	intergenic (+2/‑32)	metZ/metW	tRNA‑Met/tRNA‑Met
*	NC_000913	2,947,481	1	.	A	24.1%	189.4 / 94.8	79	intergenic (+18/‑16)	metZ/metW	tRNA‑Met/tRNA‑Met
*	NC_000913	422,429	0	T	G	23.6%	795.3 / 88.2	408	intergenic (+70/‑89)	proY/malZ	proline‑specific permease/maltodextrin glucosidase
*	NC_000913	2,818,145	0	T	C	23.3%	359.1 / 128.1	243	intergenic (‑10/+53)	argZ/argY	tRNA‑Arg/tRNA‑Arg
*	NC_000913	3,270,167	0	C	G	22.6%	401.4 / 42.1	271	intergenic (+565/+458)	yhaC/garK	pentapetide repeats‑related protein/glycerate kinase I

Marginal new junction evidence (lowest skew 10 of 41 shown)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	4542682 =	474 (0.990)	143 (0.320)	111/282	9.8	24.5%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	437 (0.970)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	= 4542690	459 (0.960)	127 (0.280)	98/282	12.7	22.9%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	422 (0.940)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	696863 =	170 (0.360)	120 (0.270) +GAAGAAACAATC	49/276	27.6	29.4%	intergenic (‑33/+2)	glnW/glnU	tRNA‑Gln/tRNA‑Gln
	?	NC_000913	= 697134	457 (0.960)					intergenic (‑1/+379)	metT/asnB	tRNA‑Met/asparagine synthetase B
*	?	NC_000913	781369 =	339 (0.710)	132 (0.280) +GAAG	45/292	31.1	33.7%	noncoding (1/76 nt)	lysZ	tRNA‑Lys
	?	NC_000913	= 2521006	195 (0.410)					noncoding (76/76 nt)	valU	tRNA‑Val
*	?	NC_000913	= 781446	302 (0.630)	68 (0.160)	37/260	31.3	17.4%	intergenic (+2/‑131)	lysZ/lysQ	tRNA‑Lys/tRNA‑Lys
	?	NC_000913	2521487 =	386 (0.930)					intergenic (+159/+106)	lysV/xapR	tRNA‑Lys/transcriptional activator of xapAB
*	?	NC_000913	781577 =	341 (0.710)	219 (0.470) +GAAG	44/292	31.5	45.6%	noncoding (1/76 nt)	lysQ	tRNA‑Lys
	?	NC_000913	= 2521006	195 (0.410)					noncoding (76/76 nt)	valU	tRNA‑Val
*	?	NC_000913	780554 =	554 (1.160)	103 (0.220) +GAAG	44/292	31.5	22.0%	noncoding (1/76 nt)	lysT	tRNA‑Lys
	?	NC_000913	= 2521006	195 (0.410)					noncoding (76/76 nt)	valU	tRNA‑Val
*	?	NC_000913	= 2357873	287 (0.600)	48 (0.100)	34/300	37.3	14.1%	pseudogene (70/198 nt)	ypaA	pseudogene, C‑terminal fragment, Transposase_31 family
	?	NC_000913	2357886 =	298 (0.620)					pseudogene (83/198 nt)	ypaA	pseudogene, C‑terminal fragment, Transposase_31 family
*	?	NC_000913	= 1287084	154 (0.320)	87 (0.210)	26/260	37.3	28.6%	intergenic (+558/+3)	narI/tpr	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/protamine‑like protein
	?	NC_000913	1287557 =	302 (0.730)					noncoding (66/85 nt)	tyrT	tRNA‑Tyr
*	?	NC_000913	781577 =	341 (0.710)	65 (0.140) +T	30/298	39.2	21.9%	noncoding (1/76 nt)	lysQ	tRNA‑Lys
	?	NC_000913	= 2521129	126 (0.260)					intergenic (+3/‑44)	valX/valY	tRNA‑Val/tRNA‑Val