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	2,947,591	0	A	.	36.5%	168.6 / 103.8	74	intergenic (+18/‑16)	metW/metV	tRNA‑Met/tRNA‑Met
*	NC_000913	1,708,901	0	A	C	34.6%	182.0 / 69.8	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	34.5%	162.1 / 151.1	114	intergenic (+4/‑30)	metZ/metW	tRNA‑Met/tRNA‑Met
*	NC_000913	1,708,930	0	C	A	33.0%	363.7 / 76.4	221	P671Q (CCG→CAG)	rsxC	SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
*	NC_000913	1,552,191	0	C	A	30.0%	746.5 / 109.1	433	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	28.6%	657.3 / 87.4	378	intergenic (+70/‑89)	proY/malZ	proline‑specific permease/maltodextrin glucosidase
*	NC_000913	1,708,880	0	C	A	27.6%	284.3 / 27.0	198	A654A (GCC→GCA)	rsxC	SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
*	NC_000913	1,708,805	0	T	A	26.7%	75.6 / 34.3	133	R629R (CGT→CGA)	rsxC	SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
*	NC_000913	915,213	0	A	C	26.6%	215.1 / 27.7	186	intergenic (‑356/+139)	ybjE/aqpZ	putative transporter/aquaporin Z
*	NC_000913	1,286,965	0	A	C	26.5%	200.6 / 39.8	227	intergenic (+439/+122)	narI/tpr	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/protamine‑like protein
*	NC_000913	2,947,481	1	.	A	26.5%	150.5 / 92.0	68	intergenic (+18/‑16)	metZ/metW	tRNA‑Met/tRNA‑Met
*	NC_000913	2,947,465	0	T	.	26.1%	385.7 / 152.1	158	intergenic (+2/‑32)	metZ/metW	tRNA‑Met/tRNA‑Met
*	NC_000913	3,233,696	0	A	C	25.4%	664.6 / 55.4	293	intergenic (+13/+32)	fadH/higA	2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked/antitoxinof the HigB‑HigA toxin‑antitoxin system
*	NC_000913	4,392,569	0	C	A	25.4%	367.0 / 13.7	214	intergenic (+22/‑14)	glyX/glyY	tRNA‑Gly/tRNA‑Gly
*	NC_000913	4,412,781	0	C	G	25.0%	986.2 / 94.9	443	S132C (TCT→TGT)	yjfM	DUF1190 family protein
*	NC_000913	1,708,883	0	C	A	24.9%	292.0 / 25.3	205	V655V (GTC→GTA)	rsxC	SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
*	NC_000913	935,551	0	A	C	24.6%	468.6 / 56.4	307	P776P (CCA→CCC)	ftsK	DNA translocase at septal ring sorting daughter chromsomes
*	NC_000913	4,296,060	0	C	T	24.5%	854.4 / inf	635	intergenic (+266/+376)	gltP/yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
*	NC_000913	2,560,996	0	G	T	24.0%	647.9 / 61.2	339	intergenic (+98/‑372)	yffL/yffM	CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein
*	NC_000913	915,226	0	T	G	23.8%	279.0 / 27.3	191	intergenic (‑369/+126)	ybjE/aqpZ	putative transporter/aquaporin Z

Marginal new junction evidence (lowest skew 10 of 50 shown)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 4542690	305 (0.700)	141 (0.340)	113/282	8.0	30.9%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	344 (0.840)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	4542682 =	298 (0.680)	134 (0.330)	108/282	9.0	29.2%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	369 (0.900)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	= 1207805	272 (0.620)	131 (0.340)	96/268	10.2	34.5%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	254 (0.650)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	1207790 =	277 (0.630)	125 (0.320)	95/268	10.4	32.4%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	275 (0.700)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	781369 =	229 (0.520)	174 (0.410) +GAAG	54/292	24.9	47.4%	noncoding (1/76 nt)	lysZ	tRNA‑Lys
	?	NC_000913	= 2521006	168 (0.380)					noncoding (76/76 nt)	valU	tRNA‑Val
*	?	NC_000913	= 1287084	159 (0.360)	72 (0.190)	44/260	25.6	26.2%	intergenic (+558/+3)	narI/tpr	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/protamine‑like protein
	?	NC_000913	1287557 =	269 (0.710)					noncoding (66/85 nt)	tyrT	tRNA‑Tyr
*	?	NC_000913	781577 =	248 (0.570)	229 (0.540) +GAAG	52/292	25.7	53.1%	noncoding (1/76 nt)	lysQ	tRNA‑Lys
	?	NC_000913	= 2521006	168 (0.380)					noncoding (76/76 nt)	valU	tRNA‑Val
*	?	NC_000913	780554 =	495 (1.130)	124 (0.290) +GAAG	52/292	25.7	27.8%	noncoding (1/76 nt)	lysT	tRNA‑Lys
	?	NC_000913	= 2521006	168 (0.380)					noncoding (76/76 nt)	valU	tRNA‑Val
*	?	NC_000913	696863 =	162 (0.370)	85 (0.210) +GAAGAAACAATC	47/276	26.0	22.1%	intergenic (‑33/+2)	glnW/glnU	tRNA‑Gln/tRNA‑Gln
	?	NC_000913	= 697134	490 (1.120)					intergenic (‑1/+379)	metT/asnB	tRNA‑Met/asparagine synthetase B
*	?	NC_000913	= 2357690	318 (0.730)	74 (0.180) +AATTAGAAGGTT	44/276	27.3	20.2%	coding (787/900 nt)	yfaD	transposase_31 family protein
	?	NC_000913	2357691 =	318 (0.730)					coding (788/900 nt)	yfaD	transposase_31 family protein