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 30 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,947,591	0	A	.	42.5%	147.0 / 122.3	73	intergenic (+18/‑16)	metW/metV	tRNA‑Met/tRNA‑Met
*	NC_000913	1,708,901	0	A	C	33.0%	194.8 / 66.4	200	R661R (CGA→CGC)	rsxC	SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
*	NC_000913	422,429	0	T	G	29.8%	581.7 / 96.8	344	intergenic (+70/‑89)	proY/malZ	proline‑specific permease/maltodextrin glucosidase
*	NC_000913	2,947,467	0	A	C	28.1%	180.9 / 86.0	89	intergenic (+4/‑30)	metZ/metW	tRNA‑Met/tRNA‑Met
*	NC_000913	1,552,191	0	C	A	28.0%	783.5 / 95.4	417	intergenic (+200/+207)	fdnI/yddM	formate dehydrogenase‑N, cytochrome B556 (gamma) subunit, nitrate‑inducible/putative DNA‑binding transcriptional regulator
*	NC_000913	1,708,910	0	G	C	26.8%	347.3 / 31.5	193	A664A (GCG→GCC)	rsxC	SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
*	NC_000913	2,818,145	0	T	C	26.1%	296.7 / 115.0	178	intergenic (‑10/+53)	argZ/argY	tRNA‑Arg/tRNA‑Arg
*	NC_000913	4,296,060	0	C	T	25.3%	630.5 / inf	487	intergenic (+266/+376)	gltP/yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
*	NC_000913	3,269,994	0	G	T	25.0%	229.1 / 12.0	163	intergenic (+392/+631)	yhaC/garK	pentapetide repeats‑related protein/glycerate kinase I
*	NC_000913	1,708,930	0	C	A	24.6%	369.1 / 39.7	198	P671Q (CCG→CAG)	rsxC	SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
*	NC_000913	4,606,192	0	G	C	24.3%	124.4 / 10.1	76	intergenic (‑27/+8)	leuV/leuP	tRNA‑Leu/tRNA‑Leu
*	NC_000913	1,308,745	0	T	G	23.9%	630.6 / 56.4	320	intergenic (‑100/‑43)	clsA/yciY	cardiolipin synthase 1/uncharacterized protein
*	NC_000913	1,708,758	0	G	C	23.7%	143.3 / 31.1	122	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	23.2%	302.4 / 83.8	169	intergenic (‑23/+40)	argZ/argY	tRNA‑Arg/tRNA‑Arg
*	NC_000913	3,270,167	0	C	G	22.4%	296.3 / 32.6	196	intergenic (+565/+458)	yhaC/garK	pentapetide repeats‑related protein/glycerate kinase I
*	NC_000913	422,432	0	T	G	22.3%	754.1 / 55.0	344	intergenic (+73/‑86)	proY/malZ	proline‑specific permease/maltodextrin glucosidase
*	NC_000913	915,213	0	A	C	22.2%	230.4 / 19.2	173	intergenic (‑356/+139)	ybjE/aqpZ	putative transporter/aquaporin Z
*	NC_000913	423,552	0	T	G	21.8%	576.9 / 41.3	262	G345G (GGT→GGG)	malZ	maltodextrin glucosidase
*	NC_000913	422,435	0	T	G	21.8%	772.5 / 51.1	344	intergenic (+76/‑83)	proY/malZ	proline‑specific permease/maltodextrin glucosidase
*	NC_000913	1,287,217	0	G	T	21.6%	720.8 / 121.9	351	intergenic (‑41/+27)	tpr/tyrV	protamine‑like protein/tRNA‑Tyr

Marginal new junction evidence (lowest skew 10 of 78 shown)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	1207790 =	302 (0.810)	63 (0.190)	57/266	15.6	18.4%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	288 (0.870)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1207805	305 (0.820)	57 (0.170)	52/266	17.2	17.1%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	281 (0.840)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	781369 =	235 (0.630)	147 (0.410) +GAAG	55/290	18.2	42.9%	noncoding (1/76 nt)	lysZ	tRNA‑Lys
	?	NC_000913	= 2521006	168 (0.450)					noncoding (76/76 nt)	valU	tRNA‑Val
*	?	NC_000913	781577 =	266 (0.710)	198 (0.550) +GAAG	50/290	19.8	48.4%	noncoding (1/76 nt)	lysQ	tRNA‑Lys
	?	NC_000913	= 2521006	168 (0.450)					noncoding (76/76 nt)	valU	tRNA‑Val
*	?	NC_000913	780554 =	386 (1.040)	108 (0.300) +GAAG	50/290	19.8	28.6%	noncoding (1/76 nt)	lysT	tRNA‑Lys
	?	NC_000913	= 2521006	168 (0.450)					noncoding (76/76 nt)	valU	tRNA‑Val
*	?	NC_000913	= 1287084	123 (0.330)	77 (0.240)	37/258	21.9	31.7%	intergenic (+558/+3)	narI/tpr	nitrate reductase 1, gamma (cytochrome b(NR)) subunit/protamine‑like protein
	?	NC_000913	1287557 =	225 (0.700)					noncoding (66/85 nt)	tyrT	tRNA‑Tyr
*	?	NC_000913	= 781446	234 (0.630)	58 (0.180)	35/258	22.7	19.2%	intergenic (+2/‑131)	lysZ/lysQ	tRNA‑Lys/tRNA‑Lys
	?	NC_000913	2521487 =	285 (0.880)					intergenic (+159/+106)	lysV/xapR	tRNA‑Lys/transcriptional activator of xapAB
*	?	NC_000913	4542682 =	452 (1.210)	41 (0.120)	38/280	23.4	8.9%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	414 (1.180)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	696863 =	114 (0.310)	74 (0.220) +GAAGAAACAATC	35/274	24.1	24.5%	intergenic (‑33/+2)	glnW/glnU	tRNA‑Gln/tRNA‑Gln
	?	NC_000913	= 697134	381 (1.020)					intergenic (‑1/+379)	metT/asnB	tRNA‑Met/asparagine synthetase B
*	?	NC_000913	= 2357690	305 (0.820)	56 (0.160) +AATTAGAAGGTT	33/274	25.0	16.7%	coding (787/900 nt)	yfaD	transposase_31 family protein
	?	NC_000913	2357691 =	305 (0.820)					coding (788/900 nt)	yfaD	transposase_31 family protein