BRESEQ :: Marginal Predictions

breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,296,060	0	C	T	31.0%	79.8 / 45.0	58	intergenic (+266/+376)	gltP/yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
*	NC_000913	1,706,079	1	.	T	23.5%	30.4 / 14.3	17	coding (313/582 nt)	rsxA	SoxR iron‑sulfur cluster reduction factor component; inner membrane protein of electron transport complex
*	NC_000913	2,282,832	0	C	G	21.6%	84.3 / 14.6	37	intergenic (+31/+108)	rplY/yejK	50S ribosomal subunit protein L25/spermidine nucleoid‑associated protein
*	NC_000913	2,282,833	0	G	A	21.6%	73.6 / 12.8	37	intergenic (+32/+107)	rplY/yejK	50S ribosomal subunit protein L25/spermidine nucleoid‑associated protein
*	NC_000913	1,499,365	0	A	T	21.4%	56.8 / 10.3	28	Q143L (CAG→CTG)	rimL	ribosomal‑protein‑L7/L12‑serine acetyltransferase
*	NC_000913	2,282,830	0	T	C	21.1%	74.9 / 14.1	38	intergenic (+29/+110)	rplY/yejK	50S ribosomal subunit protein L25/spermidine nucleoid‑associated protein
*	NC_000913	2,282,831	0	C	G	21.1%	84.4 / 19.6	38	intergenic (+30/+109)	rplY/yejK	50S ribosomal subunit protein L25/spermidine nucleoid‑associated protein
*	NC_000913	3,033,631	0	C	T	20.5%	77.1 / 15.3	39	intergenic (+18/+26)	idi/lysS	isopentenyl diphosphate isomerase/lysine tRNA synthetase, constitutive
*	NC_000913	1,555,781	0	G	C	20.0%	61.6 / 13.7	31	intergenic (‑112/+45)	maeA/sra	malate dehydrogenase, decarboxylating, NAD‑requiring; malic enzyme/stationary‑phase‑induced ribosome‑associated protein
*	NC_000913	1,555,784	0	G	C	20.0%	62.7 / 13.8	30	intergenic (‑115/+42)	maeA/sra	malate dehydrogenase, decarboxylating, NAD‑requiring; malic enzyme/stationary‑phase‑induced ribosome‑associated protein
*	NC_000913	2,814,174	0	T	A	20.0%	72.1 / 12.8	35	intergenic (+20/+44)	emrB/luxS	multidrug efflux system protein/S‑ribosylhomocysteine lyase
*	NC_000913	2,814,175	0	T	A	20.0%	74.2 / 12.0	35	intergenic (+21/+43)	emrB/luxS	multidrug efflux system protein/S‑ribosylhomocysteine lyase

Marginal new junction evidence (lowest skew 10 of 64 shown)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	1411899 =	44 (1.200)	8 (0.280)	8/190	2.0	19.4%	coding (50/936 nt)	ttcA	tRNA s(2)C32 thioltransferase, iron sulfur cluster protein
*	?	NC_000913	= 1434958	32 (1.110)	8 (0.280)	8/190	2.0	19.4%	pseudogene (51/51 nt)	ttcC	pseudogene, prophage Rac integration site ttcA duplication;Phage or Prophage Related
*	?	NC_000913	4467063 =	37 (1.010)	8 (0.230)	7/234	2.7	18.0%	coding (184/948 nt)	treR	trehalose 6‑phosphate‑inducible trehalose regulon transcriptional repressor
*	?	NC_000913	4467094 =	37 (1.040)	8 (0.230)	7/234	2.7	18.0%	coding (153/948 nt)	treR	trehalose 6‑phosphate‑inducible trehalose regulon transcriptional repressor
*	?	NC_000913	= 4081273	39 (1.060)	6 (0.180)	6/224	2.8	13.2%	coding (588/636 nt)	fdoI	formate dehydrogenase‑O, cytochrome b556 subunit
*	?	NC_000913	= 4081294	43 (1.260)	6 (0.180)	6/224	2.8	13.2%	coding (567/636 nt)	fdoI	formate dehydrogenase‑O, cytochrome b556 subunit
*	?	NC_000913	= 3385184	48 (1.310)	6 (0.170)	6/232	2.9	11.5%	intergenic (+11/‑354)	argR/yhcN	l‑arginine‑responsive arginine metabolism regulon transcriptional regulator/cadmium and peroxide resistance protein, stress‑induced
*	?	NC_000913	= 3385197	46 (1.310)	6 (0.170)	6/232	2.9	11.5%	intergenic (+24/‑341)	argR/yhcN	l‑arginine‑responsive arginine metabolism regulon transcriptional regulator/cadmium and peroxide resistance protein, stress‑induced
*	?	NC_000913	3439574 =	70 (1.910)	6 (0.180)	5/214	3.0	9.3%	intergenic (‑65/+42)	yhdN/rplQ	DUF1992 family protein/50S ribosomal subunit protein L17
*	?	NC_000913	3439604 =	55 (1.690)	6 (0.180)	5/214	3.0	9.3%	intergenic (‑95/+12)	yhdN/rplQ	DUF1992 family protein/50S ribosomal subunit protein L17
*	?	NC_000913	2349901 =	42 (1.140)	5 (0.150)	5/222	3.1	11.8%	intergenic (+8/+34)	yfaH/glpQ	pseudogene/periplasmic glycerophosphodiester phosphodiesterase
*	?	NC_000913	2349927 =	36 (1.070)	5 (0.150)	5/222	3.1	11.8%	intergenic (+34/+8)	yfaH/glpQ	pseudogene/periplasmic glycerophosphodiester phosphodiesterase
*	?	NC_000913	4599652 =	49 (1.330)	5 (0.140)	5/228	3.2	10.1%	intergenic (‑211/+43)	opgB/yjjA	OPG periplasmic biosynthetic phosphoglycerol transferases I (membrane‑bound) and II (soluble)/putative DUF2501 family periplasmic protein
*	?	NC_000913	4599685 =	43 (1.240)	5 (0.140)	5/228	3.2	10.1%	intergenic (‑244/+10)	opgB/yjjA	OPG periplasmic biosynthetic phosphoglycerol transferases I (membrane‑bound) and II (soluble)/putative DUF2501 family periplasmic protein
*	?	NC_000913	2658547 =	25 (0.680)	5 (0.140)	5/230	3.2	14.1%	coding (389/1851 nt)	hscA	DnaK‑like molecular chaperone specific for IscU
*	?	NC_000913	2658585 =	37 (1.060)	5 (0.140)	5/230	3.2	14.1%	coding (351/1851 nt)	hscA	DnaK‑like molecular chaperone specific for IscU
*	?	NC_000913	= 2533705	28 (0.760)	5 (0.150)	5/226	3.2	16.9%	intergenic (+325/‑59)	cysK/ptsH	cysteine synthase A, O‑acetylserine sulfhydrolase A subunit/phosphohistidinoprotein‑hexose phosphotransferase component of PTS system (Hpr)
*	?	NC_000913	= 2533719	23 (0.670)	5 (0.150)	5/226	3.2	16.9%	intergenic (+339/‑45)	cysK/ptsH	cysteine synthase A, O‑acetylserine sulfhydrolase A subunit/phosphohistidinoprotein‑hexose phosphotransferase component of PTS system (Hpr)
*	?	NC_000913	= 1428264	NA (NA)	16 (0.460)	5/230	3.2	94.4%	noncoding (531/1196 nt)	IS5	repeat region
*	?	NC_000913	= 2066866	1 (0.030)	16 (0.460)	5/230	3.2	94.4%	noncoding (488/1195 nt)	IS5	repeat region