breseq  version 0.35.4  revision f352f80f4bc9 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence (highest frequency 20 of 47 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	209,828	0	A	G	52.9%	4.7 / 16.0	17	G337G (GGA→GGG)	tilS	tRNA(Ile)‑lysidine synthetase
*	CP009273	3,634,341	0	C	T	41.7%	38.2 / 18.6	36	F40F (TTC→TTT)	dtpB	dipeptide and tripeptide permease B
*	CP009273	3,199,794	0	C	T	40.0%	57.4 / 27.8	50	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	CP009273	595,032	0	T	G	37.5%	66.5 / 12.8	48	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	CP009273	2,380,341	0	G	A	37.3%	75.7 / 37.5	59	intergenic (+31/‑72)	yfbL/yfbM	putative peptidase/DUF1877 family protein
*	CP009273	3,659,062	0	C	A	37.2%	164.5 / 34.2	94	A37S (GCG→TCG)	gadX	acid resistance regulon transcriptional activator; autoactivator
*	CP009273	71,566	0	C	T	36.1%	55.7 / 16.9	36	L134L (CTG→CTA)	thiB	thiamine‑, thiamine pyrophosphate‑, thiamine monophosphate‑binding ABC transporter periplasmic protein; ThiBPQ thiamine, thiamine pyrophosphate importer
*	CP009273	1,819,318	0	G	A	34.9%	69.2 / 18.3	43	intergenic (‑124/+79)	ves/spy	cold‑ and stress‑inducible protein/periplasmic ATP‑independent protein refolding chaperone, stress‑induced
*	CP009273	714,125	0	C	T	32.4%	62.8 / 12.0	37	E598K (GAA→AAA)	speF	ornithine decarboxylase isozyme, inducible
*	CP009273	5,159	0	G	A	31.3%	102.0 / 27.0	67	intergenic (+139/‑75)	thrC/yaaX	L‑threonine synthase/DUF2502 family putative periplasmic protein
*	CP009273	1,976,004	0	A	G	31.1%	79.0 / 15.9	45	intergenic (‑136/+31)	otsB/araH	trehalose‑6‑phosphate phosphatase, biosynthetic/fused L‑arabinose transporter subunits of ABC superfamily: membrane components
*	CP009273	3,285,990	0	A	T	31.0%	48.8 / 10.5	29	H235Q (CAT→CAA)	rsmI	16S rRNA C1402 2'‑O‑ribose methyltransferase, SAM‑dependent
*	CP009273	5,115	0	G	A	30.6%	115.9 / 22.6	62	intergenic (+95/‑119)	thrC/yaaX	L‑threonine synthase/DUF2502 family putative periplasmic protein
*	CP009273	3,406,257	0	C	T	30.6%	83.0 / 17.8	49	A190T (GCC→ACC)	acrS	acrAB operon transcriptional repressor
*	CP009273	2,380,362	0	C	T	29.2%	110.8 / 26.2	65	intergenic (+52/‑51)	yfbL/yfbM	putative peptidase/DUF1877 family protein
*	CP009273	3,659,058	0	T	C	29.0%	164.7 / 25.6	94	D38G (GAT→GGT)	gadX	acid resistance regulon transcriptional activator; autoactivator
*	CP009273	296,422	0	G	C	28.9%	77.9 / 10.2	38	P75R (CCG→CGG)	paoC	PaoABC aldehyde oxidoreductase, Moco‑containing subunit
*	CP009273	642,221	0	G	T	27.1%	125.6 / 13.6	59	Q249K (CAA→AAA)	citG	2‑(5''‑triphosphoribosyl)‑3'‑dephosphocoenzyme‑A synthase
*	CP009273	1,429,975	0	G	A	26.8%	116.2 / 14.2	56	intergenic (‑99/+42)	uspF/ompN	stress‑induced protein, ATP‑binding protein/outer membrane pore protein N, non‑specific
*	CP009273	5,106	0	G	A	26.6%	123.4 / 21.4	65	intergenic (+86/‑128)	thrC/yaaX	L‑threonine synthase/DUF2502 family putative periplasmic protein

Marginal new junction evidence (lowest skew 10 of 67 shown)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	= 4532507	37 (0.740)	9 (0.190)	8/216	2.8	17.4%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	CP009273	= 4532803	51 (1.100)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	CP009273	205723 =	44 (0.880)	8 (0.000)	6/218	3.4	0.074%	coding (616/960 nt)	accA	acetyl‑CoA carboxylase, carboxytransferase, alpha subunit
	?	Exported	= 2942	21646 (1.020)					intergenic (+708/–)	fdh/–	formate dehydrogenase from Pseudomonas sp. 101 with an N‑terminal his‑tag/–
*	?	CP009273	3416618 =	57 (1.130)	7 (0.150) +GAATTAATTCC	5/212	3.7	13.4%	intergenic (+65/+164)	yhdZ/rrfF	putative amino‑acid transporter subunit/5S ribosomal RNA of rrnD operon
	?	CP009273	4033989 =	43 (0.860)					noncoding (113/120 nt)	rrfA	5S ribosomal RNA of rrnA operon
*	?	CP009273	360104 =	34 (0.680)	9 (0.190) +AATTCC	5/222	3.8	19.8%	intergenic (‑38/+557)	lacZ/lacI	pseudogene, truncated/DNA‑binding transcriptional repressor
	?	CP009273	4033989 =	43 (0.860)					noncoding (113/120 nt)	rrfA	5S ribosomal RNA of rrnA operon
*	?	CP009273	= 2257783	30 (0.600)	5 (0.000)	4/220	4.1	0.052%	coding (442/1182 nt)	setB	lactose/glucose efflux system
	?	Exported	= 1719	19013 (0.890)					coding (709/1224 nt)	fdh	formate dehydrogenase from Pseudomonas sp. 101 with an N‑terminal his‑tag
*	?	CP009273	= 2763503	42 (0.840)	4 (0.000)	4/230	4.3	0.72%	coding (442/702 nt)	yfjR	CP4‑57 prophage; putative DNA‑binding transcriptional regulator
	?	Exported	9 =	1057 (0.050)					coding (784/792 nt)	aadA	aminoglycoside adenylyltransferase (Murphy, 1985)
*	?	Exported	= 905	1201 (0.050)	25 (0.000) +AAATGCTAAAATTCCAC	19/194	4.4	1.3%	intergenic (‑113/‑106)	aadA/fdh	aminoglycoside adenylyltransferase (Murphy, 1985)/formate dehydrogenase from Pseudomonas sp. 101 with an N‑terminal his‑tag
	?	KX077536	4030 =	3070 (1.410)					intergenic (+631/‑74)	unknown/unknown	transposase/cbbM
*	?	Exported	923 =	44 (0.000)	43 (0.000) +29 bp	16/176	4.5	3.9%	intergenic (‑131/‑88)	aadA/fdh	aminoglycoside adenylyltransferase (Murphy, 1985)/formate dehydrogenase from Pseudomonas sp. 101 with an N‑terminal his‑tag
	?	KX077536	1006 =	2819 (1.300)					intergenic (–/‑93)	–/unknown	–/BLA
*	?	CP009273	4432006 =	52 (1.030)	6 (0.000)	3/214	4.5	0.059%	intergenic (‑13/‑193)	msrA/tamA	methionine sulfoxide reductase A/translocation and assembly module for autotransporter export, outer membrane subunit
	?	Exported	= 1103	20142 (0.960)					coding (93/1224 nt)	fdh	formate dehydrogenase from Pseudomonas sp. 101 with an N‑terminal his‑tag
*	?	CP009273	117115 =	75 (1.490)	3 (0.000)	3/224	4.6	0.028%	coding (924/1374 nt)	aroP	aromatic amino acid transporter
	?	Exported	541 =	21542 (0.980)					coding (252/792 nt)	aadA	aminoglycoside adenylyltransferase (Murphy, 1985)