breseq  version 0.29.0  revision 8f9c342918e4 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence (highest frequency 20 of 63 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,764,771	0	T	A	45.5%	37.1 / 17.0	33	intergenic (‑385/+163)	sufA/ydiH	Fe‑S cluster assembly protein/uncharacterized protein
*	NC_000913	357,890	0	C	A	42.3%	13.3 / 11.3	26	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	4,538,109	0	A	C	42.0%	74.1 / 14.9	51	G219G (GGT→GGG)	nanM	N‑acetylneuraminic acid mutarotase
*	NC_000913	5,159	0	G	A	41.5%	47.6 / 13.5	41	intergenic (+139/‑75)	thrC/yaaX	L‑threonine synthase/DUF2502 family putative periplasmic protein
*	NC_000913	2,481,804	0	G	A	39.4%	48.5 / 10.8	33	P125S (CCA→TCA)	emrY	putative multidrug efflux system
*	NC_000913	3,206,435	0	C	T	39.3%	27.8 / 11.1	28	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	3,412,898	0	C	T	39.1%	53.6 / 27.6	48	A190T (GCC→ACC)	acrS	acrAB operon transcriptional repressor
*	NC_000913	1,163,371	0	C	T	39.0%	57.7 / 19.5	41	L38F (CTC→TTC)	thiK	thiamine kinase
*	NC_000913	5,123	0	C	A	38.9%	55.8 / 13.4	36	intergenic (+103/‑111)	thrC/yaaX	L‑threonine synthase/DUF2502 family putative periplasmic protein
*	NC_000913	2,624,517	0	G	T	38.7%	40.0 / 11.3	31	E492* (GAA→TAA)	ppk	polyphosphate kinase, component of RNA degradosome
*	NC_000913	1,504,799	0	A	G	38.5%	52.3 / 12.1	39	G361G (GGA→GGG)	insQ	IS609 transposase B
*	NC_000913	4,287,710	0	G	A	38.5%	44.6 / 13.9	39	intergenic (‑339/‑54)	acs/nrfA	acetyl‑CoA synthetase/nitrite reductase, formate‑dependent, cytochrome
*	NC_000913	2,349,145	0	A	C	38.3%	66.1 / 10.3	47	F110V (TTC→GTC)	inaA	acid‑inducible Kdo/WaaP family putative kinase
*	NC_000913	300,721	0	G	T	38.2%	42.4 / 13.1	34	Q72K (CAA→AAA)	paoC	PaoABC aldehyde oxidoreductase, Moco‑containing subunit
*	NC_000913	436,516	0	C	A	38.2%	39.7 / 10.6	34	Q295K (CAA→AAA)	thiL	thiamine monophosphate kinase
*	NC_000913	357,873	0	C	T	37.9%	26.5 / 11.3	30	S273N (AGC→AAC)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	2,903,715	0	G	A	37.5%	66.8 / 23.0	48	intergenic (+341/+1032)	ygcE/queE	putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis
*	NC_000913	357,842	0	C	A	37.1%	51.1 / 13.0	35	L283F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	3,206,452	0	C	A	37.0%	24.2 / 10.0	28	intergenic (‑196/‑11)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	3,177,748	0	C	A	36.6%	33.1 / 15.0	41	E55* (GAG→TAG)	nudF	ADP‑ribose pyrophosphatase

Marginal new junction evidence (sorted from low to high skew)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	1207790 =	25 (0.580)	11 (0.290)	11/266	3.6	30.0%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	29 (0.760)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1207805	28 (0.650)	8 (0.210)	8/266	4.6	23.2%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	28 (0.730)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 4542690	38 (0.880)	3 (0.070)	3/280	7.6	7.3%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	41 (1.010)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	4542682 =	38 (0.880)	3 (0.070)	3/280	7.6	7.2%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	42 (1.040)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)