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 447 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,578,301	0	A	C	55.7%	61.2 / 99.0	62	G142G (GGT→GGG)	gntR	d‑gluconate inducible gluconate regulon transcriptional repressor
*	NC_000913	4,346,675	0	T	G	54.4%	42.4 / 68.8	48	T218P (ACC→CCC)	fumB	anaerobic class I fumarate hydratase (fumarase B)
*	NC_000913	599,576	0	T	G	48.6%	98.7 / 29.2	70	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	3,578,287	0	T	C	46.7%	79.2 / 14.1	60	E147G (GAA→GGA)	gntR	d‑gluconate inducible gluconate regulon transcriptional repressor
*	NC_000913	1,413,735	0	A	T	45.7%	71.5 / 53.3	70	Y2* (TAT→TAA)	ydaC	DUF1187 family protein, Rac prophage; putative double‑strand break reduction protein
*	NC_000913	3,578,290	0	A	C	44.8%	87.5 / 14.5	59	V146G (GTG→GGG)	gntR	d‑gluconate inducible gluconate regulon transcriptional repressor
*	NC_000913	345,304	0	G	A	44.1%	88.2 / 38.6	68	intergenic (+313/‑100)	yahL/yahM	uncharacterized protein/uncharacterized protein
*	NC_000913	2,676,106	0	C	A	43.7%	103.3 / 36.0	71	L240F (TTG→TTT)	yphD	putative sugar ABC transporter permease
*	NC_000913	1,079,460	0	T	G	43.6%	89.1 / 14.1	55	G52G (GGT→GGG)	putP	proline:sodium symporter
*	NC_000913	2,337,723	0	A	C	43.6%	88.2 / 18.1	56	G566G (GGT→GGG)	gyrA	DNA gyrase (type II topoisomerase), subunit A
*	NC_000913	925,900	0	A	G	42.9%	122.0 / 25.2	77	noncoding (72/88 nt)	serW	tRNA‑Ser
*	NC_000913	4,536,197	0	A	T	42.9%	74.9 / 60.9	70	intergenic (+166/+417)	yjhR/nanS	pseudogene, helicase family; putative frameshift suppressor/9‑O‑acetyl N‑acetylneuraminic acid esterase
*	NC_000913	2,326,450	0	T	G	42.6%	97.5 / 10.0	54	G114G (GGT→GGG)	atoB	acetyl‑CoA acetyltransferase
*	NC_000913	357,890	0	C	A	42.4%	35.2 / 12.3	33	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	436,516	0	C	A	42.2%	95.6 / 32.4	65	Q295K (CAA→AAA)	thiL	thiamine monophosphate kinase
*	NC_000913	4,346,685	0	C	T	42.0%	51.3 / 22.5	50	E214E (GAG→GAA)	fumB	anaerobic class I fumarate hydratase (fumarase B)
*	NC_000913	589,930	0	A	G	41.7%	46.9 / 11.6	36	L342P (CTC→CCC)	nfrA	bacteriophage N4 receptor, outer membrane subunit
*	NC_000913	1,776,263	0	T	G	41.2%	147.0 / 12.6	80	V226G (GTG→GGG)	ydiF	putative acetyl‑CoA:acetoacetyl‑CoA transferase: alpha subunit/beta subunit
*	NC_000913	2,835,219	0	A	C	41.1%	102.7 / 10.8	56	V736G (GTT→GGT)	hypF	carbamoyl phosphate phosphatase and [NiFe] hydrogenase maturation protein
*	NC_000913	4,555,106	0	C	A	40.8%	137.9 / 31.4	76	N177K (AAC→AAA)	uxuR	fructuronate‑inducible hexuronate regulon transcriptional repressor; autorepressor

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	= 1207805	58 (0.770)	18 (0.270)	18/266	5.9	28.4%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	39 (0.580)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	1207790 =	60 (0.800)	13 (0.190)	13/266	7.8	21.8%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	40 (0.590)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 4542690	78 (1.040)	14 (0.200)	14/280	7.9	14.6%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	91 (1.290)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	4542682 =	85 (1.130)	14 (0.200)	14/280	7.9	14.0%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	92 (1.300)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)