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 389 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,578,143	0	A	C	51.9%	46.3 / 82.5	52	L79V (TTA→GTA)	maeB	malic enzyme: putative oxidoreductase/phosphotransacetylase
*	NC_000913	298,960	0	A	C	50.9%	65.5 / 101.1	55	Y659D (TAT→GAT)	paoC	PaoABC aldehyde oxidoreductase, Moco‑containing subunit
*	NC_000913	1,825,061	0	G	A	50.9%	49.6 / 97.9	57	intergenic (‑124/+79)	ves/spy	cold‑ and stress‑inducible protein/periplasmic ATP‑independent protein refolding chaperone, stress‑induced
*	NC_000913	2,326,450	0	T	G	50.0%	85.8 / 22.9	60	G114G (GGT→GGG)	atoB	acetyl‑CoA acetyltransferase
*	NC_000913	3,206,435	0	C	T	50.0%	38.6 / 34.1	50	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	3,412,898	0	C	T	45.1%	36.8 / 45.8	52	A190T (GCC→ACC)	acrS	acrAB operon transcriptional repressor
*	NC_000913	3,850,007	0	G	A	45.1%	39.6 / 31.5	51	P44S (CCG→TCG)	uhpB	sensory histidine kinase in two‑component regulatory sytem with UhpA
*	NC_000913	3,578,301	0	A	C	45.0%	92.6 / 12.0	60	G142G (GGT→GGG)	gntR	d‑gluconate inducible gluconate regulon transcriptional repressor
*	NC_000913	2,421,443	0	A	C	44.3%	138.4 / 23.4	79	Y40S (TAC→TCC)	folX	D‑erythro‑7,8‑dihydroneopterin triphosphate 2'‑epimerase and dihydroneopterin aldolase
*	NC_000913	3,492,834	0	T	G	43.9%	82.5 / 13.2	59	G89G (GGT→GGG)	tsgA	putative transporter
*	NC_000913	1,487,153	0	C	A	43.8%	99.5 / 22.8	48	intergenic (+190/‑82)	hrpA/ydcF	putative ATP‑dependent helicase/DUF218 superfamily protein, SAM‑binding
*	NC_000913	501,575	0	A	C	43.4%	85.3 / 13.2	53	V555G (GTG→GGG)	ybaL	inner membrane putative NAD(P)‑binding transporter
*	NC_000913	3,423,297	0	G	C	43.4%	83.3 / 29.5	53	intergenic (+103/+126)	yhdZ/rrfF	putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon
*	NC_000913	3,375,123	0	T	G	43.3%	100.6 / 13.1	60	G85G (GGT→GGG)	dcuD	putative transporter
*	NC_000913	4,538,109	0	A	C	42.4%	104.3 / 16.4	60	G219G (GGT→GGG)	nanM	N‑acetylneuraminic acid mutarotase
*	NC_000913	1,825,056	0	G	A	42.3%	73.7 / 24.4	52	intergenic (‑119/+84)	ves/spy	cold‑ and stress‑inducible protein/periplasmic ATP‑independent protein refolding chaperone, stress‑induced
*	NC_000913	3,423,294	0	T	C	42.3%	70.5 / 21.4	53	intergenic (+100/+129)	yhdZ/rrfF	putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon
*	NC_000913	298,953	0	A	C	42.1%	98.4 / 13.2	57	V661G (GTG→GGG)	paoC	PaoABC aldehyde oxidoreductase, Moco‑containing subunit
*	NC_000913	436,504	0	A	C	42.0%	80.6 / 13.9	53	T291P (ACC→CCC)	thiL	thiamine monophosphate kinase
*	NC_000913	436,516	0	C	A	41.7%	63.5 / 19.2	49	Q295K (CAA→AAA)	thiL	thiamine monophosphate kinase

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	25 (0.390)	23 (0.400)	19/266	4.2	52.7%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	19 (0.330)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related