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 345 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	987,494	0	T	G	53.7%	56.1 / 84.2	54	intergenic (‑512/+91)	ompF/asnS	outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase
*	NC_000913	4,573,500	0	A	G	51.0%	48.6 / 75.6	49	pseudogene (1087/1503 nt)	yjiT	pseudogene
*	NC_000913	4,573,496	0	A	G	50.0%	37.8 / 32.2	51	pseudogene (1083/1503 nt)	yjiT	pseudogene
*	NC_000913	1,435,727	0	G	A	48.1%	55.6 / 41.1	54	intergenic (‑108/+33)	uspF/ompN	stress‑induced protein, ATP‑binding protein/outer membrane pore protein N, non‑specific
*	NC_000913	3,585,086	0	A	C	48.1%	83.8 / 11.5	52	Y580D (TAC→GAC)	ggt	gamma‑glutamyltranspeptidase
*	NC_000913	1,487,163	0	C	T	47.5%	48.6 / 42.8	60	intergenic (+200/‑72)	hrpA/ydcF	putative ATP‑dependent helicase/DUF218 superfamily protein, SAM‑binding
*	NC_000913	3,375,123	0	T	G	47.4%	90.4 / 11.7	57	G85G (GGT→GGG)	dcuD	putative transporter
*	NC_000913	3,206,435	0	C	T	47.0%	56.8 / 45.6	66	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	2,846,674	0	T	G	46.4%	70.3 / 20.9	56	T247P (ACC→CCC)	hycD	hydrogenase 3, membrane subunit
*	NC_000913	1,413,735	0	A	T	45.2%	50.7 / 25.9	42	Y2* (TAT→TAA)	ydaC	DUF1187 family protein, Rac prophage; putative double‑strand break reduction protein
*	NC_000913	2,578,143	0	A	C	44.3%	92.5 / 24.9	61	L79V (TTA→GTA)	maeB	malic enzyme: putative oxidoreductase/phosphotransacetylase
*	NC_000913	1,435,718	0	G	A	44.2%	74.5 / 24.4	53	intergenic (‑99/+42)	uspF/ompN	stress‑induced protein, ATP‑binding protein/outer membrane pore protein N, non‑specific
*	NC_000913	993,917	0	A	C	43.6%	64.5 / 10.2	39	V43G (GTG→GGG)	ssuB	aliphatic sulfonate ABC transporter ATPase
*	NC_000913	1,435,721	0	T	A	43.4%	76.5 / 27.7	53	intergenic (‑102/+39)	uspF/ompN	stress‑induced protein, ATP‑binding protein/outer membrane pore protein N, non‑specific
*	NC_000913	2,001,918	0	A	C	43.2%	141.3 / 14.7	74	intergenic (‑129/+192)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein (flagellin)
*	NC_000913	436,516	0	C	A	42.9%	54.2 / 17.4	43	Q295K (CAA→AAA)	thiL	thiamine monophosphate kinase
*	NC_000913	3,998,178	0	G	A	42.9%	46.9 / 23.4	42	A66T (GCG→ACG)	uvrD	DNA‑dependent ATPase I and helicase II
*	NC_000913	357,890	0	C	A	42.5%	37.1 / 16.6	40	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	718,659	0	T	A	42.5%	57.9 / 16.5	40	D601V (GAT→GTT)	speF	ornithine decarboxylase isozyme, inducible
*	NC_000913	4,538,109	0	A	C	42.4%	101.4 / 16.5	61	G219G (GGT→GGG)	nanM	N‑acetylneuraminic acid mutarotase

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 =	53 (0.840)	15 (0.260)	15/266	5.4	26.0%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	38 (0.670)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1207805	50 (0.790)	14 (0.250)	13/266	6.1	25.8%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	36 (0.640)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related