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 98 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,933,409	0	T	C	52.4%	15.3 / 24.6	21	E399G (GAA→GGA)	edd	6‑phosphogluconate dehydratase
*	NC_000913	535,925	0	T	G	51.3%	52.2 / 64.3	40	G72G (GGT→GGG)	hyi	hydroxypyruvate isomerase
*	NC_000913	307,821	0	G	T	46.2%	41.7 / 20.9	39	Y504* (TAC→TAA)	ecpC	ECP production outer membrane protein
*	NC_000913	2,252,660	0	G	T	45.7%	54.3 / 19.9	36	E321* (GAA→TAA)	yeiI	putative kinase
*	NC_000913	4,536,197	0	A	T	44.7%	44.1 / 22.3	38	intergenic (+166/+417)	yjhR/nanS	pseudogene, helicase family; putative frameshift suppressor/9‑O‑acetyl N‑acetylneuraminic acid esterase
*	NC_000913	4,536,212	0	T	A	43.6%	50.8 / 16.5	39	intergenic (+181/+402)	yjhR/nanS	pseudogene, helicase family; putative frameshift suppressor/9‑O‑acetyl N‑acetylneuraminic acid esterase
*	NC_000913	1,413,735	0	A	T	43.5%	48.0 / 35.7	46	Y2* (TAT→TAA)	ydaC	DUF1187 family protein, Rac prophage; putative double‑strand break reduction protein
*	NC_000913	4,336,901	0	T	A	43.3%	29.6 / 13.5	30	Y44F (TAT→TTT)	adiC	arginine:agmatine antiporter
*	NC_000913	436,504	0	A	C	42.9%	44.2 / 12.2	36	T291P (ACC→CCC)	thiL	thiamine monophosphate kinase
*	NC_000913	2,252,657	0	C	T	42.9%	40.5 / 20.1	35	L320F (CTT→TTT)	yeiI	putative kinase
*	NC_000913	2,678,043	0	C	T	42.9%	20.3 / 14.4	28	E107K (GAA→AAA)	yphE	putative sugar ABC transporter ATPase
*	NC_000913	3,228,204	0	T	A	41.9%	44.1 / 10.5	31	I135N (ATC→AAC)	ygjJ	putative periplasmic protein
*	NC_000913	650,464	0	A	T	40.6%	45.4 / 11.4	32	R9R (CGT→CGA)	citE	citrate lyase, citryl‑ACP lyase (beta) subunit
*	NC_000913	2,248,424	0	C	A	40.6%	47.9 / 20.9	32	V37F (GTT→TTT)	lysP	lysine transporter
*	NC_000913	718,690	0	T	G	40.5%	57.7 / 12.1	37	T591P (ACC→CCC)	speF	ornithine decarboxylase isozyme, inducible
*	NC_000913	1,435,725	0	C	A	40.0%	72.8 / 16.4	41	intergenic (‑106/+35)	uspF/ompN	stress‑induced protein, ATP‑binding protein/outer membrane pore protein N, non‑specific
*	NC_000913	2,001,911	0	G	A	40.0%	46.1 / 19.1	41	intergenic (‑122/+199)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein (flagellin)
*	NC_000913	2,343,829	0	G	C	40.0%	40.6 / 11.3	26	A114G (GCC→GGC)	yfaL	adhesin
*	NC_000913	4,024,542	0	G	A	39.4%	47.2 / 10.7	33	H94Y (CAT→TAT)	rfaH	transcription antitermination protein
*	NC_000913	1,224,025	0	C	A	39.0%	96.2 / 10.2	41	intergenic (+118/+254)	ycgI/minE	pseudogene/cell division topological specificity factor

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	= 4542690	62 (1.430)	13 (0.320)	13/280	3.1	18.9%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	53 (1.300)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	4542682 =	64 (1.470)	9 (0.220)	9/280	4.3	13.6%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	54 (1.320)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)