breseq  version 0.35.4  revision f352f80f4bc9 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence (highest frequency 20 of 141 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,856,021	0	T	G	40.5%	26.7 / 14.9	43	pseudogene (943/1617 nt)	BW25113_RS19145	PTS sugar transporter subunit IIB
*	NZ_CP009273	1,995,399	0	A	C	39.6%	81.5 / 13.5	48	intergenic (‑129/+192)	fliA/fliC	RNA polymerase sigma factor FliA/H48 family flagellin FliC
*	NZ_CP009273	1,240,690	0	G	T	38.8%	94.9 / 16.4	49	L25F (TTG→TTT)	BW25113_RS06225	protein YcgY
*	NZ_CP009273	4,594,167	0	C	T	36.1%	102.1 / 35.8	72	S64F (TCT→TTT)	bglJ	DNA‑binding transcriptional activator BglJ
*	NZ_CP009273	295,837	0	A	G	35.5%	74.3 / 15.3	63	L270P (CTC→CCC)	paoC	aldehyde oxidoreductase molybdenum‑binding subunit PaoC
*	NZ_CP009273	1,995,392	0	G	A	35.3%	67.0 / 25.5	51	intergenic (‑122/+199)	fliA/fliC	RNA polymerase sigma factor FliA/H48 family flagellin FliC
*	NZ_CP009273	1,652,420	0	C	T	33.9%	105.3 / 13.2	59	S32F (TCT→TTT)	ynfE	DmsA/YnfE/YnfF family dimethyl sulfoxide reductase
*	NZ_CP009273	2,178,678	0	T	G	33.3%	87.4 / 11.1	46	T35P (ACC→CCC)	thiM	hydroxyethylthiazole kinase
*	NZ_CP009273	2,178,717	0	A	G	32.6%	90.0 / 15.4	49	S22P (TCC→CCC)	thiM	hydroxyethylthiazole kinase
*	NZ_CP009273	3,152,252	0	T	C	32.6%	174.5 / 17.6	87	intergenic (+9/+34)	yqhH/ygiQ	lipoprotein YqhH/YgiQ family radical SAM protein
*	NZ_CP009273	4,594,161	0	C	T	32.4%	118.6 / 31.0	72	S62F (TCT→TTT)	bglJ	DNA‑binding transcriptional activator BglJ
*	NZ_CP009273	1,240,692	0	C	G	32.0%	102.4 / 13.7	50	A26G (GCT→GGT)	BW25113_RS06225	protein YcgY
*	NZ_CP009273	1,995,384	0	T	C	31.9%	79.8 / 15.1	48	intergenic (‑114/+207)	fliA/fliC	RNA polymerase sigma factor FliA/H48 family flagellin FliC
*	NZ_CP009273	1,240,703	0	G	T	31.2%	105.8 / 11.1	48	E30* (GAA→TAA)	BW25113_RS06225	protein YcgY
*	NZ_CP009273	3,837,579	0	T	G	31.2%	309.2 / 26.0	142	F86V (TTT→GTT)	adeD	adenine deaminase
*	NZ_CP009273	2,330,073	0	A	C	31.0%	144.2 / 13.4	71	G17G (GGT→GGG)	yfaA	DUF2138 domain‑containing protein
*	NZ_CP009273	3,524,799	0	A	C	30.5%	367.8 / 18.0	152	Y334D (TAT→GAT)	yhgE	DUF4153 domain‑containing protein
*	NZ_CP009273	2,943,560	0	T	G	30.4%	186.4 / 15.0	81	G320G (GGT→GGG)	argA	amino‑acid N‑acetyltransferase
*	NZ_CP009273	4,538,640	0	A	C	29.7%	213.9 / 17.0	91	T6P (ACC→CCC)	fimH	type 1 fimbria D‑mannose specific adhesin FimH
*	NZ_CP009273	1,652,424	0	G	T	29.3%	120.8 / 13.1	59	L33F (TTG→TTT)	ynfE	DmsA/YnfE/YnfF family dimethyl sulfoxide reductase

Marginal new junction evidence (sorted from low to high skew)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	= 4532507	125 (1.360)	15 (0.170)	14/478	4.6	12.1%	intergenic (+57/‑425)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
	?	NZ_CP009273	= 4532803	98 (1.110)					intergenic (+353/‑129)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
*	?	NZ_CP009273	4532499 =	127 (1.380)	11 (0.120)	11/478	5.3	9.0%	intergenic (+49/‑433)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
	?	NZ_CP009273	4532813 =	99 (1.120)					intergenic (+363/‑119)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA