breseq  version 0.33.1  revision 8505477f25b3 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence (highest frequency 20 of 47 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	417,533	0	T	G	60.7%	‑5.7 / 15.7	29	V131G (GTG→GGG)	phoB	response regulator in two‑component regulatory system with PhoR
*	NC_000913	2,151,710	0	C	A	42.9%	0.7 / 10.9	14	intergenic (+64/+1)	yegJ/yegK	uncharacterized protein/ser/thr phosphatase‑related protein
*	NC_000913	540,558	0	T	G	33.3%	114.8 / 29.4	69	intergenic (+50/‑7)	allB/ybbY	allantoinase/putative uracil/xanthine transporter
*	NC_000913	2,548,026	0	A	G	33.3%	110.3 / 14.5	60	I452V (ATT→GTT)	murP	N‑acetylmuramic acid permease, EIIBC component, PTS system
*	NC_000913	1,174,605	0	T	C	32.6%	100.3 / 14.0	50	G187G (GGA→GGG)	ycfT	inner membrane protein
*	NC_000913	4,548,932	0	A	T	32.1%	49.6 / 10.1	29	Y42F (TAT→TTT)	fimH	minor component of type 1 fimbriae
*	NC_000913	3,665,698	0	T	C	30.0%	104.2 / 12.5	51	D38G (GAT→GGT)	gadX	acid resistance regulon transcriptional activator; autoactivator
*	NC_000913	2,548,033	0	T	G	29.5%	129.6 / 11.5	61	V454G (GTG→GGG)	murP	N‑acetylmuramic acid permease, EIIBC component, PTS system
*	NC_000913	540,565	0	A	T	29.2%	143.6 / 27.3	72	M1M (ATG→TTG) †	ybbY	putative uracil/xanthine transporter
*	NC_000913	1,174,626	0	G	A	28.8%	93.0 / 22.8	52	F180F (TTC→TTT)	ycfT	inner membrane protein
*	NC_000913	1,174,617	0	C	G	28.0%	114.1 / 10.6	52	T183T (ACG→ACC)	ycfT	inner membrane protein
*	NC_000913	2,288,852	0	C	T	27.7%	193.0 / 34.5	95	pseudogene (63/2525 nt)	yejO	pseudogene, autotransporter outer membrane homology;putative transport; Not classified; putative ATP‑binding component of a transport system
*	NC_000913	3,757,668	0	C	T	27.6%	115.3 / 14.4	59	A54T (GCA→ACA)	yiaY	L‑threonine dehydrogenase
*	NC_000913	3,813,272	0	C	T	27.6%	37.3 / 11.2	30	S181L (TCG→TTG)	dfp	fused 4'‑phosphopantothenoylcysteine decarboxylase/phosphopantothenoylcysteine synthetase, FMN‑binding
*	NC_000913	1,577,123	0	A	C	26.9%	192.4 / 10.4	78	V166G (GTA→GGA)	yddB	putative TonB‑dependent outer membrane receptor
*	NC_000913	12,486	0	G	A	26.6%	122.0 / 17.3	64	Q108Q (CAG→CAA)	dnaK	chaperone Hsp70, with co‑chaperone DnaJ
*	NC_000913	3,665,702	0	C	A	26.5%	133.3 / 17.2	51	A37S (GCG→TCG)	gadX	acid resistance regulon transcriptional activator; autoactivator
*	NC_000913	2,159,089	0	T	A	26.2%	91.0 / 13.2	42	L235Q (CTA→CAA)	mdtC	multidrug efflux system, subunit C
*	NC_000913	1,529,304	0	A	C	25.7%	249.2 / 16.8	106	pseudogene (1403/2037 nt)	rhsE	pseudogene, Rhs family
*	NC_000913	3,548,925	0	A	C	25.6%	166.2 / 12.0	83	G382G (GGT→GGG)	malQ	4‑alpha‑glucanotransferase (amylomaltase)

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	= 105258	72 (0.720)	5 (0.050)	5/322	6.1	6.9%	intergenic (+14/‑47)	ftsA/ftsZ	ATP‑binding cell division FtsK recruitment protein/GTP‑binding tubulin‑like cell division protein
	?	NC_000913	= 105268	66 (0.690)					intergenic (+24/‑37)	ftsA/ftsZ	ATP‑binding cell division FtsK recruitment protein/GTP‑binding tubulin‑like cell division protein
*	?	NC_000913	4094338 =	NA (NA)	27 (0.310) +23 bp	3/292	6.7	NA	noncoding (23/402 nt)	REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences	REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences
	?	NC_000913	= 4094682	NA (NA)					noncoding (367/402 nt)	REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences	REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences
*	?	NC_000913	4054641 =	82 (0.820)	4 (0.040)	4/332	6.7	4.5%	coding (638/1410 nt)	glnG	fused DNA‑binding response regulator in two‑component regulatory system with GlnL: response regulator/sigma54 interaction protein
	?	NC_000913	4054702 =	88 (0.900)					coding (577/1410 nt)	glnG	fused DNA‑binding response regulator in two‑component regulatory system with GlnL: response regulator/sigma54 interaction protein