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 180 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	380,012	1	.	G	66.7%	45.5 / 21.5	21	intergenic (‑131/+57)	frmR/yaiO	regulator protein that represses frmRAB operon/outer membrane protein
*	NC_000913	523,335	0	T	G	58.6%	13.9 / 27.5	30	G25G (GGT→GGG)	rhsD	Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor
*	NC_000913	4,378,802	0	A	C	57.6%	36.3 / 51.1	33	V48G (GTA→GGA)	ampC	penicillin‑binding protein; beta‑lactamase, intrinsically weak
*	NC_000913	646,747	0	T	G	56.2%	11.5 / 23.9	32	T255P (ACC→CCC)	citG	2‑(5''‑triphosphoribosyl)‑3'‑dephosphocoenzyme‑A synthase
*	NC_000913	954,388	0	C	T	56.2%	‑3.6 / 23.3	33	A27T (GCA→ACA)	focA	formate channel
*	NC_000913	3,177,748	0	C	A	56.1%	18.7 / 59.2	41	E55* (GAG→TAG)	nudF	ADP‑ribose pyrophosphatase
*	NC_000913	987,494	0	T	G	56.0%	24.0 / 35.7	26	intergenic (‑512/+91)	ompF/asnS	outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase
*	NC_000913	646,765	0	G	T	54.3%	23.6 / 54.0	35	Q249K (CAA→AAA)	citG	2‑(5''‑triphosphoribosyl)‑3'‑dephosphocoenzyme‑A synthase
*	NC_000913	2,578,143	0	A	C	54.0%	29.9 / 54.2	37	L79V (TTA→GTA)	maeB	malic enzyme: putative oxidoreductase/phosphotransacetylase
*	NC_000913	987,529	0	C	A	53.8%	27.1 / 51.4	26	intergenic (‑547/+56)	ompF/asnS	outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase
*	NC_000913	2,628,625	0	A	C	53.8%	5.5 / 14.3	14	V105G (GTC→GGC)	yfgF	cyclic‑di‑GMP phosphodiesterase, anaerobic
*	NC_000913	2,151,581	0	G	T	52.6%	6.5 / 27.6	19	D133Y (GAT→TAT)	yegJ	uncharacterized protein
*	NC_000913	2,434,882	0	T	G	52.3%	47.8 / 71.9	44	Y252S (TAC→TCC)	truA	tRNA pseudouridine(38‑40) synthase
*	NC_000913	1,997,114	0	T	G	51.6%	31.4 / 40.7	31	D234A (GAC→GCC)	yecC	putative ABC transporter ATPase
*	NC_000913	4,573,496	0	A	G	51.0%	32.0 / 75.8	50	pseudogene (1083/1503 nt)	yjiT	pseudogene
*	NC_000913	4,573,500	0	A	G	51.0%	57.0 / 77.6	51	pseudogene (1087/1503 nt)	yjiT	pseudogene
*	NC_000913	370,876	0	C	G	50.0%	45.4 / 29.0	43	S200R (AGC→AGG)	mhpB	2,3‑dihydroxyphenylpropionate 1,2‑dioxygenase
*	NC_000913	646,760	0	T	C	50.0%	28.3 / 10.4	35	K250K (AAA→AAG)	citG	2‑(5''‑triphosphoribosyl)‑3'‑dephosphocoenzyme‑A synthase
*	NC_000913	1,097,581	0	A	G	50.0%	35.6 / 15.9	38	noncoding (72/88 nt)	serX	tRNA‑Ser
*	NC_000913	2,151,608	0	G	A	50.0%	8.5 / 12.5	20	E142K (GAA→AAA)	yegJ	uncharacterized protein

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	1 =	0 (0.000)	13 (0.270)	12/298	3.3	100%	intergenic (–/‑189)	–/thrL	–/thr operon leader peptide
	?	NC_000913	= 4641652	0 (0.000)					intergenic (+24/–)	yjtD/–	putative methyltransferase/–
*	?	NC_000913	= 1299498	0 (0.000)	7 (0.150)	7/290	4.7	100%	intergenic (+253/‑1684)	ychE/oppA	UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
	?	NC_000913	1300698 =	0 (0.000)					intergenic (+1453/‑484)	ychE/oppA	UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
*	?	NC_000913	= 1978502	0 (0.000)	6 (0.130)	6/282	4.9	100%	intergenic (‑305/+16)	flhD/insB1	flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B
	?	NC_000913	1979279 =	0 (0.000)					intergenic (‑64/‑474)	insA/uspC	IS1 repressor TnpA/universal stress protein