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 274 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	987,494	0	T	G	58.5%	34.4 / 54.5	42	intergenic (‑512/+91)	ompF/asnS	outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase
*	NC_000913	354,288	0	T	G	52.1%	43.7 / 69.8	48	V528G (GTG→GGG)	prpE	propionate‑‑CoA ligase
*	NC_000913	987,503	0	G	A	51.2%	20.1 / 52.5	42	intergenic (‑521/+82)	ompF/asnS	outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase
*	NC_000913	987,501	0	T	A	50.0%	33.7 / 23.8	42	intergenic (‑519/+84)	ompF/asnS	outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase
*	NC_000913	941,713	0	T	G	48.8%	53.6 / 10.5	41	V252G (GTG→GGG)	dmsA	dimethyl sulfoxide reductase, anaerobic, subunit A
*	NC_000913	987,522	0	C	A	48.6%	37.5 / 17.3	37	intergenic (‑540/+63)	ompF/asnS	outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase
*	NC_000913	2,984,441	0	A	C	46.3%	93.3 / 11.2	55	G384G (GGT→GGG)	yqeF	short chain acyltransferase
*	NC_000913	4,604,344	0	C	T	46.0%	31.6 / 15.6	38	S62F (TCT→TTT)	bglJ	bgl operon transcriptional activator
*	NC_000913	993,913	0	G	C	45.2%	78.0 / 27.8	62	G44G (GGC→GGG)	ssuB	aliphatic sulfonate ABC transporter ATPase
*	NC_000913	599,576	0	T	G	44.6%	107.8 / 24.0	66	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	3,671,415	0	C	T	44.2%	48.2 / 37.5	52	K160K (AAG→AAA)	yhjB	putative DNA‑binding transcriptional response regulator
*	NC_000913	987,529	0	C	A	43.2%	69.3 / 21.0	44	intergenic (‑547/+56)	ompF/asnS	outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase
*	NC_000913	357,890	0	C	A	42.9%	39.2 / 23.4	42	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	4,538,109	0	A	C	42.6%	84.0 / 16.6	54	G219G (GGT→GGG)	nanM	N‑acetylneuraminic acid mutarotase
*	NC_000913	993,917	0	A	C	42.4%	78.0 / 22.9	59	V43G (GTG→GGG)	ssuB	aliphatic sulfonate ABC transporter ATPase
*	NC_000913	987,551	0	G	A	42.2%	29.2 / 46.5	45	intergenic (‑569/+34)	ompF/asnS	outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase
*	NC_000913	987,524	0	G	A	41.9%	40.3 / 22.7	44	intergenic (‑542/+61)	ompF/asnS	outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase
*	NC_000913	802,118	0	A	C	41.3%	99.0 / 13.2	64	T78P (ACC→CCC)	ybhI	putative DASS family tricarboxylate or dicarboxylate transporter
*	NC_000913	1,222,233	0	G	A	41.1%	56.5 / 30.5	57	pseudogene (60/75 nt)	ycgH	pseudogene; putative ATP‑binding component of a transport system
*	NC_000913	366,526	0	T	G	41.0%	97.9 / 16.9	61	T329P (ACC→CCC)	lacI	lactose‑inducible lac operon transcriptional repressor

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	= 1207805	55 (0.860)	14 (0.250)	13/266	5.8	21.5%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	53 (0.930)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	1207790 =	50 (0.780)	11 (0.190)	11/266	6.5	17.9%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	56 (0.990)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1209618	61 (0.960)	11 (0.190)	4/268	10.4	18.4%	pseudogene (2/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
	?	NC_000913	2471897 =	43 (0.750)					pseudogene (226/579 nt)	yfdL	pseudogene, CPS‑53 (KpLE1) prophage;Phage or Prophage Related