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 318 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	993,917	0	A	C	58.8%	38.6 / 68.7	51	V43G (GTG→GGG)	ssuB	aliphatic sulfonate ABC transporter ATPase
*	NC_000913	298,960	0	A	C	54.4%	46.7 / 71.6	47	Y659D (TAT→GAT)	paoC	PaoABC aldehyde oxidoreductase, Moco‑containing subunit
*	NC_000913	2,421,437	0	T	C	52.4%	50.3 / 84.9	63	I38T (ATC→ACC)	folX	D‑erythro‑7,8‑dihydroneopterin triphosphate 2'‑epimerase and dihydroneopterin aldolase
*	NC_000913	993,904	0	A	C	52.1%	65.1 / 81.0	48	G47G (GGT→GGG)	ssuB	aliphatic sulfonate ABC transporter ATPase
*	NC_000913	993,913	0	G	C	51.9%	59.0 / 86.0	52	G44G (GGC→GGG)	ssuB	aliphatic sulfonate ABC transporter ATPase
*	NC_000913	3,705,661	0	T	C	51.7%	62.4 / 86.9	58	I44V (ATC→GTC)	dppB	dipeptide/heme ABC transporter permease
*	NC_000913	357,880	0	T	C	50.0%	32.0 / 10.3	36	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	2,421,443	0	A	C	50.0%	74.8 / 21.1	66	Y40S (TAC→TCC)	folX	D‑erythro‑7,8‑dihydroneopterin triphosphate 2'‑epimerase and dihydroneopterin aldolase
*	NC_000913	3,206,435	0	C	T	50.0%	49.5 / 33.5	56	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	2,421,426	0	C	A	49.2%	59.0 / 32.2	62	I34I (ATC→ATA)	folX	D‑erythro‑7,8‑dihydroneopterin triphosphate 2'‑epimerase and dihydroneopterin aldolase
*	NC_000913	231,694	0	C	T	49.1%	46.8 / 25.6	56	F191F (TTC→TTT)	yafD	endo/exonuclease/phosphatase family protein
*	NC_000913	233,114	0	G	A	49.1%	39.7 / 31.7	53	S281F (TCC→TTC)	mltD	putative membrane‑bound lytic murein transglycosylase D
*	NC_000913	29,496	0	T	A	49.0%	38.8 / 29.3	49	intergenic (+301/‑155)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	941,713	0	T	G	47.8%	60.1 / 13.8	46	V252G (GTG→GGG)	dmsA	dimethyl sulfoxide reductase, anaerobic, subunit A
*	NC_000913	233,118	0	T	C	47.2%	47.5 / 21.6	53	I280V (ATT→GTT)	mltD	putative membrane‑bound lytic murein transglycosylase D
*	NC_000913	2,578,143	0	A	C	46.8%	61.6 / 21.4	48	L79V (TTA→GTA)	maeB	malic enzyme: putative oxidoreductase/phosphotransacetylase
*	NC_000913	3,812,792	0	C	A	46.7%	56.3 / 17.8	46	T21N (ACC→AAC)	dfp	fused 4'‑phosphopantothenoylcysteine decarboxylase/phosphopantothenoylcysteine synthetase, FMN‑binding
*	NC_000913	599,576	0	T	G	46.3%	86.9 / 13.7	56	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	2,337,723	0	A	C	46.3%	64.2 / 16.3	56	G566G (GGT→GGG)	gyrA	DNA gyrase (type II topoisomerase), subunit A
*	NC_000913	3,601,176	0	T	C	46.3%	46.1 / 37.4	54	E304G (GAA→GGA)	ftsX	putative ABC transporter permease

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	56 (0.890)	19 (0.340)	19/266	4.0	27.9%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	48 (0.860)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	1207790 =	50 (0.800)	8 (0.140)	8/266	8.2	14.3%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	51 (0.910)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 4542690	74 (1.180)	8 (0.140)	8/280	8.6	10.4%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	68 (1.150)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)