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 322 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	56.8%	4.6 / 39.4	37	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	357,880	0	T	C	56.1%	32.8 / 55.5	41	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	1,376,505	0	A	C	48.3%	92.1 / 15.7	61	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
*	NC_000913	3,556,200	0	G	A	48.2%	47.2 / 35.1	56	S217F (TCC→TTC)	rtcA	RNA 3'‑terminal phosphate cyclase
*	NC_000913	3,206,435	0	C	T	48.1%	43.7 / 34.0	52	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	357,875	0	A	T	46.5%	47.2 / 15.2	43	N272K (AAT→AAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	3,350,853	0	A	C	45.3%	81.9 / 13.9	54	S725A (TCA→GCA)	arcB	aerobic respiration control sensor histidine protein kinase, cognate to two‑component response regulators ArcA and RssB
*	NC_000913	3,556,207	0	T	C	44.6%	66.4 / 21.3	56	S215G (AGT→GGT)	rtcA	RNA 3'‑terminal phosphate cyclase
*	NC_000913	718,659	0	T	A	44.0%	67.6 / 22.2	51	D601V (GAT→GTT)	speF	ornithine decarboxylase isozyme, inducible
*	NC_000913	2,248,431	0	A	C	43.9%	83.5 / 12.0	59	G34G (GGT→GGG)	lysP	lysine transporter
*	NC_000913	1,576,080	0	G	A	42.6%	88.7 / 23.3	61	L514F (CTT→TTT)	yddB	putative TonB‑dependent outer membrane receptor
*	NC_000913	2,903,692	0	C	A	42.2%	117.6 / 48.4	71	intergenic (+318/+1055)	ygcE/queE	putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis
*	NC_000913	1,157,271	0	T	G	41.8%	86.2 / 13.3	55	G165G (GGT→GGG)	ycfH	putative DNase
*	NC_000913	4,111,747	0	G	T	41.8%	137.2 / 40.5	79	N156K (AAC→AAA)	yiiQ	DUF1454 family putative periplasmic protein
*	NC_000913	2,481,804	0	G	A	41.4%	88.0 / 24.1	58	P125S (CCA→TCA)	emrY	putative multidrug efflux system
*	NC_000913	3,177,748	0	C	A	41.4%	80.5 / 30.7	58	E55* (GAG→TAG)	nudF	ADP‑ribose pyrophosphatase
*	NC_000913	3,864,089	0	A	C	41.2%	81.4 / 10.9	51	Y64S (TAC→TCC)	yidP	UTRA domain‑containing GntR family putative transcriptional regulator
*	NC_000913	589,934	0	T	G	40.8%	77.3 / 19.8	49	T341P (ACC→CCC)	nfrA	bacteriophage N4 receptor, outer membrane subunit
*	NC_000913	2,421,443	0	A	C	40.3%	131.1 / 19.3	67	Y40S (TAC→TCC)	folX	D‑erythro‑7,8‑dihydroneopterin triphosphate 2'‑epimerase and dihydroneopterin aldolase
*	NC_000913	1,576,077	0	C	A	40.0%	101.4 / 30.9	60	D515Y (GAT→TAT)	yddB	putative TonB‑dependent outer membrane receptor

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	= 4542690	69 (1.050)	4 (0.060)	4/280	11.9	5.8%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	66 (1.070)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	4542682 =	66 (1.000)	3 (0.050)	3/280	12.7	4.4%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	67 (1.080)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)