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 609 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	51.2%	21.2 / 74.2	43	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	1,376,505	0	A	C	48.3%	61.8 / 33.1	59	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
*	NC_000913	3,206,435	0	C	T	46.2%	60.2 / 44.8	65	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	29,496	0	T	A	45.2%	96.3 / 57.9	84	intergenic (+301/‑155)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	4,538,109	0	A	C	44.9%	148.7 / 37.7	100	G219G (GGT→GGG)	nanM	N‑acetylneuraminic acid mutarotase
*	NC_000913	1,413,735	0	A	T	44.4%	67.6 / 39.5	54	Y2* (TAT→TAA)	ydaC	DUF1187 family protein, Rac prophage; putative double‑strand break reduction protein
*	NC_000913	4,287,719	0	T	A	44.1%	75.2 / 47.9	69	intergenic (‑348/‑45)	acs/nrfA	acetyl‑CoA synthetase/nitrite reductase, formate‑dependent, cytochrome
*	NC_000913	75,079	0	C	T	43.9%	73.0 / 45.6	66	L134L (CTG→CTA)	thiB	thiamine/thiamine pyrophosphate/thiamine monophosphate ABC transporter periplasmic binding protein
*	NC_000913	1,245,234	0	G	T	43.9%	74.0 / 35.0	57	L25F (TTG→TTT)	ycgY	uncharacterized protein
*	NC_000913	29,486	0	C	A	43.7%	160.1 / 48.9	87	intergenic (+291/‑165)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	3,105,499	0	A	C	43.5%	142.1 / 19.4	85	Y356S (TAC→TCC)	mltC	membrane‑bound lytic murein transglycosylase C
*	NC_000913	3,206,452	0	C	A	42.6%	84.3 / 36.7	62	intergenic (‑196/‑11)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	2,337,723	0	A	C	42.6%	80.5 / 17.3	56	G566G (GGT→GGG)	gyrA	DNA gyrase (type II topoisomerase), subunit A
*	NC_000913	2,040,075	0	C	G	42.4%	67.1 / 23.6	60	L200V (CTG→GTG)	yedY	membrane‑anchored, periplasmic TMAO, DMSO reductase
*	NC_000913	3,585,086	0	A	C	42.2%	139.9 / 16.3	83	Y580D (TAC→GAC)	ggt	gamma‑glutamyltranspeptidase
*	NC_000913	5,159	0	G	A	42.1%	89.3 / 46.0	76	intergenic (+139/‑75)	thrC/yaaX	L‑threonine synthase/DUF2502 family putative periplasmic protein
*	NC_000913	4,538,117	0	T	C	42.0%	126.1 / 49.2	104	N217D (AAT→GAT)	nanM	N‑acetylneuraminic acid mutarotase
*	NC_000913	599,576	0	T	G	41.9%	153.6 / 32.4	86	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	1,478,324	0	T	G	41.7%	90.5 / 25.4	61	G33G (GGT→GGG)	ynbB	putative CDP‑diglyceride synthase
*	NC_000913	357,875	0	A	T	41.3%	54.6 / 23.9	47	N272K (AAT→AAA)	cynR	transcriptional activator of cyn operon; autorepressor

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	4542682 =	85 (1.100)	6 (0.080)	6/280	11.6	6.4%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	95 (1.310)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)