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 282 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,043,030	0	A	G	62.5%	5.5 / 22.8	24	N206D (AAT→GAT)	srkA	Cpx stress response Thr/Ser protein kinase; MazF antagonist protein
*	NC_000913	2,984,441	0	A	C	51.2%	48.7 / 73.6	41	G384G (GGT→GGG)	yqeF	short chain acyltransferase
*	NC_000913	3,206,435	0	C	T	50.0%	36.9 / 47.8	58	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	599,576	0	T	G	47.8%	47.0 / 27.6	46	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	907,602	0	A	C	46.9%	62.2 / 13.0	49	G227G (GGT→GGG)	ybjT	putative NAD‑dependent oxidoreductase
*	NC_000913	1,376,505	0	A	C	46.4%	75.4 / 16.5	56	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
*	NC_000913	1,576,077	0	C	A	45.8%	22.3 / 14.9	24	D515Y (GAT→TAT)	yddB	putative TonB‑dependent outer membrane receptor
*	NC_000913	1,222,233	0	G	A	45.7%	30.9 / 16.4	35	pseudogene (60/75 nt)	ycgH	pseudogene; putative ATP‑binding component of a transport system
*	NC_000913	4,287,719	0	T	A	45.5%	36.0 / 33.1	44	intergenic (‑348/‑45)	acs/nrfA	acetyl‑CoA synthetase/nitrite reductase, formate‑dependent, cytochrome
*	NC_000913	941,713	0	T	G	45.2%	60.3 / 15.6	43	V252G (GTG→GGG)	dmsA	dimethyl sulfoxide reductase, anaerobic, subunit A
*	NC_000913	357,890	0	C	A	44.4%	26.3 / 10.4	27	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	753,125	0	T	A	44.0%	65.4 / 23.6	50	intergenic (‑330/+60)	ybgD/gltA	putative fimbrial‑like adhesin protein/citrate synthase
*	NC_000913	4,457,105	0	A	G	43.2%	58.1 / 13.0	44	I441V (ATC→GTC)	mpl	UDP‑N‑acetylmuramate:L‑alanyl‑gamma‑D‑glutamyl‑ meso‑diaminopimelate ligase
*	NC_000913	3,730	0	C	A	42.9%	63.3 / 20.9	42	N310K (AAC→AAA)	thrB	homoserine kinase
*	NC_000913	1,560,766	0	T	G	42.9%	21.7 / 10.7	28	Q55P (CAG→CCG)	ddpB	D,D‑dipeptide ABC transporter permease
*	NC_000913	3,285,853	0	G	T	42.5%	67.9 / 20.7	47	A126S (GCC→TCC)	agaD	N‑acetylgalactosamine‑specific enzyme IID component of PTS
*	NC_000913	646,747	0	T	G	42.5%	57.1 / 13.2	40	T255P (ACC→CCC)	citG	2‑(5''‑triphosphoribosyl)‑3'‑dephosphocoenzyme‑A synthase
*	NC_000913	3,840,646	0	T	C	41.9%	59.8 / 10.9	43	D365G (GAT→GGT)	nepI	putative transporter
*	NC_000913	2,434,882	0	T	G	41.2%	125.1 / 29.1	80	Y252S (TAC→TCC)	truA	tRNA pseudouridine(38‑40) synthase
*	NC_000913	2,001,911	0	G	A	41.0%	48.4 / 17.9	39	intergenic (‑122/+199)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein (flagellin)

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	1207790 =	42 (0.740)	5 (0.100)	5/266	7.8	10.5%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	48 (0.950)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	4542682 =	87 (1.530)	3 (0.060)	3/280	9.5	3.9%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	66 (1.230)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)