breseq  version 0.27.1  revision 87c22d663cc3 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence (highest frequency 20 of 938 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	55.6%	23.9 / 90.6	63	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	29,496	0	T	A	51.6%	90.6 / 159.4	93	intergenic (+301/‑155)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	941,713	0	T	G	50.5%	141.1 / 198.5	105	V252G (GTG→GGG)	dmsA	dimethyl sulfoxide reductase, anaerobic, subunit A
*	NC_000913	3,206,435	0	C	T	50.0%	82.7 / 69.2	92	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	3,556,207	0	T	C	48.0%	130.0 / 32.1	100	S215G (AGT→GGT)	rtcA	RNA 3'‑terminal phosphate cyclase
*	NC_000913	1,163,371	0	C	T	46.9%	73.3 / 35.3	64	L38F (CTC→TTC)	thiK	thiamine kinase
*	NC_000913	987,494	0	T	G	46.5%	181.4 / 16.9	99	intergenic (‑512/+91)	ompF/asnS	outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase
*	NC_000913	3,508,657	0	A	G	46.4%	149.8 / 22.4	97	F386S (TTC→TCC)	yhfW	phosphopentomutase‑related metalloenzyme superfamily protein
*	NC_000913	1,097,581	0	A	G	46.2%	144.2 / 27.7	91	noncoding (72/88 nt)	serX	tRNA‑Ser
*	NC_000913	3,556,200	0	G	A	46.1%	117.2 / 48.8	102	S217F (TCC→TTC)	rtcA	RNA 3'‑terminal phosphate cyclase
*	NC_000913	1,649,308	0	G	C	45.5%	128.9 / 32.2	78	intergenic (+267/‑301)	ydfC/dicB	uncharacterized protein, Qin prophage/Qin prophage; cell division inhibition protein
*	NC_000913	3,585,086	0	A	C	45.5%	159.7 / 13.8	88	Y580D (TAC→GAC)	ggt	gamma‑glutamyltranspeptidase
*	NC_000913	925,900	0	A	G	45.4%	156.2 / 30.7	98	noncoding (72/88 nt)	serW	tRNA‑Ser
*	NC_000913	1,222,596	0	G	A	45.1%	113.8 / 59.8	102	F13F (TTC→TTT)	ymgD	uncharacterized protein
*	NC_000913	3,812,792	0	C	A	44.7%	114.6 / 40.0	76	T21N (ACC→AAC)	dfp	fused 4'‑phosphopantothenoylcysteine decarboxylase/phosphopantothenoylcysteine synthetase, FMN‑binding
*	NC_000913	357,880	0	T	C	44.6%	79.9 / 21.9	65	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	4,112,578	0	T	G	44.0%	207.3 / 15.6	110	G88G (GGT→GGG)	yiiR	DUF805 family putative inner membrane protein
*	NC_000913	4,571,364	0	C	G	44.0%	152.4 / 14.3	75	A71P (GCC→CCC)	yjiR	putative DNA‑binding transcriptional regulator/putative aminotransferase
*	NC_000913	1,621,118	0	A	C	43.9%	201.1 / 22.1	123	V7G (GTG→GGG)	eamA	cysteine and O‑acetyl‑L‑serine efflux system
*	NC_000913	4,571,368	0	A	T	43.8%	111.9 / 30.2	74	R69R (CGT→CGA)	yjiR	putative DNA‑binding transcriptional regulator/putative aminotransferase

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	925901 =	96 (0.930)	27 (0.260) +C	21/298	9.5	24.0%	noncoding (71/88 nt)	serW	tRNA‑Ser
	?	NC_000913	= 1097399	76 (0.730)					intergenic (+570/+166)	ycdU/serX	putative inner membrane protein/tRNA‑Ser
*	?	NC_000913	1207790 =	94 (0.910)	16 (0.170)	16/268	10.3	17.3%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	69 (0.750)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1207805	96 (0.930)	12 (0.130)	12/268	12.2	13.5%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	68 (0.740)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 4542690	132 (1.270)	4 (0.040)	4/282	18.2	3.2%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	120 (1.230)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)