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 308 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	941,713	0	T	G	57.4%	38.4 / 76.6	54	V252G (GTG→GGG)	dmsA	dimethyl sulfoxide reductase, anaerobic, subunit A
*	NC_000913	3,131,440	0	T	C	50.9%	66.4 / 90.6	55	G323G (GGA→GGG)	yghQ	putative inner membrane polysaccharide flippase
*	NC_000913	2,642,689	0	T	G	48.1%	74.0 / 11.6	52	A52A (GCA→GCC)	rodZ	MreB assembly cytoskeletal protein
*	NC_000913	357,890	0	C	A	46.9%	43.9 / 25.8	49	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	2,984,441	0	A	C	46.9%	66.4 / 18.2	49	G384G (GGT→GGG)	yqeF	short chain acyltransferase
*	NC_000913	993,917	0	A	C	46.6%	90.0 / 14.9	60	V43G (GTG→GGG)	ssuB	aliphatic sulfonate ABC transporter ATPase
*	NC_000913	2,578,143	0	A	C	46.6%	90.5 / 17.9	58	L79V (TTA→GTA)	maeB	malic enzyme: putative oxidoreductase/phosphotransacetylase
*	NC_000913	2,151,592	0	G	T	45.0%	80.7 / 32.4	60	L136F (TTG→TTT)	yegJ	uncharacterized protein
*	NC_000913	1,622,816	0	G	A	44.6%	50.2 / 42.6	56	intergenic (+75/+144)	yneM/dgcZ	inner membrane‑associated protein/diguanylate cyclase, zinc‑sensing
*	NC_000913	1,622,802	0	A	T	43.6%	75.8 / 28.4	55	intergenic (+61/+158)	yneM/dgcZ	inner membrane‑associated protein/diguanylate cyclase, zinc‑sensing
*	NC_000913	2,781,645	0	A	C	43.4%	136.8 / 16.5	76	V361G (GTT→GGT)	ypjA	adhesin‑like autotransporter
*	NC_000913	2,865,246	0	A	G	42.2%	62.8 / 10.3	45	E49G (GAA→GGA)	ygbN	putative transporter
*	NC_000913	2,865,253	0	T	G	42.2%	74.1 / 12.7	45	G51G (GGT→GGG)	ygbN	putative transporter
*	NC_000913	3,412,898	0	C	T	42.1%	56.6 / 43.4	58	A190T (GCC→ACC)	acrS	acrAB operon transcriptional repressor
*	NC_000913	2,481,804	0	G	A	41.9%	80.1 / 27.2	62	P125S (CCA→TCA)	emrY	putative multidrug efflux system
*	NC_000913	3,206,435	0	C	T	41.5%	78.2 / 34.3	65	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	1,163,371	0	C	T	41.4%	80.7 / 30.0	59	L38F (CTC→TTC)	thiK	thiamine kinase
*	NC_000913	2,624,517	0	G	T	41.4%	71.4 / 26.7	59	E492* (GAA→TAA)	ppk	polyphosphate kinase, component of RNA degradosome
*	NC_000913	266,358	0	T	G	41.3%	111.7 / 14.1	64	T66P (ACC→CCC)	yafY	lipoprotein, inner membrane; degP regulator; CP4‑6 prophage
*	NC_000913	1,969,794	0	A	C	41.0%	104.0 / 17.0	61	G397G (GGT→GGG)	tap	methyl‑accepting protein IV

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	53 (0.830)	14 (0.250)	13/266	6.1	23.3%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	45 (0.790)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	1207790 =	52 (0.810)	8 (0.140)	8/266	8.4	14.5%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	48 (0.840)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 4542690	73 (1.140)	4 (0.070)	4/280	11.4	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	62 (1.030)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	= 1209618	57 (0.890)	13 (0.230)	3/268	11.8	19.7%	pseudogene (2/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
	?	NC_000913	2471897 =	55 (0.960)					pseudogene (226/579 nt)	yfdL	pseudogene, CPS‑53 (KpLE1) prophage;Phage or Prophage Related