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 487 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	56.7%	12.4 / 38.6	30	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	4,258,974	0	T	G	48.3%	87.0 / 15.3	58	G411G (GGT→GGG)	dinF	oxidative stress resistance protein; putative MATE family efflux pump; UV and mitomycin C inducible protein
*	NC_000913	357,880	0	T	C	46.7%	26.2 / 11.4	30	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	4,536,197	0	A	T	46.0%	58.2 / 63.6	63	intergenic (+166/+417)	yjhR/nanS	pseudogene, helicase family; putative frameshift suppressor/9‑O‑acetyl N‑acetylneuraminic acid esterase
*	NC_000913	357,873	0	C	T	45.7%	27.8 / 19.3	35	S273N (AGC→AAC)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	357,875	0	A	T	42.9%	43.4 / 11.8	35	N272K (AAT→AAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	753,125	0	T	A	42.0%	165.7 / 60.7	113	intergenic (‑330/+60)	ybgD/gltA	putative fimbrial‑like adhesin protein/citrate synthase
*	NC_000913	941,713	0	T	G	41.9%	101.8 / 18.3	62	V252G (GTG→GGG)	dmsA	dimethyl sulfoxide reductase, anaerobic, subunit A
*	NC_000913	1,435,727	0	G	A	41.9%	100.4 / 45.7	74	intergenic (‑108/+33)	uspF/ompN	stress‑induced protein, ATP‑binding protein/outer membrane pore protein N, non‑specific
*	NC_000913	925,900	0	A	G	41.8%	119.9 / 19.8	79	noncoding (72/88 nt)	serW	tRNA‑Ser
*	NC_000913	3,206,435	0	C	T	41.7%	83.3 / 41.0	73	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	2,571,036	0	T	G	41.4%	112.2 / 21.3	70	N239T (AAC→ACC)	eutE	aldehyde oxidoreductase, ethanolamine utilization protein
*	NC_000913	2,326,450	0	T	G	40.9%	122.2 / 13.2	66	G114G (GGT→GGG)	atoB	acetyl‑CoA acetyltransferase
*	NC_000913	2,984,441	0	A	C	40.5%	128.1 / 18.2	75	G384G (GGT→GGG)	yqeF	short chain acyltransferase
*	NC_000913	3,862,661	0	T	G	40.0%	49.2 / 16.8	56	pseudogene (943/1617 nt)	glvC	pseudogene, arbutin specific enzyme IIC component of PTS;enzyme; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system, arbutin‑like IIB component; PTS system, arbutin‑like IIC component
*	NC_000913	213,341	0	A	G	39.7%	117.6 / 33.1	79	G337G (GGA→GGG)	tilS	tRNA(Ile)‑lysidine synthetase
*	NC_000913	3,745,494	0	C	T	39.7%	72.4 / 26.6	63	R231C (CGC→TGC)	yiaN	2,3‑diketo‑L‑gulonate TRAP transporter large permease protein
*	NC_000913	4,378,802	0	A	C	39.7%	111.5 / 14.7	59	V48G (GTA→GGA)	ampC	penicillin‑binding protein; beta‑lactamase, intrinsically weak
*	NC_000913	4,457,105	0	A	G	39.0%	92.2 / 14.1	60	I441V (ATC→GTC)	mpl	UDP‑N‑acetylmuramate:L‑alanyl‑gamma‑D‑glutamyl‑ meso‑diaminopimelate ligase
*	NC_000913	1,413,735	0	A	T	38.6%	96.2 / 25.8	58	Y2* (TAT→TAA)	ydaC	DUF1187 family protein, Rac prophage; putative double‑strand break reduction protein

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	65 (0.800)	13 (0.180)	13/266	8.6	17.6%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	64 (0.890)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	1207790 =	62 (0.770)	13 (0.180)	13/266	8.6	17.8%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	65 (0.900)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related