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 340 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,969,794	0	A	C	57.9%	24.1 / 48.2	38	G397G (GGT→GGG)	tap	methyl‑accepting protein IV
*	NC_000913	4,040,762	0	C	G	47.5%	46.5 / 20.3	40	intergenic (+126/+144)	rrfA/mobB	5S ribosomal RNA of rrnA operon/molybdopterin‑guanine dinucleotide biosynthesis protein B
*	NC_000913	17,000	0	C	T	46.9%	44.6 / 26.8	49	intergenic (‑40/‑489)	mokC/nhaA	regulatory protein for HokC, overlaps CDS of hokC/sodium‑proton antiporter
*	NC_000913	4,279,468	0	C	G	45.5%	70.5 / 11.2	44	G330G (GGC→GGG)	ghxP	guanine/hypoxanthine permease, high affinity; guanine/hypoxanthine:H+ symporter
*	NC_000913	3,206,435	0	C	T	44.9%	60.7 / 50.9	69	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	941,713	0	T	G	44.7%	66.6 / 17.2	47	V252G (GTG→GGG)	dmsA	dimethyl sulfoxide reductase, anaerobic, subunit A
*	NC_000913	1,397,830	0	T	C	44.3%	76.1 / 19.6	61	I265V (ATT→GTT)	uspE	stress‑induced protein
*	NC_000913	4,171,882	0	C	G	44.2%	58.4 / 22.9	43	intergenic (+126/‑175)	rrfB/murB	5S ribosomal RNA of rrnB operon/UDP‑N‑acetylenolpyruvoylglucosamine reductase, FAD‑binding
*	NC_000913	4,168,221	0	T	C	44.0%	113.4 / 169.7	109	intergenic (+21/‑151)	rrsB/gltT	16S ribosomal RNA of rrnB operon/tRNA‑Glu
*	NC_000913	354,288	0	T	G	43.6%	81.3 / 18.5	56	V528G (GTG→GGG)	prpE	propionate‑‑CoA ligase
*	NC_000913	3,206,444	0	T	A	43.5%	65.4 / 39.1	69	intergenic (‑188/‑19)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	29,496	0	T	A	43.3%	75.2 / 33.4	60	intergenic (+301/‑155)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
*	NC_000913	1,376,505	0	A	C	42.9%	104.6 / 12.2	63	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
*	NC_000913	3,556,200	0	G	A	42.6%	68.9 / 36.0	62	S217F (TCC→TTC)	rtcA	RNA 3'‑terminal phosphate cyclase
*	NC_000913	3,443,277	0	A	C	42.6%	91.3 / 10.1	54	V274G (GTA→GGA)	secY	preprotein translocase membrane subunit
*	NC_000913	4,040,765	0	A	G	42.5%	49.7 / 14.1	40	intergenic (+129/+141)	rrfA/mobB	5S ribosomal RNA of rrnA operon/molybdopterin‑guanine dinucleotide biosynthesis protein B
*	NC_000913	4,604,344	0	C	T	42.3%	48.9 / 26.1	52	S62F (TCT→TTT)	bglJ	bgl operon transcriptional activator
*	NC_000913	298,960	0	A	C	42.2%	67.3 / 17.2	45	Y659D (TAT→GAT)	paoC	PaoABC aldehyde oxidoreductase, Moco‑containing subunit
*	NC_000913	213,341	0	A	G	42.1%	96.3 / 13.3	57	G337G (GGA→GGG)	tilS	tRNA(Ile)‑lysidine synthetase
*	NC_000913	2,865,870	0	C	T	42.1%	37.8 / 17.8	38	S257F (TCC→TTC)	ygbN	putative transporter

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 =	49 (0.790)	15 (0.270)	14/266	5.1	25.7%	coding (290/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	1209619 =	43 (0.780)					pseudogene (1/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1207805	51 (0.820)	11 (0.200)	11/266	6.2	20.5%	coding (305/630 nt)	stfP	e14 prophage; uncharacterized protein
	?	NC_000913	= 1209602	40 (0.720)					pseudogene (18/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
*	?	NC_000913	= 1209618	50 (0.810)	11 (0.200)	3/268	10.7	20.0%	pseudogene (2/501 nt)	stfE	pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
	?	NC_000913	2471897 =	43 (0.770)					pseudogene (226/579 nt)	yfdL	pseudogene, CPS‑53 (KpLE1) prophage;Phage or Prophage Related