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 708 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,880	0	T	C	65.2%	2.4 / 43.9	46	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	357,890	0	C	A	62.7%	‑4.6 / 45.6	51	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	2,434,861	0	G	T	48.8%	75.1 / 56.9	80	P259Q (CCA→CAA)	truA	tRNA pseudouridine(38‑40) synthase
*	NC_000913	357,875	0	A	T	48.0%	43.3 / 24.2	50	N272K (AAT→AAA)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	786,855	0	A	C	46.2%	120.6 / 18.1	78	G247G (GGT→GGG)	gpmA	phosphoglyceromutase 1
*	NC_000913	1,621,118	0	A	C	45.8%	114.3 / 18.6	83	V7G (GTG→GGG)	eamA	cysteine and O‑acetyl‑L‑serine efflux system
*	NC_000913	827,507	0	T	G	45.1%	116.1 / 11.9	71	D492A (GAC→GCC)	ybhF	putative ABC transporter ATPase
*	NC_000913	2,001,911	0	G	A	45.1%	68.4 / 37.9	71	intergenic (‑122/+199)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein (flagellin)
*	NC_000913	357,873	0	C	T	44.9%	37.3 / 26.0	50	S273N (AGC→AAC)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	1,376,505	0	A	C	44.4%	98.3 / 20.4	63	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
*	NC_000913	3,026,941	0	A	C	44.3%	104.4 / 10.6	61	E392D (GAA→GAC)	guaD	guanine deaminase
*	NC_000913	501,564	0	A	C	44.1%	113.4 / 18.6	68	*559E (TAA→GAA)	ybaL	inner membrane putative NAD(P)‑binding transporter
*	NC_000913	599,576	0	T	G	44.1%	97.7 / 20.7	59	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	357,887	0	C	A	44.0%	15.1 / 22.9	50	L268F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	2,001,918	0	A	C	43.5%	114.8 / 13.4	69	intergenic (‑129/+192)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein (flagellin)
*	NC_000913	4,378,802	0	A	C	43.5%	120.1 / 17.6	69	V48G (GTA→GGA)	ampC	penicillin‑binding protein; beta‑lactamase, intrinsically weak
*	NC_000913	2,483,268	0	T	A	43.4%	95.3 / 46.0	84	L24F (TTA→TTT)	emrK	multidrug resistance efflux pump membrane fusion protein
*	NC_000913	3,206,435	0	C	T	43.3%	78.4 / 40.5	67	intergenic (‑179/‑28)	ttdR/ttdA	transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit
*	NC_000913	1,506,028	0	A	C	43.2%	139.6 / 11.0	74	V18G (GTA→GGA)	ydcO	BenE family inner membrane putative transporter
*	NC_000913	4,457,105	0	A	G	43.2%	108.3 / 28.8	81	I441V (ATC→GTC)	mpl	UDP‑N‑acetylmuramate:L‑alanyl‑gamma‑D‑glutamyl‑ meso‑diaminopimelate ligase

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	= 781446	0 (0.000)	34 (0.500)	23/258	4.2	47.9%	intergenic (+2/‑131)	lysZ/lysQ	tRNA‑Lys/tRNA‑Lys
	?	NC_000913	2521487 =	74 (1.080)					intergenic (+159/+106)	lysV/xapR	tRNA‑Lys/transcriptional activator of xapAB
*	?	NC_000913	925901 =	70 (0.890)	11 (0.140) +C	10/296	10.0	16.9%	noncoding (71/88 nt)	serW	tRNA‑Ser
	?	NC_000913	= 1097399	39 (0.490)					intergenic (+570/+166)	ycdU/serX	putative inner membrane protein/tRNA‑Ser
*	?	NC_000913	= 4542690	90 (1.140)	3 (0.040)	3/280	14.0	3.3%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	90 (1.210)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)