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 313 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,029,959	0	A	C	51.2%	59.8 / 79.9	44	C325G (TGT→GGT)	ygfT	putative oxidoreductase, Fe‑S subunit/nucleotide‑binding subunit
*	NC_000913	993,917	0	A	C	50.0%	82.7 / 24.6	68	V43G (GTG→GGG)	ssuB	aliphatic sulfonate ABC transporter ATPase
*	NC_000913	1,510,395	0	C	A	48.4%	54.5 / 41.9	62	S131R (AGC→AGA)	ydcR	putative DNA‑binding transcriptional regulator and putative aminotransferase
*	NC_000913	987,494	0	T	G	46.8%	101.8 / 14.7	62	intergenic (‑512/+91)	ompF/asnS	outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase
*	NC_000913	1,097,581	0	A	G	46.3%	53.6 / 14.4	42	noncoding (72/88 nt)	serX	tRNA‑Ser
*	NC_000913	2,984,441	0	A	C	45.9%	83.9 / 32.2	61	G384G (GGT→GGG)	yqeF	short chain acyltransferase
*	NC_000913	993,913	0	G	C	45.8%	103.6 / 26.1	72	G44G (GGC→GGG)	ssuB	aliphatic sulfonate ABC transporter ATPase
*	NC_000913	1,487,163	0	C	T	44.9%	53.6 / 24.6	49	intergenic (+200/‑72)	hrpA/ydcF	putative ATP‑dependent helicase/DUF218 superfamily protein, SAM‑binding
*	NC_000913	2,927,501	0	T	G	44.6%	92.3 / 14.1	56	G398G (GGT→GGG)	ygdH	UPF0717 family protein
*	NC_000913	1,622,816	0	G	A	44.4%	41.4 / 50.6	54	intergenic (+75/+144)	yneM/dgcZ	inner membrane‑associated protein/diguanylate cyclase, zinc‑sensing
*	NC_000913	1,825,056	0	G	A	43.9%	78.4 / 34.8	66	intergenic (‑119/+84)	ves/spy	cold‑ and stress‑inducible protein/periplasmic ATP‑independent protein refolding chaperone, stress‑induced
*	NC_000913	4,486,580	0	A	G	43.9%	83.2 / 15.9	57	G121G (GGA→GGG)	lptF	lipopolysaccharide export ABC permease
*	NC_000913	4,536,197	0	A	T	43.1%	68.9 / 33.6	51	intergenic (+166/+417)	yjhR/nanS	pseudogene, helicase family; putative frameshift suppressor/9‑O‑acetyl N‑acetylneuraminic acid esterase
*	NC_000913	4,538,109	0	A	C	42.7%	128.4 / 22.5	76	G219G (GGT→GGG)	nanM	N‑acetylneuraminic acid mutarotase
*	NC_000913	5,159	0	G	A	42.4%	82.2 / 30.7	66	intergenic (+139/‑75)	thrC/yaaX	L‑threonine synthase/DUF2502 family putative periplasmic protein
*	NC_000913	1,079,468	0	A	G	41.7%	98.2 / 13.9	60	D55G (GAT→GGT)	putP	proline:sodium symporter
*	NC_000913	941,713	0	T	G	41.5%	108.5 / 22.0	65	V252G (GTG→GGG)	dmsA	dimethyl sulfoxide reductase, anaerobic, subunit A
*	NC_000913	599,576	0	T	G	41.5%	86.4 / 11.2	53	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	4,573,496	0	A	G	41.4%	81.8 / 27.0	58	pseudogene (1083/1503 nt)	yjiT	pseudogene
*	NC_000913	3,412,898	0	C	T	41.3%	68.0 / 44.9	63	A190T (GCC→ACC)	acrS	acrAB operon transcriptional repressor

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	4542682 =	59 (0.910)	5 (0.080)	5/280	10.9	8.0%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	4542996 =	59 (0.960)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
*	?	NC_000913	2006780 =	65 (1.000)	3 (0.050)	3/290	12.8	4.4%	coding (625/1488 nt)	amyA	cytoplasmic alpha‑amylase
	?	NC_000913	2006804 =	66 (1.040)					coding (649/1488 nt)	amyA	cytoplasmic alpha‑amylase