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 287 shown)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,352,587	0	C	A	51.6%	2.9 / 125.8	62	intergenic (‑213/‑60)	glpT/glpA	sn‑glycerol‑3‑phosphate transporter/anaerobic sn‑glycerol‑3‑phosphate dehydrogenase, large FAD/NAD(P)‑binding subunit
*	NC_000913	593,993	0	T	G	51.4%	46.1 / 58.8	35	T260P (ACC→CCC)	cusS	copper‑sensing histidine kinase in two‑component regulatory system with CusR
*	NC_000913	1,163,371	0	C	T	47.8%	51.3 / 25.4	46	L38F (CTC→TTC)	thiK	thiamine kinase
*	NC_000913	4,536,197	0	A	T	46.8%	57.4 / 54.1	62	intergenic (+166/+417)	yjhR/nanS	pseudogene, helicase family; putative frameshift suppressor/9‑O‑acetyl N‑acetylneuraminic acid esterase
*	NC_000913	3,333,757	0	T	G	46.4%	84.4 / 17.3	57	G16G (GGT→GGG)	ispB	octaprenyl diphosphate synthase
*	NC_000913	357,890	0	C	A	45.7%	30.8 / 17.6	35	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
*	NC_000913	2,984,441	0	A	C	45.6%	90.2 / 15.6	57	G384G (GGT→GGG)	yqeF	short chain acyltransferase
*	NC_000913	925,900	0	A	G	45.5%	97.7 / 16.5	66	noncoding (72/88 nt)	serW	tRNA‑Ser
*	NC_000913	1,163,377	0	G	T	44.7%	61.9 / 24.4	47	E40* (GAA→TAA)	thiK	thiamine kinase
*	NC_000913	2,386,862	0	G	A	44.6%	60.5 / 39.6	57	intergenic (+31/‑72)	yfbL/yfbM	putative M28A family peptidase/DUF1877 family protein
*	NC_000913	2,903,692	0	C	A	44.3%	129.5 / 50.7	79	intergenic (+318/+1055)	ygcE/queE	putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis
*	NC_000913	2,151,608	0	G	A	43.8%	42.3 / 29.3	50	E142K (GAA→AAA)	yegJ	uncharacterized protein
*	NC_000913	2,248,431	0	A	C	43.3%	91.2 / 13.8	61	G34G (GGT→GGG)	lysP	lysine transporter
*	NC_000913	3,601,176	0	T	C	43.3%	73.3 / 33.5	60	E304G (GAA→GGA)	ftsX	putative ABC transporter permease
*	NC_000913	1,153,573	0	T	G	43.1%	73.0 / 30.3	51	Y92D (TAC→GAC)	pabC	4‑amino‑4‑deoxychorismate lyase component of para‑aminobenzoate synthase multienzyme complex
*	NC_000913	599,576	0	T	G	42.9%	84.3 / 28.4	56	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
*	NC_000913	4,238,049	0	A	G	42.9%	119.8 / 21.7	77	E139G (GAA→GGA)	yjbH	DUF940 family extracellular polysaccharide protein
*	NC_000913	1,622,816	0	G	A	42.5%	40.9 / 36.4	47	intergenic (+75/+144)	yneM/dgcZ	inner membrane‑associated protein/diguanylate cyclase, zinc‑sensing
*	NC_000913	3,671,415	0	C	T	42.3%	66.0 / 27.1	53	K160K (AAG→AAA)	yhjB	putative DNA‑binding transcriptional response regulator
*	NC_000913	1,487,163	0	C	T	42.1%	81.8 / 19.7	57	intergenic (+200/‑72)	hrpA/ydcF	putative ATP‑dependent helicase/DUF218 superfamily protein, SAM‑binding

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	= 4542690	60 (0.960)	3 (0.050)	3/280	11.8	4.6%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	NC_000913	= 4542986	68 (1.160)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)