breseq  version 0.35.4  revision f352f80f4bc9 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence (highest frequency 20 of 120 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	2,354,816	0	A	C	57.9%	10.0 / 17.7	19	G26G (GGT→GGG)	rhmD	L‑rhamnonate dehydratase
*	NZ_CP009273	1,995,399	0	A	C	51.8%	64.8 / 90.6	56	intergenic (‑129/+192)	fliA/fliC	RNA polymerase sigma factor FliA/H48 family flagellin FliC
*	NZ_CP009273	595,032	0	T	G	51.7%	19.7 / 43.7	29	V288G (GTG→GGG)	cusA	Cu(+)/Ag(+) efflux RND transporter permease subunit CusA
*	NZ_CP009273	1,995,392	0	G	A	47.3%	38.0 / 37.4	55	intergenic (‑122/+199)	fliA/fliC	RNA polymerase sigma factor FliA/H48 family flagellin FliC
*	NZ_CP009273	2,428,361	0	T	G	44.7%	65.7 / 17.0	47	Y252S (TAC→TCC)	truA	tRNA pseudouridine(38‑40) synthase TruA
*	NZ_CP009273	1,257,298	0	T	G	44.0%	82.7 / 10.4	50	T12P (ACC→CCC)	prs	ribose‑phosphate diphosphokinase
*	NZ_CP009273	2,897,051	0	C	A	43.8%	91.4 / 53.6	64	intergenic (+318/+1055)	ygcE/queE	FGGY‑family carbohydrate kinase/7‑carboxy‑7‑deazaguanine synthase QueE
*	NZ_CP009273	748,581	0	T	A	43.1%	69.1 / 23.6	51	intergenic (‑330/+60)	ybgD/gltA	fimbrial protein/citrate synthase
*	NZ_CP009273	4,277,647	0	T	A	41.9%	49.8 / 26.0	43	intergenic (‑348/‑45)	acs/nrfA	acetate‑‑CoA ligase/ammonia‑forming nitrite reductase cytochrome c552 subunit
*	NZ_CP009273	1,377,979	0	G	A	41.7%	82.2 / 29.3	60	F80F (TTC→TTT)	ycjW	LacI family DNA‑binding transcriptional regulator
*	NZ_CP009273	3,725,084	0	G	A	41.5%	84.7 / 14.9	53	L198L (TTG→TTA)	xylF	D‑xylose ABC transporter substrate‑binding protein
*	NZ_CP009273	3,823,685	0	G	A	40.9%	50.2 / 18.6	44	E461K (GAA→AAA)	xanP	xanthine/proton symporter XanP
*	NZ_CP009273	792,856	0	G	T	40.6%	57.5 / 10.1	32	V283F (GTT→TTT)	modC	molybdenum ABC transporter ATP‑binding protein ModC
*	NZ_CP009273	2,319,929	0	T	G	40.5%	50.8 / 17.8	37	G114G (GGT→GGG)	atoB	acetyl‑CoA acetyltransferase
*	NZ_CP009273	4,049,475	0	A	C	40.3%	93.9 / 14.1	62	G75G (GGT→GGG)	glnL	nitrogen regulation protein NR(II)
*	NZ_CP009273	29,486	0	C	A	40.0%	90.1 / 17.4	50	intergenic (+291/‑165)	dapB/carA	4‑hydroxy‑tetrahydrodipicolinate reductase/glutamine‑hydrolyzing carbamoyl‑phosphate synthase small subunit
*	NZ_CP009273	117,994	0	A	T	40.0%	81.2 / 24.8	55	L15L (CTT→CTA)	aroP	aromatic amino acid transporter AroP
*	NZ_CP009273	858,015	0	G	T	39.2%	89.5 / 17.3	51	H16Q (CAC→CAA)	ybiW	glycyl radical protein
*	NZ_CP009273	646,723	0	A	T	38.9%	48.0 / 11.6	36	L197* (TTA→TAA)	citC	[citrate (pro‑3S)‑lyase] ligase
*	NZ_CP009273	29,496	0	T	A	38.8%	79.6 / 19.9	49	intergenic (+301/‑155)	dapB/carA	4‑hydroxy‑tetrahydrodipicolinate reductase/glutamine‑hydrolyzing carbamoyl‑phosphate synthase small subunit

Marginal new junction evidence (sorted from low to high skew)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	3416618 =	24 (0.430)	4 (0.190) +152 bp	4/190	3.7	32.2%	intergenic (+65/+166)	yhdZ/rrf	amino acid ABC transporter ATP‑binding protein/5S ribosomal RNA
	?	NZ_CP009273	= 3416648	20 (0.360)					intergenic (+95/+136)	yhdZ/rrf	amino acid ABC transporter ATP‑binding protein/5S ribosomal RNA