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 449 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	4,036,390	0	A	G	57.6%	35.2 / 70.4	59	N206D (AAT→GAT)	srkA	stress response kinase SrkA
*	NZ_CP009273	4,036,353	0	C	T	46.8%	36.7 / 24.3	62	F193F (TTC→TTT)	srkA	stress response kinase SrkA
*	NZ_CP009273	2,145,154	0	T	G	46.0%	58.7 / 20.9	54	intergenic (+27/+38)	yegJ/pphC	DUF2314 domain‑containing protein/protein‑serine/threonine phosphatase PphC
*	NZ_CP009273	681,493	0	C	A	45.5%	6.5 / 10.7	22	S211S (TCG→TCT)	gltJ	glutamate/aspartate ABC transporter permease GltJ
*	NZ_CP009273	684,970	0	A	C	44.4%	76.8 / 10.5	45	G456G (GGT→GGG)	lnt	apolipoprotein N‑acyltransferase
*	NZ_CP009273	2,145,111	0	C	A	43.1%	88.9 / 29.2	54	A149E (GCA→GAA)	yegJ	DUF2314 domain‑containing protein
*	NZ_CP009273	2,380,341	0	G	A	42.2%	65.6 / 56.6	64	intergenic (+31/‑72)	yfbL/yfbM	M28 family metallopeptidase/YfbM family protein
*	NZ_CP009273	3,806,632	0	C	T	40.2%	107.8 / 37.9	92	S181L (TCG→TTG)	coaBC	bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate‑‑cysteine ligase CoaBC
*	NZ_CP009273	2,145,105	0	T	A	40.0%	86.9 / 18.3	54	L147Q (CTA→CAA)	yegJ	DUF2314 domain‑containing protein
*	NZ_CP009273	2,826,926	0	T	G	39.8%	170.9 / 11.7	93	G364G (GGT→GGG)	norV	anaerobic nitric oxide reductase flavorubredoxin
*	NZ_CP009273	2,428,361	0	T	G	39.7%	152.4 / 13.2	78	Y252S (TAC→TCC)	truA	tRNA pseudouridine(38‑40) synthase TruA
*	NZ_CP009273	4,612,067	0	A	G	39.5%	144.0 / 35.6	86	E161G (GAG→GGG)	yjjJ	type II toxin‑antitoxin system HipA family toxin YjjJ
*	NZ_CP009273	2,997,280	0	T	G	39.2%	145.1 / 13.6	79	Y145D (TAT→GAT)	xdhC	xanthine dehydrogenase iron sulfur‑binding subunit XdhC
*	NZ_CP009273	4,570,451	0	C	T	39.2%	125.3 / 31.5	79	E277K (GAA→AAA)	hsdS	type I restriction‑modification system specificity subunit
*	NZ_CP009273	4,058,940	0	T	A	39.2%	140.6 / 41.6	97	T63S (ACC→TCC)	yihO	MFS transporter
*	NZ_CP009273	2,145,164	0	A	T	38.9%	74.9 / 21.1	54	intergenic (+37/+28)	yegJ/pphC	DUF2314 domain‑containing protein/protein‑serine/threonine phosphatase PphC
*	NZ_CP009273	1,429,984	0	G	A	38.5%	147.4 / 46.5	91	intergenic (‑108/+33)	uspF/ompN	universal stress protein UspF/porin OmpN
*	NZ_CP009273	4,049,475	0	A	C	38.4%	150.8 / 22.7	87	G75G (GGT→GGG)	glnL	nitrogen regulation protein NR(II)
*	NZ_CP009273	1,861,959	0	T	A	38.2%	105.6 / 33.9	68	F265L (TTT→TTA)	yeaG	protein kinase YeaG
*	NZ_CP009273	4,277,638	0	G	A	38.2%	100.1 / 29.2	68	intergenic (‑339/‑54)	acs/nrfA	acetate‑‑CoA ligase/ammonia‑forming nitrite reductase cytochrome c552 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	= 1203261	79 (0.820)	16 (0.180)	16/462	9.2	18.7%	coding (305/630 nt)	BW25113_RS05990	protein StfP
	?	NZ_CP009273	= 1205058	65 (0.720)					coding (57/540 nt)	BW25113_RS06005	phage tail protein
*	?	NZ_CP009273	1203246 =	79 (0.820)	14 (0.160)	14/462	10.0	16.8%	coding (290/630 nt)	BW25113_RS05990	protein StfP
	?	NZ_CP009273	1205075 =	65 (0.720)					coding (40/540 nt)	BW25113_RS06005	phage tail protein
*	?	NZ_CP009273	= 4532507	104 (1.080)	7 (0.080)	7/476	14.0	6.6%	intergenic (+57/‑425)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
	?	NZ_CP009273	= 4532803	97 (1.050)					intergenic (+353/‑129)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
*	?	NZ_CP009273	4532499 =	104 (1.080)	4 (0.040)	4/476	16.1	3.9%	intergenic (+49/‑433)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
	?	NZ_CP009273	4532813 =	98 (1.060)					intergenic (+363/‑119)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA