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 257 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	2,221,754	0	T	C	48.0%	47.4 / 14.8	51	pseudogene (484/1436 nt)	mdtQ	multidrug resistance outer membrane protein MdtQ
*	NZ_CP009273	4,036,390	0	A	G	41.7%	63.6 / 11.4	48	N206D (AAT→GAT)	srkA	stress response kinase SrkA
*	NZ_CP009273	4,594,167	0	C	T	38.8%	93.6 / 29.4	67	S64F (TCT→TTT)	bglJ	DNA‑binding transcriptional activator BglJ
*	NZ_CP009273	748,581	0	T	A	38.7%	141.1 / 49.9	93	intergenic (‑330/+60)	ybgD/gltA	fimbrial protein/citrate synthase
*	NZ_CP009273	4,245,997	0	G	C	37.3%	134.2 / 27.4	67	P133R (CCG→CGG)	plsB	glycerol‑3‑phosphate 1‑O‑acyltransferase PlsB
*	NZ_CP009273	1,429,975	0	G	A	37.2%	138.5 / 30.7	78	intergenic (‑99/+42)	uspF/ompN	universal stress protein UspF/porin OmpN
*	NZ_CP009273	1,429,984	0	G	A	36.7%	129.5 / 38.7	79	intergenic (‑108/+33)	uspF/ompN	universal stress protein UspF/porin OmpN
*	NZ_CP009273	3,659,062	0	C	A	35.3%	179.8 / 39.2	105	A37S (GCG→TCG)	gadX	acid resistance transcriptional activator GadX
*	NZ_CP009273	1,407,992	0	A	T	35.2%	132.3 / 28.4	71	Y2* (TAT→TAA)  *65K (TAA→AAA)	rcbA ralR	double‑strand break reduction protein RcbA type I toxin‑antitoxin system endodeoxyribonuclease toxin RalR
*	NZ_CP009273	3,806,632	0	C	T	35.2%	96.8 / 27.5	71	S181L (TCG→TTG)	coaBC	bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate‑‑cysteine ligase CoaBC
*	NZ_CP009273	4,551,032	0	G	A	34.9%	109.5 / 29.5	83	E96K (GAA→AAA)	kptA	RNA 2'‑phosphotransferase
*	NZ_CP009273	3,171,107	0	C	A	34.7%	145.5 / 40.7	95	E55* (GAG→TAG)	nudF	ADP‑ribose diphosphatase
*	NZ_CP009273	1,615,375	0	A	C	34.7%	155.3 / 18.2	75	V7G (GTG→GGG)	eamA	O‑acetylserine/cysteine exporter
*	NZ_CP009273	1,076,312	0	T	G	33.9%	122.3 / 13.1	65	intergenic (+43/‑500)	putP/BW25113_RS05295	sodium/proline symporter PutP/FTR1 family protein
*	NZ_CP009273	1,429,978	0	T	A	33.3%	171.6 / 24.6	81	intergenic (‑102/+39)	uspF/ompN	universal stress protein UspF/porin OmpN
*	NZ_CP009273	2,089,571	0	A	G	33.3%	136.0 / 10.1	72	I83V (ATT→GTT)	hisF	imidazole glycerol phosphate synthase subunit HisF
*	NZ_CP009273	4,594,161	0	C	T	32.8%	108.5 / 21.8	67	S62F (TCT→TTT)	bglJ	DNA‑binding transcriptional activator BglJ
*	NZ_CP009273	2,476,747	0	T	A	32.6%	201.6 / 29.9	98	L24F (TTA→TTT)	emrK	multidrug efflux MFS transporter periplasmic adaptor subunit EmrK
*	NZ_CP009273	1,980,476	0	A	C	32.4%	148.4 / 13.0	71	Y24S (TAC→TCC)	ftnB	non‑heme ferritin‑like protein
*	NZ_CP009273	29,486	0	C	A	32.0%	177.6 / 25.1	78	intergenic (+291/‑165)	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	= 692197	60 (0.650)	3 (0.050)	3/340	12.6	6.1%	intergenic (‑1/+15)	BW25113_RS03450/BW25113_RS03455	tRNA‑Met/tRNA‑Gln
	?	NZ_CP009273	692591 =	52 (0.830)					intergenic (‑2/+378)	BW25113_RS03470/asnB	tRNA‑Met/asparagine synthase B
*	?	NZ_CP009273	= 4532507	104 (1.130)	6 (0.070)	6/478	13.7	5.8%	intergenic (+57/‑425)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
	?	NZ_CP009273	= 4532803	96 (1.090)					intergenic (+353/‑129)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
*	?	NZ_CP009273	4532499 =	107 (1.170)	3 (0.030)	3/478	16.0	2.9%	intergenic (+49/‑433)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
	?	NZ_CP009273	4532813 =	96 (1.090)					intergenic (+363/‑119)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA