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 352 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,995,399	0	A	C	46.0%	77.0 / 11.7	50	intergenic (‑129/+192)	fliA/fliC	RNA polymerase sigma factor FliA/H48 family flagellin FliC
*	NZ_CP009273	1,995,392	0	G	A	44.2%	55.1 / 25.8	52	intergenic (‑122/+199)	fliA/fliC	RNA polymerase sigma factor FliA/H48 family flagellin FliC
*	NZ_CP009273	2,145,154	0	T	G	43.5%	52.3 / 19.0	48	intergenic (+27/+38)	yegJ/pphC	DUF2314 domain‑containing protein/protein‑serine/threonine phosphatase PphC
*	NZ_CP009273	921,356	0	A	G	43.1%	66.4 / 21.0	52	noncoding (72/88 nt)	BW25113_RS04585	tRNA‑Ser
*	NZ_CP009273	636,336	0	T	G	41.5%	104.7 / 13.5	66	G376G (GGT→GGG)	ahpF	alkyl hydroperoxide reductase subunit F
*	NZ_CP009273	29,486	0	C	A	41.4%	143.9 / 45.0	87	intergenic (+291/‑165)	dapB/carA	4‑hydroxy‑tetrahydrodipicolinate reductase/glutamine‑hydrolyzing carbamoyl‑phosphate synthase small subunit
*	NZ_CP009273	4,036,353	0	C	T	41.3%	43.3 / 12.9	46	F193F (TTC→TTT)	srkA	stress response kinase SrkA
*	NZ_CP009273	1,819,313	0	G	A	41.1%	80.7 / 29.6	56	intergenic (‑119/+84)	ves/spy	environmental stress‑induced protein Ves/ATP‑independent periplasmic protein‑refolding chaperone Spy
*	NZ_CP009273	4,245,997	0	G	C	41.0%	91.7 / 26.5	61	P133R (CCG→CGG)	plsB	glycerol‑3‑phosphate 1‑O‑acyltransferase PlsB
*	NZ_CP009273	4,245,989	0	C	T	40.4%	66.3 / 18.7	57	E136K (GAA→AAA)	plsB	glycerol‑3‑phosphate 1‑O‑acyltransferase PlsB
*	NZ_CP009273	2,178,678	0	T	G	39.1%	118.5 / 13.1	64	T35P (ACC→CCC)	thiM	hydroxyethylthiazole kinase
*	NZ_CP009273	3,659,062	0	C	A	38.9%	136.5 / 39.4	90	A37S (GCG→TCG)	gadX	acid resistance transcriptional activator GadX
*	NZ_CP009273	2,819,821	0	G	A	38.8%	120.7 / 38.5	80	G24E (GGA→GAA)	srlE	PTS glucitol/sorbitol transporter subunit IIB
*	NZ_CP009273	4,526,014	0	A	T	38.6%	108.1 / 80.8	88	intergenic (+166/+102)	yjhR/BW25113_RS26295	helicase YjhR/HNH endonuclease
*	NZ_CP009273	2,145,134	0	G	T	38.3%	83.1 / 13.0	47	intergenic (+7/+58)	yegJ/pphC	DUF2314 domain‑containing protein/protein‑serine/threonine phosphatase PphC
*	NZ_CP009273	4,594,161	0	C	T	38.1%	96.3 / 22.4	63	S62F (TCT→TTT)	bglJ	DNA‑binding transcriptional activator BglJ
*	NZ_CP009273	29,496	0	T	A	37.8%	149.4 / 41.2	90	intergenic (+301/‑155)	dapB/carA	4‑hydroxy‑tetrahydrodipicolinate reductase/glutamine‑hydrolyzing carbamoyl‑phosphate synthase small subunit
*	NZ_CP009273	3,199,794	0	C	T	37.6%	86.6 / 57.2	85	intergenic (‑179/‑28)	ttdR/ttdA	DNA‑binding transcriptional activator TtdR/L(+)‑tartrate dehydratase subunit alpha
*	NZ_CP009273	2,145,084	0	C	A	37.1%	58.6 / 14.2	35	P140Q (CCA→CAA)	yegJ	DUF2314 domain‑containing protein
*	NZ_CP009273	782,311	0	A	C	37.1%	161.8 / 13.9	89	G247G (GGT→GGG)	gpmA	2,3‑diphosphoglycerate‑dependent phosphoglycerate mutase

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	56 (0.630)	7 (0.110)	7/340	8.7	13.3%	intergenic (‑1/+15)	BW25113_RS03450/BW25113_RS03455	tRNA‑Met/tRNA‑Gln
	?	NZ_CP009273	692591 =	53 (0.870)					intergenic (‑2/+378)	BW25113_RS03470/asnB	tRNA‑Met/asparagine synthase B