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 403 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	2,145,111	0	C	A	53.4%	58.9 / 107.5	61	A149E (GCA→GAA)	yegJ	DUF2314 domain‑containing protein
*	NZ_CP009273	4,036,353	0	C	T	50.0%	25.7 / 26.7	56	F193F (TTC→TTT)	srkA	stress response kinase SrkA
*	NZ_CP009273	4,036,390	0	A	G	47.2%	53.2 / 17.3	53	N206D (AAT→GAT)	srkA	stress response kinase SrkA
*	NZ_CP009273	383,643	0	T	G	45.5%	106.1 / 16.2	79	G131G (GGT→GGG)	tauD	taurine dioxygenase
*	NZ_CP009273	1,995,399	0	A	C	42.9%	152.7 / 22.1	91	intergenic (‑129/+192)	fliA/fliC	RNA polymerase sigma factor FliA/H48 family flagellin FliC
*	NZ_CP009273	2,145,146	0	G	T	41.9%	88.4 / 23.3	63	intergenic (+19/+46)	yegJ/pphC	DUF2314 domain‑containing protein/protein‑serine/threonine phosphatase PphC
*	NZ_CP009273	107,682	0	T	G	41.0%	120.7 / 16.4	78	V51G (GTG→GGG)	mutT	8‑oxo‑dGTP diphosphatase MutT
*	NZ_CP009273	2,221,754	0	T	C	40.9%	64.9 / 15.6	67	pseudogene (484/1436 nt)	mdtQ	multidrug resistance outer membrane protein MdtQ
*	NZ_CP009273	4,594,161	0	C	T	39.8%	114.8 / 42.9	89	S62F (TCT→TTT)	bglJ	DNA‑binding transcriptional activator BglJ
*	NZ_CP009273	2,145,084	0	C	A	39.7%	95.4 / 34.9	58	P140Q (CCA→CAA)	yegJ	DUF2314 domain‑containing protein
*	NZ_CP009273	3,199,794	0	C	T	39.2%	97.9 / 35.4	79	intergenic (‑179/‑28)	ttdR/ttdA	DNA‑binding transcriptional activator TtdR/L(+)‑tartrate dehydratase subunit alpha
*	NZ_CP009273	2,145,167	0	G	T	38.7%	53.4 / 16.9	63	intergenic (+40/+25)	yegJ/pphC	DUF2314 domain‑containing protein/protein‑serine/threonine phosphatase PphC
*	NZ_CP009273	2,476,733	0	G	A	38.5%	197.4 / 49.4	123	S29L (TCA→TTA)	emrK	multidrug efflux MFS transporter periplasmic adaptor subunit EmrK
*	NZ_CP009273	2,145,134	0	G	T	37.7%	92.9 / 18.3	61	intergenic (+7/+58)	yegJ/pphC	DUF2314 domain‑containing protein/protein‑serine/threonine phosphatase PphC
*	NZ_CP009273	4,594,167	0	C	T	37.5%	124.8 / 34.2	89	S64F (TCT→TTT)	bglJ	DNA‑binding transcriptional activator BglJ
*	NZ_CP009273	2,145,143	0	A	T	37.3%	79.0 / 22.3	60	intergenic (+16/+49)	yegJ/pphC	DUF2314 domain‑containing protein/protein‑serine/threonine phosphatase PphC
*	NZ_CP009273	2,089,571	0	A	G	37.1%	117.3 / 22.2	70	I83V (ATT→GTT)	hisF	imidazole glycerol phosphate synthase subunit HisF
*	NZ_CP009273	2,145,154	0	T	G	37.1%	81.3 / 13.0	65	intergenic (+27/+38)	yegJ/pphC	DUF2314 domain‑containing protein/protein‑serine/threonine phosphatase PphC
*	NZ_CP009273	2,145,105	0	T	A	36.4%	88.5 / 17.5	59	L147Q (CTA→CAA)	yegJ	DUF2314 domain‑containing protein
*	NZ_CP009273	1,819,313	0	G	A	36.2%	140.7 / 30.5	80	intergenic (‑119/+84)	ves/spy	environmental stress‑induced protein Ves/ATP‑independent periplasmic protein‑refolding chaperone Spy

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	= 3541908	75 (0.740)	9 (0.100) +23 bp	9/448	13.0	11.3%	coding (1522/2085 nt)	malQ	4‑alpha‑glucanotransferase
	?	NZ_CP009273	3541932 =	81 (0.800)					coding (1498/2085 nt)	malQ	4‑alpha‑glucanotransferase
*	?	NZ_CP009273	4532499 =	125 (1.230)	5 (0.050)	5/478	16.3	4.1%	intergenic (+49/‑433)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
	?	NZ_CP009273	4532813 =	114 (1.170)					intergenic (+363/‑119)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA