breseq  version 0.33.1  revision 8505477f25b3 mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence (highest frequency 20 of 22 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,741,229	0	A	C	64.9%	‑2.9 / 27.3	37	intergenic (+466/+287)	gltA/yeiW	citrate synthase/putative oxidoreductase
*	NC_002947	4,741,231	0	C	G	62.2%	‑3.9 / 47.3	37	intergenic (+468/+285)	gltA/yeiW	citrate synthase/putative oxidoreductase
*	NC_002947	4,741,236	0	G	T	62.2%	54.7 / NA	37	intergenic (+473/+280)	gltA/yeiW	citrate synthase/putative oxidoreductase
*	NC_002947	4,741,239	0	A	G	62.2%	‑6.4 / 28.7	37	intergenic (+476/+277)	gltA/yeiW	citrate synthase/putative oxidoreductase
*	NC_002947	4,741,245	0	A	C	62.2%	19.7 / 52.9	37	intergenic (+482/+271)	gltA/yeiW	citrate synthase/putative oxidoreductase
*	NC_002947	4,741,237	0	C	G	60.0%	12.3 / 48.3	37	intergenic (+474/+279)	gltA/yeiW	citrate synthase/putative oxidoreductase
*	NC_002947	4,741,244	0	C	G	59.5%	‑5.1 / 53.2	37	intergenic (+481/+272)	gltA/yeiW	citrate synthase/putative oxidoreductase
*	NC_002947	699,722	0	A	G	53.1%	260.9 / 316.0	260	intergenic (+115/‑129)	PP_t06/PP_23SD	tRNA‑Ala/23S ribosomal RNA
*	NC_002947	4,348,705	0	A	G	51.6%	179.5 / inf	308	intergenic (‑70/+404)	PP_3820/galU	group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase
*	NC_002947	1,327,121	0	C	T	47.3%	209.8 / inf	296	intergenic (+97/‑196)	PP_16SE/PP_23SE	16S ribosomal RNA/23S ribosomal RNA
*	NC_002947	195,634	0	C	T	40.7%	3.4 / 193.4	221	T380T (ACC→ACT)	PP_0168	putative surface adhesion protein
*	NC_002947	4,741,235	0	C	T	38.9%	‑4.0 / 28.4	37	intergenic (+472/+281)	gltA/yeiW	citrate synthase/putative oxidoreductase
*	NC_002947	4,741,232	0	C	T	37.8%	12.5 / 33.6	37	intergenic (+469/+284)	gltA/yeiW	citrate synthase/putative oxidoreductase
*	NC_002947	4,741,238	0	C	G	37.8%	3.4 / 44.7	37	intergenic (+475/+278)	gltA/yeiW	citrate synthase/putative oxidoreductase
*	NC_002947	4,741,240	0	A	C	37.8%	31.6 / 10.1	37	intergenic (+477/+276)	gltA/yeiW	citrate synthase/putative oxidoreductase
*	NC_002947	4,741,241	0	C	T	37.8%	‑0.7 / 35.0	37	intergenic (+478/+275)	gltA/yeiW	citrate synthase/putative oxidoreductase
*	NC_002947	4,741,228	1	.	C	35.1%	8.2 / 66.7	37	intergenic (+465/+288)	gltA/yeiW	citrate synthase/putative oxidoreductase
*	NC_002947	4,741,230	0	A	G	35.1%	41.4 / 13.5	37	intergenic (+467/+286)	gltA/yeiW	citrate synthase/putative oxidoreductase
*	NC_002947	2,087,210	0	T	G	26.9%	220.4 / 51.5	183	intergenic (+23/+895)	PP_1865/aroH	transposase/3‑deoxy‑7‑phosphoheptulonate synthase
*	NC_002947	195,559	0	C	A	25.6%	122.0 / 74.2	156	T355T (ACC→ACA)	PP_0168	putative surface adhesion protein

Marginal new junction evidence (sorted from low to high skew)
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	1 =	0 (0.000)	52 (0.290)	30/234	8.8	100%	intergenic (–/+146)	–/parB	–/chromosome‑partitioning protein
	?	NC_002947	= 6181873	0 (0.000)					intergenic (‑3/–)	atpI/–	ATP synthase protein I/–
*	?	NC_002947	= 3534746	201 (1.110)	8 (0.050)	8/220	16.0	4.1%	intergenic (+33/‑122)	atoB/PP_3124	3‑oxoacid CoA‑transferase subunit B/short chain fatty acid transporter
	?	NC_002947	3534791 =	182 (1.070)					intergenic (+78/‑77)	atoB/PP_3124	3‑oxoacid CoA‑transferase subunit B/short chain fatty acid transporter
*	?	NC_002947	= 4808174	8 (0.040)	11 (0.070)	5/206	17.2	10.4%	intergenic (‑283/‑272)	PP_4234/dsbD‑II	bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
	?	NC_002947	5737599 =	182 (1.140)					intergenic (‑154/+48)	hutU/PP_5034	urocanate hydratase/hypothetical protein