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 53 shown, sorted by frequency from high to low)
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,350,671	0	A	G	55.8%	‑0.5 / 51.8	43	intergenic (‑70/+404)	PP_3820/galU	group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase
*	NC_002947	3,449,251	0	A	C	55.6%	1.3 / 10.0	37	S18R (AGC→CGC)	PP_5556	bacteriophage lysis protein
*	NC_002947	3,294,637	0	T	A	53.8%	8.7 / 20.0	26	T652T (ACT→ACA)	PP_2893	hypothetical protein
*	NC_002947	3,449,271	0	A	C	50.0%	28.1 / 14.8	41	A24A (GCA→GCC)	PP_5556	bacteriophage lysis protein
*	NC_002947	4,160,447	0	A	C	47.8%	17.6 / 13.2	23	H164P (CAT→CCT)	PP_3661	membrane protein
*	NC_002947	3,449,256	0	T	G	46.0%	6.4 / 14.3	38	A19A (GCT→GCG)	PP_5556	bacteriophage lysis protein
*	NC_002947	1,327,127	0	C	T	45.0%	10.4 / 21.2	20	intergenic (+97/‑196)	PP_16SE/PP_23SE	16S ribosomal RNA/23S ribosomal RNA
*	NC_002947	3,635,014	0	T	G	43.6%	35.0 / 24.7	55	V174G (GTG→GGG)	PP_3201	BNR domain‑containing protein
*	NC_002947	527,898	0	C	.	42.9%	32.3 / 31.7	21	noncoding (1133/2902 nt)	PP_23SC	23S ribosomal RNA
*	NC_002947	699,725	0	A	G	42.9%	8.5 / 22.6	21	intergenic (+115/‑129)	PP_t06/PP_23SD	tRNA‑Ala/23S ribosomal RNA
*	NC_002947	1,728,864	0	A	C	42.9%	15.6 / 13.7	28	G95G (GGT→GGG)	PP_1523	hypothetical protein
*	NC_002947	100,464	0	A	C	41.7%	7.9 / 11.7	24	intergenic (‑56/+66)	PP_0094/PP_0095	5'‑nucleotidase/hypothetical protein
*	NC_002947	527,921	0	G	C	38.5%	48.6 / 26.7	26	noncoding (1156/2902 nt)	PP_23SC	23S ribosomal RNA
*	NC_002947	3,595,316	0	C	A	37.9%	83.9 / 15.9	58	F129L (TTC→TTA)	PP_3171	hypothetical protein
*	NC_002947	196,351	0	C	G	34.8%	21.5 / 24.2	23	T619T (ACC→ACG)	PP_0168	putative surface adhesion protein
*	NC_002947	2,089,416	0	G	A	34.8%	18.5 / 17.2	23	intergenic (+264/+654)	PP_1865/aroH	transposase/3‑deoxy‑7‑phosphoheptulonate synthase
*	NC_002947	5,990,889	0	A	.	34.8%	28.9 / 27.2	29	intergenic (+205/‑341)	kefB‑III/PP_mr64	glutathione‑regulated potassium/H+ antiporter/C4 ncRNA
*	NC_002947	527,917	0	A	G	34.6%	48.1 / 22.7	26	noncoding (1152/2902 nt)	PP_23SC	23S ribosomal RNA
*	NC_002947	3,793,692	0	T	G	34.0%	68.7 / 10.9	52	S531R (AGC→CGC)	PP_3354	acyl‑CoA dehydrogenase
*	NC_002947	527,922	0	T	A	33.3%	46.2 / 23.0	27	noncoding (1157/2902 nt)	PP_23SC	23S ribosomal RNA

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	= 5990749	89 (2.290)	4 (0.110)	4/248	2.0	6.1%	intergenic (+65/‑481)	kefB‑III/PP_mr64	glutathione‑regulated potassium/H+ antiporter/C4 ncRNA
	?	NC_002947	5990941 =	39 (1.070)					intergenic (+257/‑289)	kefB‑III/PP_mr64	glutathione‑regulated potassium/H+ antiporter/C4 ncRNA
*	?	NC_002947	= 5990646	86 (2.220)	4 (0.110)	4/250	2.0	6.2%	coding (1750/1788 nt)	kefB‑III	glutathione‑regulated potassium/H+ antiporter
	?	NC_002947	5990934 =	39 (1.060)					intergenic (+250/‑296)	kefB‑III/PP_mr64	glutathione‑regulated potassium/H+ antiporter/C4 ncRNA
*	?	NC_002947	= 4810097	10 (0.260)	4 (0.110)	3/258	2.4	14.1%	intergenic (‑239/‑316)	PP_4234/dsbD‑II	bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
	?	NC_002947	= 5990944	39 (1.030)					intergenic (+260/‑286)	kefB‑III/PP_mr64	glutathione‑regulated potassium/H+ antiporter/C4 ncRNA