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Detailed information for vg0806013173:

Variant ID: vg0806013173 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 6013173
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATCAGTTGCAGGAATGCAGTAGCTAAGCTATAGTATGATAGCAGTGCCAGTAGGTGCGGTGGCAGTCATGCCAATTGGGCAATTTGGTACTAAATGGATT[C/T]
CATTAATTTCTTCAAAAATAAATGTAGTCTTTTCACAAAGTAATTGGTGTCAACGTATTTTAATGACAAGTGCTTATTCATATTTCCGGCACATGCATGT

Reverse complement sequence

ACATGCATGTGCCGGAAATATGAATAAGCACTTGTCATTAAAATACGTTGACACCAATTACTTTGTGAAAAGACTACATTTATTTTTGAAGAAATTAATG[G/A]
AATCCATTTAGTACCAAATTGCCCAATTGGCATGACTGCCACCGCACCTACTGGCACTGCTATCATACTATAGCTTAGCTACTGCATTCCTGCAACTGAT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	68.10%	10.00%	1.67%	20.25%	NA
All Indica	2759	67.70%	0.10%	1.45%	30.66%	NA
All Japonica	1512	65.90%	30.20%	2.18%	1.79%	NA
Aus	269	91.40%	0.00%	0.00%	8.55%	NA
Indica I	595	55.60%	0.20%	2.02%	42.18%	NA
Indica II	465	59.40%	0.20%	1.94%	38.49%	NA
Indica III	913	77.00%	0.10%	0.99%	21.91%	NA
Indica Intermediate	786	71.10%	0.10%	1.27%	27.48%	NA
Temperate Japonica	767	65.40%	30.80%	3.78%	0.00%	NA
Tropical Japonica	504	66.70%	28.60%	0.79%	3.97%	NA
Japonica Intermediate	241	65.60%	31.50%	0.00%	2.90%	NA
VI/Aromatic	96	45.80%	0.00%	4.17%	50.00%	NA
Intermediate	90	71.10%	12.20%	2.22%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0806013173	C -> T	LOC_Os08g10310.1	upstream_gene_variant ; 2572.0bp to feature; MODIFIER	silent_mutation	Average:19.99; most accessible tissue: Callus, score: 80.124	N	N	N	N
vg0806013173	C -> T	LOC_Os08g10310.2	upstream_gene_variant ; 2572.0bp to feature; MODIFIER	silent_mutation	Average:19.99; most accessible tissue: Callus, score: 80.124	N	N	N	N
vg0806013173	C -> T	LOC_Os08g10310.3	upstream_gene_variant ; 2572.0bp to feature; MODIFIER	silent_mutation	Average:19.99; most accessible tissue: Callus, score: 80.124	N	N	N	N
vg0806013173	C -> T	LOC_Os08g10304-LOC_Os08g10310	intergenic_region ; MODIFIER	silent_mutation	Average:19.99; most accessible tissue: Callus, score: 80.124	N	N	N	N
vg0806013173	C -> DEL	N	N	silent_mutation	Average:19.99; most accessible tissue: Callus, score: 80.124	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0806013173	3.81E-06	NA	mr1594_2	All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0806013173	NA	2.67E-06	mr1594_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251