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Detailed information for vg0808279687:

Variant ID: vg0808279687 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 8279687
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.62, C: 0.37, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:

AGTGGATGACTCGGCGAGGAAGCTGTGGGCGGTGATGGCAGGGACGGCAGTAGGTAGAGTGTAGAGGTCCCCACGACTATTGCAACGAAGAATCACGCGC[T/C]
GGGTTTGAAGGTCCTTCACAAAGAAACCAAACTCGTCAAATTCAATTGAGCATTTGTTGTCGCGGGTAAATTGACGAACAGAAAGTAAGTTTCGAACCAA

Reverse complement sequence

TTGGTTCGAAACTTACTTTCTGTTCGTCAATTTACCCGCGACAACAAATGCTCAATTGAATTTGACGAGTTTGGTTTCTTTGTGAAGGACCTTCAAACCC[A/G]
GCGCGTGATTCTTCGTTGCAATAGTCGTGGGGACCTCTACACTCTACCTACTGCCGTCCCTGCCATCACCGCCCACAGCTTCCTCGCCGAGTCATCCACT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	29.70%	4.30%	1.86%	64.09%	NA
All Indica	2759	5.00%	0.40%	1.49%	93.04%	NA
All Japonica	1512	81.60%	7.40%	0.00%	10.98%	NA
Aus	269	0.70%	2.20%	15.99%	81.04%	NA
Indica I	595	8.20%	0.00%	1.85%	89.92%	NA
Indica II	465	6.00%	0.20%	1.29%	92.47%	NA
Indica III	913	1.80%	0.90%	0.99%	96.39%	NA
Indica Intermediate	786	5.90%	0.40%	1.91%	91.86%	NA
Temperate Japonica	767	93.50%	4.00%	0.00%	2.48%	NA
Tropical Japonica	504	75.40%	3.00%	0.00%	21.63%	NA
Japonica Intermediate	241	56.80%	27.40%	0.00%	15.77%	NA
VI/Aromatic	96	2.10%	72.90%	0.00%	25.00%	NA
Intermediate	90	30.00%	5.60%	4.44%	60.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0808279687	T -> C	LOC_Os08g13870.1	downstream_gene_variant ; 3275.0bp to feature; MODIFIER	silent_mutation	Average:9.872; most accessible tissue: Callus, score: 34.609	N	N	N	N
vg0808279687	T -> C	LOC_Os08g13860.1	intron_variant ; MODIFIER	silent_mutation	Average:9.872; most accessible tissue: Callus, score: 34.609	N	N	N	N
vg0808279687	T -> DEL	N	N	silent_mutation	Average:9.872; most accessible tissue: Callus, score: 34.609	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0808279687	NA	1.01E-13	mr1641	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
vg0808279687	NA	5.25E-15	mr1909	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
vg0808279687	NA	3.94E-12	mr1921	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
vg0808279687	NA	4.74E-24	mr1024_2	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
vg0808279687	NA	3.30E-09	mr1232_2	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
vg0808279687	NA	1.75E-12	mr1258_2	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
vg0808279687	NA	3.97E-07	mr1334_2	Ind_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
vg0808279687	NA	2.59E-14	mr1529_2	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
vg0808279687	NA	1.13E-11	mr1641_2	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
vg0808279687	NA	2.52E-12	mr1714_2	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
vg0808279687	NA	7.83E-15	mr1767_2	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
vg0808279687	NA	4.00E-09	mr1909_2	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
vg0808279687	NA	3.36E-08	mr1921_2	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
vg0808279687	NA	1.03E-24	mr1968_2	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
vg0808279687	1.37E-06	1.01E-07	mr1987_2	Ind_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