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Detailed information for vg0816832964:

Variant ID: vg0816832964 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 16832964
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:

TTTTGGTTGTATTTTCAAAATTGAGCTGTCGCGATTTCGACGTTCGGTGAGCTATGCTTCGACCGATTCGTCCCCCCCCCCCGGTGTGTTCACTGATCAG[A/G]
CGTTTGCCTTGGGGTTTTTCCACGAAGACATCATTCACACAAAAAGGCGAAAAGACACAAAGATTTTTATACTGGTTCGGGCCTCTAAGGTGGATAATAA

Reverse complement sequence

TTATTATCCACCTTAGAGGCCCGAACCAGTATAAAAATCTTTGTGTCTTTTCGCCTTTTTGTGTGAATGATGTCTTCGTGGAAAAACCCCAAGGCAAACG[T/C]
CTGATCAGTGAACACACCGGGGGGGGGGGACGAATCGGTCGAAGCATAGCTCACCGAACGTCGAAATCGCGACAGCTCAATTTTGAAAATACAACCAAAA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	68.70%	5.30%	2.56%	23.44%	NA
All Indica	2759	48.90%	8.80%	4.06%	38.20%	NA
All Japonica	1512	99.10%	0.10%	0.07%	0.79%	NA
Aus	269	89.20%	0.70%	0.37%	9.67%	NA
Indica I	595	80.70%	5.50%	1.68%	12.10%	NA
Indica II	465	37.60%	3.90%	3.23%	55.27%	NA
Indica III	913	31.90%	14.30%	6.57%	47.21%	NA
Indica Intermediate	786	51.40%	7.80%	3.44%	37.40%	NA
Temperate Japonica	767	99.20%	0.00%	0.00%	0.78%	NA
Tropical Japonica	504	98.60%	0.20%	0.20%	0.99%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	88.50%	1.00%	3.12%	7.29%	NA
Intermediate	90	81.10%	4.40%	4.44%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0816832964	A -> G	LOC_Os08g27610.1	upstream_gene_variant ; 2143.0bp to feature; MODIFIER	silent_mutation	Average:29.892; most accessible tissue: Zhenshan97 flag leaf, score: 68.25	N	N	N	N
vg0816832964	A -> G	LOC_Os08g27620.1	downstream_gene_variant ; 220.0bp to feature; MODIFIER	silent_mutation	Average:29.892; most accessible tissue: Zhenshan97 flag leaf, score: 68.25	N	N	N	N
vg0816832964	A -> G	LOC_Os08g27630.1	downstream_gene_variant ; 1214.0bp to feature; MODIFIER	silent_mutation	Average:29.892; most accessible tissue: Zhenshan97 flag leaf, score: 68.25	N	N	N	N
vg0816832964	A -> G	LOC_Os08g27610-LOC_Os08g27620	intergenic_region ; MODIFIER	silent_mutation	Average:29.892; most accessible tissue: Zhenshan97 flag leaf, score: 68.25	N	N	N	N
vg0816832964	A -> DEL	N	N	silent_mutation	Average:29.892; most accessible tissue: Zhenshan97 flag leaf, score: 68.25	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0816832964	NA	7.77E-06	mr1011	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
vg0816832964	2.27E-06	2.27E-06	mr1012	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