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Detailed information for vg0806930067:

Variant ID: vg0806930067 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 6930067
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:

CTATTGCGCGTACCACGGTCGATCCTCGCATACCACCGAGCAATGCCGAAATATCTGGCAGCGTGGCAACAATCAAGACCCAAGGCCGCAACAAGGGGCT[A/G]
CTGTCGAAGCACCTCGCGAAGCTGCTCAAGAACAAGCACCCCCGGTCGAACAGCGCCAAGACAACCAGAGCAGAGTAATCCAAGTGATTACAAGAGCCGA

Reverse complement sequence

TCGGCTCTTGTAATCACTTGGATTACTCTGCTCTGGTTGTCTTGGCGCTGTTCGACCGGGGGTGCTTGTTCTTGAGCAGCTTCGCGAGGTGCTTCGACAG[T/C]
AGCCCCTTGTTGCGGCCTTGGGTCTTGATTGTTGCCACGCTGCCAGATATTTCGGCATTGCTCGGTGGTATGCGAGGATCGACCGTGGTACGCGCAATAG

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	99.90%	0.00%	0.11%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	99.50%	0.10%	0.33%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.00%	0.20%	0.79%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0806930067	A -> G	LOC_Os08g11810.1	missense_variant ; p.Thr353Ala; MODERATE	N	Average:52.849; most accessible tissue: Minghui63 flag leaf, score: 80.516	N	N	N	N
vg0806930067	A -> G	LOC_Os08g11800.1	upstream_gene_variant ; 3288.0bp to feature; MODIFIER	N	Average:52.849; most accessible tissue: Minghui63 flag leaf, score: 80.516	N	N	N	N
vg0806930067	A -> G	LOC_Os08g11820.1	downstream_gene_variant ; 1181.0bp to feature; MODIFIER	N	Average:52.849; most accessible tissue: Minghui63 flag leaf, score: 80.516	N	N	N	N
vg0806930067	A -> G	LOC_Os08g11830.1	downstream_gene_variant ; 4910.0bp to feature; MODIFIER	N	Average:52.849; most accessible tissue: Minghui63 flag leaf, score: 80.516	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0806930067	3.22E-06	3.22E-06	mr1877_2	Jap_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