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Detailed information for vg0119110815:

Variant ID: vg0119110815 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 19110815
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

TTTCGTGAGTGGTGCAACATGTGAAACACTTTGTGATAATATAGTGCAACACCGTCCGATCTATTGCAAAAGATCGGACGTCCGATTTGTAGCAACCTCC[A/G]
CACTTTTGTTTCCCCTACGCCGCACCACGCCACCCCGCACGGCTGCTGGCTCGATACACCTGCCCGCCCAACATGTGCAGGATTAATATCATGTTTTTCA

Reverse complement sequence

TGAAAAACATGATATTAATCCTGCACATGTTGGGCGGGCAGGTGTATCGAGCCAGCAGCCGTGCGGGGTGGCGTGGTGCGGCGTAGGGGAAACAAAAGTG[T/C]
GGAGGTTGCTACAAATCGGACGTCCGATCTTTTGCAATAGATCGGACGGTGTTGCACTATATTATCACAAAGTGTTTCACATGTTGCACCACTCACGAAA

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	97.50%	2.00%	0.49%	0.00%	NA
All Indica	2759	99.90%	0.00%	0.11%	0.00%	NA
All Japonica	1512	92.60%	6.20%	1.19%	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	99.80%	0.00%	0.22%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.00%	0.25%	0.00%	NA
Temperate Japonica	767	95.30%	3.90%	0.78%	0.00%	NA
Tropical Japonica	504	90.30%	7.70%	1.98%	0.00%	NA
Japonica Intermediate	241	88.80%	10.40%	0.83%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	2.20%	2.22%	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
vg0119110815	A -> G	LOC_Os01g34660.1	downstream_gene_variant ; 93.0bp to feature; MODIFIER	silent_mutation	Average:66.722; most accessible tissue: Callus, score: 82.843	N	N	N	N
vg0119110815	A -> G	LOC_Os01g34670.1	downstream_gene_variant ; 4431.0bp to feature; MODIFIER	silent_mutation	Average:66.722; most accessible tissue: Callus, score: 82.843	N	N	N	N
vg0119110815	A -> G	LOC_Os01g34630-LOC_Os01g34660	intergenic_region ; MODIFIER	silent_mutation	Average:66.722; most accessible tissue: Callus, score: 82.843	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0119110815	2.67E-06	2.67E-06	mr1610_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