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Detailed information for vg0202013925:

Variant ID: vg0202013925 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 2013925
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.75, G: 0.26, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:

GGTCAGCTAGGCAGCCTGACCAAACTTCGAGGACATCTCCATATCATGAATCTTGAGAATGTGCAAAATAGGAATGCGGCAAAGGATGCAAAGCTCCAAG[A/G]
AAAAGCCAATCTTGATGCATTGCGGTTGGTGTGGAACCATGACACATACAAGAACAACAATGTTGACTTGGAGGTACTCGAGGGACTTGAGCCTTCTTCA

Reverse complement sequence

TGAAGAAGGCTCAAGTCCCTCGAGTACCTCCAAGTCAACATTGTTGTTCTTGTATGTGTCATGGTTCCACACCAACCGCAATGCATCAAGATTGGCTTTT[T/C]
CTTGGAGCTTTGCATCCTTTGCCGCATTCCTATTTTGCACATTCTCAAGATTCATGATATGGAGATGTCCTCGAAGTTTGGTCAGGCTGCCTAGCTGACC

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	76.10%	23.70%	0.21%	0.00%	NA
All Indica	2759	60.20%	39.50%	0.33%	0.00%	NA
All Japonica	1512	99.80%	0.20%	0.00%	0.00%	NA
Aus	269	94.40%	5.60%	0.00%	0.00%	NA
Indica I	595	46.20%	53.30%	0.50%	0.00%	NA
Indica II	465	52.30%	47.50%	0.22%	0.00%	NA
Indica III	913	76.50%	23.40%	0.11%	0.00%	NA
Indica Intermediate	786	56.50%	43.00%	0.51%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	86.70%	12.20%	1.11%	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
vg0202013925	A -> G	LOC_Os02g04530.1	missense_variant ; p.Glu740Gly; MODERATE	nonsynonymous_codon ; E740G	Average:69.367; most accessible tissue: Callus, score: 85.852	unknown	unknown	DELETERIOUS	0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0202013925	NA	4.50E-07	mr1220	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
vg0202013925	NA	8.04E-07	mr1881	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
vg0202013925	NA	2.69E-06	mr1984_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
vg0202013925	1.98E-06	1.98E-06	mr1984_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