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Detailed information for vg0202217757:

Variant ID: vg0202217757 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 2217757
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.03, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:

AATATCCAAAAGAGAATCATGTTGATAGGTGATTTTTTTTTCTCTTAATCCATTATCCAAACTGGCTCAAACACCACCTAAGATGGTATTTGAATCTTCT[G/A]
AAGATGGAGATGAAGATGAATATTAAGTTTTTTACGTAAAACGAGGTGGTATTAACGTATGATTGATTGAGTTTTAATTATTACAAATTTTAAAAATGGA

Reverse complement sequence

TCCATTTTTAAAATTTGTAATAATTAAAACTCAATCAATCATACGTTAATACCACCTCGTTTTACGTAAAAAACTTAATATTCATCTTCATCTCCATCTT[C/T]
AGAAGATTCAAATACCATCTTAGGTGGTGTTTGAGCCAGTTTGGATAATGGATTAAGAGAAAAAAAAATCACCTATCAACATGATTCTCTTTTGGATATT

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	53.60%	46.30%	0.06%	0.00%	NA
All Indica	2759	86.20%	13.80%	0.00%	0.00%	NA
All Japonica	1512	0.70%	99.20%	0.07%	0.00%	NA
Aus	269	9.30%	90.70%	0.00%	0.00%	NA
Indica I	595	81.00%	19.00%	0.00%	0.00%	NA
Indica II	465	96.60%	3.40%	0.00%	0.00%	NA
Indica III	913	81.50%	18.50%	0.00%	0.00%	NA
Indica Intermediate	786	89.30%	10.70%	0.00%	0.00%	NA
Temperate Japonica	767	0.10%	99.90%	0.00%	0.00%	NA
Tropical Japonica	504	0.60%	99.40%	0.00%	0.00%	NA
Japonica Intermediate	241	2.90%	96.70%	0.41%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	32.20%	65.60%	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
vg0202217757	G -> A	LOC_Os02g04810.1	upstream_gene_variant ; 3125.0bp to feature; MODIFIER	silent_mutation	Average:48.749; most accessible tissue: Minghui63 panicle, score: 78.92	N	N	N	N
vg0202217757	G -> A	LOC_Os02g04810-LOC_Os02g04820	intergenic_region ; MODIFIER	silent_mutation	Average:48.749; most accessible tissue: Minghui63 panicle, score: 78.92	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0202217757	4.71E-07	1.87E-06	mr1229	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
vg0202217757	NA	1.56E-08	mr1260	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
vg0202217757	NA	6.45E-23	mr1571	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
vg0202217757	NA	2.27E-30	mr1638	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
vg0202217757	NA	1.16E-22	mr1164_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
vg0202217757	NA	8.03E-12	mr1666_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
vg0202217757	NA	9.44E-41	mr1745_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
vg0202217757	NA	6.30E-09	mr1851_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