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Detailed information for vg0308314436:

Variant ID: vg0308314436 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 8314436
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.59, A: 0.40, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

TCTGGAAGACGAGAAATGGTTTATGGAATTTATAGAAATAATATTCTCAAGAATATTATTGACAGTCACTGACGTGCGGGACCAAAGGAAAATGATTCAT[A/G]
GAATTTTGGAATAAAGAATTTTATTTATGAAACAAAGGAAAAGGATTTATTAAATCCCTTGGAAAATTAAAGGGATGAGGGATGTGATTTGGACTTTTCT

Reverse complement sequence

AGAAAAGTCCAAATCACATCCCTCATCCCTTTAATTTTCCAAGGGATTTAATAAATCCTTTTCCTTTGTTTCATAAATAAAATTCTTTATTCCAAAATTC[T/C]
ATGAATCATTTTCCTTTGGTCCCGCACGTCAGTGACTGTCAATAATATTCTTGAGAATATTATTTCTATAAATTCCATAAACCATTTCTCGTCTTCCAGA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	91.00%	7.00%	1.86%	0.15%	NA
All Indica	2759	99.70%	0.20%	0.07%	0.04%	NA
All Japonica	1512	73.00%	20.90%	5.69%	0.40%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.70%	0.20%	0.00%	0.17%	NA
Indica II	465	99.60%	0.40%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.40%	0.40%	0.25%	0.00%	NA
Temperate Japonica	767	50.50%	39.20%	9.65%	0.65%	NA
Tropical Japonica	504	98.20%	0.20%	1.39%	0.20%	NA
Japonica Intermediate	241	92.10%	5.80%	2.07%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	10.00%	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
vg0308314436	A -> DEL	N	N	silent_mutation	Average:8.799; most accessible tissue: Zhenshan97 flower, score: 13.891	N	N	N	N
vg0308314436	A -> G	LOC_Os03g15190.1	upstream_gene_variant ; 2879.0bp to feature; MODIFIER	silent_mutation	Average:8.799; most accessible tissue: Zhenshan97 flower, score: 13.891	N	N	N	N
vg0308314436	A -> G	LOC_Os03g15190-LOC_Os03g15200	intergenic_region ; MODIFIER	silent_mutation	Average:8.799; most accessible tissue: Zhenshan97 flower, score: 13.891	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0308314436	NA	8.63E-07	mr1026	Jap_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
vg0308314436	NA	2.58E-06	mr1171	Jap_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
vg0308314436	5.53E-06	NA	mr1210	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
vg0308314436	7.28E-06	NA	mr1305	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
vg0308314436	NA	5.41E-07	mr1310	Jap_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
vg0308314436	1.40E-07	NA	mr1585	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
vg0308314436	3.18E-06	9.34E-09	mr1585	Jap_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
vg0308314436	NA	1.41E-14	mr1712	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
vg0308314436	NA	4.34E-06	mr1712	Jap_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
vg0308314436	6.77E-06	6.77E-06	mr1779	Jap_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
vg0308314436	7.39E-06	NA	mr1926	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
vg0308314436	NA	7.21E-08	mr1926	Jap_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
vg0308314436	NA	2.61E-08	mr1946	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
vg0308314436	NA	6.38E-10	mr1977	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
vg0308314436	NA	3.03E-06	mr1977	Jap_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