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Detailed information for vg0220330014:

Variant ID: vg0220330014 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 20330014
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.85, A: 0.15, others allele: 0.00, population size: 108. )

Flanking Sequence (100 bp) in Reference Genome:

TTTCGACTATTTAAAGATAAAACCTATTACTCTATAAATTTAAGCAAATATAGCTATAGATTTTGACTTAAATGGGTGAATCTAATATTTTAAACCATTA[A/G]
ATTAGATGTATATTATTTTAAAAACTAATACCTTATTACTCTGTGTACATAAACGGGAGAAATATATAACTGTTAGGCTAGAAAAAGAAAGAAAACACAT

Reverse complement sequence

ATGTGTTTTCTTTCTTTTTCTAGCCTAACAGTTATATATTTCTCCCGTTTATGTACACAGAGTAATAAGGTATTAGTTTTTAAAATAATATACATCTAAT[T/C]
TAATGGTTTAAAATATTAGATTCACCCATTTAAGTCAAAATCTATAGCTATATTTGCTTAAATTTATAGAGTAATAGGTTTTATCTTTAAATAGTCGAAA

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	81.70%	18.00%	0.30%	0.00%	NA
All Indica	2759	97.00%	3.00%	0.04%	0.00%	NA
All Japonica	1512	49.80%	49.30%	0.86%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	92.00%	8.00%	0.00%	0.00%	NA
Indica III	913	97.60%	2.40%	0.00%	0.00%	NA
Indica Intermediate	786	96.90%	2.90%	0.13%	0.00%	NA
Temperate Japonica	767	42.00%	56.30%	1.69%	0.00%	NA
Tropical Japonica	504	54.60%	45.40%	0.00%	0.00%	NA
Japonica Intermediate	241	64.70%	35.30%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	76.70%	23.30%	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
vg0220330014	A -> G	LOC_Os02g34030.1	upstream_gene_variant ; 2606.0bp to feature; MODIFIER	silent_mutation	Average:26.266; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N
vg0220330014	A -> G	LOC_Os02g34030-LOC_Os02g34040	intergenic_region ; MODIFIER	silent_mutation	Average:26.266; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0220330014	NA	4.68E-13	mr1035_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
vg0220330014	NA	7.57E-06	mr1173_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
vg0220330014	NA	1.67E-08	mr1299_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
vg0220330014	NA	1.18E-06	mr1577_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
vg0220330014	1.41E-07	NA	mr1622_2	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
vg0220330014	NA	3.53E-06	mr1648_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
vg0220330014	8.23E-06	8.23E-06	mr1657_2	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
vg0220330014	NA	7.46E-08	mr1700_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