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Detailed information for vg0222019892:

Variant ID: vg0222019892 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 22019892
Reference Allele: C	Alternative Allele: A
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.90, A: 0.10, others allele: 0.00, population size: 92. )

Flanking Sequence (100 bp) in Reference Genome:

AGTATGATTTGGTTTTCCTTTTTGACTGTTGTCCGATTCGAGTGGCTTAGTATGCCTTTTTTTTCCCTTTCTTCAGTTTTTAACTAATCCTAATTCTAGT[C/A]
TAGTTCTATTTTTCTTTTTTTTTATTTTTTTTATTAATGTGAGAATTTCTAAGCTGTGAGAGCGAACGTGGAGGCTCTTTTTTCTATTAATTTATAGATA

Reverse complement sequence

TATCTATAAATTAATAGAAAAAAGAGCCTCCACGTTCGCTCTCACAGCTTAGAAATTCTCACATTAATAAAAAAAATAAAAAAAAAGAAAAATAGAACTA[G/T]
ACTAGAATTAGGATTAGTTAAAAACTGAAGAAAGGGAAAAAAAAGGCATACTAAGCCACTCGAATCGGACAACAGTCAAAAAGGAAAACCAAATCATACT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	62.60%	36.70%	0.66%	0.00%	NA
All Indica	2759	91.30%	7.60%	1.12%	0.00%	NA
All Japonica	1512	8.10%	91.90%	0.00%	0.00%	NA
Aus	269	96.70%	3.30%	0.00%	0.00%	NA
Indica I	595	95.30%	3.90%	0.84%	0.00%	NA
Indica II	465	97.40%	1.70%	0.86%	0.00%	NA
Indica III	913	89.50%	9.30%	1.20%	0.00%	NA
Indica Intermediate	786	86.60%	12.00%	1.40%	0.00%	NA
Temperate Japonica	767	1.40%	98.60%	0.00%	0.00%	NA
Tropical Japonica	504	19.80%	80.20%	0.00%	0.00%	NA
Japonica Intermediate	241	5.00%	95.00%	0.00%	0.00%	NA
VI/Aromatic	96	12.50%	87.50%	0.00%	0.00%	NA
Intermediate	90	52.20%	47.80%	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
vg0222019892	C -> A	LOC_Os02g36460.1	upstream_gene_variant ; 734.0bp to feature; MODIFIER	silent_mutation	Average:49.926; most accessible tissue: Minghui63 flower, score: 72.615	N	N	N	N
vg0222019892	C -> A	LOC_Os02g36450.1	downstream_gene_variant ; 2245.0bp to feature; MODIFIER	silent_mutation	Average:49.926; most accessible tissue: Minghui63 flower, score: 72.615	N	N	N	N
vg0222019892	C -> A	LOC_Os02g36450.2	downstream_gene_variant ; 2247.0bp to feature; MODIFIER	silent_mutation	Average:49.926; most accessible tissue: Minghui63 flower, score: 72.615	N	N	N	N
vg0222019892	C -> A	LOC_Os02g36450-LOC_Os02g36460	intergenic_region ; MODIFIER	silent_mutation	Average:49.926; most accessible tissue: Minghui63 flower, score: 72.615	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0222019892	4.65E-06	4.65E-06	mr1311	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