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Detailed information for vg0220102123:

Variant ID: vg0220102123 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 20102123
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:

TATGAAATATGTAAAACTATATGTATACATAAAAGTATATTTAATAATAAATCAAATAATAGAAAACAAATTAATAATTATTTAAATTTTTAAATAAGAC[G/A]
AACGGTTAAATATGTTTAAAAAAATCAACGACATCGTGTCAGAGACGAGGAGTATATTTTAAAACGCAGAGGTAATCGATACTTTAGGACGGAGAGATAG

Reverse complement sequence

CTATCTCTCCGTCCTAAAGTATCGATTACCTCTGCGTTTTAAAATATACTCCTCGTCTCTGACACGATGTCGTTGATTTTTTTAAACATATTTAACCGTT[C/T]
GTCTTATTTAAAAATTTAAATAATTATTAATTTGTTTTCTATTATTTGATTTATTATTAAATATACTTTTATGTATACATATAGTTTTACATATTTCATA

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	88.40%	11.50%	0.13%	0.00%	NA
All Indica	2759	86.90%	13.00%	0.14%	0.00%	NA
All Japonica	1512	99.40%	0.60%	0.00%	0.00%	NA
Aus	269	36.40%	62.80%	0.74%	0.00%	NA
Indica I	595	93.10%	6.90%	0.00%	0.00%	NA
Indica II	465	74.20%	25.20%	0.65%	0.00%	NA
Indica III	913	88.50%	11.50%	0.00%	0.00%	NA
Indica Intermediate	786	87.80%	12.10%	0.13%	0.00%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.80%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	94.40%	5.60%	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
vg0220102123	G -> A	LOC_Os02g33700.1	upstream_gene_variant ; 645.0bp to feature; MODIFIER	silent_mutation	Average:45.885; most accessible tissue: Zhenshan97 panicle, score: 69.946	N	N	N	N
vg0220102123	G -> A	LOC_Os02g33705.1	downstream_gene_variant ; 1839.0bp to feature; MODIFIER	silent_mutation	Average:45.885; most accessible tissue: Zhenshan97 panicle, score: 69.946	N	N	N	N
vg0220102123	G -> A	LOC_Os02g33690-LOC_Os02g33700	intergenic_region ; MODIFIER	silent_mutation	Average:45.885; most accessible tissue: Zhenshan97 panicle, score: 69.946	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0220102123	1.48E-06	NA	mr1102	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
vg0220102123	NA	9.52E-07	mr1114	Ind_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
vg0220102123	NA	3.27E-06	mr1884	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