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Detailed information for vg1002138376:

Variant ID: vg1002138376 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 2138376
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.63, A: 0.37, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:

AAATCAGCTCTCCTCTTCCATTTTACACCCAATTTCAGGTCCCATGGCTGCCACATCATCAACCAAGGTGGCACTGAGAGCGTTAAAGGATGGGATTTGT[G/A]
CCTTACCCCAGCGGGCACTTAGATGGAGCCATAACCCCCAAAATCCAAACCCTAGACAATCCGATATGCAACAAAAACAACCAAATCTGAGACAAATTGT

Reverse complement sequence

ACAATTTGTCTCAGATTTGGTTGTTTTTGTTGCATATCGGATTGTCTAGGGTTTGGATTTTGGGGGTTATGGCTCCATCTAAGTGCCCGCTGGGGTAAGG[C/T]
ACAAATCCCATCCTTTAACGCTCTCAGTGCCACCTTGGTTGATGATGTGGCAGCCATGGGACCTGAAATTGGGTGTAAAATGGAAGAGGAGAGCTGATTT

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	35.30%	31.00%	1.80%	31.97%	NA
All Indica	2759	15.40%	29.40%	2.17%	53.03%	NA
All Japonica	1512	78.40%	20.40%	0.00%	1.26%	NA
Aus	269	4.50%	84.80%	7.43%	3.35%	NA
Indica I	595	4.40%	41.70%	4.87%	49.08%	NA
Indica II	465	17.80%	18.90%	0.65%	62.58%	NA
Indica III	913	20.70%	25.20%	1.75%	52.35%	NA
Indica Intermediate	786	16.20%	31.20%	1.53%	51.15%	NA
Temperate Japonica	767	79.40%	19.90%	0.00%	0.65%	NA
Tropical Japonica	504	80.20%	17.50%	0.00%	2.38%	NA
Japonica Intermediate	241	71.40%	27.80%	0.00%	0.83%	NA
VI/Aromatic	96	11.50%	81.20%	3.12%	4.17%	NA
Intermediate	90	37.80%	42.20%	2.22%	17.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1002138376	G -> A	LOC_Os10g04500.1	upstream_gene_variant ; 4872.0bp to feature; MODIFIER	silent_mutation	Average:26.177; most accessible tissue: Zhenshan97 flag leaf, score: 54.545	N	N	N	N
vg1002138376	G -> A	LOC_Os10g04510.1	upstream_gene_variant ; 4988.0bp to feature; MODIFIER	silent_mutation	Average:26.177; most accessible tissue: Zhenshan97 flag leaf, score: 54.545	N	N	N	N
vg1002138376	G -> A	LOC_Os10g04500-LOC_Os10g04510	intergenic_region ; MODIFIER	silent_mutation	Average:26.177; most accessible tissue: Zhenshan97 flag leaf, score: 54.545	N	N	N	N
vg1002138376	G -> DEL	N	N	silent_mutation	Average:26.177; most accessible tissue: Zhenshan97 flag leaf, score: 54.545	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1002138376	3.55E-06	NA	mr1486	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
vg1002138376	NA	6.52E-08	mr1486	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
vg1002138376	NA	6.41E-06	mr1548	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
vg1002138376	1.19E-07	NA	mr1486_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
vg1002138376	NA	2.80E-08	mr1486_2	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