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Detailed information for vg1125800615:

Variant ID: vg1125800615 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 25800615
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, G: 0.02, others allele: 0.00, population size: 100. )

Flanking Sequence (100 bp) in Reference Genome:

TCTAATATTATTTTCATATAATATGTTAACAAGAATAATAGCTATACTTCACAAAAATAGTCTAATAATTGCCTACAAAGATGTACAGAGTCTCCAATAC[A/G]
GGAGAATAGATGATGAAACAAAAGTCGTGTAGGAGATGGAAAAAAAAATCGATGGATCCTATCCGATCAAATGTCCATCAATTTAGCTTTTCTTTTAACA

Reverse complement sequence

TGTTAAAAGAAAAGCTAAATTGATGGACATTTGATCGGATAGGATCCATCGATTTTTTTTTCCATCTCCTACACGACTTTTGTTTCATCATCTATTCTCC[T/C]
GTATTGGAGACTCTGTACATCTTTGTAGGCAATTATTAGACTATTTTTGTGAAGTATAGCTATTATTCTTGTTAACATATTATATGAAAATAATATTAGA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	67.30%	6.50%	0.76%	25.45%	NA
All Indica	2759	53.10%	7.40%	1.16%	38.38%	NA
All Japonica	1512	94.40%	1.20%	0.07%	4.37%	NA
Aus	269	52.40%	30.90%	0.37%	16.36%	NA
Indica I	595	80.50%	2.40%	0.34%	16.81%	NA
Indica II	465	42.20%	3.90%	1.08%	52.90%	NA
Indica III	913	51.00%	5.00%	1.42%	42.50%	NA
Indica Intermediate	786	41.10%	16.00%	1.53%	41.35%	NA
Temperate Japonica	767	97.30%	1.70%	0.13%	0.91%	NA
Tropical Japonica	504	92.30%	0.20%	0.00%	7.54%	NA
Japonica Intermediate	241	89.60%	1.70%	0.00%	8.71%	NA
VI/Aromatic	96	84.40%	0.00%	0.00%	15.62%	NA
Intermediate	90	75.60%	1.10%	2.22%	21.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1125800615	A -> DEL	N	N	silent_mutation	Average:29.356; most accessible tissue: Zhenshan97 flag leaf, score: 55.285	N	N	N	N
vg1125800615	A -> G	LOC_Os11g42830.1	upstream_gene_variant ; 3558.0bp to feature; MODIFIER	silent_mutation	Average:29.356; most accessible tissue: Zhenshan97 flag leaf, score: 55.285	N	N	N	N
vg1125800615	A -> G	LOC_Os11g42840.1	intron_variant ; MODIFIER	silent_mutation	Average:29.356; most accessible tissue: Zhenshan97 flag leaf, score: 55.285	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1125800615	NA	6.10E-10	mr1133	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
vg1125800615	NA	4.81E-07	mr1667	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
vg1125800615	NA	1.31E-09	mr1133_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
vg1125800615	2.27E-06	1.40E-09	mr1667_2	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