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Detailed information for vg0216335484:

Variant ID: vg0216335484 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 16335484
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: 108. )

Flanking Sequence (100 bp) in Reference Genome:

ATGCAAGGTTTAAAATCTCCGGCTAAGCCCTTTAGCTGCTGGGCTTTTCATCAGCTATGGCCAGCTATGGCCGGCTATAGCTGCAGTTAAGCCATTTAGC[G/A]
GATTTGCAAAAATTGAACATAAACTTGCCAATATCAGAATAAATTCGTGACAACATCAGAGATTCAAAATAGTTCAAAACACTTCAATTCTTCAACACTC

Reverse complement sequence

GAGTGTTGAAGAATTGAAGTGTTTTGAACTATTTTGAATCTCTGATGTTGTCACGAATTTATTCTGATATTGGCAAGTTTATGTTCAATTTTTGCAAATC[C/T]
GCTAAATGGCTTAACTGCAGCTATAGCCGGCCATAGCTGGCCATAGCTGATGAAAAGCCCAGCAGCTAAAGGGCTTAGCCGGAGATTTTAAACCTTGCAT

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	49.50%	27.30%	5.42%	17.77%	NA
All Indica	2759	19.00%	45.40%	8.37%	27.26%	NA
All Japonica	1512	98.80%	0.20%	0.26%	0.73%	NA
Aus	269	88.10%	5.20%	3.72%	2.97%	NA
Indica I	595	17.30%	45.70%	11.09%	25.88%	NA
Indica II	465	12.90%	64.50%	6.88%	15.70%	NA
Indica III	913	19.70%	38.30%	8.00%	33.95%	NA
Indica Intermediate	786	23.00%	42.00%	7.63%	27.35%	NA
Temperate Japonica	767	99.30%	0.00%	0.00%	0.65%	NA
Tropical Japonica	504	98.80%	0.20%	0.40%	0.60%	NA
Japonica Intermediate	241	97.10%	0.80%	0.83%	1.24%	NA
VI/Aromatic	96	35.40%	4.20%	3.12%	57.29%	NA
Intermediate	90	57.80%	17.80%	8.89%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0216335484	G -> A	LOC_Os02g27590.1	downstream_gene_variant ; 3279.0bp to feature; MODIFIER	silent_mutation	Average:32.072; most accessible tissue: Minghui63 flag leaf, score: 60.569	N	N	N	N
vg0216335484	G -> A	LOC_Os02g27580.1	intron_variant ; MODIFIER	silent_mutation	Average:32.072; most accessible tissue: Minghui63 flag leaf, score: 60.569	N	N	N	N
vg0216335484	G -> DEL	N	N	silent_mutation	Average:32.072; most accessible tissue: Minghui63 flag leaf, score: 60.569	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0216335484	NA	2.48E-06	mr1129	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
vg0216335484	NA	1.29E-17	mr1255	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
vg0216335484	NA	2.06E-08	mr1610	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
vg0216335484	NA	4.22E-13	mr1914	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
vg0216335484	1.02E-06	3.60E-07	mr1914	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
vg0216335484	NA	2.77E-07	mr1129_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
vg0216335484	NA	1.23E-20	mr1627_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