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Detailed information for vg0235058313:

Variant ID: vg0235058313 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 35058313
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: 304. )

Flanking Sequence (100 bp) in Reference Genome:

TGAAGTAATGAGAGGGAGGGAGAAAGGAAACCTGTGAAGCTCTTGAAGTTGATGTAGTTACTTTTCTTTCATCCAAGTATCTGACAAAGCTCCTATGAGA[G/A]
ACAAACATATATATTAACCTAAAATAATGGTCATGGAACTCTTAGGAAACAAGATGTTTTTTAAGAAAAAAAGGTTAAAGTGCCTTAACTATTAAGGTGA

Reverse complement sequence

TCACCTTAATAGTTAAGGCACTTTAACCTTTTTTTCTTAAAAAACATCTTGTTTCCTAAGAGTTCCATGACCATTATTTTAGGTTAATATATATGTTTGT[C/T]
TCTCATAGGAGCTTTGTCAGATACTTGGATGAAAGAAAAGTAACTACATCAACTTCAAGAGCTTCACAGGTTTCCTTTCTCCCTCCCTCTCATTACTTCA

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	94.00%	4.50%	1.57%	0.00%	NA
All Indica	2759	94.00%	4.10%	1.88%	0.00%	NA
All Japonica	1512	99.30%	0.10%	0.53%	0.00%	NA
Aus	269	64.30%	31.60%	4.09%	0.00%	NA
Indica I	595	88.10%	4.50%	7.39%	0.00%	NA
Indica II	465	89.20%	10.50%	0.22%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	94.40%	4.70%	0.89%	0.00%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	98.60%	0.00%	1.39%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	90.60%	6.20%	3.12%	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
vg0235058313	G -> A	LOC_Os02g57210.1	downstream_gene_variant ; 3970.0bp to feature; MODIFIER	silent_mutation	Average:50.442; most accessible tissue: Callus, score: 80.543	N	N	N	N
vg0235058313	G -> A	LOC_Os02g57220.1	intron_variant ; MODIFIER	silent_mutation	Average:50.442; most accessible tissue: Callus, score: 80.543	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0235058313	3.89E-06	3.89E-06	mr1450	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