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Detailed information for vg0202090631:

Variant ID: vg0202090631 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 2090631
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

AAGGTATGGGCTCAATGCATGCCGAACAGCAGTATCTAAAACAACAGTTTAGGCAACAGATAAGTCATGTGCTAAAGAAAAAATATACATTTTGCAGTGC[G/A]
CCTCAGAAATTCAAGCAGCTAATTTCATTTCAAGTCCTGACTTTTGCTCTCTGAATTTGTTTCAAAGTTAAGTTTGTAGAGCACCACTATTACTTAAAAC

Reverse complement sequence

GTTTTAAGTAATAGTGGTGCTCTACAAACTTAACTTTGAAACAAATTCAGAGAGCAAAAGTCAGGACTTGAAATGAAATTAGCTGCTTGAATTTCTGAGG[C/T]
GCACTGCAAAATGTATATTTTTTCTTTAGCACATGACTTATCTGTTGCCTAAACTGTTGTTTTAGATACTGCTGTTCGGCATGCATTGAGCCCATACCTT

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	75.50%	24.50%	0.02%	0.00%	NA
All Indica	2759	58.60%	41.30%	0.04%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	97.80%	2.20%	0.00%	0.00%	NA
Indica I	595	58.30%	41.70%	0.00%	0.00%	NA
Indica II	465	70.80%	29.20%	0.00%	0.00%	NA
Indica III	913	47.10%	52.90%	0.00%	0.00%	NA
Indica Intermediate	786	65.10%	34.70%	0.13%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	88.90%	11.10%	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
vg0202090631	G -> A	LOC_Os02g04660.1	intron_variant ; MODIFIER	silent_mutation	Average:36.522; most accessible tissue: Callus, score: 48.49	N	N	N	N
vg0202090631	G -> A	LOC_Os02g04660.2	intron_variant ; MODIFIER	silent_mutation	Average:36.522; most accessible tissue: Callus, score: 48.49	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0202090631	3.17E-06	1.23E-06	mr1733	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