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Detailed information for vg0802257334:

Variant ID: vg0802257334 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 2257334
Reference Allele: C	Alternative Allele: G
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, G: 0.08, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:

ACTCCGGCGAGGTCACCGACCTCAAGGACATGCAGGTCGGCGTCGGCCGCCGCTTCCGGGGGCTCAAGCTCTGGATGGTCATGCGCACCTACGGCGTCGC[C/G]
AAGCTGCAGGAGCACATCCGGAGCGACGTCGCCATGGCCAAGGTGTTCGAGGACCTCGTCCGCGGCGACGACAGGTTCGAGGTCGTCGTGCCGAGGAACT

Reverse complement sequence

AGTTCCTCGGCACGACGACCTCGAACCTGTCGTCGCCGCGGACGAGGTCCTCGAACACCTTGGCCATGGCGACGTCGCTCCGGATGTGCTCCTGCAGCTT[G/C]
GCGACGCCGTAGGTGCGCATGACCATCCAGAGCTTGAGCCCCCGGAAGCGGCGGCCGACGCCGACCTGCATGTCCTTGAGGTCGGTGACCTCGCCGGAGT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	57.00%	43.00%	0.04%	0.02%	NA
All Indica	2759	88.30%	11.60%	0.04%	0.04%	NA
All Japonica	1512	1.50%	98.50%	0.00%	0.00%	NA
Aus	269	65.80%	34.20%	0.00%	0.00%	NA
Indica I	595	93.90%	6.10%	0.00%	0.00%	NA
Indica II	465	94.40%	5.40%	0.00%	0.22%	NA
Indica III	913	81.20%	18.80%	0.00%	0.00%	NA
Indica Intermediate	786	88.70%	11.20%	0.13%	0.00%	NA
Temperate Japonica	767	1.40%	98.60%	0.00%	0.00%	NA
Tropical Japonica	504	1.20%	98.80%	0.00%	0.00%	NA
Japonica Intermediate	241	2.10%	97.90%	0.00%	0.00%	NA
VI/Aromatic	96	11.50%	88.50%	0.00%	0.00%	NA
Intermediate	90	52.20%	46.70%	1.11%	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
vg0802257334	C -> G	LOC_Os08g04540.1	synonymous_variant ; p.Ala399Ala; LOW	synonymous_codon	Average:75.496; most accessible tissue: Zhenshan97 root, score: 85.912	N	N	N	N
vg0802257334	C -> DEL	LOC_Os08g04540.1	N	frameshift_variant	Average:75.496; most accessible tissue: Zhenshan97 root, score: 85.912	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0802257334	NA	5.97E-07	mr1761	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
vg0802257334	NA	2.89E-17	mr1913	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
vg0802257334	3.92E-06	2.36E-06	mr1425_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