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Detailed information for vg0821107181:

Variant ID: vg0821107181 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 21107181
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, T: 0.02, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:

GAAGGCCAGCGAGGTGGTTGTGTACTCCGGTCCCGGTGTGAATGGGAGGTTACGAGTTTGATTTTTTTTACCTGGAAATAGTGGGGGAAACCCCCATGGT[G/T]
AATTTTCATATATATGAAAAAGGGAAAAAAGAACTGTACAAAGGTTAAAAATCACAGGTTGTCAAGCCATGATTTCAGAAAAGGTCTAGAAACTAATCTA

Reverse complement sequence

TAGATTAGTTTCTAGACCTTTTCTGAAATCATGGCTTGACAACCTGTGATTTTTAACCTTTGTACAGTTCTTTTTTCCCTTTTTCATATATATGAAAATT[C/A]
ACCATGGGGGTTTCCCCCACTATTTCCAGGTAAAAAAAATCAAACTCGTAACCTCCCATTCACACCGGGACCGGAGTACACAACCACCTCGCTGGCCTTC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	95.20%	4.40%	0.40%	0.00%	NA
All Indica	2759	97.30%	2.20%	0.47%	0.00%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	50.60%	47.20%	2.23%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	95.50%	3.30%	1.20%	0.00%	NA
Indica Intermediate	786	95.90%	3.80%	0.25%	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	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	89.60%	10.40%	0.00%	0.00%	NA
Intermediate	90	95.60%	4.40%	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
vg0821107181	G -> T	LOC_Os08g33750-LOC_Os08g33760	intergenic_region ; MODIFIER	silent_mutation	Average:59.341; most accessible tissue: Callus, score: 73.678	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0821107181	NA	1.03E-08	mr1654	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
vg0821107181	2.19E-06	NA	mr1134_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
vg0821107181	NA	7.26E-07	mr1608_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