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Detailed information for vg0823689104:

Variant ID: vg0823689104 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 23689104
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.02, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:

TTTTATTTGAGAAACTTAGTACAAGCGTGGCCATGAACATACACACCCACAATCTAAACCGACCTATAAGCACATATTTAATTAAAAACTAGTTGGATGG[C/T]
CCGCGCAATTACTCGGCTAACACCCAAACAAAATCATATAATTTTTAAGTATGATTTTACTTAAAATTTATTAAATAGCTATCTTCTTCTCTTAGGACTT

Reverse complement sequence

AAGTCCTAAGAGAAGAAGATAGCTATTTAATAAATTTTAAGTAAAATCATACTTAAAAATTATATGATTTTGTTTGGGTGTTAGCCGAGTAATTGCGCGG[G/A]
CCATCCAACTAGTTTTTAATTAAATATGTGCTTATAGGTCGGTTTAGATTGTGGGTGTGTATGTTCATGGCCACGCTTGTACTAAGTTTCTCAAATAAAA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	69.80%	26.80%	3.36%	0.00%	NA
All Indica	2759	90.50%	6.80%	2.68%	0.00%	NA
All Japonica	1512	47.70%	47.20%	5.16%	0.00%	NA
Aus	269	4.80%	94.80%	0.37%	0.00%	NA
Indica I	595	86.90%	7.20%	5.88%	0.00%	NA
Indica II	465	89.70%	8.40%	1.94%	0.00%	NA
Indica III	913	95.20%	4.60%	0.22%	0.00%	NA
Indica Intermediate	786	88.30%	8.10%	3.56%	0.00%	NA
Temperate Japonica	767	38.30%	53.80%	7.82%	0.00%	NA
Tropical Japonica	504	62.30%	35.50%	2.18%	0.00%	NA
Japonica Intermediate	241	46.90%	50.20%	2.90%	0.00%	NA
VI/Aromatic	96	8.30%	91.70%	0.00%	0.00%	NA
Intermediate	90	66.70%	26.70%	6.67%	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
vg0823689104	C -> T	LOC_Os08g37410-LOC_Os08g37420	intergenic_region ; MODIFIER	silent_mutation	Average:54.817; most accessible tissue: Minghui63 panicle, score: 85.556	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0823689104	NA	8.50E-06	mr1030	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
vg0823689104	NA	1.95E-09	mr1321	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
vg0823689104	NA	1.46E-06	mr1568	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
vg0823689104	NA	2.54E-06	mr1614	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
vg0823689104	NA	4.39E-06	mr1621	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
vg0823689104	1.53E-06	1.53E-06	mr1728	Jap_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
vg0823689104	NA	1.23E-07	mr1989	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