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Detailed information for vg0208618283:

Variant ID: vg0208618283 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 8618283
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.78, T: 0.20, others allele: 0.00, population size: 45. )

Flanking Sequence (100 bp) in Reference Genome:

ATTGTTTTGGATGTCAGGTGCTGACTCGGTTTGGAAATGATTTAAAATTATCGGATGTTATGTGCATATACAATCATACAACATCTAGTTAGCAATACAA[C/T]
GGATAACAATAAAATAATCAATTAATGATCCATTGTAATAACTATATGCTTAAGTGCAAAATAACATGAATACAAGATATCCATAACATAAAAGCACAAC

Reverse complement sequence

GTTGTGCTTTTATGTTATGGATATCTTGTATTCATGTTATTTTGCACTTAAGCATATAGTTATTACAATGGATCATTAATTGATTATTTTATTGTTATCC[G/A]
TTGTATTGCTAACTAGATGTTGTATGATTGTATATGCACATAACATCCGATAATTTTAAATCATTTCCAAACCGAGTCAGCACCTGACATCCAAAACAAT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	24.60%	20.00%	0.23%	55.23%	NA
All Indica	2759	10.00%	25.00%	0.29%	64.73%	NA
All Japonica	1512	56.40%	1.10%	0.07%	42.46%	NA
Aus	269	2.60%	70.30%	0.37%	26.77%	NA
Indica I	595	20.70%	10.10%	0.50%	68.74%	NA
Indica II	465	5.20%	37.00%	0.43%	57.42%	NA
Indica III	913	1.90%	30.20%	0.00%	67.91%	NA
Indica Intermediate	786	14.20%	23.00%	0.38%	62.34%	NA
Temperate Japonica	767	81.50%	0.30%	0.13%	18.12%	NA
Tropical Japonica	504	28.80%	1.80%	0.00%	69.44%	NA
Japonica Intermediate	241	34.40%	2.10%	0.00%	63.49%	NA
VI/Aromatic	96	2.10%	24.00%	0.00%	73.96%	NA
Intermediate	90	25.60%	30.00%	1.11%	43.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0208618283	C -> T	LOC_Os02g15410-LOC_Os02g15420	intergenic_region ; MODIFIER	silent_mutation	Average:12.095; most accessible tissue: Callus, score: 76.023	N	N	N	N
vg0208618283	C -> DEL	N	N	silent_mutation	Average:12.095; most accessible tissue: Callus, score: 76.023	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0208618283	4.02E-06	3.79E-07	mr1068_2	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