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Detailed information for vg0226125510:

Variant ID: vg0226125510 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 26125510
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

ATGCAATAATGTGTGCTCCGTTTTGCGTTAGGGAACCCCTCCTCCCTAACGCAACCAATTACCCAGTTTACGTGTAAATTGCGAGACGAATCTTTTAAGC[C/T]
TAATTGCGTCATGATTTGACAATGTGGTGCTACAGTAAATATTTGCTAATGATGGATTAATTAGGCTTAATAAATTCGTCTCGCAGTTTCCTGGCGGAAT

Reverse complement sequence

ATTCCGCCAGGAAACTGCGAGACGAATTTATTAAGCCTAATTAATCCATCATTAGCAAATATTTACTGTAGCACCACATTGTCAAATCATGACGCAATTA[G/A]
GCTTAAAAGATTCGTCTCGCAATTTACACGTAAACTGGGTAATTGGTTGCGTTAGGGAGGAGGGGTTCCCTAACGCAAAACGGAGCACACATTATTGCAT

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	84.00%	16.00%	0.02%	0.00%	NA
All Indica	2759	76.60%	23.40%	0.04%	0.00%	NA
All Japonica	1512	97.60%	2.40%	0.00%	0.00%	NA
Aus	269	74.30%	25.70%	0.00%	0.00%	NA
Indica I	595	74.80%	25.20%	0.00%	0.00%	NA
Indica II	465	71.60%	28.40%	0.00%	0.00%	NA
Indica III	913	87.80%	12.20%	0.00%	0.00%	NA
Indica Intermediate	786	67.80%	32.10%	0.13%	0.00%	NA
Temperate Japonica	767	99.50%	0.50%	0.00%	0.00%	NA
Tropical Japonica	504	94.20%	5.80%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	92.20%	7.80%	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
vg0226125510	C -> T	LOC_Os02g43314.1	upstream_gene_variant ; 597.0bp to feature; MODIFIER	silent_mutation	Average:38.165; most accessible tissue: Callus, score: 63.511	N	N	N	N
vg0226125510	C -> T	LOC_Os02g43310-LOC_Os02g43314	intergenic_region ; MODIFIER	silent_mutation	Average:38.165; most accessible tissue: Callus, score: 63.511	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0226125510	4.39E-06	NA	mr1682	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