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Detailed information for vg0224550937:

Variant ID: vg0224550937 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 24550937
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.03, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

TGGGCTAATAAGCTAGAGCAAAAGCCAAAATTTGAATTTTTAAACTTAATTTTGAAGTTGATTTAAGATATACTTAACTTAGTTTCTTTTTCAGCATTGG[T/C]
TTTTAAGTCGCTAAGAATAAATATATAAAATTTTTATCTATAAATTAATTTTTATTTCCTAATAAGTGGCTTATTAGGGAATATAGTCAACCAAGAAGAC

Reverse complement sequence

GTCTTCTTGGTTGACTATATTCCCTAATAAGCCACTTATTAGGAAATAAAAATTAATTTATAGATAAAAATTTTATATATTTATTCTTAGCGACTTAAAA[A/G]
CCAATGCTGAAAAAGAAACTAAGTTAAGTATATCTTAAATCAACTTCAAAATTAAGTTTAAAAATTCAAATTTTGGCTTTTGCTCTAGCTTATTAGCCCA

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	90.50%	9.50%	0.04%	0.00%	NA
All Indica	2759	95.60%	4.30%	0.07%	0.00%	NA
All Japonica	1512	80.40%	19.60%	0.00%	0.00%	NA
Aus	269	92.90%	7.10%	0.00%	0.00%	NA
Indica I	595	99.20%	0.70%	0.17%	0.00%	NA
Indica II	465	95.70%	4.10%	0.22%	0.00%	NA
Indica III	913	94.40%	5.60%	0.00%	0.00%	NA
Indica Intermediate	786	94.10%	5.90%	0.00%	0.00%	NA
Temperate Japonica	767	77.20%	22.80%	0.00%	0.00%	NA
Tropical Japonica	504	84.50%	15.50%	0.00%	0.00%	NA
Japonica Intermediate	241	81.70%	18.30%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	86.70%	13.30%	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
vg0224550937	T -> C	LOC_Os02g40480.1	upstream_gene_variant ; 2349.0bp to feature; MODIFIER	silent_mutation	Average:51.547; most accessible tissue: Callus, score: 91.471	N	N	N	N
vg0224550937	T -> C	LOC_Os02g40480-LOC_Os02g40490	intergenic_region ; MODIFIER	silent_mutation	Average:51.547; most accessible tissue: Callus, score: 91.471	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0224550937	NA	9.63E-07	mr1940	Jap_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
vg0224550937	1.85E-06	NA	mr1360_2	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