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Detailed information for vg0224480783:

Variant ID: vg0224480783 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 24480783
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.91, T: 0.09, others allele: 0.00, population size: 115. )

Flanking Sequence (100 bp) in Reference Genome:

GCTTCTTAGTTTATTTTTCAGAATCTGTAACTACAGATTCTTAGAAGCTGTGGACTGTTTGGGGTAGCTTCTAGTAGAAGCAGCTTTTTGGGAAAAGCTA[T/C]
AGTTGGGACAAGCTCCCCCAAACAGGGCCTTTGGCACAAACCAACCAAGTCCAAAATTCCATGCAAAGAGCATGAAAGTCCAAAGAATATGTTTGGTTTG

Reverse complement sequence

CAAACCAAACATATTCTTTGGACTTTCATGCTCTTTGCATGGAATTTTGGACTTGGTTGGTTTGTGCCAAAGGCCCTGTTTGGGGGAGCTTGTCCCAACT[A/G]
TAGCTTTTCCCAAAAAGCTGCTTCTACTAGAAGCTACCCCAAACAGTCCACAGCTTCTAAGAATCTGTAGTTACAGATTCTGAAAAATAAACTAAGAAGC

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	84.50%	15.40%	0.13%	0.00%	NA
All Indica	2759	89.50%	10.50%	0.00%	0.00%	NA
All Japonica	1512	75.10%	24.50%	0.33%	0.00%	NA
Aus	269	87.00%	13.00%	0.00%	0.00%	NA
Indica I	595	98.70%	1.30%	0.00%	0.00%	NA
Indica II	465	86.70%	13.30%	0.00%	0.00%	NA
Indica III	913	86.30%	13.70%	0.00%	0.00%	NA
Indica Intermediate	786	87.80%	12.20%	0.00%	0.00%	NA
Temperate Japonica	767	69.50%	30.00%	0.52%	0.00%	NA
Tropical Japonica	504	83.50%	16.30%	0.20%	0.00%	NA
Japonica Intermediate	241	75.50%	24.50%	0.00%	0.00%	NA
VI/Aromatic	96	82.30%	17.70%	0.00%	0.00%	NA
Intermediate	90	85.60%	13.30%	1.11%	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
vg0224480783	T -> C	LOC_Os02g40410.1	upstream_gene_variant ; 3460.0bp to feature; MODIFIER	silent_mutation	Average:44.316; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N
vg0224480783	T -> C	LOC_Os02g40420.1	downstream_gene_variant ; 2207.0bp to feature; MODIFIER	silent_mutation	Average:44.316; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N
vg0224480783	T -> C	LOC_Os02g40410-LOC_Os02g40420	intergenic_region ; MODIFIER	silent_mutation	Average:44.316; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0224480783	7.95E-07	NA	mr1099_2	Ind_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
vg0224480783	1.77E-06	NA	mr1123_2	Ind_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
vg0224480783	NA	1.84E-06	mr1188_2	Ind_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