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Detailed information for vg0210259508:

Variant ID: vg0210259508 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 10259508
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, C: 0.01, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:

GTTTGAACTGGAAACCTGCCAGGAGGTTCCGGGCAAAAGTGTCAGGAACTTCCGGGCAGCACTTAGGAAAATTTTTGCTTTGAAACGGCGCCCGGAAGTT[T/C]
CGGCCAGAACCTCCGGGTAGCCCTCTCTGTCCCGGGGAGAAAATCATTTTTCAAAAATGATTCAAAAAATCTTTTGACTCATGGATATGACTAAGAGCAC

Reverse complement sequence

GTGCTCTTAGTCATATCCATGAGTCAAAAGATTTTTTGAATCATTTTTGAAAAATGATTTTCTCCCCGGGACAGAGAGGGCTACCCGGAGGTTCTGGCCG[A/G]
AACTTCCGGGCGCCGTTTCAAAGCAAAAATTTTCCTAAGTGCTGCCCGGAAGTTCCTGACACTTTTGCCCGGAACCTCCTGGCAGGTTTCCAGTTCAAAC

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	46.90%	1.30%	3.68%	48.14%	NA
All Indica	2759	16.90%	2.00%	3.41%	77.71%	NA
All Japonica	1512	98.40%	0.00%	0.07%	1.52%	NA
Aus	269	43.50%	1.90%	28.25%	26.39%	NA
Indica I	595	6.90%	1.20%	1.85%	90.08%	NA
Indica II	465	9.00%	1.50%	1.94%	87.53%	NA
Indica III	913	30.30%	3.20%	4.82%	61.66%	NA
Indica Intermediate	786	13.50%	1.50%	3.82%	81.17%	NA
Temperate Japonica	767	99.00%	0.00%	0.00%	1.04%	NA
Tropical Japonica	504	97.40%	0.00%	0.00%	2.58%	NA
Japonica Intermediate	241	98.80%	0.00%	0.41%	0.83%	NA
VI/Aromatic	96	93.80%	0.00%	0.00%	6.25%	NA
Intermediate	90	60.00%	2.20%	3.33%	34.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0210259508	T -> DEL	N	N	silent_mutation	Average:10.32; most accessible tissue: Callus, score: 28.971	N	N	N	N
vg0210259508	T -> C	LOC_Os02g17760.1	upstream_gene_variant ; 2478.0bp to feature; MODIFIER	silent_mutation	Average:10.32; most accessible tissue: Callus, score: 28.971	N	N	N	N
vg0210259508	T -> C	LOC_Os02g17750-LOC_Os02g17760	intergenic_region ; MODIFIER	silent_mutation	Average:10.32; most accessible tissue: Callus, score: 28.971	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0210259508	NA	3.05E-08	mr1278	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
vg0210259508	NA	4.09E-09	mr1302	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
vg0210259508	NA	2.14E-08	mr1604	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
vg0210259508	NA	6.22E-07	mr1810	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
vg0210259508	NA	3.22E-07	mr1824	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
vg0210259508	NA	1.46E-07	mr1886	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
vg0210259508	3.99E-06	3.99E-06	mr1894	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