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Detailed information for vg0332502505:

Variant ID: vg0332502505 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 32502505
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, C: 0.01, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:

TGAGTGTAAAAATAAAAGTTATCAAGGGAAACTCATAACTGATGACAATCTGACATCATTTACAAGCACTGTGATTTGCAATACCCATGACAAATTTTCG[T/C]
GAATAATATATATAAATCAACGGAGTAGAAAAGATAAAAAGAATATATGCTGCATGGATTAAAAATCAAAAATTAGTTACTCCTATAAAAAAAAGAGGGA

Reverse complement sequence

TCCCTCTTTTTTTTATAGGAGTAACTAATTTTTGATTTTTAATCCATGCAGCATATATTCTTTTTATCTTTTCTACTCCGTTGATTTATATATATTATTC[A/G]
CGAAAATTTGTCATGGGTATTGCAAATCACAGTGCTTGTAAATGATGTCAGATTGTCATCAGTTATGAGTTTCCCTTGATAACTTTTATTTTTACACTCA

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	53.10%	46.40%	0.53%	0.00%	NA
All Indica	2759	21.00%	78.10%	0.87%	0.00%	NA
All Japonica	1512	99.30%	0.70%	0.00%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	10.60%	88.90%	0.50%	0.00%	NA
Indica II	465	14.60%	84.10%	1.29%	0.00%	NA
Indica III	913	27.90%	71.60%	0.44%	0.00%	NA
Indica Intermediate	786	24.70%	73.90%	1.40%	0.00%	NA
Temperate Japonica	767	99.50%	0.50%	0.00%	0.00%	NA
Tropical Japonica	504	98.80%	1.20%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	71.10%	27.80%	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
vg0332502505	T -> C	LOC_Os03g57020-LOC_Os03g57030	intergenic_region ; MODIFIER	silent_mutation	Average:40.015; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0332502505	NA	9.47E-26	mr1181	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
vg0332502505	NA	2.96E-10	mr1524	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
vg0332502505	NA	1.93E-07	mr1716	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
vg0332502505	4.82E-07	NA	mr1723	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
vg0332502505	1.74E-06	8.86E-10	mr1723	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
vg0332502505	NA	3.10E-14	mr1807	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
vg0332502505	4.33E-06	1.60E-34	mr1723_2	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
vg0332502505	NA	1.77E-10	mr1723_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