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Detailed information for vg0316482623:

Variant ID: vg0316482623 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 16482623
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.03, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:

CCGAGGAGTAGGCTTCGTCCGGGCCGTCGAGGATGCCTGTGGAGTGGTGTTCCCGCTGCAATCCAAGTCAAGGCTTAGCTCTATTTATCTTTTAATTTTC[C/T]
GCTGCATTTATGTAAGACTTTTATGATGTTTGTAAGATGTGGATCTGTATGTCAACTTTGTCGTTTGTGTACCCCGGCCGGTCCTGGACGGGGATTTTAA

Reverse complement sequence

TTAAAATCCCCGTCCAGGACCGGCCGGGGTACACAAACGACAAAGTTGACATACAGATCCACATCTTACAAACATCATAAAAGTCTTACATAAATGCAGC[G/A]
GAAAATTAAAAGATAAATAGAGCTAAGCCTTGACTTGGATTGCAGCGGGAACACCACTCCACAGGCATCCTCGACGGCCCGGACGAAGCCTACTCCTCGG

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	49.80%	39.40%	0.80%	9.94%	NA
All Indica	2759	75.50%	22.40%	0.58%	1.52%	NA
All Japonica	1512	1.70%	71.80%	0.73%	25.79%	NA
Aus	269	72.90%	13.40%	2.60%	11.15%	NA
Indica I	595	60.00%	40.00%	0.00%	0.00%	NA
Indica II	465	92.00%	6.70%	0.00%	1.29%	NA
Indica III	913	77.90%	20.60%	0.66%	0.88%	NA
Indica Intermediate	786	74.70%	20.50%	1.27%	3.56%	NA
Temperate Japonica	767	1.70%	56.20%	0.91%	41.20%	NA
Tropical Japonica	504	1.80%	90.10%	0.60%	7.54%	NA
Japonica Intermediate	241	1.20%	83.40%	0.41%	14.94%	NA
VI/Aromatic	96	9.40%	89.60%	0.00%	1.04%	NA
Intermediate	90	46.70%	41.10%	4.44%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0316482623	C -> T	LOC_Os03g29035.1	downstream_gene_variant ; 4011.0bp to feature; MODIFIER	silent_mutation	Average:70.3; most accessible tissue: Zhenshan97 flag leaf, score: 87.472	N	N	N	N
vg0316482623	C -> T	LOC_Os03g29020-LOC_Os03g29035	intergenic_region ; MODIFIER	silent_mutation	Average:70.3; most accessible tissue: Zhenshan97 flag leaf, score: 87.472	N	N	N	N
vg0316482623	C -> DEL	N	N	silent_mutation	Average:70.3; most accessible tissue: Zhenshan97 flag leaf, score: 87.472	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0316482623	NA	2.99E-06	mr1130	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
vg0316482623	NA	1.56E-08	mr1542	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
vg0316482623	NA	1.15E-08	mr1644	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
vg0316482623	1.00E-06	1.96E-10	mr1542_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
vg0316482623	NA	2.64E-09	mr1749_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
vg0316482623	NA	1.04E-11	mr1761_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