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Detailed information for vg0209301301:

Variant ID: vg0209301301 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 9301301
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:

TCGAGATCAGCTCGTCATTACTAGGATACCATGCTTGTCATCATGAGCATATCATGCTTGTCATTTACTTCTAACCTGCCACCAACTGCCTCATATTAGC[T/C]
TTCCTAGTCTCCGGGTGATAACTACTTCTGCTATTTGATGCAAGGGTCGATAACTTTGCCTTTGAATTATGTTTCCCAAGAGAACCAACTTATCCCACTT

Reverse complement sequence

AAGTGGGATAAGTTGGTTCTCTTGGGAAACATAATTCAAAGGCAAAGTTATCGACCCTTGCATCAAATAGCAGAAGTAGTTATCACCCGGAGACTAGGAA[A/G]
GCTAATATGAGGCAGTTGGTGGCAGGTTAGAAGTAAATGACAAGCATGATATGCTCATGATGACAAGCATGGTATCCTAGTAATGACGAGCTGATCTCGA

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	43.30%	10.20%	4.89%	41.62%	NA
All Indica	2759	13.40%	12.80%	6.63%	67.09%	NA
All Japonica	1512	98.10%	0.10%	0.20%	1.65%	NA
Aus	269	16.70%	42.80%	13.01%	27.51%	NA
Indica I	595	22.50%	10.60%	5.04%	61.85%	NA
Indica II	465	15.10%	5.40%	8.82%	70.75%	NA
Indica III	913	5.30%	17.20%	7.01%	70.54%	NA
Indica Intermediate	786	15.10%	13.90%	6.11%	64.89%	NA
Temperate Japonica	767	99.50%	0.00%	0.00%	0.52%	NA
Tropical Japonica	504	96.20%	0.00%	0.40%	3.37%	NA
Japonica Intermediate	241	97.50%	0.40%	0.41%	1.66%	NA
VI/Aromatic	96	89.60%	6.20%	3.12%	1.04%	NA
Intermediate	90	68.90%	5.60%	7.78%	17.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0209301301	T -> DEL	N	N	silent_mutation	Average:10.665; most accessible tissue: Callus, score: 26.684	N	N	N	N
vg0209301301	T -> C	LOC_Os02g16350.1	upstream_gene_variant ; 1909.0bp to feature; MODIFIER	silent_mutation	Average:10.665; most accessible tissue: Callus, score: 26.684	N	N	N	N
vg0209301301	T -> C	LOC_Os02g16340.1	downstream_gene_variant ; 3481.0bp to feature; MODIFIER	silent_mutation	Average:10.665; most accessible tissue: Callus, score: 26.684	N	N	N	N
vg0209301301	T -> C	LOC_Os02g16340-LOC_Os02g16350	intergenic_region ; MODIFIER	silent_mutation	Average:10.665; most accessible tissue: Callus, score: 26.684	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0209301301	3.69E-06	NA	mr1946	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
vg0209301301	NA	2.27E-06	mr1547_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