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Detailed information for vg0111639734:

Variant ID: vg0111639734 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 11639734
Reference Allele: G	Alternative Allele: T
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.76, T: 0.23, A: 0.01, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:

TCTAGTAATTTATTTATGCACCTAAAGTTTATACACCTCAAGTTTACACATCTAAAGTTTAGAGACCAAAAGTTTATATATCCGATTCAAATTTGAATTT[G/T]
AATTCAAATATATTTTATATATAGTATTTCTATACATCTAAAGTTTATACACCTAAAGTTTATAGACTTAAAGTTTATAAGTCCAAAGTTTATATATCCG

Reverse complement sequence

CGGATATATAAACTTTGGACTTATAAACTTTAAGTCTATAAACTTTAGGTGTATAAACTTTAGATGTATAGAAATACTATATATAAAATATATTTGAATT[C/A]
AAATTCAAATTTGAATCGGATATATAAACTTTTGGTCTCTAAACTTTAGATGTGTAAACTTGAGGTGTATAAACTTTAGGTGCATAAATAAATTACTAGA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	60.10%	39.70%	0.28%	0.00%	NA
All Indica	2759	88.90%	10.70%	0.43%	0.00%	NA
All Japonica	1512	3.20%	96.80%	0.00%	0.00%	NA
Aus	269	78.80%	21.20%	0.00%	0.00%	NA
Indica I	595	98.30%	1.30%	0.34%	0.00%	NA
Indica II	465	78.90%	20.90%	0.22%	0.00%	NA
Indica III	913	89.80%	10.00%	0.22%	0.00%	NA
Indica Intermediate	786	86.50%	12.60%	0.89%	0.00%	NA
Temperate Japonica	767	1.40%	98.60%	0.00%	0.00%	NA
Tropical Japonica	504	5.60%	94.40%	0.00%	0.00%	NA
Japonica Intermediate	241	3.70%	96.30%	0.00%	0.00%	NA
VI/Aromatic	96	81.20%	18.80%	0.00%	0.00%	NA
Intermediate	90	54.40%	44.40%	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
vg0111639734	G -> T	LOC_Os01g20860.1	upstream_gene_variant ; 2658.0bp to feature; MODIFIER	silent_mutation	Average:71.881; most accessible tissue: Zhenshan97 flower, score: 86.268	N	N	N	N
vg0111639734	G -> T	LOC_Os01g20860-LOC_Os01g20870	intergenic_region ; MODIFIER	silent_mutation	Average:71.881; most accessible tissue: Zhenshan97 flower, score: 86.268	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0111639734	2.91E-06	2.91E-06	mr1848_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