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Detailed information for vg0818017838:

Variant ID: vg0818017838 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 18017838
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, T: 0.01, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:

GTTTGGTGTTATGGATAACAAACTGTCTAAGCTATTAAAATGTTGGCACAATCAATTGAAACTAGGTGAAACCTCGCACGTTGCTGCGGGAGTTCAGTAG[G/T]
ATAACAATAGGTAAAAAATAATGTATAAGATAGCTAAACAACATAAACTTACATAAACACTAAAAACAATTGATCTGATATGGCTTAATTAGAGAATAGA

Reverse complement sequence

TCTATTCTCTAATTAAGCCATATCAGATCAATTGTTTTTAGTGTTTATGTAAGTTTATGTTGTTTAGCTATCTTATACATTATTTTTTACCTATTGTTAT[C/A]
CTACTGAACTCCCGCAGCAACGTGCGAGGTTTCACCTAGTTTCAATTGATTGTGCCAACATTTTAATAGCTTAGACAGTTTGTTATCCATAACACCAAAC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	58.80%	41.10%	0.08%	0.00%	NA
All Indica	2759	31.60%	68.30%	0.07%	0.00%	NA
All Japonica	1512	98.70%	1.30%	0.00%	0.00%	NA
Aus	269	98.50%	1.10%	0.37%	0.00%	NA
Indica I	595	42.90%	57.10%	0.00%	0.00%	NA
Indica II	465	10.10%	89.90%	0.00%	0.00%	NA
Indica III	913	29.90%	70.00%	0.11%	0.00%	NA
Indica Intermediate	786	37.90%	62.00%	0.13%	0.00%	NA
Temperate Japonica	767	99.00%	1.00%	0.00%	0.00%	NA
Tropical Japonica	504	98.60%	1.40%	0.00%	0.00%	NA
Japonica Intermediate	241	97.90%	2.10%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	60.00%	38.90%	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
vg0818017838	G -> T	LOC_Os08g29370.1	upstream_gene_variant ; 2279.0bp to feature; MODIFIER	silent_mutation	Average:40.685; most accessible tissue: Minghui63 flag leaf, score: 56.489	N	N	N	N
vg0818017838	G -> T	LOC_Os08g29370.2	upstream_gene_variant ; 2243.0bp to feature; MODIFIER	silent_mutation	Average:40.685; most accessible tissue: Minghui63 flag leaf, score: 56.489	N	N	N	N
vg0818017838	G -> T	LOC_Os08g29360-LOC_Os08g29370	intergenic_region ; MODIFIER	silent_mutation	Average:40.685; most accessible tissue: Minghui63 flag leaf, score: 56.489	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0818017838	NA	5.67E-11	mr1249	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