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Detailed information for vg0820374951:

Variant ID: vg0820374951 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 20374951
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 127. )

Flanking Sequence (100 bp) in Reference Genome:

AAAGAATATATGATTGGTCTTAGCATATCCTGACACATGATTTGGTTTGATGTACTTGTATATACTTGCAGCCATGAATGTTCCCGTTGAAAATTATTTT[G/T]
TACGTGCCTATTTAGATTGCTACCAAAAACATACCATACCAATATTTTGGTAATTTAAATAGTACTTGTGTTTGATTTGAATTGAAGCCCATTCATTGGT

Reverse complement sequence

ACCAATGAATGGGCTTCAATTCAAATCAAACACAAGTACTATTTAAATTACCAAAATATTGGTATGGTATGTTTTTGGTAGCAATCTAAATAGGCACGTA[C/A]
AAAATAATTTTCAACGGGAACATTCATGGCTGCAAGTATATACAAGTACATCAAACCAAATCATGTGTCAGGATATGCTAAGACCAATCATATATTCTTT

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	94.70%	5.10%	0.21%	0.00%	NA
All Indica	2759	96.40%	3.50%	0.11%	0.00%	NA
All Japonica	1512	94.40%	5.20%	0.40%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	96.60%	3.20%	0.22%	0.00%	NA
Indica III	913	94.90%	5.10%	0.00%	0.00%	NA
Indica Intermediate	786	95.50%	4.30%	0.13%	0.00%	NA
Temperate Japonica	767	97.70%	2.00%	0.39%	0.00%	NA
Tropical Japonica	504	90.30%	9.70%	0.00%	0.00%	NA
Japonica Intermediate	241	92.50%	6.20%	1.24%	0.00%	NA
VI/Aromatic	96	44.80%	54.20%	1.04%	0.00%	NA
Intermediate	90	85.60%	14.40%	0.00%	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
vg0820374951	G -> T	LOC_Os08g32870.1	upstream_gene_variant ; 4843.0bp to feature; MODIFIER	silent_mutation	Average:46.447; most accessible tissue: Zhenshan97 panicle, score: 63.607	N	N	N	N
vg0820374951	G -> T	LOC_Os08g32860.1	downstream_gene_variant ; 2480.0bp to feature; MODIFIER	silent_mutation	Average:46.447; most accessible tissue: Zhenshan97 panicle, score: 63.607	N	N	N	N
vg0820374951	G -> T	LOC_Os08g32860-LOC_Os08g32870	intergenic_region ; MODIFIER	silent_mutation	Average:46.447; most accessible tissue: Zhenshan97 panicle, score: 63.607	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0820374951	9.39E-07	NA	mr1439	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
vg0820374951	NA	2.36E-06	mr1177_2	Jap_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
vg0820374951	NA	1.59E-06	mr1252_2	Jap_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