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Detailed information for vg0803057970:

Variant ID: vg0803057970 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 3057970
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:

CCTCGTTTTGATTTTGATCGTGTTTCACATCTTGAAACTGCACATGAGATTTGGATTGCTTTAGAAAACTTTCATCAAGGAACTTCAAATATCAAGGAAC[T/C]
ACGCAAAGATGTTTTCAAAAAGGATTACATAAAATTTGAGAAGAAACATGGAGAGGCTTTGGATGATTACCTTGCATGCTTTGACAAAGTTTTGAGTAAT

Reverse complement sequence

ATTACTCAAAACTTTGTCAAAGCATGCAAGGTAATCATCCAAAGCCTCTCCATGTTTCTTCTCAAATTTTATGTAATCCTTTTTGAAAACATCTTTGCGT[A/G]
GTTCCTTGATATTTGAAGTTCCTTGATGAAAGTTTTCTAAAGCAATCCAAATCTCATGTGCAGTTTCAAGATGTGAAACACGATCAAAATCAAAACGAGG

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	92.80%	2.80%	4.34%	0.00%	NA
All Indica	2759	88.10%	4.60%	7.32%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	78.00%	4.50%	17.48%	0.00%	NA
Indica II	465	96.80%	1.50%	1.72%	0.00%	NA
Indica III	913	90.30%	7.10%	2.63%	0.00%	NA
Indica Intermediate	786	88.00%	3.60%	8.40%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	92.20%	4.40%	3.33%	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
vg0803057970	T -> C	LOC_Os08g05700.1	upstream_gene_variant ; 574.0bp to feature; MODIFIER	silent_mutation	Average:29.554; most accessible tissue: Callus, score: 59.044	N	N	N	N
vg0803057970	T -> C	LOC_Os08g05710.1	upstream_gene_variant ; 3896.0bp to feature; MODIFIER	silent_mutation	Average:29.554; most accessible tissue: Callus, score: 59.044	N	N	N	N
vg0803057970	T -> C	LOC_Os08g05690.1	downstream_gene_variant ; 1897.0bp to feature; MODIFIER	silent_mutation	Average:29.554; most accessible tissue: Callus, score: 59.044	N	N	N	N
vg0803057970	T -> C	LOC_Os08g05690-LOC_Os08g05700	intergenic_region ; MODIFIER	silent_mutation	Average:29.554; most accessible tissue: Callus, score: 59.044	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0803057970	NA	4.47E-07	mr1425_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
vg0803057970	NA	8.97E-06	mr1425_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