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Detailed information for vg0825346640:

Variant ID: vg0825346640 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 25346640
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.70, C: 0.25, A: 0.05, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:

TCCGTTGTTCATTAGCTAATGCCTTTCAGTTGCAATAGGAATGGAGAACAGTATAAGAATACACAGTCATCTTAAGCTTCAGAGGCACGAACAAGGAACG[T/A]
ATGAATTTGTGAAAAGCAATAAGAGAAAAGGAAAAATGCTAGCATATGAGTTTGTCAAGACACGGACAGTGAAGTGGAGATTCATCAGCTGGTGCACTCC

Reverse complement sequence

GGAGTGCACCAGCTGATGAATCTCCACTTCACTGTCCGTGTCTTGACAAACTCATATGCTAGCATTTTTCCTTTTCTCTTATTGCTTTTCACAAATTCAT[A/T]
CGTTCCTTGTTCGTGCCTCTGAAGCTTAAGATGACTGTGTATTCTTATACTGTTCTCCATTCCTATTGCAACTGAAAGGCATTAGCTAATGAACAACGGA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	85.10%	14.90%	0.04%	0.00%	NA
All Indica	2759	81.70%	18.20%	0.07%	0.00%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	33.10%	66.90%	0.00%	0.00%	NA
Indica I	595	81.80%	18.20%	0.00%	0.00%	NA
Indica II	465	94.40%	5.60%	0.00%	0.00%	NA
Indica III	913	81.10%	18.90%	0.00%	0.00%	NA
Indica Intermediate	786	74.80%	24.90%	0.25%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	88.90%	11.10%	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
vg0825346640	T -> A	LOC_Os08g40020.1	3_prime_UTR_variant ; 365.0bp to feature; MODIFIER	silent_mutation	Average:42.353; most accessible tissue: Callus, score: 63.595	N	N	N	N
vg0825346640	T -> A	LOC_Os08g40010.1	downstream_gene_variant ; 2691.0bp to feature; MODIFIER	silent_mutation	Average:42.353; most accessible tissue: Callus, score: 63.595	N	N	N	N
vg0825346640	T -> A	LOC_Os08g40030.1	downstream_gene_variant ; 4884.0bp to feature; MODIFIER	silent_mutation	Average:42.353; most accessible tissue: Callus, score: 63.595	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0825346640	NA	5.45E-06	mr1207	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
vg0825346640	NA	1.45E-06	mr1587	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
vg0825346640	NA	4.17E-06	mr1665	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