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Detailed information for vg0825755939:

Variant ID: vg0825755939 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 25755939
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:

TGACATTCAAAATAAATGCAATAGTTGAATAGAAACAATAGCTTTAAACGGAATCAACATGCTCAAAGGGTTGTTTAGGATCTGTGTGACTTGACTTGCT[G/A]
ACCTTGGAACTCTTCAAAGTCTTCTCCTGCAAACTCAGACTCTCCGGGAACGTCGGAATGTAAGCATAAAAGAGCAAAAATCACCAAAACAGTACATAAA

Reverse complement sequence

TTTATGTACTGTTTTGGTGATTTTTGCTCTTTTATGCTTACATTCCGACGTTCCCGGAGAGTCTGAGTTTGCAGGAGAAGACTTTGAAGAGTTCCAAGGT[C/T]
AGCAAGTCAAGTCACACAGATCCTAAACAACCCTTTGAGCATGTTGATTCCGTTTAAAGCTATTGTTTCTATTCAACTATTGCATTTATTTTGAATGTCA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	79.50%	20.40%	0.13%	0.02%	NA
All Indica	2759	66.30%	33.50%	0.22%	0.04%	NA
All Japonica	1512	98.40%	1.60%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	84.70%	15.10%	0.17%	0.00%	NA
Indica II	465	81.50%	18.30%	0.22%	0.00%	NA
Indica III	913	44.90%	54.70%	0.33%	0.11%	NA
Indica Intermediate	786	68.20%	31.70%	0.13%	0.00%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	98.60%	1.40%	0.00%	0.00%	NA
Japonica Intermediate	241	93.80%	6.20%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	82.20%	17.80%	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
vg0825755939	G -> A	LOC_Os08g40670.1	upstream_gene_variant ; 2613.0bp to feature; MODIFIER	silent_mutation	Average:34.765; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N
vg0825755939	G -> A	LOC_Os08g40680.1	downstream_gene_variant ; 2912.0bp to feature; MODIFIER	silent_mutation	Average:34.765; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N
vg0825755939	G -> A	LOC_Os08g40670-LOC_Os08g40680	intergenic_region ; MODIFIER	silent_mutation	Average:34.765; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N
vg0825755939	G -> DEL	N	N	silent_mutation	Average:34.765; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0825755939	NA	6.22E-06	mr1536	Ind_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
vg0825755939	NA	6.34E-09	mr1536_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