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Detailed information for vg0910802971:

Variant ID: vg0910802971 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 10802971
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.69, G: 0.32, others allele: 0.00, population size: 182. )

Flanking Sequence (100 bp) in Reference Genome:

ACCATATTCGTATTCATATCCGGGAGAAAATATCCGTATTCGTATCCGTATCCGAACTATCTGAGAATTATCCGATCCGAAAAGTATTCGTATTCGTTTT[G/A]
AGCGGACAGAAACTATCTGCTCCGTTTTCATCCCTACATGACAGTCCAACAATTTCCTCTTATTAATTAGGAAGGGAATCCTTCCTAGCTGCACCGACCT

Reverse complement sequence

AGGTCGGTGCAGCTAGGAAGGATTCCCTTCCTAATTAATAAGAGGAAATTGTTGGACTGTCATGTAGGGATGAAAACGGAGCAGATAGTTTCTGTCCGCT[C/T]
AAAACGAATACGAATACTTTTCGGATCGGATAATTCTCAGATAGTTCGGATACGGATACGAATACGGATATTTTCTCCCGGATATGAATACGAATATGGT

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	75.20%	24.50%	0.21%	0.00%	NA
All Indica	2759	69.90%	29.80%	0.25%	0.00%	NA
All Japonica	1512	94.90%	5.00%	0.07%	0.00%	NA
Aus	269	14.90%	84.80%	0.37%	0.00%	NA
Indica I	595	81.30%	18.30%	0.34%	0.00%	NA
Indica II	465	54.80%	45.20%	0.00%	0.00%	NA
Indica III	913	75.90%	23.80%	0.33%	0.00%	NA
Indica Intermediate	786	63.20%	36.50%	0.25%	0.00%	NA
Temperate Japonica	767	95.60%	4.40%	0.00%	0.00%	NA
Tropical Japonica	504	92.70%	7.30%	0.00%	0.00%	NA
Japonica Intermediate	241	97.50%	2.10%	0.41%	0.00%	NA
VI/Aromatic	96	83.30%	16.70%	0.00%	0.00%	NA
Intermediate	90	80.00%	18.90%	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
vg0910802971	G -> A	LOC_Os09g17670.1	upstream_gene_variant ; 1578.0bp to feature; MODIFIER	silent_mutation	Average:55.057; most accessible tissue: Callus, score: 87.322	N	N	N	N
vg0910802971	G -> A	LOC_Os09g17650.1	downstream_gene_variant ; 4582.0bp to feature; MODIFIER	silent_mutation	Average:55.057; most accessible tissue: Callus, score: 87.322	N	N	N	N
vg0910802971	G -> A	LOC_Os09g17660.1	downstream_gene_variant ; 591.0bp to feature; MODIFIER	silent_mutation	Average:55.057; most accessible tissue: Callus, score: 87.322	N	N	N	N
vg0910802971	G -> A	LOC_Os09g17660-LOC_Os09g17670	intergenic_region ; MODIFIER	silent_mutation	Average:55.057; most accessible tissue: Callus, score: 87.322	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0910802971	NA	3.80E-07	mr1367	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