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Detailed information for vg0809876655:

Variant ID: vg0809876655 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 9876655
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:

GAGCGGCACAGTAAAAAGCCCACGAAGGGAAAGCCCAATACTGTTCCGTTCGGCCCGGGAAAAGAAAATAATAATAACCACCAATCGCAGGAGGCGAAGT[G/A]
TGGCAAAATAATAATAGCCGCACAAGTAACAAACTTCATTCGCAGGGATAATGTAGGTTTCGGCAGGAGCATCGGTCGAAAGGGGGCGCCGCATACCATA

Reverse complement sequence

TATGGTATGCGGCGCCCCCTTTCGACCGATGCTCCTGCCGAAACCTACATTATCCCTGCGAATGAAGTTTGTTACTTGTGCGGCTATTATTATTTTGCCA[C/T]
ACTTCGCCTCCTGCGATTGGTGGTTATTATTATTTTCTTTTCCCGGGCCGAACGGAACAGTATTGGGCTTTCCCTTCGTGGGCTTTTTACTGTGCCGCTC

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	82.10%	8.90%	1.04%	7.98%	NA
All Indica	2759	84.80%	14.80%	0.43%	0.00%	NA
All Japonica	1512	73.10%	0.20%	2.05%	24.60%	NA
Aus	269	98.50%	1.50%	0.00%	0.00%	NA
Indica I	595	95.80%	4.00%	0.17%	0.00%	NA
Indica II	465	91.60%	8.20%	0.22%	0.00%	NA
Indica III	913	73.50%	25.70%	0.77%	0.00%	NA
Indica Intermediate	786	85.60%	14.00%	0.38%	0.00%	NA
Temperate Japonica	767	98.00%	0.00%	0.00%	1.96%	NA
Tropical Japonica	504	45.40%	0.60%	5.36%	48.61%	NA
Japonica Intermediate	241	51.90%	0.00%	1.66%	46.47%	NA
VI/Aromatic	96	96.90%	1.00%	1.04%	1.04%	NA
Intermediate	90	83.30%	6.70%	5.56%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0809876655	G -> A	LOC_Os08g16190.1	downstream_gene_variant ; 2437.0bp to feature; MODIFIER	silent_mutation	Average:48.296; most accessible tissue: Zhenshan97 flag leaf, score: 71.238	N	N	N	N
vg0809876655	G -> A	LOC_Os08g16200.1	intron_variant ; MODIFIER	silent_mutation	Average:48.296; most accessible tissue: Zhenshan97 flag leaf, score: 71.238	N	N	N	N
vg0809876655	G -> DEL	N	N	silent_mutation	Average:48.296; most accessible tissue: Zhenshan97 flag leaf, score: 71.238	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0809876655	1.38E-06	NA	mr1342	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
vg0809876655	7.48E-06	7.48E-06	mr1342	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