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Detailed information for vg0806335787:

Variant ID: vg0806335787 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 6335787
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, A: 0.01, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:

ATATTACAAGATTCATCTTTTAAAGTACTTTTATGTGAAGCTAATTTCATATTTGTTGGGAACATAACATAAAATAAATTAATGGTCAAAGTATGTCATT[G/A]
AAGACCGTGTAAAAAAATATTGGCCTTATAATTTGGGACGGAGGGAGTACTAGCGCACAGTTTGGCATATCTTTTAGTTTATAATCGGTCTTCAGTTTGG

Reverse complement sequence

CCAAACTGAAGACCGATTATAAACTAAAAGATATGCCAAACTGTGCGCTAGTACTCCCTCCGTCCCAAATTATAAGGCCAATATTTTTTTACACGGTCTT[C/T]
AATGACATACTTTGACCATTAATTTATTTTATGTTATGTTCCCAACAAATATGAAATTAGCTTCACATAAAAGTACTTTAAAAGATGAATCTTGTAATAT

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	60.20%	5.70%	3.96%	30.07%	NA
All Indica	2759	36.00%	7.40%	6.49%	50.16%	NA
All Japonica	1512	98.60%	0.30%	0.20%	0.86%	NA
Aus	269	77.30%	21.60%	0.00%	1.12%	NA
Indica I	595	28.10%	0.00%	7.23%	64.71%	NA
Indica II	465	23.70%	31.20%	5.38%	39.78%	NA
Indica III	913	40.70%	0.30%	7.34%	51.59%	NA
Indica Intermediate	786	43.60%	7.10%	5.60%	43.64%	NA
Temperate Japonica	767	98.60%	0.10%	0.26%	1.04%	NA
Tropical Japonica	504	99.00%	0.20%	0.00%	0.79%	NA
Japonica Intermediate	241	97.90%	1.20%	0.41%	0.41%	NA
VI/Aromatic	96	97.90%	1.00%	1.04%	0.00%	NA
Intermediate	90	68.90%	3.30%	4.44%	23.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0806335787	G -> A	LOC_Os08g10770.1	downstream_gene_variant ; 1952.0bp to feature; MODIFIER	silent_mutation	Average:35.265; most accessible tissue: Callus, score: 63.167	N	N	N	N
vg0806335787	G -> A	LOC_Os08g10780.1	intron_variant ; MODIFIER	silent_mutation	Average:35.265; most accessible tissue: Callus, score: 63.167	N	N	N	N
vg0806335787	G -> DEL	N	N	silent_mutation	Average:35.265; most accessible tissue: Callus, score: 63.167	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0806335787	NA	4.91E-07	mr1082	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
vg0806335787	5.07E-07	3.65E-07	mr1083	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
vg0806335787	3.99E-06	3.32E-10	mr1410	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
vg0806335787	6.22E-06	7.74E-08	mr1411	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
vg0806335787	NA	4.58E-06	mr1425	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