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Detailed information for vg0801766010:

Variant ID: vg0801766010 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 1766010
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, A: 0.05, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

TTTATGTACATATATAGATAGAAAAAAATAAAGGATTCTATAGTACTTTCGCCTGTTTCATATTGTAAGTTGTTTTGACTTTTTTCTTAATTAAACTTTT[G/A]
TAAGTTTGACTAAATTTATAGATAAATTTAACAACATTTATAACATAAAATTAGTTTTATTCAAACTAATATTTAATATATTTTAATAATATGTTTGTTT

Reverse complement sequence

AAACAAACATATTATTAAAATATATTAAATATTAGTTTGAATAAAACTAATTTTATGTTATAAATGTTGTTAAATTTATCTATAAATTTAGTCAAACTTA[C/T]
AAAAGTTTAATTAAGAAAAAAGTCAAAACAACTTACAATATGAAACAGGCGAAAGTACTATAGAATCCTTTATTTTTTTCTATCTATATATGTACATAAA

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	86.60%	12.00%	0.06%	1.29%	NA
All Indica	2759	86.90%	12.80%	0.07%	0.29%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	4.50%	75.80%	0.37%	19.33%	NA
Indica I	595	72.10%	27.90%	0.00%	0.00%	NA
Indica II	465	98.90%	1.10%	0.00%	0.00%	NA
Indica III	913	88.90%	10.70%	0.00%	0.33%	NA
Indica Intermediate	786	88.50%	10.60%	0.25%	0.64%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	92.20%	6.70%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0801766010	G -> A	LOC_Os08g03720.1	intron_variant ; MODIFIER	silent_mutation	Average:34.214; most accessible tissue: Callus, score: 63.775	N	N	N	N
vg0801766010	G -> DEL	N	N	silent_mutation	Average:34.214; most accessible tissue: Callus, score: 63.775	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0801766010	NA	2.10E-06	mr1621	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
vg0801766010	NA	2.78E-06	mr1706	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
vg0801766010	NA	2.85E-08	mr1739	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
vg0801766010	NA	2.43E-12	mr1739	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
vg0801766010	NA	1.49E-17	mr1765	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
vg0801766010	NA	6.20E-26	mr1817	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
vg0801766010	NA	9.25E-06	mr1817	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
vg0801766010	NA	2.36E-12	mr1918	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
vg0801766010	NA	4.60E-06	mr1265_2	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
vg0801766010	NA	8.03E-06	mr1296_2	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
vg0801766010	NA	7.85E-09	mr1347_2	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
vg0801766010	NA	9.76E-06	mr1483_2	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
vg0801766010	NA	8.71E-08	mr1510_2	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
vg0801766010	NA	4.20E-06	mr1722_2	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
vg0801766010	NA	5.51E-12	mr1739_2	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
vg0801766010	NA	6.46E-12	mr1739_2	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
vg0801766010	NA	3.86E-08	mr1895_2	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
vg0801766010	NA	5.77E-06	mr1895_2	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
vg0801766010	NA	1.64E-06	mr1929_2	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