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Detailed information for vg0320217493:

Variant ID: vg0320217493 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 20217493
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.07, others allele: 0.00, population size: 61. )

Flanking Sequence (100 bp) in Reference Genome:

TTGATTTTAATATCTTGTGCATAAATATTCGTAGGGTTAAATATATTCTTGTAAATTATATCTATTGCTTAAATGTCGATCTTTTCTTTACTTTCTTTGT[G/A]
ATCATTTACGGTTTGGCAAGCCATAGCAATCATAACAACCAGCATGCTGCAAAAGTTTTAAAAAGTTCGAAATTTTAGTAATTTTTATTGTGAGGAATTT

Reverse complement sequence

AAATTCCTCACAATAAAAATTACTAAAATTTCGAACTTTTTAAAACTTTTGCAGCATGCTGGTTGTTATGATTGCTATGGCTTGCCAAACCGTAAATGAT[C/T]
ACAAAGAAAGTAAAGAAAAGATCGACATTTAAGCAATAGATATAATTTACAAGAATATATTTAACCCTACGAATATTTATGCACAAGATATTAAAATCAA

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	84.70%	14.30%	0.38%	0.61%	NA
All Indica	2759	81.00%	18.30%	0.58%	0.11%	NA
All Japonica	1512	87.40%	10.90%	0.13%	1.52%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	94.30%	5.20%	0.50%	0.00%	NA
Indica II	465	77.00%	21.30%	1.72%	0.00%	NA
Indica III	913	71.50%	28.10%	0.33%	0.00%	NA
Indica Intermediate	786	84.40%	15.00%	0.25%	0.38%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	69.80%	29.80%	0.20%	0.20%	NA
Japonica Intermediate	241	84.20%	6.20%	0.41%	9.13%	NA
VI/Aromatic	96	96.90%	0.00%	0.00%	3.12%	NA
Intermediate	90	93.30%	6.70%	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
vg0320217493	G -> A	LOC_Os03g36520.1	upstream_gene_variant ; 4020.0bp to feature; MODIFIER	silent_mutation	Average:42.723; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0320217493	G -> A	LOC_Os03g36500.1	intron_variant ; MODIFIER	silent_mutation	Average:42.723; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0320217493	G -> DEL	N	N	silent_mutation	Average:42.723; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0320217493	NA	1.93E-07	mr1217	Jap_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
vg0320217493	3.87E-06	NA	mr1362	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
vg0320217493	3.60E-07	3.06E-08	mr1439	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
vg0320217493	NA	4.32E-07	mr1845	Jap_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
vg0320217493	2.78E-06	6.41E-09	mr1852	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
vg0320217493	NA	9.33E-09	mr1852	Jap_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
vg0320217493	NA	5.80E-08	mr1136_2	Jap_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
vg0320217493	NA	9.53E-07	mr1439_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