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Detailed information for vg1121223361:

Variant ID: vg1121223361 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21223361
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:

TAATTAACATGTCAAGTTTGTGTTAAATCTCAGACATTAAAATCTATGCCTCTTATAATCCAATGGTGTAAATAATTCATATTTTTTTCGATTAATGTAG[G/A]
AATTTCTAGCCTCCACGGTGAACGTGGTGTCTTCTTTTCGAGCTGTCTTAATAATATAATAGATAGATGAAAAAAGTAATACGCCATAATCTTATTAATA

Reverse complement sequence

TATTAATAAGATTATGGCGTATTACTTTTTTCATCTATCTATTATATTATTAAGACAGCTCGAAAAGAAGACACCACGTTCACCGTGGAGGCTAGAAATT[C/T]
CTACATTAATCGAAAAAAATATGAATTATTTACACCATTGGATTATAAGAGGCATAGATTTTAATGTCTGAGATTTAACACAAACTTGACATGTTAATTA

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	87.10%	12.20%	0.06%	0.68%	NA
All Indica	2759	94.40%	5.30%	0.00%	0.25%	NA
All Japonica	1512	76.90%	22.90%	0.13%	0.07%	NA
Aus	269	90.70%	0.70%	0.37%	8.18%	NA
Indica I	595	95.60%	4.40%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	90.10%	9.40%	0.00%	0.44%	NA
Indica Intermediate	786	95.30%	4.30%	0.00%	0.38%	NA
Temperate Japonica	767	89.60%	10.30%	0.13%	0.00%	NA
Tropical Japonica	504	69.40%	30.60%	0.00%	0.00%	NA
Japonica Intermediate	241	52.30%	46.90%	0.41%	0.41%	NA
VI/Aromatic	96	31.20%	67.70%	0.00%	1.04%	NA
Intermediate	90	80.00%	18.90%	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
vg1121223361	G -> A	LOC_Os11g36100.1	upstream_gene_variant ; 1441.0bp to feature; MODIFIER	silent_mutation	Average:50.167; most accessible tissue: Zhenshan97 panicle, score: 72.468	N	N	N	N
vg1121223361	G -> A	LOC_Os11g36110.1	upstream_gene_variant ; 3838.0bp to feature; MODIFIER	silent_mutation	Average:50.167; most accessible tissue: Zhenshan97 panicle, score: 72.468	N	N	N	N
vg1121223361	G -> A	LOC_Os11g36090-LOC_Os11g36100	intergenic_region ; MODIFIER	silent_mutation	Average:50.167; most accessible tissue: Zhenshan97 panicle, score: 72.468	N	N	N	N
vg1121223361	G -> DEL	N	N	silent_mutation	Average:50.167; most accessible tissue: Zhenshan97 panicle, score: 72.468	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121223361	NA	1.35E-06	mr1280	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
vg1121223361	1.96E-06	1.95E-06	mr1597	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
vg1121223361	NA	1.87E-06	mr1729	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