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Detailed information for vg1121466812:

Variant ID: vg1121466812 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21466812
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.01, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

AAAGGGCTTCCTTTGCAACGGTGGCCGATAAGATCCTGTGTTGGCTAGGGCTTAAGGGATTCCCTAGCCACCCAGCCTAGTGCCGTCCCCCGCTGAGGTC[G/A]
ACTTGCTATGCTCCATGCTTGTGTATTTTGTCCCTTTGTCTCTCTTCTTCTTTACATAATGGATAGAAATTTGGCATTTATATCCATATACGTACGTAGC

Reverse complement sequence

GCTACGTACGTATATGGATATAAATGCCAAATTTCTATCCATTATGTAAAGAAGAAGAGAGACAAAGGGACAAAATACACAAGCATGGAGCATAGCAAGT[C/T]
GACCTCAGCGGGGGACGGCACTAGGCTGGGTGGCTAGGGAATCCCTTAAGCCCTAGCCAACACAGGATCTTATCGGCCACCGTTGCAAAGGAAGCCCTTT

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	91.20%	3.80%	0.15%	4.89%	NA
All Indica	2759	99.10%	0.40%	0.00%	0.51%	NA
All Japonica	1512	84.00%	1.30%	0.40%	14.29%	NA
Aus	269	72.50%	27.50%	0.00%	0.00%	NA
Indica I	595	99.20%	0.20%	0.00%	0.67%	NA
Indica II	465	99.40%	0.20%	0.00%	0.43%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	98.10%	0.90%	0.00%	1.02%	NA
Temperate Japonica	767	90.70%	2.20%	0.13%	6.91%	NA
Tropical Japonica	504	76.80%	0.20%	0.60%	22.42%	NA
Japonica Intermediate	241	77.60%	0.80%	0.83%	20.75%	NA
VI/Aromatic	96	33.30%	66.70%	0.00%	0.00%	NA
Intermediate	90	85.60%	12.20%	1.11%	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
vg1121466812	G -> A	LOC_Os11g36400.1	upstream_gene_variant ; 2326.0bp to feature; MODIFIER	silent_mutation	Average:54.307; most accessible tissue: Zhenshan97 young leaf, score: 77.422	N	N	N	N
vg1121466812	G -> A	LOC_Os11g36410.1	downstream_gene_variant ; 1939.0bp to feature; MODIFIER	silent_mutation	Average:54.307; most accessible tissue: Zhenshan97 young leaf, score: 77.422	N	N	N	N
vg1121466812	G -> A	LOC_Os11g36400-LOC_Os11g36410	intergenic_region ; MODIFIER	silent_mutation	Average:54.307; most accessible tissue: Zhenshan97 young leaf, score: 77.422	N	N	N	N
vg1121466812	G -> DEL	N	N	silent_mutation	Average:54.307; most accessible tissue: Zhenshan97 young leaf, score: 77.422	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121466812	NA	1.11E-13	mr1570	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