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Detailed information for vg1122436158:

Variant ID: vg1122436158 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 22436158
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, A: 0.08, others allele: 0.00, population size: 66. )

Flanking Sequence (100 bp) in Reference Genome:

GGCCAACGAGCTTGGCTGCGCCGCCGCCGTCGTCAAAGGACCCGAGGGGCTTTTAACTATTTGCCACTCTTACGAGTGGTGCTTAACGATTTGCCACTAG[G/A]
CCCACATGTTATAGACATATGAGAGCCCACATGTCATAGACACGGTGTGGCAAATCGTTAATTGCAATGTCATAAGAGTGGCAAATAGTTAAATTTCCCG

Reverse complement sequence

CGGGAAATTTAACTATTTGCCACTCTTATGACATTGCAATTAACGATTTGCCACACCGTGTCTATGACATGTGGGCTCTCATATGTCTATAACATGTGGG[C/T]
CTAGTGGCAAATCGTTAAGCACCACTCGTAAGAGTGGCAAATAGTTAAAAGCCCCTCGGGTCCTTTGACGACGGCGGCGGCGCAGCCAAGCTCGTTGGCC

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	34.30%	1.90%	0.80%	62.95%	NA
All Indica	2759	7.60%	2.90%	0.87%	88.69%	NA
All Japonica	1512	78.60%	0.10%	0.93%	20.37%	NA
Aus	269	68.00%	0.40%	0.00%	31.60%	NA
Indica I	595	2.90%	0.20%	0.50%	96.47%	NA
Indica II	465	6.20%	1.90%	0.65%	91.18%	NA
Indica III	913	9.90%	6.40%	1.75%	82.04%	NA
Indica Intermediate	786	9.30%	1.40%	0.25%	89.06%	NA
Temperate Japonica	767	82.40%	0.10%	0.52%	16.95%	NA
Tropical Japonica	504	81.50%	0.20%	0.79%	17.46%	NA
Japonica Intermediate	241	60.20%	0.00%	2.49%	37.34%	NA
VI/Aromatic	96	8.30%	6.20%	0.00%	85.42%	NA
Intermediate	90	37.80%	3.30%	0.00%	58.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1122436158	G -> A	LOC_Os11g37860.1	downstream_gene_variant ; 751.0bp to feature; MODIFIER	silent_mutation	Average:28.946; most accessible tissue: Callus, score: 65.453	N	N	N	N
vg1122436158	G -> A	LOC_Os11g37860-LOC_Os11g37870	intergenic_region ; MODIFIER	silent_mutation	Average:28.946; most accessible tissue: Callus, score: 65.453	N	N	N	N
vg1122436158	G -> DEL	N	N	silent_mutation	Average:28.946; most accessible tissue: Callus, score: 65.453	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1122436158	NA	1.27E-07	mr1662	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
vg1122436158	1.56E-06	NA	mr1558_2	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
vg1122436158	NA	1.18E-07	mr1662_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