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Detailed information for vg1108631112:

Variant ID: vg1108631112 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 8631112
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.84, A: 0.18, others allele: 0.00, population size: 55. )

Flanking Sequence (100 bp) in Reference Genome:

TTTTATAAAGCGTCGTAGGAACGTCTCTGTTTGCACCATCTCAAAATTATAGAGACGCTTTTTAAAGCGTATCTATATTATTTAAGACGTTGCTAGAGAC[G/A]
TGTAAATTGCATCTCTATAAATATAGAGACGCTTTTATAGAACCACCTGCACAACGTCTTAATTAATATAGGCACGTACGTAAAGACGTTTTTTGCTGTC

Reverse complement sequence

GACAGCAAAAAACGTCTTTACGTACGTGCCTATATTAATTAAGACGTTGTGCAGGTGGTTCTATAAAAGCGTCTCTATATTTATAGAGATGCAATTTACA[C/T]
GTCTCTAGCAACGTCTTAAATAATATAGATACGCTTTAAAAAGCGTCTCTATAATTTTGAGATGGTGCAAACAGAGACGTTCCTACGACGCTTTATAAAA

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	44.20%	34.40%	1.86%	19.53%	NA
All Indica	2759	10.90%	55.10%	2.86%	31.10%	NA
All Japonica	1512	95.60%	1.60%	0.53%	2.31%	NA
Aus	269	74.70%	20.80%	0.00%	4.46%	NA
Indica I	595	11.80%	70.60%	2.02%	15.63%	NA
Indica II	465	2.80%	43.40%	2.80%	50.97%	NA
Indica III	913	12.70%	54.20%	3.29%	29.79%	NA
Indica Intermediate	786	13.10%	51.30%	3.05%	32.57%	NA
Temperate Japonica	767	98.00%	1.80%	0.00%	0.13%	NA
Tropical Japonica	504	94.60%	1.60%	0.20%	3.57%	NA
Japonica Intermediate	241	89.60%	0.80%	2.90%	6.64%	NA
VI/Aromatic	96	97.90%	0.00%	0.00%	2.08%	NA
Intermediate	90	50.00%	31.10%	1.11%	17.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1108631112	G -> A	LOC_Os11g15280.1	downstream_gene_variant ; 517.0bp to feature; MODIFIER	silent_mutation	Average:15.458; most accessible tissue: Callus, score: 41.04	N	N	N	N
vg1108631112	G -> A	LOC_Os11g15260-LOC_Os11g15280	intergenic_region ; MODIFIER	silent_mutation	Average:15.458; most accessible tissue: Callus, score: 41.04	N	N	N	N
vg1108631112	G -> DEL	N	N	silent_mutation	Average:15.458; most accessible tissue: Callus, score: 41.04	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1108631112	8.50E-06	5.58E-06	mr1940	Ind_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