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Detailed information for vg1116397481:

Variant ID: vg1116397481 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 16397481
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, A: 0.04, others allele: 0.00, population size: 49. )

Flanking Sequence (100 bp) in Reference Genome:

AAGAACGGATCATAGCCATATACTACTAGGCAAAATTTGTTGCAGGACATCTAAACAACGTGCAAGAACACGTTTATGCTATAGGGCACTATAAAAAAGT[G/A]
GTAATTAGTTGCTCGATACACACAACATTATTTTATTATATCCGGAGGAATTGGAAAGTGAAACCGCTGCGAAAGTATGTTTTTACCCATCGGACCCAAT

Reverse complement sequence

ATTGGGTCCGATGGGTAAAAACATACTTTCGCAGCGGTTTCACTTTCCAATTCCTCCGGATATAATAAAATAATGTTGTGTGTATCGAGCAACTAATTAC[C/T]
ACTTTTTTATAGTGCCCTATAGCATAAACGTGTTCTTGCACGTTGTTTAGATGTCCTGCAACAAATTTTGCCTAGTAGTATATGGCTATGATCCGTTCTT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	65.00%	25.00%	0.15%	9.90%	NA
All Indica	2759	78.10%	8.00%	0.22%	13.63%	NA
All Japonica	1512	43.50%	56.00%	0.07%	0.40%	NA
Aus	269	68.80%	2.60%	0.00%	28.62%	NA
Indica I	595	75.80%	9.20%	0.17%	14.79%	NA
Indica II	465	91.80%	3.70%	0.00%	4.52%	NA
Indica III	913	72.40%	6.10%	0.22%	21.25%	NA
Indica Intermediate	786	78.50%	11.80%	0.38%	9.29%	NA
Temperate Japonica	767	15.00%	84.70%	0.13%	0.13%	NA
Tropical Japonica	504	72.20%	27.20%	0.00%	0.60%	NA
Japonica Intermediate	241	74.30%	24.90%	0.00%	0.83%	NA
VI/Aromatic	96	11.50%	88.50%	0.00%	0.00%	NA
Intermediate	90	66.70%	23.30%	0.00%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1116397481	G -> A	LOC_Os11g28480.1	upstream_gene_variant ; 2286.0bp to feature; MODIFIER	silent_mutation	Average:45.892; most accessible tissue: Callus, score: 87.071	N	N	N	N
vg1116397481	G -> A	LOC_Os11g28480-LOC_Os11g28490	intergenic_region ; MODIFIER	silent_mutation	Average:45.892; most accessible tissue: Callus, score: 87.071	N	N	N	N
vg1116397481	G -> DEL	N	N	silent_mutation	Average:45.892; most accessible tissue: Callus, score: 87.071	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1116397481	2.83E-07	NA	Awn_length	All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1116397481	8.06E-06	NA	mr1265	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
vg1116397481	NA	4.61E-07	mr1617	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
vg1116397481	NA	1.59E-06	mr1627	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
vg1116397481	NA	2.46E-06	mr1668	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