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Detailed information for vg1121318047:

Variant ID: vg1121318047 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21318047
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.93, A: 0.07, others allele: 0.00, population size: 68. )

Flanking Sequence (100 bp) in Reference Genome:

GAGTGTCCACTAGTTGGGGTTTCGTTTATTCTAGGGTGAGCAAAGAAATAATAACAATAACAATAATAAGGTCATAACAAAGGTAAATAGGCATGGCTAA[T/A]
TAAAACAATGATAACACGGGAATTTAAATAAAGCGATAATGCATTAATTTAAATCAAATTAATTTTATAAACTGGGATTCAATATGCTCAAGGATGATGT

Reverse complement sequence

ACATCATCCTTGAGCATATTGAATCCCAGTTTATAAAATTAATTTGATTTAAATTAATGCATTATCGCTTTATTTAAATTCCCGTGTTATCATTGTTTTA[A/T]
TTAGCCATGCCTATTTACCTTTGTTATGACCTTATTATTGTTATTGTTATTATTTCTTTGCTCACCCTAGAATAAACGAAACCCCAACTAGTGGACACTC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	26.10%	18.60%	18.64%	36.61%	NA
All Indica	2759	8.00%	25.70%	23.96%	42.37%	NA
All Japonica	1512	64.40%	8.10%	7.94%	19.64%	NA
Aus	269	5.20%	13.00%	16.73%	65.06%	NA
Indica I	595	24.20%	7.40%	16.81%	51.60%	NA
Indica II	465	4.30%	27.10%	18.49%	50.11%	NA
Indica III	913	1.40%	33.60%	32.20%	32.75%	NA
Indica Intermediate	786	5.60%	29.40%	23.03%	41.98%	NA
Temperate Japonica	767	78.90%	3.10%	6.65%	11.34%	NA
Tropical Japonica	504	52.20%	14.90%	6.35%	26.59%	NA
Japonica Intermediate	241	43.60%	9.50%	15.35%	31.54%	NA
VI/Aromatic	96	1.00%	3.10%	42.71%	53.12%	NA
Intermediate	90	27.80%	14.40%	15.56%	42.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1121318047	T -> A	LOC_Os11g36220.1	upstream_gene_variant ; 439.0bp to feature; MODIFIER	silent_mutation	Average:12.448; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N
vg1121318047	T -> A	LOC_Os11g36220-LOC_Os11g36230	intergenic_region ; MODIFIER	silent_mutation	Average:12.448; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N
vg1121318047	T -> DEL	N	N	silent_mutation	Average:12.448; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121318047	NA	3.46E-06	mr1188	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
vg1121318047	9.85E-06	3.27E-07	mr1448	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
vg1121318047	4.82E-07	4.82E-07	mr1855	Jap_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
vg1121318047	4.65E-06	NA	mr1055_2	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