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Detailed information for vg1119948255:

Variant ID: vg1119948255 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 19948255
Reference Allele: T	Alternative Allele: A
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.59, A: 0.41, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

TAAGCTAGGTTAATAGTCAAACATATATAAATAAAAACAATAACGTCTTACATCAAAATTCAGAGGAAGTACTACACACATATCAATACTACTTCTCTTG[T/A]
GGAAATGCCATTGCCGTAGACAATGAATCACGTGATCCACGTGCCTGCAGGACGATGTTCCTTCCTTTGGGCACAAACCTAGCAATTTTTTTTTGTTACA

Reverse complement sequence

TGTAACAAAAAAAAATTGCTAGGTTTGTGCCCAAAGGAAGGAACATCGTCCTGCAGGCACGTGGATCACGTGATTCATTGTCTACGGCAATGGCATTTCC[A/T]
CAAGAGAAGTAGTATTGATATGTGTGTAGTACTTCCTCTGAATTTTGATGTAAGACGTTATTGTTTTTATTTATATATGTTTGACTATTAACCTAGCTTA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	59.60%	40.20%	0.19%	0.02%	NA
All Indica	2759	85.20%	14.50%	0.29%	0.04%	NA
All Japonica	1512	7.90%	92.10%	0.07%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	89.40%	10.10%	0.50%	0.00%	NA
Indica II	465	97.20%	2.80%	0.00%	0.00%	NA
Indica III	913	77.30%	22.20%	0.44%	0.00%	NA
Indica Intermediate	786	84.00%	15.80%	0.13%	0.13%	NA
Temperate Japonica	767	5.90%	94.00%	0.13%	0.00%	NA
Tropical Japonica	504	10.50%	89.50%	0.00%	0.00%	NA
Japonica Intermediate	241	8.70%	91.30%	0.00%	0.00%	NA
VI/Aromatic	96	30.20%	69.80%	0.00%	0.00%	NA
Intermediate	90	55.60%	44.40%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1119948255	T -> A	LOC_Os11g34090.1	upstream_gene_variant ; 1378.0bp to feature; MODIFIER	silent_mutation	Average:53.119; most accessible tissue: Callus, score: 91.414	N	N	N	N
vg1119948255	T -> A	LOC_Os11g34080-LOC_Os11g34090	intergenic_region ; MODIFIER	silent_mutation	Average:53.119; most accessible tissue: Callus, score: 91.414	N	N	N	N
vg1119948255	T -> DEL	N	N	silent_mutation	Average:53.119; most accessible tissue: Callus, score: 91.414	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1119948255	5.52E-06	5.52E-06	mr1417	Ind_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
vg1119948255	4.49E-06	4.49E-06	mr1497	Ind_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
vg1119948255	NA	1.28E-08	mr1595	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
vg1119948255	8.84E-07	3.02E-07	mr1988	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