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Detailed information for vg0311227346:

Variant ID: vg0311227346 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 11227346
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:

TGAGCCAAAATTCTTTGTGAATAATGGCATGAATTAGTATCTCTAACCCATCTAAGGCTTTCCAAATGTCAAACTTCATAAAAATCTTATTTGGATGTGA[T/A]
TTGACACTTTGGTTGAGATTTATTGACTTGAATGGCCTACAAAACTCTCTTTGACATTTCTCTTGAAAGAAAAATCTTTTTTGAGAAATTCTTTTTGGAA

Reverse complement sequence

TTCCAAAAAGAATTTCTCAAAAAAGATTTTTCTTTCAAGAGAAATGTCAAAGAGAGTTTTGTAGGCCATTCAAGTCAATAAATCTCAACCAAAGTGTCAA[A/T]
TCACATCCAAATAAGATTTTTATGAAGTTTGACATTTGGAAAGCCTTAGATGGGTTAGAGATACTAATTCATGCCATTATTCACAAAGAATTTTGGCTCA

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	58.80%	35.00%	2.37%	3.81%	NA
All Indica	2759	31.80%	57.80%	3.95%	6.45%	NA
All Japonica	1512	99.40%	0.60%	0.00%	0.00%	NA
Aus	269	93.30%	5.60%	0.37%	0.74%	NA
Indica I	595	72.80%	25.90%	0.50%	0.84%	NA
Indica II	465	5.20%	80.90%	4.95%	9.03%	NA
Indica III	913	14.30%	70.40%	5.91%	9.31%	NA
Indica Intermediate	786	36.60%	53.80%	3.69%	5.85%	NA
Temperate Japonica	767	99.50%	0.50%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	93.80%	5.20%	1.04%	0.00%	NA
Intermediate	90	67.80%	31.10%	1.11%	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
vg0311227346	T -> A	LOC_Os03g19950.1	upstream_gene_variant ; 2349.0bp to feature; MODIFIER	silent_mutation	Average:15.493; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N
vg0311227346	T -> A	LOC_Os03g19950-LOC_Os03g19960	intergenic_region ; MODIFIER	silent_mutation	Average:15.493; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N
vg0311227346	T -> DEL	N	N	silent_mutation	Average:15.493; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0311227346	NA	7.68E-06	mr1030	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
vg0311227346	4.62E-06	NA	mr1168	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
vg0311227346	9.59E-07	NA	mr1383	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
vg0311227346	NA	1.36E-10	mr1524	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