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Detailed information for vg0318779823:

Variant ID: vg0318779823 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 18779823
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.92, A: 0.08, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:

CTCGAGAACATGTGGCCTTTCTACTCATGTGGCTGGAAAAGTTTCTTTTCTGTGGATCTAGCTGTGGTCCTACAACCAAGTGGCAGTTTGCAGCCGAAGC[T/A]
CTTGAGTCAAAACGAGAATTTCCTCTAGGCAAAATCCTCCTCGGCTACTTATACCAAATGCTGAACAATGCATCGGCCAAAATAGCCATCGGCTCAGTGG

Reverse complement sequence

CCACTGAGCCGATGGCTATTTTGGCCGATGCATTGTTCAGCATTTGGTATAAGTAGCCGAGGAGGATTTTGCCTAGAGGAAATTCTCGTTTTGACTCAAG[A/T]
GCTTCGGCTGCAAACTGCCACTTGGTTGTAGGACCACAGCTAGATCCACAGAAAAGAAACTTTTCCAGCCACATGAGTAGAAAGGCCACATGTTCTCGAG

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	47.80%	40.40%	0.55%	11.19%	NA
All Indica	2759	22.60%	65.00%	0.72%	11.71%	NA
All Japonica	1512	98.30%	1.60%	0.07%	0.07%	NA
Aus	269	10.00%	21.20%	1.12%	67.66%	NA
Indica I	595	8.20%	52.80%	1.51%	37.48%	NA
Indica II	465	26.70%	69.20%	0.86%	3.23%	NA
Indica III	913	31.40%	67.30%	0.00%	1.31%	NA
Indica Intermediate	786	20.90%	69.00%	0.89%	9.29%	NA
Temperate Japonica	767	99.50%	0.50%	0.00%	0.00%	NA
Tropical Japonica	504	96.20%	3.80%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	0.40%	0.41%	0.41%	NA
VI/Aromatic	96	75.00%	6.20%	0.00%	18.75%	NA
Intermediate	90	56.70%	35.60%	2.22%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0318779823	T -> A	LOC_Os03g32820.1	synonymous_variant ; p.Ala230Ala; LOW	synonymous_codon	Average:28.472; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N
vg0318779823	T -> DEL	LOC_Os03g32820.1	N	frameshift_variant	Average:28.472; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0318779823	NA	1.52E-07	mr1785	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
vg0318779823	2.84E-06	5.18E-08	mr1439_2	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
vg0318779823	NA	8.60E-06	mr1669_2	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