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Detailed information for vg0212064522:

Variant ID: vg0212064522 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 12064522
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 336. )

Flanking Sequence (100 bp) in Reference Genome:

GTCACGCTTTTACAGCTCCCTGAAGAAAACTATGCTCTCATATTTCTCTTTATAAATTGCAGAGGGGACCTTAGACTTTTGCTCATCCCAGAAATCCTCC[T/A]
GATGCTGTTCATCTTCAAGAACAAGCTATATGTTCGCTGCAGAAAAAGAATACAAAGATCACCAGAGGCATGGAGACTGCGCCTAAGTCACAAAGTTTAC

Reverse complement sequence

GTAAACTTTGTGACTTAGGCGCAGTCTCCATGCCTCTGGTGATCTTTGTATTCTTTTTCTGCAGCGAACATATAGCTTGTTCTTGAAGATGAACAGCATC[A/T]
GGAGGATTTCTGGGATGAGCAAAAGTCTAAGGTCCCCTCTGCAATTTATAAAGAGAAATATGAGAGCATAGTTTTCTTCAGGGAGCTGTAAAAGCGTGAC

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	99.40%	0.50%	0.17%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	98.30%	1.20%	0.53%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.10%	0.00%	0.00%	NA
Temperate Japonica	767	97.30%	2.00%	0.78%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	97.90%	1.20%	0.83%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg0212064522	T -> A	LOC_Os02g20450.1	missense_variant ; p.Leu66Gln; MODERATE	nonsynonymous_codon ; L66Q	Average:74.613; most accessible tissue: Callus, score: 92.559	unknown	unknown	DELETERIOUS	0.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0212064522	1.12E-06	NA	mr1157	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
vg0212064522	9.90E-07	NA	mr1328	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
vg0212064522	2.92E-08	1.41E-06	mr1446	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
vg0212064522	1.77E-06	1.71E-06	mr1989	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