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Detailed information for vg0224663540:

Variant ID: vg0224663540 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 24663540
Reference Allele: G	Alternative Allele: A,T
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.89, A: 0.08, T: 0.02, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

AAGAAAATTTGATGATAAATCAAGTCACAATAAAATAAATTATAATTACATAAATTTTTTGAATAAGACGAAAAGTCAAACGTTTATCAAAAAGTCAACG[G/A,T]
CGTCATACATTAAAATACGGAGGGAGTATATTAGTTACTCCCTCGGTCCCATAATATAGTAACCTAGTATAGGATGTGACACTTCATACTTCATAGTACA

Reverse complement sequence

TGTACTATGAAGTATGAAGTGTCACATCCTATACTAGGTTACTATATTATGGGACCGAGGGAGTAACTAATATACTCCCTCCGTATTTTAATGTATGACG[C/T,A]
CGTTGACTTTTTGATAAACGTTTGACTTTTCGTCTTATTCAAAAAATTTATGTAATTATAATTTATTTTATTGTGACTTGATTTATCATCAAATTTTCTT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	93.40%	5.50%	0.32%	0.15%	T: 0.63%
All Indica	2759	90.10%	8.90%	0.43%	0.25%	T: 0.33%
All Japonica	1512	98.90%	0.10%	0.00%	0.00%	T: 0.99%
Aus	269	95.50%	2.60%	0.37%	0.00%	T: 1.49%
Indica I	595	98.20%	0.30%	0.84%	0.67%	NA
Indica II	465	86.70%	12.00%	1.08%	0.22%	NA
Indica III	913	86.20%	12.70%	0.00%	0.11%	T: 0.99%
Indica Intermediate	786	90.50%	9.20%	0.25%	0.13%	NA
Temperate Japonica	767	99.90%	0.00%	0.00%	0.00%	T: 0.13%
Tropical Japonica	504	98.60%	0.20%	0.00%	0.00%	T: 1.19%
Japonica Intermediate	241	96.70%	0.00%	0.00%	0.00%	T: 3.32%
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	88.90%	6.70%	2.22%	0.00%	T: 2.22%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0224663540	G -> A	LOC_Os02g40680.1	upstream_gene_variant ; 3711.0bp to feature; MODIFIER	silent_mutation	Average:53.637; most accessible tissue: Callus, score: 72.788	N	N	N	N
vg0224663540	G -> A	LOC_Os02g40664-LOC_Os02g40680	intergenic_region ; MODIFIER	silent_mutation	Average:53.637; most accessible tissue: Callus, score: 72.788	N	N	N	N
vg0224663540	G -> T	LOC_Os02g40680.1	upstream_gene_variant ; 3711.0bp to feature; MODIFIER	silent_mutation	Average:53.637; most accessible tissue: Callus, score: 72.788	N	N	N	N
vg0224663540	G -> T	LOC_Os02g40664-LOC_Os02g40680	intergenic_region ; MODIFIER	silent_mutation	Average:53.637; most accessible tissue: Callus, score: 72.788	N	N	N	N
vg0224663540	G -> DEL	N	N	silent_mutation	Average:53.637; most accessible tissue: Callus, score: 72.788	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0224663540	3.40E-06	3.40E-06	mr1673	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