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Detailed information for vg0200903122:

Variant ID: vg0200903122 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 903122
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.70, G: 0.30, others allele: 0.00, population size: 77. )

Flanking Sequence (100 bp) in Reference Genome:

TGGGAAAAGAAAATACTTCCTCCGTCCTCTAATATAAGGGATTTTGATATTTTGTTTTTACCATTCATCTTATTAAAAATTTGTTCAAATATAAAAAAAT[G/A]
AAAAGTTGTACTTAAAATACTTTGGTTAATAAAGTAAGTCACAAATAAAATAATTAATATTTTTTTAAAAAAATTATTAAGACGAATAGTTAAACCGTAC

Reverse complement sequence

GTACGGTTTAACTATTCGTCTTAATAATTTTTTTAAAAAAATATTAATTATTTTATTTGTGACTTACTTTATTAACCAAAGTATTTTAAGTACAACTTTT[C/T]
ATTTTTTTATATTTGAACAAATTTTTAATAAGATGAATGGTAAAAACAAAATATCAAAATCCCTTATATTAGAGGACGGAGGAAGTATTTTCTTTTCCCA

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	44.90%	24.10%	16.48%	14.52%	NA
All Indica	2759	10.40%	39.80%	26.68%	23.09%	NA
All Japonica	1512	94.00%	1.70%	1.59%	2.71%	NA
Aus	269	93.70%	2.20%	4.09%	0.00%	NA
Indica I	595	3.70%	34.10%	16.97%	45.21%	NA
Indica II	465	27.30%	15.70%	31.61%	25.38%	NA
Indica III	913	3.90%	62.10%	27.82%	6.13%	NA
Indica Intermediate	786	13.00%	32.60%	29.77%	24.68%	NA
Temperate Japonica	767	99.50%	0.30%	0.26%	0.00%	NA
Tropical Japonica	504	88.50%	4.00%	3.77%	3.77%	NA
Japonica Intermediate	241	88.00%	1.70%	1.24%	9.13%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	74.40%	7.80%	8.89%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0200903122	G -> A	LOC_Os02g02530.1	upstream_gene_variant ; 3442.0bp to feature; MODIFIER	silent_mutation	Average:15.192; most accessible tissue: Zhenshan97 panicle, score: 24.575	N	N	N	N
vg0200903122	G -> A	LOC_Os02g02530.3	upstream_gene_variant ; 3442.0bp to feature; MODIFIER	silent_mutation	Average:15.192; most accessible tissue: Zhenshan97 panicle, score: 24.575	N	N	N	N
vg0200903122	G -> A	LOC_Os02g02530.2	upstream_gene_variant ; 3442.0bp to feature; MODIFIER	silent_mutation	Average:15.192; most accessible tissue: Zhenshan97 panicle, score: 24.575	N	N	N	N
vg0200903122	G -> A	LOC_Os02g02520.1	downstream_gene_variant ; 2745.0bp to feature; MODIFIER	silent_mutation	Average:15.192; most accessible tissue: Zhenshan97 panicle, score: 24.575	N	N	N	N
vg0200903122	G -> A	LOC_Os02g02524.1	intron_variant ; MODIFIER	silent_mutation	Average:15.192; most accessible tissue: Zhenshan97 panicle, score: 24.575	N	N	N	N
vg0200903122	G -> DEL	N	N	silent_mutation	Average:15.192; most accessible tissue: Zhenshan97 panicle, score: 24.575	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0200903122	NA	8.36E-15	mr1744	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
vg0200903122	NA	1.63E-09	mr1660_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
vg0200903122	NA	1.55E-06	mr1660_2	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