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Detailed information for vg0223948926:

Variant ID: vg0223948926 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 23948926
Reference Allele: G	Alternative Allele: A,T
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCAGCAGCAGCGGCTTCGGTGGCAGCAAAGAGGAGGGGTGGTGGCGGTGACCGGCGGCAGCAACTCCCGCGCGTGAGTAACAGATCTGGTGGTGGCGGAC[G/A,T]
GGCTCGGCAGAGTGGGGTGGCGTAGGGGAGCCTAGCTCCTCCCCTCTCCATTTCCGGAGTGGGGTGACAAAGGGGAGTATCGTCTCTCCGGGCTCAGCAG

Reverse complement sequence

CTGCTGAGCCCGGAGAGACGATACTCCCCTTTGTCACCCCACTCCGGAAATGGAGAGGGGAGGAGCTAGGCTCCCCTACGCCACCCCACTCTGCCGAGCC[C/T,A]
GTCCGCCACCACCAGATCTGTTACTCACGCGCGGGAGTTGCTGCCGCCGGTCACCGCCACCACCCCTCCTCTTTGCTGCCACCGAAGCCGCTGCTGCTGG

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	96.30%	3.20%	0.55%	0.00%	T: 0.02%
All Indica	2759	99.80%	0.10%	0.00%	0.00%	T: 0.04%
All Japonica	1512	89.40%	9.10%	1.59%	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	99.80%	0.10%	0.00%	0.00%	T: 0.11%
Indica Intermediate	786	99.70%	0.30%	0.00%	0.00%	NA
Temperate Japonica	767	97.80%	1.30%	0.91%	0.00%	NA
Tropical Japonica	504	78.40%	19.20%	2.38%	0.00%	NA
Japonica Intermediate	241	85.50%	12.40%	2.07%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	88.90%	8.90%	2.22%	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
vg0223948926	G -> A	LOC_Os02g39650.1	upstream_gene_variant ; 2414.0bp to feature; MODIFIER	silent_mutation	Average:76.5; most accessible tissue: Zhenshan97 young leaf, score: 85.001	N	N	N	N
vg0223948926	G -> A	LOC_Os02g39660.1	upstream_gene_variant ; 4000.0bp to feature; MODIFIER	silent_mutation	Average:76.5; most accessible tissue: Zhenshan97 young leaf, score: 85.001	N	N	N	N
vg0223948926	G -> A	LOC_Os02g39650-LOC_Os02g39660	intergenic_region ; MODIFIER	silent_mutation	Average:76.5; most accessible tissue: Zhenshan97 young leaf, score: 85.001	N	N	N	N
vg0223948926	G -> T	LOC_Os02g39650.1	upstream_gene_variant ; 2414.0bp to feature; MODIFIER	silent_mutation	Average:76.5; most accessible tissue: Zhenshan97 young leaf, score: 85.001	N	N	N	N
vg0223948926	G -> T	LOC_Os02g39660.1	upstream_gene_variant ; 4000.0bp to feature; MODIFIER	silent_mutation	Average:76.5; most accessible tissue: Zhenshan97 young leaf, score: 85.001	N	N	N	N
vg0223948926	G -> T	LOC_Os02g39650-LOC_Os02g39660	intergenic_region ; MODIFIER	silent_mutation	Average:76.5; most accessible tissue: Zhenshan97 young leaf, score: 85.001	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0223948926	1.92E-06	1.57E-08	mr1156_2	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