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Detailed information for vg0208319048:

Variant ID: vg0208319048 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 8319048
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCGTTGTGTTTTATATCAACATTTACAAAATTCCGATGCAAAATGATTATTTAAAAATAAATTTATTTCGGGACAAATGGAAGGGAAAAAAATTATTTTA[G/A]
AACGAAGGGAGTACAAAGTTAGTAAGAATGTAAAGAATTTACTATCTCTGTCTTAAAATATACTAACTATTCCTACCTTTCTGTTTTAAAATTTACACTA

Reverse complement sequence

TAGTGTAAATTTTAAAACAGAAAGGTAGGAATAGTTAGTATATTTTAAGACAGAGATAGTAAATTCTTTACATTCTTACTAACTTTGTACTCCCTTCGTT[C/T]
TAAAATAATTTTTTTCCCTTCCATTTGTCCCGAAATAAATTTATTTTTAAATAATCATTTTGCATCGGAATTTTGTAAATGTTGATATAAAACACAACGG

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	95.90%	3.10%	1.04%	0.00%	NA
All Indica	2759	99.80%	0.20%	0.04%	0.00%	NA
All Japonica	1512	88.60%	8.50%	2.91%	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	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.50%	0.40%	0.13%	0.00%	NA
Temperate Japonica	767	97.40%	0.50%	2.09%	0.00%	NA
Tropical Japonica	504	76.40%	21.00%	2.58%	0.00%	NA
Japonica Intermediate	241	86.30%	7.50%	6.22%	0.00%	NA
VI/Aromatic	96	91.70%	7.30%	1.04%	0.00%	NA
Intermediate	90	91.10%	5.60%	3.33%	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
vg0208319048	G -> A	LOC_Os02g14910.1	upstream_gene_variant ; 4843.0bp to feature; MODIFIER	silent_mutation	Average:43.513; most accessible tissue: Callus, score: 84.802	N	N	N	N
vg0208319048	G -> A	LOC_Os02g14900.1	downstream_gene_variant ; 1857.0bp to feature; MODIFIER	silent_mutation	Average:43.513; most accessible tissue: Callus, score: 84.802	N	N	N	N
vg0208319048	G -> A	LOC_Os02g14900-LOC_Os02g14910	intergenic_region ; MODIFIER	silent_mutation	Average:43.513; most accessible tissue: Callus, score: 84.802	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0208319048	1.78E-06	NA	mr1301_2	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
vg0208319048	4.46E-07	NA	mr1410_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