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Detailed information for vg0208003316:

Variant ID: vg0208003316 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 8003316
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTGAACAATCGTCATAAACAGCCTCTGTTTATAACATATATGTGTTCTGTCATCAGGTAATCGTCACAGAAGCCCAGATTTGTTGTAGTGATCATCCCTC[A/G]
ACCATAAACAGGGTATAATGCATTCCCATCTTCGAAAGTTGCTGCAATTAGACTTCTTTGGTGGCTGAGAAAGTTGTTTTTTGTTGGCATGACCAGTTAA

Reverse complement sequence

TTAACTGGTCATGCCAACAAAAAACAACTTTCTCAGCCACCAAAGAAGTCTAATTGCAGCAACTTTCGAAGATGGGAATGCATTATACCCTGTTTATGGT[T/C]
GAGGGATGATCACTACAACAAATCTGGGCTTCTGTGACGATTACCTGATGACAGAACACATATATGTTATAAACAGAGGCTGTTTATGACGATTGTTCAC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	63.00%	36.90%	0.08%	0.02%	NA
All Indica	2759	38.50%	61.30%	0.11%	0.04%	NA
All Japonica	1512	98.30%	1.60%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	32.60%	67.20%	0.17%	0.00%	NA
Indica II	465	19.60%	80.20%	0.22%	0.00%	NA
Indica III	913	53.00%	47.00%	0.00%	0.00%	NA
Indica Intermediate	786	37.40%	62.30%	0.13%	0.13%	NA
Temperate Japonica	767	98.60%	1.40%	0.00%	0.00%	NA
Tropical Japonica	504	98.20%	1.60%	0.20%	0.00%	NA
Japonica Intermediate	241	97.90%	2.10%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	67.80%	32.20%	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
vg0208003316	A -> G	LOC_Os02g14520.1	upstream_gene_variant ; 1437.0bp to feature; MODIFIER	silent_mutation	Average:72.005; most accessible tissue: Callus, score: 82.016	N	N	N	N
vg0208003316	A -> G	LOC_Os02g14530.1	upstream_gene_variant ; 1665.0bp to feature; MODIFIER	silent_mutation	Average:72.005; most accessible tissue: Callus, score: 82.016	N	N	N	N
vg0208003316	A -> G	LOC_Os02g14520-LOC_Os02g14530	intergenic_region ; MODIFIER	silent_mutation	Average:72.005; most accessible tissue: Callus, score: 82.016	N	N	N	N
vg0208003316	A -> DEL	N	N	silent_mutation	Average:72.005; most accessible tissue: Callus, score: 82.016	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0208003316	NA	3.64E-06	mr1215	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
vg0208003316	1.06E-06	5.43E-07	mr1416	Ind_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
vg0208003316	NA	5.29E-06	mr1448	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
vg0208003316	NA	2.99E-06	mr1508	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
vg0208003316	NA	1.52E-07	mr1781	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