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Detailed information for vg0817500434:

Variant ID: vg0817500434 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 17500434
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.50, A: 0.49, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:

TGTGACAGGCTGGGAATCGCAACCAGATTGGAGAGATGCTACAGATGCAAAAGGATAGAGAAGAAGAAAACAAGATGCAACAAGGAAAAACCGATCTACT[A/G]
CACAAAGAAGGGGATCTAGCCGATGGGCATGGACCTCTGCATACTCGGCCGATGGCGCGGCAGTCGGGCTGGCGGAAGTCGATATCGCCGCGGGCAAAAG

Reverse complement sequence

CTTTTGCCCGCGGCGATATCGACTTCCGCCAGCCCGACTGCCGCGCCATCGGCCGAGTATGCAGAGGTCCATGCCCATCGGCTAGATCCCCTTCTTTGTG[T/C]
AGTAGATCGGTTTTTCCTTGTTGCATCTTGTTTTCTTCTTCTCTATCCTTTTGCATCTGTAGCATCTCTCCAATCTGGTTGCGATTCCCAGCCTGTCACA

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	30.20%	23.00%	3.09%	43.72%	NA
All Indica	2759	3.10%	30.20%	4.89%	61.87%	NA
All Japonica	1512	80.30%	4.60%	0.26%	14.81%	NA
Aus	269	1.50%	61.70%	1.86%	34.94%	NA
Indica I	595	4.40%	37.50%	2.02%	56.13%	NA
Indica II	465	4.10%	10.10%	5.59%	80.22%	NA
Indica III	913	1.10%	41.00%	5.59%	52.35%	NA
Indica Intermediate	786	3.80%	23.90%	5.85%	66.41%	NA
Temperate Japonica	767	97.10%	1.00%	0.00%	1.83%	NA
Tropical Japonica	504	54.00%	8.50%	0.60%	36.90%	NA
Japonica Intermediate	241	81.70%	7.90%	0.41%	9.96%	NA
VI/Aromatic	96	89.60%	2.10%	0.00%	8.33%	NA
Intermediate	90	42.20%	18.90%	2.22%	36.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0817500434	A -> G	LOC_Os08g28640.1	upstream_gene_variant ; 864.0bp to feature; MODIFIER	silent_mutation	Average:13.99; most accessible tissue: Callus, score: 61.454	N	N	N	N
vg0817500434	A -> G	LOC_Os08g28650.1	upstream_gene_variant ; 23.0bp to feature; MODIFIER	silent_mutation	Average:13.99; most accessible tissue: Callus, score: 61.454	N	N	N	N
vg0817500434	A -> G	LOC_Os08g28630.1	downstream_gene_variant ; 3608.0bp to feature; MODIFIER	silent_mutation	Average:13.99; most accessible tissue: Callus, score: 61.454	N	N	N	N
vg0817500434	A -> G	LOC_Os08g28640-LOC_Os08g28650	intergenic_region ; MODIFIER	silent_mutation	Average:13.99; most accessible tissue: Callus, score: 61.454	N	N	N	N
vg0817500434	A -> DEL	N	N	silent_mutation	Average:13.99; most accessible tissue: Callus, score: 61.454	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0817500434	8.09E-07	NA	mr1539_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