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Detailed information for vg0808847695:

Variant ID: vg0808847695 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 8847695
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCCTTCCTCCTCTTCTCCATCTGATCGATCGACGCCGCCTCAATTGCCATTGGCAAGACCGACAGTGAGTGGATCTGGCGCCGTGTGCTTGCTGGTGGCT[A/G]
AATGCGCCGTTGCATGCTCGGGGGTGACCGAATCCGCCGCCGCAACCACGGGGGTGGCTATCTCGATGACGGCAACAATAGCGATGGAAGCTCTCTGTAC

Reverse complement sequence

GTACAGAGAGCTTCCATCGCTATTGTTGCCGTCATCGAGATAGCCACCCCCGTGGTTGCGGCGGCGGATTCGGTCACCCCCGAGCATGCAACGGCGCATT[T/C]
AGCCACCAGCAAGCACACGGCGCCAGATCCACTCACTGTCGGTCTTGCCAATGGCAATTGAGGCGGCGTCGATCGATCAGATGGAGAAGAGGAGGAAGGA

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	54.50%	45.30%	0.19%	0.00%	NA
All Indica	2759	78.00%	21.70%	0.22%	0.00%	NA
All Japonica	1512	13.40%	86.50%	0.07%	0.00%	NA
Aus	269	61.30%	38.70%	0.00%	0.00%	NA
Indica I	595	76.50%	23.50%	0.00%	0.00%	NA
Indica II	465	96.60%	3.20%	0.22%	0.00%	NA
Indica III	913	64.50%	35.40%	0.11%	0.00%	NA
Indica Intermediate	786	84.00%	15.50%	0.51%	0.00%	NA
Temperate Japonica	767	4.60%	95.40%	0.00%	0.00%	NA
Tropical Japonica	504	23.00%	76.80%	0.20%	0.00%	NA
Japonica Intermediate	241	21.60%	78.40%	0.00%	0.00%	NA
VI/Aromatic	96	5.20%	94.80%	0.00%	0.00%	NA
Intermediate	90	55.60%	42.20%	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
vg0808847695	A -> G	LOC_Os08g14720.1	upstream_gene_variant ; 1634.0bp to feature; MODIFIER	silent_mutation	Average:57.48; most accessible tissue: Callus, score: 77.908	N	N	N	N
vg0808847695	A -> G	LOC_Os08g14710.1	downstream_gene_variant ; 3624.0bp to feature; MODIFIER	silent_mutation	Average:57.48; most accessible tissue: Callus, score: 77.908	N	N	N	N
vg0808847695	A -> G	LOC_Os08g14720-LOC_Os08g14730	intergenic_region ; MODIFIER	silent_mutation	Average:57.48; most accessible tissue: Callus, score: 77.908	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0808847695	3.67E-07	NA	mr1178	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