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Detailed information for vg0817500785:

Variant ID: vg0817500785 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 17500785
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AACGGTTGGAAAAACAACAATGAGCGATATTCTTGGAGGAGCAGATATGGCAAATCCGAAACATTACCAAATATTCCGGACTTGGGGGGCATGTGTTAAC[G/A]
ACCAAATTTGGTAATTCAGGTATCGGAGATGAAGATAAAACCGAAGTGGAATCCAAGATAGAAATCATTCCGGAAACAGAGCAAGAATCGGCTGAAGTCC

Reverse complement sequence

GGACTTCAGCCGATTCTTGCTCTGTTTCCGGAATGATTTCTATCTTGGATTCCACTTCGGTTTTATCTTCATCTCCGATACCTGAATTACCAAATTTGGT[C/T]
GTTAACACATGCCCCCCAAGTCCGGAATATTTGGTAATGTTTCGGATTTGCCATATCTGCTCCTCCAAGAATATCGCTCATTGTTGTTTTTCCAACCGTT

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	87.70%	1.60%	4.32%	6.43%	NA
All Indica	2759	85.00%	0.20%	6.60%	8.23%	NA
All Japonica	1512	91.40%	4.50%	0.99%	3.11%	NA
Aus	269	91.10%	0.00%	1.12%	7.81%	NA
Indica I	595	80.80%	0.00%	12.10%	7.06%	NA
Indica II	465	81.30%	0.00%	8.82%	9.89%	NA
Indica III	913	89.20%	0.40%	2.30%	8.11%	NA
Indica Intermediate	786	85.50%	0.10%	6.11%	8.27%	NA
Temperate Japonica	767	96.70%	1.00%	1.17%	1.04%	NA
Tropical Japonica	504	84.90%	8.10%	0.79%	6.15%	NA
Japonica Intermediate	241	88.00%	7.90%	0.83%	3.32%	NA
VI/Aromatic	96	97.90%	0.00%	0.00%	2.08%	NA
Intermediate	90	85.60%	2.20%	4.44%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0817500785	G -> A	LOC_Os08g28640.1	upstream_gene_variant ; 1215.0bp to feature; MODIFIER	silent_mutation	Average:16.126; most accessible tissue: Callus, score: 38.988	N	N	N	N
vg0817500785	G -> A	LOC_Os08g28630.1	downstream_gene_variant ; 3959.0bp to feature; MODIFIER	silent_mutation	Average:16.126; most accessible tissue: Callus, score: 38.988	N	N	N	N
vg0817500785	G -> A	LOC_Os08g28650.1	intron_variant ; MODIFIER	silent_mutation	Average:16.126; most accessible tissue: Callus, score: 38.988	N	N	N	N
vg0817500785	G -> DEL	N	N	silent_mutation	Average:16.126; most accessible tissue: Callus, score: 38.988	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0817500785	1.86E-06	1.86E-06	mr1881	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