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Detailed information for vg0809657696:

Variant ID: vg0809657696 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 9657696
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAAACCAAAGAGTCGGGGGCTACACAAATACATGGCTCAAAATTCGACAAGCTTTATGTCAAGATGAAGCAATCAATTAATCAGCCAACGAGTCAACTCT[G/A]
GGAGTCATCAATTTTGTCTTCGCTTTAGAGCAGTAGGTCAAGATTAAATTTACATGTCTGGGAGTTTGGATTCATCAACCAATCAACTCATATCAGATTC

Reverse complement sequence

GAATCTGATATGAGTTGATTGGTTGATGAATCCAAACTCCCAGACATGTAAATTTAATCTTGACCTACTGCTCTAAAGCGAAGACAAAATTGATGACTCC[C/T]
AGAGTTGACTCGTTGGCTGATTAATTGATTGCTTCATCTTGACATAAAGCTTGTCGAATTTTGAGCCATGTATTTGTGTAGCCCCCGACTCTTTGGTTTG

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	94.80%	0.10%	0.25%	4.85%	NA
All Indica	2759	99.70%	0.10%	0.04%	0.07%	NA
All Japonica	1512	85.30%	0.10%	0.73%	13.96%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	99.80%	0.00%	0.00%	0.22%	NA
Indica III	913	99.80%	0.10%	0.11%	0.00%	NA
Indica Intermediate	786	99.60%	0.30%	0.00%	0.13%	NA
Temperate Japonica	767	91.10%	0.10%	0.65%	8.08%	NA
Tropical Japonica	504	74.40%	0.00%	1.19%	24.40%	NA
Japonica Intermediate	241	89.20%	0.00%	0.00%	10.79%	NA
VI/Aromatic	96	87.50%	0.00%	0.00%	12.50%	NA
Intermediate	90	95.60%	0.00%	0.00%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0809657696	G -> A	LOC_Os08g15870.1	upstream_gene_variant ; 4773.0bp to feature; MODIFIER	silent_mutation	Average:31.538; most accessible tissue: Minghui63 flag leaf, score: 46.761	N	N	N	N
vg0809657696	G -> A	LOC_Os08g15870-LOC_Os08g15880	intergenic_region ; MODIFIER	silent_mutation	Average:31.538; most accessible tissue: Minghui63 flag leaf, score: 46.761	N	N	N	N
vg0809657696	G -> DEL	N	N	silent_mutation	Average:31.538; most accessible tissue: Minghui63 flag leaf, score: 46.761	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0809657696	NA	1.22E-06	mr1201	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
vg0809657696	2.49E-07	6.30E-08	mr1219	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
vg0809657696	NA	1.80E-06	mr1201_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
vg0809657696	8.01E-07	5.88E-08	mr1219_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