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Detailed information for vg0908091687:

Variant ID: vg0908091687 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 8091687
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGGCTATTCGAATAGATTTAGTTTACTCACACTGCAGTGGATGTACACTTTACCCGCACTCCGCGACTGCCCAACACATGAGCCTCATCCCAACACATGA[A/G]
ACGCGTCACGGCAAAGCTTTTCGATAACCTCACATTGGCAGTACCCGCTCCATGAACTTTACATCCTCATGCACTCTAGGCGTCATACGTTTCTAGCAGT

Reverse complement sequence

ACTGCTAGAAACGTATGACGCCTAGAGTGCATGAGGATGTAAAGTTCATGGAGCGGGTACTGCCAATGTGAGGTTATCGAAAAGCTTTGCCGTGACGCGT[T/C]
TCATGTGTTGGGATGAGGCTCATGTGTTGGGCAGTCGCGGAGTGCGGGTAAAGTGTACATCCACTGCAGTGTGAGTAAACTAAATCTATTCGAATAGCCG

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	58.20%	1.80%	22.18%	17.84%	NA
All Indica	2759	55.50%	0.40%	25.19%	18.96%	NA
All Japonica	1512	59.30%	4.80%	18.52%	17.33%	NA
Aus	269	62.80%	0.00%	22.30%	14.87%	NA
Indica I	595	50.80%	1.80%	20.17%	27.23%	NA
Indica II	465	74.20%	0.00%	11.61%	14.19%	NA
Indica III	913	47.40%	0.00%	38.01%	14.57%	NA
Indica Intermediate	786	57.30%	0.00%	22.14%	20.61%	NA
Temperate Japonica	767	87.50%	6.60%	1.04%	4.82%	NA
Tropical Japonica	504	29.80%	0.40%	42.46%	27.38%	NA
Japonica Intermediate	241	31.50%	8.30%	24.07%	36.10%	NA
VI/Aromatic	96	86.50%	0.00%	4.17%	9.38%	NA
Intermediate	90	78.90%	1.10%	10.00%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0908091687	A -> G	LOC_Os09g13800.1	upstream_gene_variant ; 2593.0bp to feature; MODIFIER	silent_mutation	Average:33.341; most accessible tissue: Minghui63 flag leaf, score: 64.284	N	N	N	N
vg0908091687	A -> G	LOC_Os09g13800-LOC_Os09g13810	intergenic_region ; MODIFIER	silent_mutation	Average:33.341; most accessible tissue: Minghui63 flag leaf, score: 64.284	N	N	N	N
vg0908091687	A -> DEL	N	N	silent_mutation	Average:33.341; most accessible tissue: Minghui63 flag leaf, score: 64.284	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0908091687	NA	3.37E-06	mr1397	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
vg0908091687	NA	1.42E-06	mr1603	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