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Detailed information for vg0709664645:

Variant ID: vg0709664645 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 9664645
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTTTTCCAGTTGGATCTATGTCGGATGGTTTCCTGCAAAGTGTTCTTTCAATATTTAGTATCATTTTCATGAGAGAGGCATGCCGACATGAAATGGTACC[A/G]
AGAGGTTTATACCTGGAAGATGTTCTAATCTTTGGCATTGGACGGCCAGCCAGTTTTTTCCTGGGCATGGTACGCTTTGGGAGTTTATTAGGCGAGCCCT

Reverse complement sequence

AGGGCTCGCCTAATAAACTCCCAAAGCGTACCATGCCCAGGAAAAAACTGGCTGGCCGTCCAATGCCAAAGATTAGAACATCTTCCAGGTATAAACCTCT[T/C]
GGTACCATTTCATGTCGGCATGCCTCTCTCATGAAAATGATACTAAATATTGAAAGAACACTTTGCAGGAAACCATCCGACATAGATCCAACTGGAAAAG

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	99.50%	0.40%	0.08%	0.00%	NA
All Indica	2759	99.30%	0.70%	0.07%	0.00%	NA
All Japonica	1512	99.70%	0.10%	0.13%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	99.50%	0.50%	0.00%	0.00%	NA
Indica II	465	99.10%	0.60%	0.22%	0.00%	NA
Indica III	913	99.50%	0.50%	0.00%	0.00%	NA
Indica Intermediate	786	99.00%	0.90%	0.13%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	99.20%	0.40%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	0.00%	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
vg0709664645	A -> G	LOC_Os07g16480.1	downstream_gene_variant ; 1858.0bp to feature; MODIFIER	N	Average:40.166; most accessible tissue: Zhenshan97 flag leaf, score: 74.162	N	N	N	N
vg0709664645	A -> G	LOC_Os07g16490.1	intron_variant ; MODIFIER	N	Average:40.166; most accessible tissue: Zhenshan97 flag leaf, score: 74.162	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0709664645	2.26E-06	4.28E-06	mr1256	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