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Detailed information for vg0708261838:

Variant ID: vg0708261838 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 8261838
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 115. )

Flanking Sequence (100 bp) in Reference Genome:

AAAGGTCGGTAATATCCTCCAACCGCCATAGGGGAGCCATCCACACCGTCCAGCGCCAACCCTGGATCCAGCGGCTGCACGGCAGGTTCAGTCGAACCCA[G/A]
GGGTTCAGCCGAACCCTGGGCTGGGCCAAACCAGCCCAATCTCGGTTGGCGGCCTCCTCGTTTGCTCCTCTCCGCAGACTTGTGAATTTTGGGCTTGTTG

Reverse complement sequence

CAACAAGCCCAAAATTCACAAGTCTGCGGAGAGGAGCAAACGAGGAGGCCGCCAACCGAGATTGGGCTGGTTTGGCCCAGCCCAGGGTTCGGCTGAACCC[C/T]
TGGGTTCGACTGAACCTGCCGTGCAGCCGCTGGATCCAGGGTTGGCGCTGGACGGTGTGGATGGCTCCCCTATGGCGGTTGGAGGATATTACCGACCTTT

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	96.80%	1.50%	0.89%	0.85%	NA
All Indica	2759	95.40%	2.60%	0.58%	1.41%	NA
All Japonica	1512	98.20%	0.00%	1.72%	0.07%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.20%	0.30%	0.17%	0.34%	NA
Indica II	465	96.60%	1.30%	1.08%	1.08%	NA
Indica III	913	97.20%	1.80%	0.77%	0.33%	NA
Indica Intermediate	786	89.90%	6.00%	0.38%	3.69%	NA
Temperate Japonica	767	98.80%	0.00%	1.04%	0.13%	NA
Tropical Japonica	504	99.00%	0.00%	0.99%	0.00%	NA
Japonica Intermediate	241	94.60%	0.00%	5.39%	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
vg0708261838	G -> DEL	N	N	silent_mutation	Average:21.691; most accessible tissue: Zhenshan97 flag leaf, score: 31.305	N	N	N	N
vg0708261838	G -> A	LOC_Os07g14490.1	downstream_gene_variant ; 3586.0bp to feature; MODIFIER	silent_mutation	Average:21.691; most accessible tissue: Zhenshan97 flag leaf, score: 31.305	N	N	N	N
vg0708261838	G -> A	LOC_Os07g14500.1	downstream_gene_variant ; 1585.0bp to feature; MODIFIER	silent_mutation	Average:21.691; most accessible tissue: Zhenshan97 flag leaf, score: 31.305	N	N	N	N
vg0708261838	G -> A	LOC_Os07g14514.1	downstream_gene_variant ; 2933.0bp to feature; MODIFIER	silent_mutation	Average:21.691; most accessible tissue: Zhenshan97 flag leaf, score: 31.305	N	N	N	N
vg0708261838	G -> A	LOC_Os07g14514.5	downstream_gene_variant ; 2933.0bp to feature; MODIFIER	silent_mutation	Average:21.691; most accessible tissue: Zhenshan97 flag leaf, score: 31.305	N	N	N	N
vg0708261838	G -> A	LOC_Os07g14514.3	downstream_gene_variant ; 2933.0bp to feature; MODIFIER	silent_mutation	Average:21.691; most accessible tissue: Zhenshan97 flag leaf, score: 31.305	N	N	N	N
vg0708261838	G -> A	LOC_Os07g14514.2	downstream_gene_variant ; 2933.0bp to feature; MODIFIER	silent_mutation	Average:21.691; most accessible tissue: Zhenshan97 flag leaf, score: 31.305	N	N	N	N
vg0708261838	G -> A	LOC_Os07g14514.4	downstream_gene_variant ; 2933.0bp to feature; MODIFIER	silent_mutation	Average:21.691; most accessible tissue: Zhenshan97 flag leaf, score: 31.305	N	N	N	N
vg0708261838	G -> A	LOC_Os07g14514.6	downstream_gene_variant ; 2933.0bp to feature; MODIFIER	silent_mutation	Average:21.691; most accessible tissue: Zhenshan97 flag leaf, score: 31.305	N	N	N	N
vg0708261838	G -> A	LOC_Os07g14500-LOC_Os07g14514	intergenic_region ; MODIFIER	silent_mutation	Average:21.691; most accessible tissue: Zhenshan97 flag leaf, score: 31.305	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0708261838	1.57E-06	1.57E-06	mr1582	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
vg0708261838	2.98E-06	6.31E-06	mr1582	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