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Detailed information for vg0706932173:

Variant ID: vg0706932173 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 6932173
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.77, A: 0.22, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:

AAAACATGAAAAAATAAAAAAATCGTCCCGGATTCGAGGTCCCGGTTTGCAAACCGGGAGTAAAGATGGGTTCCCCAGCAATGCATAGTCGGCTTCCTCA[G/A]
CGAATACTGTGATCGTGTCACCATCTTCGTTCTTGGTGAGTCCTCACGCACACCTTGGTCCACGACACCATCCAACATGGCCACTCCATGGCGCTCCTTG

Reverse complement sequence

CAAGGAGCGCCATGGAGTGGCCATGTTGGATGGTGTCGTGGACCAAGGTGTGCGTGAGGACTCACCAAGAACGAAGATGGTGACACGATCACAGTATTCG[C/T]
TGAGGAAGCCGACTATGCATTGCTGGGGAACCCATCTTTACTCCCGGTTTGCAAACCGGGACCTCGAATCCGGGACGATTTTTTTATTTTTTCATGTTTT

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	40.10%	18.20%	0.47%	41.24%	NA
All Indica	2759	8.20%	23.00%	0.80%	68.00%	NA
All Japonica	1512	99.40%	0.30%	0.00%	0.33%	NA
Aus	269	8.20%	75.50%	0.00%	16.36%	NA
Indica I	595	6.90%	43.90%	0.67%	48.57%	NA
Indica II	465	6.20%	12.70%	0.65%	80.43%	NA
Indica III	913	3.30%	11.50%	0.66%	84.56%	NA
Indica Intermediate	786	16.00%	26.70%	1.15%	56.11%	NA
Temperate Japonica	767	99.70%	0.10%	0.00%	0.13%	NA
Tropical Japonica	504	99.60%	0.00%	0.00%	0.40%	NA
Japonica Intermediate	241	97.90%	1.20%	0.00%	0.83%	NA
VI/Aromatic	96	97.90%	1.00%	0.00%	1.04%	NA
Intermediate	90	56.70%	17.80%	0.00%	25.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0706932173	G -> DEL	N	N	silent_mutation	Average:13.382; most accessible tissue: Callus, score: 38.628	N	N	N	N
vg0706932173	G -> A	LOC_Os07g12304.1	upstream_gene_variant ; 2059.0bp to feature; MODIFIER	silent_mutation	Average:13.382; most accessible tissue: Callus, score: 38.628	N	N	N	N
vg0706932173	G -> A	LOC_Os07g12310.1	downstream_gene_variant ; 4772.0bp to feature; MODIFIER	silent_mutation	Average:13.382; most accessible tissue: Callus, score: 38.628	N	N	N	N
vg0706932173	G -> A	LOC_Os07g12300-LOC_Os07g12304	intergenic_region ; MODIFIER	silent_mutation	Average:13.382; most accessible tissue: Callus, score: 38.628	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0706932173	3.20E-07	3.20E-07	mr1300	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