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Detailed information for vg0826039982:

Variant ID: vg0826039982 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 26039982
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGGGAACGTCTCTCCGCCGACGACGAAGGAGACGCCATGGAGTCGGGCGTTGGGTGGGCACTGCTGGATCTGGATGATAGCGTGAGCTAGTGGCGGAACT[A/G]
AGGGGGGTGGCAGGGGCCATGGCGCCTCCCAATAAATTTTTTTTTAATTACCCCTATATATGGTACCCAGGTCCAACAGGCCACCGTATGGCCCAATTCA

Reverse complement sequence

TGAATTGGGCCATACGGTGGCCTGTTGGACCTGGGTACCATATATAGGGGTAATTAAAAAAAAATTTATTGGGAGGCGCCATGGCCCCTGCCACCCCCCT[T/C]
AGTTCCGCCACTAGCTCACGCTATCATCCAGATCCAGCAGTGCCCACCCAACGCCCGACTCCATGGCGTCTCCTTCGTCGTCGGCGGAGAGACGTTCCCT

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	38.00%	5.80%	7.89%	48.31%	NA
All Indica	2759	4.50%	9.60%	12.36%	73.54%	NA
All Japonica	1512	97.70%	0.00%	0.53%	1.79%	NA
Aus	269	24.90%	0.70%	7.43%	66.91%	NA
Indica I	595	4.70%	2.50%	15.80%	76.97%	NA
Indica II	465	4.10%	10.50%	15.05%	70.32%	NA
Indica III	913	3.70%	16.10%	5.70%	74.48%	NA
Indica Intermediate	786	5.30%	7.00%	15.90%	71.76%	NA
Temperate Japonica	767	97.50%	0.00%	0.65%	1.83%	NA
Tropical Japonica	504	98.40%	0.00%	0.40%	1.19%	NA
Japonica Intermediate	241	96.70%	0.00%	0.41%	2.90%	NA
VI/Aromatic	96	87.50%	0.00%	1.04%	11.46%	NA
Intermediate	90	52.20%	4.40%	3.33%	40.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0826039982	A -> G	LOC_Os08g41230.1	upstream_gene_variant ; 2131.0bp to feature; MODIFIER	silent_mutation	Average:52.886; most accessible tissue: Zhenshan97 panicle, score: 72.468	N	N	N	N
vg0826039982	A -> G	LOC_Os08g41240.1	downstream_gene_variant ; 4285.0bp to feature; MODIFIER	silent_mutation	Average:52.886; most accessible tissue: Zhenshan97 panicle, score: 72.468	N	N	N	N
vg0826039982	A -> G	LOC_Os08g41230-LOC_Os08g41240	intergenic_region ; MODIFIER	silent_mutation	Average:52.886; most accessible tissue: Zhenshan97 panicle, score: 72.468	N	N	N	N
vg0826039982	A -> DEL	N	N	silent_mutation	Average:52.886; most accessible tissue: Zhenshan97 panicle, score: 72.468	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0826039982	2.65E-06	NA	mr1874_2	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