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Detailed information for vg0817358722:

Variant ID: vg0817358722 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 17358722
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATGATTCAAATACCTCATTATTCGTTTGACCGCTTGACGATGTGAAGCATGAGGAGAAGCTTGAAAGCGTGCAGACAAACACACAGCAAACTGTATGTCT[A/G]
GCCTAGAAGCAGTTAGATACAACAAAAAGATTCAATCATACTTCTATACTCCTTTTGATCAATAGCTTCACCATCTTCATCAGGATCCAACACAACTGTA

Reverse complement sequence

TACAGTTGTGTTGGATCCTGATGAAGATGGTGAAGCTATTGATCAAAAGGAGTATAGAAGTATGATTGAATCTTTTTGTTGTATCTAACTGCTTCTAGGC[T/C]
AGACATACAGTTTGCTGTGTGTTTGTCTGCACGCTTTCAAGCTTCTCCTCATGCTTCACATCGTCAAGCGGTCAAACGAATAATGAGGTATTTGAATCAT

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	36.00%	6.20%	0.95%	56.77%	NA
All Indica	2759	4.90%	6.80%	1.56%	86.70%	NA
All Japonica	1512	94.10%	1.90%	0.13%	3.84%	NA
Aus	269	1.10%	27.50%	0.00%	71.38%	NA
Indica I	595	8.40%	3.00%	0.84%	87.73%	NA
Indica II	465	4.30%	5.80%	1.94%	87.96%	NA
Indica III	913	2.50%	13.10%	1.20%	83.13%	NA
Indica Intermediate	786	5.50%	2.90%	2.29%	89.31%	NA
Temperate Japonica	767	95.40%	3.70%	0.00%	0.91%	NA
Tropical Japonica	504	90.90%	0.20%	0.00%	8.93%	NA
Japonica Intermediate	241	96.70%	0.00%	0.83%	2.49%	NA
VI/Aromatic	96	92.70%	0.00%	0.00%	7.29%	NA
Intermediate	90	57.80%	4.40%	0.00%	37.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0817358722	A -> G	LOC_Os08g28450.1	downstream_gene_variant ; 1050.0bp to feature; MODIFIER	silent_mutation	Average:8.516; most accessible tissue: Callus, score: 34.324	N	N	N	N
vg0817358722	A -> G	LOC_Os08g28430-LOC_Os08g28450	intergenic_region ; MODIFIER	silent_mutation	Average:8.516; most accessible tissue: Callus, score: 34.324	N	N	N	N
vg0817358722	A -> DEL	N	N	silent_mutation	Average:8.516; most accessible tissue: Callus, score: 34.324	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0817358722	5.41E-07	7.59E-08	mr1040	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
vg0817358722	1.04E-07	1.04E-07	mr1040	Ind_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
vg0817358722	NA	5.46E-08	mr1836	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
vg0817358722	1.79E-06	1.79E-06	mr1852	Ind_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