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Detailed information for vg0117282717:

Variant ID: vg0117282717 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 17282717
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.57, G: 0.42, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

ACCCTTTTTACTTTTATTTTGTTTCGACGAGTTCTTACTTTCGGGTTGAGCTGCATCGGTTTCGATCTTCAACAAGAGGTAAAACTTGTTATGGCGGCTT[A/G]
CGTTCTCGGGATTAGTGCTTCCATCTTTATGATACTCTAGTCTTGTTTATGTAATTTGTCGAGTTATCATATATCTAACATAATCTCTAGTAATATCGCT

Reverse complement sequence

AGCGATATTACTAGAGATTATGTTAGATATATGATAACTCGACAAATTACATAAACAAGACTAGAGTATCATAAAGATGGAAGCACTAATCCCGAGAACG[T/C]
AAGCCGCCATAACAAGTTTTACCTCTTGTTGAAGATCGAAACCGATGCAGCTCAACCCGAAAGTAAGAACTCGTCGAAACAAAATAAAAGTAAAAAGGGT

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	55.10%	37.80%	1.44%	5.61%	NA
All Indica	2759	89.80%	3.20%	2.39%	4.64%	NA
All Japonica	1512	0.90%	97.50%	0.00%	1.59%	NA
Aus	269	29.00%	31.60%	0.37%	39.03%	NA
Indica I	595	89.90%	1.20%	1.68%	7.23%	NA
Indica II	465	91.60%	4.70%	1.08%	2.58%	NA
Indica III	913	91.70%	1.30%	3.50%	3.50%	NA
Indica Intermediate	786	86.40%	6.00%	2.42%	5.22%	NA
Temperate Japonica	767	0.80%	99.20%	0.00%	0.00%	NA
Tropical Japonica	504	0.80%	94.60%	0.00%	4.56%	NA
Japonica Intermediate	241	1.70%	97.90%	0.00%	0.41%	NA
VI/Aromatic	96	3.10%	93.80%	0.00%	3.12%	NA
Intermediate	90	37.80%	55.60%	1.11%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0117282717	A -> G	LOC_Os01g31590.1	upstream_gene_variant ; 4595.0bp to feature; MODIFIER	silent_mutation	Average:11.696; most accessible tissue: Callus, score: 34.916	N	N	N	N
vg0117282717	A -> G	LOC_Os01g31580-LOC_Os01g31590	intergenic_region ; MODIFIER	silent_mutation	Average:11.696; most accessible tissue: Callus, score: 34.916	N	N	N	N
vg0117282717	A -> DEL	N	N	silent_mutation	Average:11.696; most accessible tissue: Callus, score: 34.916	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0117282717	4.91E-06	1.31E-09	mr1705_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
vg0117282717	3.36E-06	1.72E-06	mr1705_2	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
vg0117282717	NA	2.10E-08	mr1783_2	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
vg0117282717	NA	7.44E-08	mr1804_2	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