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Detailed information for vg0119308289:

Variant ID: vg0119308289 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 19308289
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:

CACATAACGCTGAAGGATGCACAAAAGATATGTACTTTATAAAATGTAATGGGTGTTCAGCAACTTACGTTAACATGAGATTTAAGATGTTTTCATAAAG[A/G]
CCTTTTTCACGGGAATCCTTTGATGCCTTATGCATGCCATAGAGTTGGCAGGAAACAACATAAGTGAATTTTATATCAGCAATGGCCTTGGACCTTGCAG

Reverse complement sequence

CTGCAAGGTCCAAGGCCATTGCTGATATAAAATTCACTTATGTTGTTTCCTGCCAACTCTATGGCATGCATAAGGCATCAAAGGATTCCCGTGAAAAAGG[T/C]
CTTTATGAAAACATCTTAAATCTCATGTTAACGTAAGTTGCTGAACACCCATTACATTTTATAAAGTACATATCTTTTGTGCATCCTTCAGCGTTATGTG

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	90.10%	9.20%	0.72%	0.00%	NA
All Indica	2759	83.60%	15.40%	1.05%	0.00%	NA
All Japonica	1512	99.70%	0.20%	0.13%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.00%	0.80%	0.17%	0.00%	NA
Indica II	465	54.20%	43.90%	1.94%	0.00%	NA
Indica III	913	90.90%	8.80%	0.33%	0.00%	NA
Indica Intermediate	786	80.80%	17.20%	2.04%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.40%	0.20%	0.40%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	88.90%	7.80%	3.33%	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
vg0119308289	A -> G	LOC_Os01g34930.1	upstream_gene_variant ; 2253.0bp to feature; MODIFIER	silent_mutation	Average:45.115; most accessible tissue: Callus, score: 72.788	N	N	N	N
vg0119308289	A -> G	LOC_Os01g34930-LOC_Os01g34940	intergenic_region ; MODIFIER	silent_mutation	Average:45.115; most accessible tissue: Callus, score: 72.788	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0119308289	NA	5.66E-06	mr1195	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
vg0119308289	NA	9.01E-06	mr1231	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
vg0119308289	NA	9.99E-07	mr1441	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
vg0119308289	NA	4.24E-11	mr1565	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
vg0119308289	NA	1.32E-08	mr1565	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
vg0119308289	NA	9.72E-08	mr1593	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
vg0119308289	3.22E-07	3.22E-07	mr1762	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
vg0119308289	NA	9.37E-06	mr1402_2	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
vg0119308289	NA	7.36E-06	mr1482_2	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
vg0119308289	NA	7.33E-06	mr1510_2	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