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Detailed information for vg0412128903:

Variant ID: vg0412128903 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 12128903
Reference Allele: G	Alternative Allele: T
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, T: 0.01, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:

TCCCCGCCAACGGCGCCAGAATTGCTTGTTGGTATTTCTTAACGGCATTACAAGAAATATAATTCCCAACAATGGCGCAGAAATATTTCTGGTATATTAT[G/T]
GTTACAGAGTTCATCCGCAAGCGCATGGATATACCATTGTAGCATTTCACCTTAGAGTATTCCAATGGTATCGTATTTATTTTATCCCGTGGGAAGATCA

Reverse complement sequence

TGATCTTCCCACGGGATAAAATAAATACGATACCATTGGAATACTCTAAGGTGAAATGCTACAATGGTATATCCATGCGCTTGCGGATGAACTCTGTAAC[C/A]
ATAATATACCAGAAATATTTCTGCGCCATTGTTGGGAATTATATTTCTTGTAATGCCGTTAAGAAATACCAACAAGCAATTCTGGCGCCGTTGGCGGGGA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	57.60%	41.50%	0.89%	0.00%	NA
All Indica	2759	92.10%	6.50%	1.41%	0.00%	NA
All Japonica	1512	0.90%	99.10%	0.00%	0.00%	NA
Aus	269	48.00%	51.70%	0.37%	0.00%	NA
Indica I	595	98.80%	0.80%	0.34%	0.00%	NA
Indica II	465	94.40%	4.70%	0.86%	0.00%	NA
Indica III	913	86.60%	10.50%	2.85%	0.00%	NA
Indica Intermediate	786	91.90%	7.30%	0.89%	0.00%	NA
Temperate Japonica	767	0.40%	99.60%	0.00%	0.00%	NA
Tropical Japonica	504	1.00%	99.00%	0.00%	0.00%	NA
Japonica Intermediate	241	2.10%	97.90%	0.00%	0.00%	NA
VI/Aromatic	96	2.10%	97.90%	0.00%	0.00%	NA
Intermediate	90	41.10%	56.70%	2.22%	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
vg0412128903	G -> T	LOC_Os04g21450.1	upstream_gene_variant ; 580.0bp to feature; MODIFIER	silent_mutation	Average:22.258; most accessible tissue: Zhenshan97 flag leaf, score: 37.1	N	N	N	N
vg0412128903	G -> T	LOC_Os04g21450-LOC_Os04g21460	intergenic_region ; MODIFIER	silent_mutation	Average:22.258; most accessible tissue: Zhenshan97 flag leaf, score: 37.1	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0412128903	1.07E-06	1.54E-07	mr1071	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
vg0412128903	NA	2.75E-06	mr1080	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
vg0412128903	NA	8.06E-06	mr1140	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
vg0412128903	NA	4.01E-16	mr1156	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
vg0412128903	NA	8.26E-16	mr1700	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
vg0412128903	NA	2.46E-53	mr1795	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
vg0412128903	NA	1.15E-07	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