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Detailed information for vg0222612606:

Variant ID: vg0222612606 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 22612606
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 120. )

Flanking Sequence (100 bp) in Reference Genome:

GCGTGGCTGCCACATGGCCGCCACGTGTGCGCCACGTCGGCGCCACATGTGCACCACGTGGTGTGCCGCCCCTTTCCCGGTCCGTGGACCCAGTCCACCG[C/T]
GGACAGCCACCCGATTCACTGCCATGTGCCATGTGGGGCCCGCATGTCGGCGCCGCCCTCTCTCTCCCCGGGATTTTAATTATTGCGCAATAAATCAATT

Reverse complement sequence

AATTGATTTATTGCGCAATAATTAAAATCCCGGGGAGAGAGAGGGCGGCGCCGACATGCGGGCCCCACATGGCACATGGCAGTGAATCGGGTGGCTGTCC[G/A]
CGGTGGACTGGGTCCACGGACCGGGAAAGGGGCGGCACACCACGTGGTGCACATGTGGCGCCGACGTGGCGCACACGTGGCGGCCATGTGGCAGCCACGC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	93.50%	6.50%	0.08%	0.00%	NA
All Indica	2759	95.70%	4.20%	0.07%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	36.40%	63.60%	0.00%	0.00%	NA
Indica I	595	99.00%	1.00%	0.00%	0.00%	NA
Indica II	465	94.80%	4.90%	0.22%	0.00%	NA
Indica III	913	97.30%	2.60%	0.11%	0.00%	NA
Indica Intermediate	786	91.90%	8.10%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	87.50%	11.50%	1.04%	0.00%	NA
Intermediate	90	94.40%	4.40%	1.11%	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
vg0222612606	C -> T	LOC_Os02g37450.1	upstream_gene_variant ; 523.0bp to feature; MODIFIER	silent_mutation	Average:62.617; most accessible tissue: Minghui63 panicle, score: 82.128	N	N	N	N
vg0222612606	C -> T	LOC_Os02g37460.1	upstream_gene_variant ; 1685.0bp to feature; MODIFIER	silent_mutation	Average:62.617; most accessible tissue: Minghui63 panicle, score: 82.128	N	N	N	N
vg0222612606	C -> T	LOC_Os02g37470.1	upstream_gene_variant ; 4897.0bp to feature; MODIFIER	silent_mutation	Average:62.617; most accessible tissue: Minghui63 panicle, score: 82.128	N	N	N	N
vg0222612606	C -> T	LOC_Os02g37440.1	downstream_gene_variant ; 3398.0bp to feature; MODIFIER	silent_mutation	Average:62.617; most accessible tissue: Minghui63 panicle, score: 82.128	N	N	N	N
vg0222612606	C -> T	LOC_Os02g37450-LOC_Os02g37460	intergenic_region ; MODIFIER	silent_mutation	Average:62.617; most accessible tissue: Minghui63 panicle, score: 82.128	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0222612606	2.39E-06	NA	mr1101	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
vg0222612606	NA	1.04E-13	mr1496	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
vg0222612606	NA	2.76E-07	mr1706	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
vg0222612606	NA	2.19E-06	mr1378_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
vg0222612606	NA	7.85E-10	mr1968_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