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Detailed information for vg0121350184:

Variant ID: vg0121350184 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 21350184
Reference Allele: A	Alternative Allele: T
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.95, T: 0.05, others allele: 0.00, population size: 186. )

Flanking Sequence (100 bp) in Reference Genome:

TGCGAGGCACAAGGTGCGTATAGTTGAAAAGAGTAAAAAGGTACACAACTGCAAAAATCAGCTCGGTCTACAACCGCTTAAAATTACGTTCCGTCCTTAT[A/T]
TATAGATTCATTTGTTTCTACCTTATTTCTCCCTCTGTTTTTTCTCTATTTGACATTGAACTAACCAACATCAGAAGTTTGGAAACATAGACATTATTAA

Reverse complement sequence

TTAATAATGTCTATGTTTCCAAACTTCTGATGTTGGTTAGTTCAATGTCAAATAGAGAAAAAACAGAGGGAGAAATAAGGTAGAAACAAATGAATCTATA[T/A]
ATAAGGACGGAACGTAATTTTAAGCGGTTGTAGACCGAGCTGATTTTTGCAGTTGTGTACCTTTTTACTCTTTTCAACTATACGCACCTTGTGCCTCGCA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	54.70%	45.30%	0.06%	0.00%	NA
All Indica	2759	85.50%	14.40%	0.11%	0.00%	NA
All Japonica	1512	1.10%	98.90%	0.00%	0.00%	NA
Aus	269	48.30%	51.70%	0.00%	0.00%	NA
Indica I	595	99.50%	0.50%	0.00%	0.00%	NA
Indica II	465	75.50%	24.30%	0.22%	0.00%	NA
Indica III	913	91.70%	8.20%	0.11%	0.00%	NA
Indica Intermediate	786	73.80%	26.10%	0.13%	0.00%	NA
Temperate Japonica	767	1.00%	99.00%	0.00%	0.00%	NA
Tropical Japonica	504	0.80%	99.20%	0.00%	0.00%	NA
Japonica Intermediate	241	2.10%	97.90%	0.00%	0.00%	NA
VI/Aromatic	96	50.00%	50.00%	0.00%	0.00%	NA
Intermediate	90	32.20%	67.80%	0.00%	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
vg0121350184	A -> T	LOC_Os01g38120.1	upstream_gene_variant ; 510.0bp to feature; MODIFIER	silent_mutation	Average:70.125; most accessible tissue: Callus, score: 80.173	N	N	N	N
vg0121350184	A -> T	LOC_Os01g38140.1	upstream_gene_variant ; 4286.0bp to feature; MODIFIER	silent_mutation	Average:70.125; most accessible tissue: Callus, score: 80.173	N	N	N	N
vg0121350184	A -> T	LOC_Os01g38130.1	intron_variant ; MODIFIER	silent_mutation	Average:70.125; most accessible tissue: Callus, score: 80.173	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0121350184	NA	5.88E-09	mr1047	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
vg0121350184	NA	1.09E-06	mr1189	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
vg0121350184	NA	3.05E-06	mr1625	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
vg0121350184	2.78E-06	2.54E-25	mr1698	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
vg0121350184	NA	4.89E-06	mr1698	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
vg0121350184	NA	8.35E-06	mr1782	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
vg0121350184	NA	9.62E-08	mr1796	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
vg0121350184	NA	1.66E-07	mr1990	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
vg0121350184	NA	1.97E-21	mr1698_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
vg0121350184	NA	2.91E-06	mr1925_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