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Detailed information for vg0412966608:

Variant ID: vg0412966608 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 12966608
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.75, T: 0.27, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

CCTCTTCCACAGCATTGTTCATTTCTTAAAAAAATGAAAAAAATCGTCCTTCCATCCGAATGAAAATAAATTTAATAGAGGCAAACCCAACTTTTCAATG[T/C]
AGGTACTGAATACTTTTATAAACATGTAATGGAATCATTATGTGTTTGCTAAAAAAAATAAAAAACAAAAAGGTGTCTACACTATTCCATTTATAAAAGT

Reverse complement sequence

ACTTTTATAAATGGAATAGTGTAGACACCTTTTTGTTTTTTATTTTTTTTAGCAAACACATAATGATTCCATTACATGTTTATAAAAGTATTCAGTACCT[A/G]
CATTGAAAAGTTGGGTTTGCCTCTATTAAATTTATTTTCATTCGGATGGAAGGACGATTTTTTTCATTTTTTTAAGAAATGAACAATGCTGTGGAAGAGG

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	65.00%	34.90%	0.15%	0.00%	NA
All Indica	2759	98.40%	1.40%	0.22%	0.00%	NA
All Japonica	1512	2.30%	97.60%	0.07%	0.00%	NA
Aus	269	98.90%	1.10%	0.00%	0.00%	NA
Indica I	595	99.00%	0.50%	0.50%	0.00%	NA
Indica II	465	97.00%	3.00%	0.00%	0.00%	NA
Indica III	913	99.30%	0.50%	0.11%	0.00%	NA
Indica Intermediate	786	97.70%	2.00%	0.25%	0.00%	NA
Temperate Japonica	767	2.30%	97.50%	0.13%	0.00%	NA
Tropical Japonica	504	1.20%	98.80%	0.00%	0.00%	NA
Japonica Intermediate	241	4.60%	95.40%	0.00%	0.00%	NA
VI/Aromatic	96	11.50%	88.50%	0.00%	0.00%	NA
Intermediate	90	48.90%	51.10%	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
vg0412966608	T -> C	LOC_Os04g22870-LOC_Os04g22880	intergenic_region ; MODIFIER	silent_mutation	Average:31.092; most accessible tissue: Zhenshan97 panicle, score: 46.362	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0412966608	NA	4.52E-76	mr1100	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
vg0412966608	NA	2.23E-15	mr1324	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
vg0412966608	3.86E-06	NA	mr1549	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
vg0412966608	NA	6.99E-66	mr1619	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
vg0412966608	NA	5.29E-26	mr1686	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
vg0412966608	NA	1.99E-07	mr1690	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
vg0412966608	NA	2.89E-53	mr1889	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
vg0412966608	NA	3.09E-69	mr1896	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
vg0412966608	NA	1.98E-76	mr1907	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
vg0412966608	NA	3.59E-34	mr1932	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
vg0412966608	NA	9.16E-17	mr1416_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
vg0412966608	9.20E-10	NA	mr1549_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
vg0412966608	NA	5.03E-35	mr1888_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