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Detailed information for vg0921121859:

Variant ID: vg0921121859 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 21121859
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, T: 0.05, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:

AAATGAGGATGGTTTGATTGTGAGAAATAAAGCTAGACTTGTTGCTAAAGGTTTTACTCAAGTTGAGGGTTTGGATTTTGATGAAACTTTTGCTCCTGTT[T/G]
CTAGAATTGAGGCAATTAGACTTTTGTTGGCTTTTGCTGCTTCAAAAGGTTTTAAATTGTATCAAATGGATGTGAAAAGTGCTTTTCTAAATGGTTTTAT

Reverse complement sequence

ATAAAACCATTTAGAAAAGCACTTTTCACATCCATTTGATACAATTTAAAACCTTTTGAAGCAGCAAAAGCCAACAAAAGTCTAATTGCCTCAATTCTAG[A/C]
AACAGGAGCAAAAGTTTCATCAAAATCCAAACCCTCAACTTGAGTAAAACCTTTAGCAACAAGTCTAGCTTTATTTCTCACAATCAAACCATCCTCATTT

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	63.20%	36.70%	0.11%	0.00%	NA
All Indica	2759	44.40%	55.40%	0.18%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	30.50%	69.50%	0.00%	0.00%	NA
Indica I	595	11.10%	88.70%	0.17%	0.00%	NA
Indica II	465	65.60%	34.20%	0.22%	0.00%	NA
Indica III	913	50.40%	49.60%	0.00%	0.00%	NA
Indica Intermediate	786	50.30%	49.40%	0.38%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	85.60%	14.40%	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
vg0921121859	T -> G	LOC_Os09g36610.1	missense_variant ; p.Ser1208Ala; MODERATE	nonsynonymous_codon ; S1208A	Average:14.736; most accessible tissue: Minghui63 young leaf, score: 21.268	unknown	unknown	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0921121859	NA	7.66E-08	mr1439	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
vg0921121859	NA	9.04E-07	mr1598	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
vg0921121859	NA	8.82E-06	mr1927	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
vg0921121859	NA	3.79E-06	mr1970	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
vg0921121859	NA	1.17E-13	mr1050_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
vg0921121859	NA	3.26E-06	mr1050_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
vg0921121859	NA	1.21E-08	mr1272_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
vg0921121859	NA	8.81E-07	mr1480_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
vg0921121859	NA	6.95E-08	mr1607_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
vg0921121859	NA	3.75E-06	mr1629_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
vg0921121859	NA	2.10E-06	mr1793_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
vg0921121859	NA	9.93E-14	mr1904_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
vg0921121859	NA	8.82E-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
vg0921121859	NA	4.11E-06	mr1970_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