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Detailed information for vg0919961970:

Variant ID: vg0919961970 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 19961970
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, T: 0.06, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:

CTCCTCTTTGTCTGCCCAATTACCTTTTTCAGACCAGAAGAAAAATGCAAAACCAGAGGGGTCTTCTGGCTCGCAAAGGGGAGCTCCCCCGGCACCTGAT[G/T]
CAGGCCTTCCCAATCCTTTTGATTTTTCTCAGTTTAGCAACTTGCTCAATGTAAGTTCTTTTTTTTTTCGCGCAGCTAAAAGCATGATATGTGCTCTCTT

Reverse complement sequence

AAGAGAGCACATATCATGCTTTTAGCTGCGCGAAAAAAAAAAGAACTTACATTGAGCAAGTTGCTAAACTGAGAAAAATCAAAAGGATTGGGAAGGCCTG[C/A]
ATCAGGTGCCGGGGGAGCTCCCCTTTGCGAGCCAGAAGACCCCTCTGGTTTTGCATTTTTCTTCTGGTCTGAAAAAGGTAATTGGGCAGACAAAGAGGAG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	90.10%	9.80%	0.11%	0.00%	NA
All Indica	2759	91.10%	8.70%	0.18%	0.00%	NA
All Japonica	1512	98.90%	1.10%	0.00%	0.00%	NA
Aus	269	37.90%	62.10%	0.00%	0.00%	NA
Indica I	595	97.10%	2.90%	0.00%	0.00%	NA
Indica II	465	91.60%	8.20%	0.22%	0.00%	NA
Indica III	913	90.50%	9.40%	0.11%	0.00%	NA
Indica Intermediate	786	87.00%	12.60%	0.38%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	98.20%	1.80%	0.00%	0.00%	NA
Japonica Intermediate	241	96.70%	3.30%	0.00%	0.00%	NA
VI/Aromatic	96	74.00%	26.00%	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
vg0919961970	G -> T	LOC_Os09g33810.1	missense_variant ; p.Ala49Ser; MODERATE	nonsynonymous_codon ; A49S	Average:74.879; most accessible tissue: Callus, score: 88.327	unknown	unknown	TOLERATED	0.29
vg0919961970	G -> T	LOC_Os09g33810.2	missense_variant ; p.Ala26Ser; MODERATE	nonsynonymous_codon ; A26S	Average:74.879; most accessible tissue: Callus, score: 88.327	unknown	unknown	TOLERATED	0.26
vg0919961970	G -> T	LOC_Os09g33810.3	missense_variant ; p.Ala26Ser; MODERATE	nonsynonymous_codon ; A26S	Average:74.879; most accessible tissue: Callus, score: 88.327	unknown	unknown	TOLERATED	0.26
vg0919961970	G -> T	LOC_Os09g33810.4	missense_variant ; p.Ala26Ser; MODERATE	nonsynonymous_codon ; A26S	Average:74.879; most accessible tissue: Callus, score: 88.327	unknown	unknown	TOLERATED	0.21

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0919961970	1.14E-07	2.43E-14	mr1216	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
vg0919961970	5.40E-08	1.78E-15	mr1216	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
vg0919961970	NA	4.94E-07	mr1510	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
vg0919961970	NA	6.87E-07	mr1702	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
vg0919961970	NA	1.28E-06	mr1158_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
vg0919961970	NA	1.18E-08	mr1510_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
vg0919961970	2.06E-06	NA	mr1793_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
vg0919961970	6.34E-06	8.72E-18	mr1817_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