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Detailed information for vg0919531759:

Variant ID: vg0919531759 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 19531759
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, A: 0.05, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:

TTTTTCCTCCTTGGCCTGTACCTTTCCCCCAACAATCAATTAAAGATTTTCGACAAATATAGTCCTAATTTTGTCTACTATAGTATATCTCCTTGTTGAC[C/A]
TCTTCCCAAATTACATGCATGATCCGACAATTCTTAAACAATGCTAGGCCGTCTTTATGTTCCTCAAACAAAATTAACAAAAACAATTATGTAGCCCTTT

Reverse complement sequence

AAAGGGCTACATAATTGTTTTTGTTAATTTTGTTTGAGGAACATAAAGACGGCCTAGCATTGTTTAAGAATTGTCGGATCATGCATGTAATTTGGGAAGA[G/T]
GTCAACAAGGAGATATACTATAGTAGACAAAATTAGGACTATATTTGTCGAAAATCTTTAATTGATTGTTGGGGGAAAGGTACAGGCCAAGGAGGAAAAA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	53.50%	46.40%	0.06%	0.00%	NA
All Indica	2759	22.70%	77.20%	0.07%	0.00%	NA
All Japonica	1512	99.50%	0.50%	0.00%	0.00%	NA
Aus	269	88.10%	11.90%	0.00%	0.00%	NA
Indica I	595	60.80%	39.20%	0.00%	0.00%	NA
Indica II	465	8.60%	91.40%	0.00%	0.00%	NA
Indica III	913	7.30%	92.60%	0.11%	0.00%	NA
Indica Intermediate	786	20.10%	79.80%	0.13%	0.00%	NA
Temperate Japonica	767	99.30%	0.70%	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	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	73.30%	25.60%	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
vg0919531759	C -> A	LOC_Os09g32740.1	upstream_gene_variant ; 3972.0bp to feature; MODIFIER	silent_mutation	Average:51.009; most accessible tissue: Callus, score: 82.919	N	N	N	N
vg0919531759	C -> A	LOC_Os09g32750.1	upstream_gene_variant ; 1261.0bp to feature; MODIFIER	silent_mutation	Average:51.009; most accessible tissue: Callus, score: 82.919	N	N	N	N
vg0919531759	C -> A	LOC_Os09g32740-LOC_Os09g32750	intergenic_region ; MODIFIER	silent_mutation	Average:51.009; most accessible tissue: Callus, score: 82.919	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0919531759	NA	9.37E-06	mr1532	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
vg0919531759	4.71E-06	5.27E-06	mr1676_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
vg0919531759	NA	2.87E-10	mr1761_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