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Detailed information for vg0824785295:

Variant ID: vg0824785295 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 24785295
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:

CTGCATTCATCGGCATCAATGCCAATATTTTATAGAGATATTAAATCTTCCAATATACTTCTTGATGACAACCTAACAGCAAAGGTATCCGACTTTAGAG[C/T]
TTCAAGATATATCTCAATCAATGAAACAGGAATAACTACTGCAGTTCAAGGAACGATTGGCTACTTGGATCCTATGTACTATTATACGGGACGACTTACG

Reverse complement sequence

CGTAAGTCGTCCCGTATAATAGTACATAGGATCCAAGTAGCCAATCGTTCCTTGAACTGCAGTAGTTATTCCTGTTTCATTGATTGAGATATATCTTGAA[G/A]
CTCTAAAGTCGGATACCTTTGCTGTTAGGTTGTCATCAAGAAGTATATTGGAAGATTTAATATCTCTATAAAATATTGGCATTGATGCCGATGAATGCAG

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	91.30%	6.00%	2.62%	0.11%	NA
All Indica	2759	85.20%	10.20%	4.39%	0.18%	NA
All Japonica	1512	99.90%	0.10%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	64.70%	21.70%	13.11%	0.50%	NA
Indica II	465	92.00%	5.20%	2.58%	0.22%	NA
Indica III	913	93.10%	6.70%	0.22%	0.00%	NA
Indica Intermediate	786	87.70%	8.50%	3.69%	0.13%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	2.20%	2.22%	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
vg0824785295	C -> T	LOC_Os08g39240.1	missense_variant ; p.Ala533Val; MODERATE	nonsynonymous_codon ; A533V	Average:33.189; most accessible tissue: Callus, score: 59.483	unknown	unknown	DELETERIOUS	0.00
vg0824785295	C -> T	LOC_Os08g39240.2	missense_variant ; p.Ala186Val; MODERATE	nonsynonymous_codon ; A186V	Average:33.189; most accessible tissue: Callus, score: 59.483	unknown	unknown	DELETERIOUS	0.00
vg0824785295	C -> DEL	LOC_Os08g39240.1	N	frameshift_variant	Average:33.189; most accessible tissue: Callus, score: 59.483	N	N	N	N
vg0824785295	C -> DEL	LOC_Os08g39240.2	N	frameshift_variant	Average:33.189; most accessible tissue: Callus, score: 59.483	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0824785295	NA	1.42E-06	mr1038	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
vg0824785295	NA	3.65E-06	mr1038	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
vg0824785295	NA	1.18E-06	mr1389	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
vg0824785295	9.40E-06	NA	mr1436	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
vg0824785295	NA	1.26E-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
vg0824785295	NA	8.80E-06	mr1874_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