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Detailed information for vg0820734484:

Variant ID: vg0820734484 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 20734484
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.04, others allele: 0.00, population size: 49. )

Flanking Sequence (100 bp) in Reference Genome:

CCTTTAGCACAGAGCTCAATCCTGAGATTCAACATTTTGTCAAGGAAAAGTGCAGAAATAGCATCAAATGGATCGAAAAGCTATGAAACTTTCCAGTTTG[T/C]
AGTGGAAGAGATGGACAAAATTGCTAAACAATTGGAATTATTGTGTTCAAATAAAGATGCTGAGCAGGAGATCAATGATTCAGATCCAAATGCAGAAGAC

Reverse complement sequence

GTCTTCTGCATTTGGATCTGAATCATTGATCTCCTGCTCAGCATCTTTATTTGAACACAATAATTCCAATTGTTTAGCAATTTTGTCCATCTCTTCCACT[A/G]
CAAACTGGAAAGTTTCATAGCTTTTCGATCCATTTGATGCTATTTCTGCACTTTTCCTTGACAAAATGTTGAATCTCAGGATTGAGCTCTGTGCTAAAGG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	36.50%	5.10%	9.94%	48.50%	NA
All Indica	2759	5.70%	2.50%	11.13%	80.65%	NA
All Japonica	1512	96.40%	2.40%	0.07%	1.12%	NA
Aus	269	2.60%	32.30%	56.88%	8.18%	NA
Indica I	595	4.70%	0.20%	3.53%	91.60%	NA
Indica II	465	5.60%	0.20%	6.45%	87.74%	NA
Indica III	913	4.60%	3.90%	18.84%	72.62%	NA
Indica Intermediate	786	7.80%	4.10%	10.69%	77.48%	NA
Temperate Japonica	767	98.30%	0.90%	0.00%	0.78%	NA
Tropical Japonica	504	95.60%	2.40%	0.00%	1.98%	NA
Japonica Intermediate	241	91.70%	7.50%	0.41%	0.41%	NA
VI/Aromatic	96	61.50%	36.50%	2.08%	0.00%	NA
Intermediate	90	47.80%	13.30%	7.78%	31.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0820734484	T -> C	LOC_Os08g33270.1	missense_variant ; p.Val966Ala; MODERATE	nonsynonymous_codon ; V966A	Average:6.638; most accessible tissue: Callus, score: 23.478	unknown	unknown	TOLERATED	0.33
vg0820734484	T -> DEL	LOC_Os08g33270.1	N	frameshift_variant	Average:6.638; most accessible tissue: Callus, score: 23.478	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0820734484	7.49E-07	NA	mr1066	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
vg0820734484	NA	1.64E-07	mr1612_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