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Detailed information for vg0820747994:

Variant ID: vg0820747994 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 20747994
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.82, T: 0.18, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:

CTTCTAAGCAGACTCAACCATTCACCATTTATGAAGGGACGCTAAAAATTTTCTTTCTCAACCTTAGTTAAGCAACCTATAGTTCTTACATATTGACGTG[C/T]
AATTCTTTTACGCATTCGGAAATAAAAAAGTTAAGCAACCTATAGCTAGCTATACTTACGTTTTAAAATGGACTGTGGTATACGTCCATATGCATGCATT

Reverse complement sequence

AATGCATGCATATGGACGTATACCACAGTCCATTTTAAAACGTAAGTATAGCTAGCTATAGGTTGCTTAACTTTTTTATTTCCGAATGCGTAAAAGAATT[G/A]
CACGTCAATATGTAAGAACTATAGGTTGCTTAACTAAGGTTGAGAAAGAAAATTTTTAGCGTCCCTTCATAAATGGTGAATGGTTGAGTCTGCTTAGAAG

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	55.20%	44.40%	0.25%	0.19%	NA
All Indica	2759	91.90%	7.40%	0.33%	0.33%	NA
All Japonica	1512	1.30%	98.70%	0.07%	0.00%	NA
Aus	269	9.30%	90.70%	0.00%	0.00%	NA
Indica I	595	96.80%	2.00%	0.50%	0.67%	NA
Indica II	465	93.30%	6.00%	0.43%	0.22%	NA
Indica III	913	92.30%	7.60%	0.11%	0.00%	NA
Indica Intermediate	786	86.90%	12.20%	0.38%	0.51%	NA
Temperate Japonica	767	1.00%	99.00%	0.00%	0.00%	NA
Tropical Japonica	504	2.00%	97.80%	0.20%	0.00%	NA
Japonica Intermediate	241	0.40%	99.60%	0.00%	0.00%	NA
VI/Aromatic	96	1.00%	97.90%	1.04%	0.00%	NA
Intermediate	90	31.10%	67.80%	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
vg0820747994	C -> T	LOC_Os08g33290.1	downstream_gene_variant ; 2490.0bp to feature; MODIFIER	silent_mutation	Average:61.559; most accessible tissue: Callus, score: 85.17	N	N	N	N
vg0820747994	C -> T	LOC_Os08g33290-LOC_Os08g33300	intergenic_region ; MODIFIER	silent_mutation	Average:61.559; most accessible tissue: Callus, score: 85.17	N	N	N	N
vg0820747994	C -> DEL	N	N	silent_mutation	Average:61.559; most accessible tissue: Callus, score: 85.17	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0820747994	NA	3.91E-26	mr1039	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
vg0820747994	NA	1.68E-10	mr1151	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
vg0820747994	NA	8.24E-06	mr1157	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
vg0820747994	5.92E-06	3.03E-06	mr1328	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
vg0820747994	NA	6.11E-09	mr1352	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
vg0820747994	5.30E-07	8.84E-08	mr1446	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
vg0820747994	NA	4.37E-25	mr1571	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
vg0820747994	NA	5.08E-20	mr1580	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
vg0820747994	NA	1.28E-25	mr1632	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
vg0820747994	2.48E-07	2.25E-07	mr1712	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
vg0820747994	NA	3.75E-30	mr1793	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
vg0820747994	NA	2.53E-17	mr1825	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
vg0820747994	NA	2.18E-27	mr1039_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
vg0820747994	NA	5.12E-14	mr1514_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