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Detailed information for vg0816234574:

Variant ID: vg0816234574 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 16234574
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:

CACTTTTTGACACAATTTGCTACTATGGACTAGCAAATACCAAATGCCAAATTGCCAACTTTTGCTACTAGTGTTTAGATCCAAAATAGCAAAAAGTGCT[A/C]
CAAAATGGCAAAACTTTTGCCATTTTGGAGGATCTAAACAGGGCCTTACGTAGAGAGAAACGGAAAAGAGAAATAATGGTAACGAGGTAGCAAGTAAAGT

Reverse complement sequence

ACTTTACTTGCTACCTCGTTACCATTATTTCTCTTTTCCGTTTCTCTCTACGTAAGGCCCTGTTTAGATCCTCCAAAATGGCAAAAGTTTTGCCATTTTG[T/G]
AGCACTTTTTGCTATTTTGGATCTAAACACTAGTAGCAAAAGTTGGCAATTTGGCATTTGGTATTTGCTAGTCCATAGTAGCAAATTGTGTCAAAAAGTG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	40.60%	0.90%	0.63%	57.91%	NA
All Indica	2759	21.80%	1.40%	0.98%	75.75%	NA
All Japonica	1512	74.40%	0.00%	0.13%	25.46%	NA
Aus	269	17.50%	0.00%	0.37%	82.16%	NA
Indica I	595	46.60%	2.40%	0.84%	50.25%	NA
Indica II	465	23.20%	1.70%	1.72%	73.33%	NA
Indica III	913	3.60%	0.00%	0.44%	95.95%	NA
Indica Intermediate	786	23.40%	2.30%	1.27%	73.03%	NA
Temperate Japonica	767	98.80%	0.00%	0.00%	1.17%	NA
Tropical Japonica	504	36.70%	0.00%	0.20%	63.10%	NA
Japonica Intermediate	241	75.50%	0.00%	0.41%	24.07%	NA
VI/Aromatic	96	91.70%	1.00%	0.00%	7.29%	NA
Intermediate	90	61.10%	1.10%	0.00%	37.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0816234574	A -> C	LOC_Os08g26690.1	downstream_gene_variant ; 1628.0bp to feature; MODIFIER	silent_mutation	Average:15.184; most accessible tissue: Callus, score: 32.265	N	N	N	N
vg0816234574	A -> C	LOC_Os08g26700.1	downstream_gene_variant ; 4009.0bp to feature; MODIFIER	silent_mutation	Average:15.184; most accessible tissue: Callus, score: 32.265	N	N	N	N
vg0816234574	A -> C	LOC_Os08g26700.2	downstream_gene_variant ; 2888.0bp to feature; MODIFIER	silent_mutation	Average:15.184; most accessible tissue: Callus, score: 32.265	N	N	N	N
vg0816234574	A -> C	LOC_Os08g26700.3	downstream_gene_variant ; 2888.0bp to feature; MODIFIER	silent_mutation	Average:15.184; most accessible tissue: Callus, score: 32.265	N	N	N	N
vg0816234574	A -> C	LOC_Os08g26690-LOC_Os08g26700	intergenic_region ; MODIFIER	silent_mutation	Average:15.184; most accessible tissue: Callus, score: 32.265	N	N	N	N
vg0816234574	A -> DEL	N	N	silent_mutation	Average:15.184; most accessible tissue: Callus, score: 32.265	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0816234574	NA	7.73E-08	mr1680	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
vg0816234574	NA	2.37E-16	mr1040_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
vg0816234574	2.80E-06	NA	mr1134_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