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Detailed information for vg0208782569:

Variant ID: vg0208782569 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 8782569
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, C: 0.03, others allele: 0.00, population size: 101. )

Flanking Sequence (100 bp) in Reference Genome:

CTCATCATCAAATACTTATATAAGAATAAATCTAACAAAATATAGTTATAATCCTTTATATTTTACCAAACTTGGGTATAGAATGATATATGAAACATGT[T/C]
TAGATTGCTACCTTGACATGCCAAAATTTAGCATAAGGTGTGTTTAGTTTTTTTGTGTAAAGTTTTTGAAGTATACAGACACACATTTGATGTATTAAAC

Reverse complement sequence

GTTTAATACATCAAATGTGTGTCTGTATACTTCAAAAACTTTACACAAAAAAACTAAACACACCTTATGCTAAATTTTGGCATGTCAAGGTAGCAATCTA[A/G]
ACATGTTTCATATATCATTCTATACCCAAGTTTGGTAAAATATAAAGGATTATAACTATATTTTGTTAGATTTATTCTTATATAAGTATTTGATGATGAG

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	72.50%	27.50%	0.04%	0.00%	NA
All Indica	2759	55.70%	44.30%	0.07%	0.00%	NA
All Japonica	1512	99.40%	0.60%	0.00%	0.00%	NA
Aus	269	81.40%	18.60%	0.00%	0.00%	NA
Indica I	595	31.80%	68.10%	0.17%	0.00%	NA
Indica II	465	60.90%	39.10%	0.00%	0.00%	NA
Indica III	913	76.70%	23.30%	0.00%	0.00%	NA
Indica Intermediate	786	46.30%	53.60%	0.13%	0.00%	NA
Temperate Japonica	767	99.10%	0.90%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	80.00%	20.00%	0.00%	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
vg0208782569	T -> C	LOC_Os02g15630.1	upstream_gene_variant ; 1352.0bp to feature; MODIFIER	silent_mutation	Average:39.372; most accessible tissue: Callus, score: 67.927	N	N	N	N
vg0208782569	T -> C	LOC_Os02g15620.1	downstream_gene_variant ; 946.0bp to feature; MODIFIER	silent_mutation	Average:39.372; most accessible tissue: Callus, score: 67.927	N	N	N	N
vg0208782569	T -> C	LOC_Os02g15620-LOC_Os02g15630	intergenic_region ; MODIFIER	silent_mutation	Average:39.372; most accessible tissue: Callus, score: 67.927	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0208782569	1.28E-06	2.41E-06	mr1002	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
vg0208782569	1.72E-06	NA	mr1399	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