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Detailed information for vg0208856189:

Variant ID: vg0208856189 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 8856189
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.60, T: 0.40, others allele: 0.00, population size: 93. )

Flanking Sequence (100 bp) in Reference Genome:

TCTGCTTCTTGAAGAGTTGTTTGGATTTGATGGTTTTGTAGTGGCTAAGCAAATGAGCTGGTGGCCAGGGTGGACATCAACGCATTGTTCGCTGCGCAGC[T/C]
AGCAATCTGACCTACTCGATGATGAGAGAGATGCGTCAGAGTAAGGCTAAAAGTGGGGTGGGCCTGCCACTAACCCGCTGGGCTAGCCCACCCCACTTAC

Reverse complement sequence

GTAAGTGGGGTGGGCTAGCCCAGCGGGTTAGTGGCAGGCCCACCCCACTTTTAGCCTTACTCTGACGCATCTCTCTCATCATCGAGTAGGTCAGATTGCT[A/G]
GCTGCGCAGCGAACAATGCGTTGATGTCCACCCTGGCCACCAGCTCATTTGCTTAGCCACTACAAAACCATCAAATCCAAACAACTCTTCAAGAAGCAGA

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	54.70%	24.80%	1.57%	18.96%	NA
All Indica	2759	34.30%	39.60%	2.14%	24.03%	NA
All Japonica	1512	97.90%	1.30%	0.00%	0.79%	NA
Aus	269	7.10%	17.10%	4.46%	71.38%	NA
Indica I	595	4.40%	46.40%	3.03%	46.22%	NA
Indica II	465	24.10%	40.40%	2.58%	32.90%	NA
Indica III	913	63.10%	29.50%	0.99%	6.46%	NA
Indica Intermediate	786	29.40%	45.70%	2.54%	22.39%	NA
Temperate Japonica	767	98.40%	0.90%	0.00%	0.65%	NA
Tropical Japonica	504	97.80%	2.00%	0.00%	0.20%	NA
Japonica Intermediate	241	96.70%	0.80%	0.00%	2.49%	NA
VI/Aromatic	96	82.30%	0.00%	1.04%	16.67%	NA
Intermediate	90	65.60%	17.80%	2.22%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0208856189	T -> DEL	N	N	silent_mutation	Average:66.838; most accessible tissue: Callus, score: 81.229	N	N	N	N
vg0208856189	T -> C	LOC_Os02g15710.1	upstream_gene_variant ; 1204.0bp to feature; MODIFIER	silent_mutation	Average:66.838; most accessible tissue: Callus, score: 81.229	N	N	N	N
vg0208856189	T -> C	LOC_Os02g15720.1	upstream_gene_variant ; 377.0bp to feature; MODIFIER	silent_mutation	Average:66.838; most accessible tissue: Callus, score: 81.229	N	N	N	N
vg0208856189	T -> C	LOC_Os02g15704.1	downstream_gene_variant ; 4292.0bp to feature; MODIFIER	silent_mutation	Average:66.838; most accessible tissue: Callus, score: 81.229	N	N	N	N
vg0208856189	T -> C	LOC_Os02g15710-LOC_Os02g15720	intergenic_region ; MODIFIER	silent_mutation	Average:66.838; most accessible tissue: Callus, score: 81.229	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0208856189	2.66E-06	NA	mr1929	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