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Detailed information for vg0206245186:

Variant ID: vg0206245186 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 6245186
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, T: 0.08, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:

GTAGGCCATCTTTTATTGGCAAAATTTTACTTTGGACCTTTCTTAAACTAATCTTTCCATTTTGAATCGGGTAATTTTAACATTTTTTCGGTTTGGACTA[C/T]
CCTCAACGACTTCTTCATCACCCAACAACAACCTCACTCAAATTAGTTTGGGTACACCGATGAACTTCCTTGTCTATATGCAAGTCATATCTTCACTAGA

Reverse complement sequence

TCTAGTGAAGATATGACTTGCATATAGACAAGGAAGTTCATCGGTGTACCCAAACTAATTTGAGTGAGGTTGTTGTTGGGTGATGAAGAAGTCGTTGAGG[G/A]
TAGTCCAAACCGAAAAAATGTTAAAATTACCCGATTCAAAATGGAAAGATTAGTTTAAGAAAGGTCCAAAGTAAAATTTTGCCAATAAAAGATGGCCTAC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	54.70%	44.90%	0.40%	0.00%	NA
All Indica	2759	37.80%	61.60%	0.58%	0.00%	NA
All Japonica	1512	96.80%	3.20%	0.07%	0.00%	NA
Aus	269	2.20%	97.80%	0.00%	0.00%	NA
Indica I	595	51.40%	47.90%	0.67%	0.00%	NA
Indica II	465	50.10%	49.00%	0.86%	0.00%	NA
Indica III	913	27.80%	71.90%	0.33%	0.00%	NA
Indica Intermediate	786	31.80%	67.60%	0.64%	0.00%	NA
Temperate Japonica	767	98.20%	1.80%	0.00%	0.00%	NA
Tropical Japonica	504	95.80%	4.00%	0.20%	0.00%	NA
Japonica Intermediate	241	94.20%	5.80%	0.00%	0.00%	NA
VI/Aromatic	96	32.30%	66.70%	1.04%	0.00%	NA
Intermediate	90	48.90%	50.00%	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
vg0206245186	C -> T	LOC_Os02g12030.1	downstream_gene_variant ; 1897.0bp to feature; MODIFIER	silent_mutation	Average:51.59; most accessible tissue: Callus, score: 82.145	N	N	N	N
vg0206245186	C -> T	LOC_Os02g12020-LOC_Os02g12030	intergenic_region ; MODIFIER	silent_mutation	Average:51.59; most accessible tissue: Callus, score: 82.145	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0206245186	3.46E-07	3.21E-18	mr1170	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
vg0206245186	3.90E-07	1.29E-11	mr1170	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
vg0206245186	1.20E-07	8.28E-18	mr1170_2	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
vg0206245186	4.47E-06	2.02E-10	mr1170_2	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
vg0206245186	NA	2.75E-07	mr1691_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
vg0206245186	NA	2.28E-07	mr1743_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
vg0206245186	NA	2.22E-07	mr1749_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