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Detailed information for vg0314584521:

Variant ID: vg0314584521 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 14584521
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.95, C: 0.05, others allele: 0.00, population size: 108. )

Flanking Sequence (100 bp) in Reference Genome:

GTGGCCGGCCGGCGTGGAGAGGAGGCGGCAGCGGCCGGCCGGCGTCTCTGTGATTTTTTTTTTTTAGAATTTGTGATTTATTGCATGATCCTGTGATGTA[T/C]
TGATTTGTGTGTGATGTATTTGCGATGAATTTTGTAGAACTTGTGATGTAATTTGATTTGTGTGCAATTTTATTTTAGGATTTGTGATGTATTTGATTTG

Reverse complement sequence

CAAATCAAATACATCACAAATCCTAAAATAAAATTGCACACAAATCAAATTACATCACAAGTTCTACAAAATTCATCGCAAATACATCACACACAAATCA[A/G]
TACATCACAGGATCATGCAATAAATCACAAATTCTAAAAAAAAAAAATCACAGAGACGCCGGCCGGCCGCTGCCGCCTCCTCTCCACGCCGGCCGGCCAC

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	75.80%	24.10%	0.17%	0.00%	NA
All Indica	2759	68.80%	31.00%	0.18%	0.00%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	7.10%	92.20%	0.74%	0.00%	NA
Indica I	595	51.10%	48.70%	0.17%	0.00%	NA
Indica II	465	59.10%	40.60%	0.22%	0.00%	NA
Indica III	913	81.10%	18.70%	0.22%	0.00%	NA
Indica Intermediate	786	73.70%	26.20%	0.13%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	90.60%	9.40%	0.00%	0.00%	NA
Intermediate	90	75.60%	23.30%	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
vg0314584521	T -> C	LOC_Os03g25540.1	downstream_gene_variant ; 1528.0bp to feature; MODIFIER	silent_mutation	Average:32.788; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N
vg0314584521	T -> C	LOC_Os03g25540-LOC_Os03g25550	intergenic_region ; MODIFIER	silent_mutation	Average:32.788; most accessible tissue: Minghui63 panicle, score: 62.157	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0314584521	NA	3.90E-06	mr1516	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
vg0314584521	1.59E-06	NA	mr1542	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
vg0314584521	NA	2.67E-08	mr1542	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
vg0314584521	5.79E-07	NA	mr1542_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
vg0314584521	NA	5.50E-09	mr1542_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