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Detailed information for vg0629450401:

Variant ID: vg0629450401 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 29450401
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, C: 0.01, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

TGTACCCTGGACATGAAAAATAAACTTTTGCACATTTTTATTTGGATTCGAAATAAGATCTCCAAATCACAGTTATATGTATATGCTGTTATGTCATTAG[T/C]
GTGCACTAATTTAGAGCAATTTTACTTGTGTGGATCATTTTGGCCCAGTTCGCACCAACTAGCCAAGTTATTATATCAAAGTGAGCAATTTGTAAGTTGT

Reverse complement sequence

ACAACTTACAAATTGCTCACTTTGATATAATAACTTGGCTAGTTGGTGCGAACTGGGCCAAAATGATCCACACAAGTAAAATTGCTCTAAATTAGTGCAC[A/G]
CTAATGACATAACAGCATATACATATAACTGTGATTTGGAGATCTTATTTCGAATCCAAATAAAAATGTGCAAAAGTTTATTTTTCATGTCCAGGGTACA

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	81.50%	18.20%	0.30%	0.00%	NA
All Indica	2759	73.90%	25.70%	0.43%	0.00%	NA
All Japonica	1512	91.30%	8.70%	0.07%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	44.20%	55.00%	0.84%	0.00%	NA
Indica II	465	69.90%	29.20%	0.86%	0.00%	NA
Indica III	913	94.50%	5.40%	0.11%	0.00%	NA
Indica Intermediate	786	74.80%	24.90%	0.25%	0.00%	NA
Temperate Japonica	767	97.70%	2.30%	0.00%	0.00%	NA
Tropical Japonica	504	80.40%	19.40%	0.20%	0.00%	NA
Japonica Intermediate	241	93.80%	6.20%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	77.80%	21.10%	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
vg0629450401	T -> C	LOC_Os06g48680.1	upstream_gene_variant ; 2866.0bp to feature; MODIFIER	silent_mutation	Average:28.868; most accessible tissue: Minghui63 root, score: 46.493	N	N	N	N
vg0629450401	T -> C	LOC_Os06g48680-LOC_Os06g48690	intergenic_region ; MODIFIER	silent_mutation	Average:28.868; most accessible tissue: Minghui63 root, score: 46.493	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0629450401	2.50E-06	2.50E-06	mr1736	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