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Detailed information for vg0114539233:

Variant ID: vg0114539233 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 14539233
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

CATGCCAATTGTTGTGTGCCTTCTACCTTGCATCAATGTTTAATTCAATGGGACGGTGATGATGTTGAAATTGTTCAAGCGGATACATTGGCCGAGGTTG[C/T]
AATGGCCGATGCTACTTTTGAGTGGCGTCATGGGAATATCCAATGCTTATCGGGGAGGGATCTTTCTAGCTATGATTTTATTAGTATCTCCGATGGCAAA

Reverse complement sequence

TTTGCCATCGGAGATACTAATAAAATCATAGCTAGAAAGATCCCTCCCCGATAAGCATTGGATATTCCCATGACGCCACTCAAAAGTAGCATCGGCCATT[G/A]
CAACCTCGGCCAATGTATCCGCTTGAACAATTTCAACATCATCACCGTCCCATTGAATTAAACATTGATGCAAGGTAGAAGGCACACAACAATTGGCATG

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	62.80%	12.30%	14.11%	10.73%	NA
All Indica	2759	61.70%	20.50%	17.51%	0.25%	NA
All Japonica	1512	60.70%	0.20%	6.55%	32.54%	NA
Aus	269	81.80%	0.40%	17.84%	0.00%	NA
Indica I	595	68.10%	5.20%	26.39%	0.34%	NA
Indica II	465	47.50%	30.10%	21.72%	0.65%	NA
Indica III	913	66.20%	25.10%	8.76%	0.00%	NA
Indica Intermediate	786	60.20%	21.10%	18.45%	0.25%	NA
Temperate Japonica	767	86.30%	0.10%	0.65%	12.91%	NA
Tropical Japonica	504	26.20%	0.40%	14.88%	58.53%	NA
Japonica Intermediate	241	51.50%	0.00%	7.88%	40.66%	NA
VI/Aromatic	96	71.90%	2.10%	20.83%	5.21%	NA
Intermediate	90	65.60%	12.20%	18.89%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0114539233	C -> T	LOC_Os01g25640.1	downstream_gene_variant ; 4758.0bp to feature; MODIFIER	silent_mutation	Average:10.979; most accessible tissue: Callus, score: 28.892	N	N	N	N
vg0114539233	C -> T	LOC_Os01g25650.1	intron_variant ; MODIFIER	silent_mutation	Average:10.979; most accessible tissue: Callus, score: 28.892	N	N	N	N
vg0114539233	C -> DEL	N	N	silent_mutation	Average:10.979; most accessible tissue: Callus, score: 28.892	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0114539233	1.86E-06	1.86E-06	mr1492	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