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Detailed information for vg0205094542:

Variant ID: vg0205094542 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 5094542
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:

AAAATCCCAATGAGATTTGCCTTTTCCAATGTACTGTTTATATACCAGCGGTTCGATGGAGACCGATTAAGGTTGAACATCCACCTAGAACTCCAAGTTA[C/T]
ACTTACTCACAACTTGAACAATGGACTACGCCTTGAATTGCAAGTCTTGTGCAAGCAAGTTTCACTCAGAGTCTTATCTGGTACTAGACCGTCTGTAGAC

Reverse complement sequence

GTCTACAGACGGTCTAGTACCAGATAAGACTCTGAGTGAAACTTGCTTGCACAAGACTTGCAATTCAAGGCGTAGTCCATTGTTCAAGTTGTGAGTAAGT[G/A]
TAACTTGGAGTTCTAGGTGGATGTTCAACCTTAATCGGTCTCCATCGAACCGCTGGTATATAAACAGTACATTGGAAAAGGCAAATCTCATTGGGATTTT

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	51.40%	45.50%	3.07%	0.00%	NA
All Indica	2759	75.20%	21.00%	3.73%	0.00%	NA
All Japonica	1512	1.00%	98.90%	0.07%	0.00%	NA
Aus	269	82.90%	8.90%	8.18%	0.00%	NA
Indica I	595	56.60%	39.30%	4.03%	0.00%	NA
Indica II	465	82.80%	12.50%	4.73%	0.00%	NA
Indica III	913	83.60%	13.70%	2.74%	0.00%	NA
Indica Intermediate	786	75.20%	20.70%	4.07%	0.00%	NA
Temperate Japonica	767	0.50%	99.30%	0.13%	0.00%	NA
Tropical Japonica	504	0.60%	99.40%	0.00%	0.00%	NA
Japonica Intermediate	241	3.30%	96.70%	0.00%	0.00%	NA
VI/Aromatic	96	78.10%	8.30%	13.54%	0.00%	NA
Intermediate	90	44.40%	48.90%	6.67%	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
vg0205094542	C -> T	LOC_Os02g09860.1	upstream_gene_variant ; 3227.0bp to feature; MODIFIER	silent_mutation	Average:20.172; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0205094542	C -> T	LOC_Os02g09870.1	downstream_gene_variant ; 437.0bp to feature; MODIFIER	silent_mutation	Average:20.172; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0205094542	C -> T	LOC_Os02g09860-LOC_Os02g09870	intergenic_region ; MODIFIER	silent_mutation	Average:20.172; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0205094542	NA	2.47E-06	mr1011	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
vg0205094542	4.24E-06	NA	mr1526	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