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Detailed information for vg1003471515:

Variant ID: vg1003471515 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 3471515
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.04, others allele: 0.00, population size: 49. )

Flanking Sequence (100 bp) in Reference Genome:

AGAGCAAGTTTAGTAGTATAGCTAACTACTAGTTTCAAATCATCGATAGTCAATTTAATAGTCAATTCATACTACACTATTAATATATGGTTCCACAAAT[C/T]
ATACACATATTGTGTCTTAGAGTTCGTGCTACGGCTGGTTACAAATCTGTAGCTCGCTATTCTTTTCTCTTCTTTTATTTCCTTGACGTGTGTTATAGCT

Reverse complement sequence

AGCTATAACACACGTCAAGGAAATAAAAGAAGAGAAAAGAATAGCGAGCTACAGATTTGTAACCAGCCGTAGCACGAACTCTAAGACACAATATGTGTAT[G/A]
ATTTGTGGAACCATATATTAATAGTGTAGTATGAATTGACTATTAAATTGACTATCGATGATTTGAAACTAGTAGTTAGCTATACTACTAAACTTGCTCT

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	62.20%	3.30%	1.21%	33.35%	NA
All Indica	2759	40.50%	5.20%	1.56%	52.74%	NA
All Japonica	1512	99.40%	0.20%	0.00%	0.40%	NA
Aus	269	84.00%	0.40%	3.72%	11.90%	NA
Indica I	595	39.20%	0.50%	0.50%	59.83%	NA
Indica II	465	33.30%	23.40%	6.67%	36.56%	NA
Indica III	913	35.70%	0.10%	0.11%	64.07%	NA
Indica Intermediate	786	51.40%	3.80%	1.02%	43.77%	NA
Temperate Japonica	767	99.50%	0.10%	0.00%	0.39%	NA
Tropical Japonica	504	99.80%	0.00%	0.00%	0.20%	NA
Japonica Intermediate	241	98.30%	0.80%	0.00%	0.83%	NA
VI/Aromatic	96	34.40%	1.00%	1.04%	63.54%	NA
Intermediate	90	65.60%	6.70%	3.33%	24.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1003471515	C -> T	LOC_Os10g06710.1	upstream_gene_variant ; 643.0bp to feature; MODIFIER	silent_mutation	Average:30.786; most accessible tissue: Callus, score: 85.462	N	N	N	N
vg1003471515	C -> T	LOC_Os10g06700.1	downstream_gene_variant ; 2195.0bp to feature; MODIFIER	silent_mutation	Average:30.786; most accessible tissue: Callus, score: 85.462	N	N	N	N
vg1003471515	C -> T	LOC_Os10g06720.1	downstream_gene_variant ; 4027.0bp to feature; MODIFIER	silent_mutation	Average:30.786; most accessible tissue: Callus, score: 85.462	N	N	N	N
vg1003471515	C -> T	LOC_Os10g06720.2	downstream_gene_variant ; 4027.0bp to feature; MODIFIER	silent_mutation	Average:30.786; most accessible tissue: Callus, score: 85.462	N	N	N	N
vg1003471515	C -> T	LOC_Os10g06700-LOC_Os10g06710	intergenic_region ; MODIFIER	silent_mutation	Average:30.786; most accessible tissue: Callus, score: 85.462	N	N	N	N
vg1003471515	C -> DEL	N	N	silent_mutation	Average:30.786; most accessible tissue: Callus, score: 85.462	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1003471515	2.73E-06	2.73E-06	mr1197	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
vg1003471515	NA	9.12E-09	mr1877	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