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Detailed information for vg0613866615:

Variant ID: vg0613866615 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 13866615
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGGGAAACTATCAAAGCTTGAATTAATTTGTGAGCAAAGTTTGGAGAGGGAATGAAAATGTGTTGAAATGGGGTGGACTTCCCTCTCTCAGCCAGCTGGC[A/T]
TTAGTAATGCACCCACAACGGTCAAAACAACCTGTGGGGCCCACTAGCCGTTACCCTGCCAAAAATGGCAGGTAGCCGTTGCCTAGCTGGTTCGGCCGAA

Reverse complement sequence

TTCGGCCGAACCAGCTAGGCAACGGCTACCTGCCATTTTTGGCAGGGTAACGGCTAGTGGGCCCCACAGGTTGTTTTGACCGTTGTGGGTGCATTACTAA[T/A]
GCCAGCTGGCTGAGAGAGGGAAGTCCACCCCATTTCAACACATTTTCATTCCCTCTCCAAACTTTGCTCACAAATTAATTCAAGCTTTGATAGTTTCCCT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	35.10%	6.00%	0.53%	58.38%	NA
All Indica	2759	8.30%	1.80%	0.83%	89.05%	NA
All Japonica	1512	91.50%	6.20%	0.07%	2.31%	NA
Aus	269	1.50%	45.70%	0.37%	52.42%	NA
Indica I	595	16.50%	3.90%	0.84%	78.82%	NA
Indica II	465	8.20%	1.90%	0.65%	89.25%	NA
Indica III	913	1.40%	0.20%	0.88%	97.48%	NA
Indica Intermediate	786	10.20%	2.00%	0.89%	86.90%	NA
Temperate Japonica	767	97.00%	0.10%	0.13%	2.74%	NA
Tropical Japonica	504	82.90%	15.70%	0.00%	1.39%	NA
Japonica Intermediate	241	91.70%	5.40%	0.00%	2.90%	NA
VI/Aromatic	96	5.20%	4.20%	0.00%	90.62%	NA
Intermediate	90	43.30%	13.30%	0.00%	43.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0613866615	A -> T	LOC_Os06g23720.1	upstream_gene_variant ; 1569.0bp to feature; MODIFIER	silent_mutation	Average:9.274; most accessible tissue: Callus, score: 39.629	N	N	N	N
vg0613866615	A -> T	LOC_Os06g23730.1	intron_variant ; MODIFIER	silent_mutation	Average:9.274; most accessible tissue: Callus, score: 39.629	N	N	N	N
vg0613866615	A -> DEL	N	N	silent_mutation	Average:9.274; most accessible tissue: Callus, score: 39.629	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0613866615	NA	1.51E-06	mr1603	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
vg0613866615	NA	1.57E-06	mr1126_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
vg0613866615	4.72E-06	NA	mr1170_2	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
vg0613866615	NA	7.45E-06	mr1603_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