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Detailed information for vg0616146874:

Variant ID: vg0616146874 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 16146874
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, T: 0.01, others allele: 0.00, population size: 92. )

Flanking Sequence (100 bp) in Reference Genome:

ATTTGGACATTATGGAATTGTTGGATTATGTGGAAATGGACACACACCTCCCCCTCTATTCAAAACCCTCAAAATGGTTTTAGGCTGGGCTCGAGGTGCA[A/T]
GGTTTTGATAGTAGCACCTCAGCCACTATAAGGACCGGTCTTCGGGCCTCTGTTGCAAAGCACCACCGTACTTCCACATGTCTAGTGGGTAAAGCTTAGT

Reverse complement sequence

ACTAAGCTTTACCCACTAGACATGTGGAAGTACGGTGGTGCTTTGCAACAGAGGCCCGAAGACCGGTCCTTATAGTGGCTGAGGTGCTACTATCAAAACC[T/A]
TGCACCTCGAGCCCAGCCTAAAACCATTTTGAGGGTTTTGAATAGAGGGGGAGGTGTGTGTCCATTTCCACATAATCCAACAATTCCATAATGTCCAAAT

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	72.50%	7.10%	19.40%	0.93%	NA
All Indica	2759	55.50%	12.00%	31.10%	1.45%	NA
All Japonica	1512	98.60%	0.10%	1.06%	0.20%	NA
Aus	269	87.00%	1.10%	11.90%	0.00%	NA
Indica I	595	88.70%	3.20%	6.89%	1.18%	NA
Indica II	465	77.60%	3.90%	17.20%	1.29%	NA
Indica III	913	16.60%	23.50%	59.69%	0.11%	NA
Indica Intermediate	786	62.20%	10.10%	24.43%	3.31%	NA
Temperate Japonica	767	98.00%	0.10%	1.43%	0.39%	NA
Tropical Japonica	504	99.20%	0.20%	0.60%	0.00%	NA
Japonica Intermediate	241	99.20%	0.00%	0.83%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	85.60%	1.10%	12.22%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0616146874	A -> T	LOC_Os06g28390.1	upstream_gene_variant ; 3858.0bp to feature; MODIFIER	silent_mutation	Average:35.5; most accessible tissue: Zhenshan97 flag leaf, score: 84.146	N	N	N	N
vg0616146874	A -> T	LOC_Os06g28380.1	downstream_gene_variant ; 2113.0bp to feature; MODIFIER	silent_mutation	Average:35.5; most accessible tissue: Zhenshan97 flag leaf, score: 84.146	N	N	N	N
vg0616146874	A -> T	LOC_Os06g28380-LOC_Os06g28390	intergenic_region ; MODIFIER	silent_mutation	Average:35.5; most accessible tissue: Zhenshan97 flag leaf, score: 84.146	N	N	N	N
vg0616146874	A -> DEL	N	N	silent_mutation	Average:35.5; most accessible tissue: Zhenshan97 flag leaf, score: 84.146	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0616146874	3.94E-06	6.77E-07	mr1850	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