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Detailed information for vg0816140925:

Variant ID: vg0816140925 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 16140925
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 73. )

Flanking Sequence (100 bp) in Reference Genome:

TTCATTATATGTTCTACAGTGTACTTAGAAGAGGGAGAGAGTAAAGTAGAAGATGTCGGAGGAATCCCAGAGTTGTCGGTAATCCTGTCCTTATTCTTTT[T/A]
CTTTGTTAATTACTCTGGTTCAATAGAAATATCATTTTGAGTAATTAAGATTTGCTTCGTGAGAATTATTCTTGGTTAGTTCCTAATTAGCATACGGGAT

Reverse complement sequence

ATCCCGTATGCTAATTAGGAACTAACCAAGAATAATTCTCACGAAGCAAATCTTAATTACTCAAAATGATATTTCTATTGAACCAGAGTAATTAACAAAG[A/T]
AAAAGAATAAGGACAGGATTACCGACAACTCTGGGATTCCTCCGACATCTTCTACTTTACTCTCTCCCTCTTCTAAGTACACTGTAGAACATATAATGAA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	25.70%	0.70%	4.74%	68.79%	NA
All Indica	2759	7.50%	1.00%	7.29%	84.23%	NA
All Japonica	1512	56.70%	0.10%	0.46%	42.72%	NA
Aus	269	6.30%	1.10%	4.83%	87.73%	NA
Indica I	595	15.60%	0.50%	11.43%	72.44%	NA
Indica II	465	8.40%	1.30%	4.73%	85.59%	NA
Indica III	913	1.30%	1.30%	6.24%	91.13%	NA
Indica Intermediate	786	8.00%	0.80%	6.87%	84.35%	NA
Temperate Japonica	767	96.50%	0.00%	0.00%	3.52%	NA
Tropical Japonica	504	6.90%	0.20%	0.99%	91.87%	NA
Japonica Intermediate	241	34.40%	0.00%	0.83%	64.73%	NA
VI/Aromatic	96	92.70%	2.10%	1.04%	4.17%	NA
Intermediate	90	50.00%	2.20%	2.22%	45.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0816140925	T -> A	LOC_Os08g26500.1	downstream_gene_variant ; 878.0bp to feature; MODIFIER	silent_mutation	Average:12.378; most accessible tissue: Callus, score: 19.445	N	N	N	N
vg0816140925	T -> A	LOC_Os08g26520.1	downstream_gene_variant ; 4464.0bp to feature; MODIFIER	silent_mutation	Average:12.378; most accessible tissue: Callus, score: 19.445	N	N	N	N
vg0816140925	T -> A	LOC_Os08g26510.1	intron_variant ; MODIFIER	silent_mutation	Average:12.378; most accessible tissue: Callus, score: 19.445	N	N	N	N
vg0816140925	T -> DEL	N	N	silent_mutation	Average:12.378; most accessible tissue: Callus, score: 19.445	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0816140925	2.66E-06	2.66E-06	mr1575	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