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Detailed information for vg0811941721:

Variant ID: vg0811941721 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 11941721
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.95, T: 0.05, others allele: 0.00, population size: 63. )

Flanking Sequence (100 bp) in Reference Genome:

GCCAACAGGAAGGATGCATGGGCTGATTGCAGCTGAGAAAACTTCCCTGGACTTTTGGTATCTTTCATGATTGATGTCTTCAAATCTAAAGTCCGATGGG[A/T]
GCTCAAGGTTTGCTGAATCTTCATAAGGAAACCAAACTCAAGCATCTTTTTGAAAGCCCTCATAGAAACTGCAGAACCGGTCCTTGAGCAGTTCAACCAA

Reverse complement sequence

TTGGTTGAACTGCTCAAGGACCGGTTCTGCAGTTTCTATGAGGGCTTTCAAAAAGATGCTTGAGTTTGGTTTCCTTATGAAGATTCAGCAAACCTTGAGC[T/A]
CCCATCGGACTTTAGATTTGAAGACATCAATCATGAAAGATACCAAAAGTCCAGGGAAGTTTTCTCAGCTGCAATCAGCCCATGCATCCTTCCTGTTGGC

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	39.30%	23.80%	5.52%	31.32%	NA
All Indica	2759	12.50%	39.50%	7.00%	40.92%	NA
All Japonica	1512	89.00%	1.10%	1.39%	8.53%	NA
Aus	269	7.40%	3.00%	14.87%	74.72%	NA
Indica I	595	7.10%	26.60%	8.24%	58.15%	NA
Indica II	465	11.60%	29.50%	4.30%	54.62%	NA
Indica III	913	16.60%	54.00%	7.67%	21.69%	NA
Indica Intermediate	786	12.50%	38.50%	6.87%	42.11%	NA
Temperate Japonica	767	88.30%	0.90%	0.65%	10.17%	NA
Tropical Japonica	504	92.10%	0.80%	1.59%	5.56%	NA
Japonica Intermediate	241	85.10%	2.10%	3.32%	9.54%	NA
VI/Aromatic	96	96.90%	0.00%	1.04%	2.08%	NA
Intermediate	90	60.00%	12.20%	6.67%	21.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0811941721	A -> T	LOC_Os08g19940.1	upstream_gene_variant ; 245.0bp to feature; MODIFIER	silent_mutation	Average:11.518; most accessible tissue: Callus, score: 30.441	N	N	N	N
vg0811941721	A -> T	LOC_Os08g19930.1	downstream_gene_variant ; 2838.0bp to feature; MODIFIER	silent_mutation	Average:11.518; most accessible tissue: Callus, score: 30.441	N	N	N	N
vg0811941721	A -> T	LOC_Os08g19950.1	downstream_gene_variant ; 38.0bp to feature; MODIFIER	silent_mutation	Average:11.518; most accessible tissue: Callus, score: 30.441	N	N	N	N
vg0811941721	A -> T	LOC_Os08g19960.1	downstream_gene_variant ; 4489.0bp to feature; MODIFIER	silent_mutation	Average:11.518; most accessible tissue: Callus, score: 30.441	N	N	N	N
vg0811941721	A -> T	LOC_Os08g19940-LOC_Os08g19950	intergenic_region ; MODIFIER	silent_mutation	Average:11.518; most accessible tissue: Callus, score: 30.441	N	N	N	N
vg0811941721	A -> DEL	N	N	silent_mutation	Average:11.518; most accessible tissue: Callus, score: 30.441	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0811941721	2.81E-07	2.81E-07	mr1900	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
vg0811941721	NA	6.59E-10	mr1945	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