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Detailed information for vg0802260819:

Variant ID: vg0802260819 (JBrowse)	Variation Type: INDEL
Chromosome: chr08	Position: 2260819
Reference Allele: T	Alternative Allele: A,TAAA,TA
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.79, T: 0.21, others allele: 0.00, population size: 100. )

Flanking Sequence (100 bp) in Reference Genome:

TCTTTTGTGGTTCCTAAGTTTAACAAATTTTAAAGAAAAAGTTTAACAAATTTAAAACCCCATCCCTATACATACTTGGCAAATATTTACTTAATTTTTT[T/A,TAAA,TA]
AAAAAACATAGAATGTACATGAAACTTTTAGTTGTTGATTTGTTGATTAAGGTTGTCAGTTTAACTTTTCACTACTTTGAAAAATATTATCTCAGATATA

Reverse complement sequence

TATATCTGAGATAATATTTTTCAAAGTAGTGAAAAGTTAAACTGACAACCTTAATCAACAAATCAACAACTAAAAGTTTCATGTACATTCTATGTTTTTT[A/T,TTTA,TA]
AAAAAATTAAGTAAATATTTGCCAAGTATGTATAGGGATGGGGTTTTAAATTTGTTAAACTTTTTCTTTAAAATTTGTTAAACTTAGGAACCACAAAAGA

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	61.20%	32.60%	0.21%	0.00%	TA: 3.64%; TAAA: 2.29%
All Indica	2759	95.40%	1.10%	0.11%	0.00%	TA: 2.97%; TAAA: 0.40%
All Japonica	1512	10.30%	89.50%	0.13%	0.00%	TA: 0.07%
Aus	269	20.10%	14.10%	1.49%	0.00%	TAAA: 34.57%; TA: 29.74%
Indica I	595	99.30%	0.30%	0.17%	0.00%	TA: 0.17%
Indica II	465	91.60%	1.70%	0.22%	0.00%	TA: 6.24%; TAAA: 0.22%
Indica III	913	98.50%	0.20%	0.11%	0.00%	TA: 0.88%; TAAA: 0.33%
Indica Intermediate	786	91.20%	2.30%	0.00%	0.00%	TA: 5.60%; TAAA: 0.89%
Temperate Japonica	767	18.50%	81.20%	0.26%	0.00%	NA
Tropical Japonica	504	1.20%	98.60%	0.00%	0.00%	TA: 0.20%
Japonica Intermediate	241	3.30%	96.70%	0.00%	0.00%	NA
VI/Aromatic	96	4.20%	88.50%	0.00%	0.00%	TA: 5.21%; TAAA: 2.08%
Intermediate	90	51.10%	41.10%	1.11%	0.00%	TA: 4.44%; TAAA: 2.22%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0802260819	T -> TA	LOC_Os08g04540.1	downstream_gene_variant ; 2900.0bp to feature; MODIFIER	silent_mutation	Average:30.221; most accessible tissue: Callus, score: 58.795	N	N	N	N
vg0802260819	T -> TA	LOC_Os08g04540-LOC_Os08g04550	intergenic_region ; MODIFIER	silent_mutation	Average:30.221; most accessible tissue: Callus, score: 58.795	N	N	N	N
vg0802260819	T -> A	LOC_Os08g04540.1	downstream_gene_variant ; 2899.0bp to feature; MODIFIER	silent_mutation	Average:30.221; most accessible tissue: Callus, score: 58.795	N	N	N	N
vg0802260819	T -> A	LOC_Os08g04540-LOC_Os08g04550	intergenic_region ; MODIFIER	silent_mutation	Average:30.221; most accessible tissue: Callus, score: 58.795	N	N	N	N
vg0802260819	T -> TAAA	LOC_Os08g04540.1	downstream_gene_variant ; 2900.0bp to feature; MODIFIER	silent_mutation	Average:30.221; most accessible tissue: Callus, score: 58.795	N	N	N	N
vg0802260819	T -> TAAA	LOC_Os08g04540-LOC_Os08g04550	intergenic_region ; MODIFIER	silent_mutation	Average:30.221; most accessible tissue: Callus, score: 58.795	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0802260819	NA	2.64E-08	mr1249	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
vg0802260819	NA	2.17E-17	mr1261	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
vg0802260819	NA	9.58E-13	mr1531	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
vg0802260819	NA	1.60E-18	mr1552	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
vg0802260819	NA	3.94E-35	mr1793	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
vg0802260819	NA	1.11E-15	mr1916	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
vg0802260819	NA	1.23E-48	mr1793_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