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Detailed information for vg0212113401:

Variant ID: vg0212113401 (JBrowse)	Variation Type: INDEL
Chromosome: chr02	Position: 12113401
Reference Allele: T	Alternative Allele: A,TA
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, A: 0.01, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:

AGTTTGGCAAGTGCTATATGGTTGGGGAATATATACTATGTACACAAGCTTCCTGTGCACACTCCGTACACATCAACTAGCAAATGTCACAAATTTTTTT[T/A,TA]
AAAAAAATTGGACACATACTTCCAATAGTATTACACCTACCTGTGAAATCTTATCTTTAAATTCATTATATTTTAGTCATAAAGAAAAAGACAAAATTCT

Reverse complement sequence

AGAATTTTGTCTTTTTCTTTATGACTAAAATATAATGAATTTAAAGATAAGATTTCACAGGTAGGTGTAATACTATTGGAAGTATGTGTCCAATTTTTTT[A/T,TA]
AAAAAAATTTGTGACATTTGCTAGTTGATGTGTACGGAGTGTGCACAGGAAGCTTGTGTACATAGTATATATTCCCCAACCATATAGCACTTGCCAAACT

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	52.50%	44.10%	3.13%	0.00%	TA: 0.25%
All Indica	2759	81.60%	12.80%	5.11%	0.00%	TA: 0.43%
All Japonica	1512	1.70%	98.30%	0.00%	0.00%	NA
Aus	269	63.20%	36.10%	0.74%	0.00%	NA
Indica I	595	81.20%	5.20%	13.11%	0.00%	TA: 0.50%
Indica II	465	88.60%	8.00%	3.23%	0.00%	TA: 0.22%
Indica III	913	83.00%	15.90%	0.55%	0.00%	TA: 0.55%
Indica Intermediate	786	76.20%	17.90%	5.47%	0.00%	TA: 0.38%
Temperate Japonica	767	1.00%	99.00%	0.00%	0.00%	NA
Tropical Japonica	504	2.60%	97.40%	0.00%	0.00%	NA
Japonica Intermediate	241	1.70%	98.30%	0.00%	0.00%	NA
VI/Aromatic	96	0.00%	100.00%	0.00%	0.00%	NA
Intermediate	90	40.00%	54.40%	5.56%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0212113401	T -> A	LOC_Os02g20530.1	downstream_gene_variant ; 3174.0bp to feature; MODIFIER	silent_mutation	Average:26.97; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0212113401	T -> A	LOC_Os02g20540.1	downstream_gene_variant ; 433.0bp to feature; MODIFIER	silent_mutation	Average:26.97; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0212113401	T -> A	LOC_Os02g20540.2	downstream_gene_variant ; 433.0bp to feature; MODIFIER	silent_mutation	Average:26.97; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0212113401	T -> A	LOC_Os02g20530-LOC_Os02g20540	intergenic_region ; MODIFIER	silent_mutation	Average:26.97; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0212113401	T -> TA	LOC_Os02g20530.1	downstream_gene_variant ; 3175.0bp to feature; MODIFIER	silent_mutation	Average:26.97; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0212113401	T -> TA	LOC_Os02g20540.1	downstream_gene_variant ; 432.0bp to feature; MODIFIER	silent_mutation	Average:26.97; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0212113401	T -> TA	LOC_Os02g20540.2	downstream_gene_variant ; 432.0bp to feature; MODIFIER	silent_mutation	Average:26.97; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0212113401	T -> TA	LOC_Os02g20530-LOC_Os02g20540	intergenic_region ; MODIFIER	silent_mutation	Average:26.97; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0212113401	NA	7.44E-06	mr1425	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
vg0212113401	NA	6.01E-08	mr1506	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
vg0212113401	NA	1.27E-10	mr1751	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
vg0212113401	NA	4.44E-16	mr1968	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
vg0212113401	NA	4.96E-06	mr1425_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