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Detailed information for vg0229962990:

Variant ID: vg0229962990 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 29962990
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 309. )

Flanking Sequence (100 bp) in Reference Genome:

GAATCGGCTGAAGTCCAGATCGGCTACGATTAAGATCGGCTGGGTCTGAGTCGGACTAGGTGAGCCGATGCAGCCGATTCTGACAGTATAATTTGGTGTA[T/G]
GACATTGGGTTGAATTGAGGTGCTTCAAGATGATTGCCGCACATGGATAGAGTCCCGAGAAGACAATTGTATCTATTAATTAGGATGTTTTATGTAACTT

Reverse complement sequence

AAGTTACATAAAACATCCTAATTAATAGATACAATTGTCTTCTCGGGACTCTATCCATGTGCGGCAATCATCTTGAAGCACCTCAATTCAACCCAATGTC[A/C]
TACACCAAATTATACTGTCAGAATCGGCTGCATCGGCTCACCTAGTCCGACTCAGACCCAGCCGATCTTAATCGTAGCCGATCTGGACTTCAGCCGATTC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	88.60%	4.70%	6.24%	0.44%	NA
All Indica	2759	88.50%	3.30%	7.47%	0.76%	NA
All Japonica	1512	99.50%	0.40%	0.13%	0.00%	NA
Aus	269	22.30%	46.50%	31.23%	0.00%	NA
Indica I	595	97.10%	0.00%	2.86%	0.00%	NA
Indica II	465	99.40%	0.60%	0.00%	0.00%	NA
Indica III	913	80.30%	5.00%	12.81%	1.86%	NA
Indica Intermediate	786	85.10%	5.20%	9.16%	0.51%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	98.80%	1.00%	0.20%	0.00%	NA
Japonica Intermediate	241	99.20%	0.40%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	3.30%	3.33%	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
vg0229962990	T -> G	LOC_Os02g48990-LOC_Os02g49010	intergenic_region ; MODIFIER	silent_mutation	Average:25.889; most accessible tissue: Callus, score: 35.546	N	N	N	N
vg0229962990	T -> DEL	N	N	silent_mutation	Average:25.889; most accessible tissue: Callus, score: 35.546	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0229962990	NA	6.30E-06	mr1184	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
vg0229962990	NA	2.00E-06	mr1320	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
vg0229962990	NA	1.21E-07	mr1365	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
vg0229962990	4.15E-06	4.14E-06	mr1421	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
vg0229962990	NA	5.31E-06	mr1621	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
vg0229962990	NA	5.31E-09	mr1741_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