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Detailed information for vg0622383384:

Variant ID: vg0622383384 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 22383384
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.07, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:

AGAGGAAATAGAGATAAATAACATATTTTATTCTATATGGGCAACCCATATGCTTATGGGTGGCTTTTGCTATTTTCTTACTATGGACTAGTTCCACAAT[A/G]
TGGTTAGGTGGCTAAATGGAATATTTTATTGCTTATGGACTAGTTTTAGACTACATTAAGGATGCCCTAAGAGTTGATAGCTGGGGGAATAAACAATTAT

Reverse complement sequence

ATAATTGTTTATTCCCCCAGCTATCAACTCTTAGGGCATCCTTAATGTAGTCTAAAACTAGTCCATAAGCAATAAAATATTCCATTTAGCCACCTAACCA[T/C]
ATTGTGGAACTAGTCCATAGTAAGAAAATAGCAAAAGCCACCCATAAGCATATGGGTTGCCCATATAGAATAAAATATGTTATTTATCTCTATTTCCTCT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	64.50%	35.50%	0.06%	0.00%	NA
All Indica	2759	78.50%	21.50%	0.04%	0.00%	NA
All Japonica	1512	35.20%	64.70%	0.13%	0.00%	NA
Aus	269	89.20%	10.80%	0.00%	0.00%	NA
Indica I	595	83.40%	16.60%	0.00%	0.00%	NA
Indica II	465	88.20%	11.80%	0.00%	0.00%	NA
Indica III	913	71.10%	28.90%	0.00%	0.00%	NA
Indica Intermediate	786	77.70%	22.10%	0.13%	0.00%	NA
Temperate Japonica	767	24.60%	75.10%	0.26%	0.00%	NA
Tropical Japonica	504	55.40%	44.60%	0.00%	0.00%	NA
Japonica Intermediate	241	26.60%	73.40%	0.00%	0.00%	NA
VI/Aromatic	96	52.10%	47.90%	0.00%	0.00%	NA
Intermediate	90	64.40%	35.60%	0.00%	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
vg0622383384	A -> G	LOC_Os06g37830.1	upstream_gene_variant ; 4983.0bp to feature; MODIFIER	silent_mutation	Average:43.339; most accessible tissue: Minghui63 young leaf, score: 51.901	N	N	N	N
vg0622383384	A -> G	LOC_Os06g37820.1	intron_variant ; MODIFIER	silent_mutation	Average:43.339; most accessible tissue: Minghui63 young leaf, score: 51.901	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0622383384	NA	8.48E-07	mr1037	Ind_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
vg0622383384	NA	1.43E-07	mr1040	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
vg0622383384	6.68E-08	NA	mr1066	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
vg0622383384	NA	2.72E-08	mr1066	Ind_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
vg0622383384	NA	1.00E-05	mr1656	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
vg0622383384	NA	1.61E-06	mr1708	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
vg0622383384	NA	1.36E-06	mr1846	Ind_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