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Detailed information for vg0631229654:

Variant ID: vg0631229654 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 31229654
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

AGTCTCCAGGAAATCTAAGAAGTTTGATTCTCTTCATAGCCATTCTTGAAAAAGTTCTATTAAGACTATTATTGCTGTTAAGCCGATTAATCCTCCTAAA[G/T]
TTTCTTCTTCCAAGTTGCTTAATCTTTCTAAAGTTTCTACTGCTAAGTTGATTAATCCTCCAAAGGTTTCAACTGTTAATAAGTCTAGCAATTTCAAGCG

Reverse complement sequence

CGCTTGAAATTGCTAGACTTATTAACAGTTGAAACCTTTGGAGGATTAATCAACTTAGCAGTAGAAACTTTAGAAAGATTAAGCAACTTGGAAGAAGAAA[C/A]
TTTAGGAGGATTAATCGGCTTAACAGCAATAATAGTCTTAATAGAACTTTTTCAAGAATGGCTATGAAGAGAATCAAACTTCTTAGATTTCCTGGAGACT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	37.40%	4.50%	21.88%	36.23%	NA
All Indica	2759	4.40%	7.40%	35.77%	52.37%	NA
All Japonica	1512	88.10%	0.10%	0.60%	11.24%	NA
Aus	269	69.90%	1.50%	9.67%	18.96%	NA
Indica I	595	2.90%	6.60%	40.50%	50.08%	NA
Indica II	465	2.80%	8.20%	32.47%	56.56%	NA
Indica III	913	5.10%	8.20%	34.94%	51.70%	NA
Indica Intermediate	786	5.70%	6.70%	35.11%	52.42%	NA
Temperate Japonica	767	94.00%	0.00%	0.78%	5.22%	NA
Tropical Japonica	504	78.20%	0.00%	0.60%	21.23%	NA
Japonica Intermediate	241	90.00%	0.40%	0.00%	9.54%	NA
VI/Aromatic	96	92.70%	0.00%	1.04%	6.25%	NA
Intermediate	90	40.00%	3.30%	12.22%	44.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0631229654	G -> T	LOC_Os06g51530.1	upstream_gene_variant ; 3068.0bp to feature; MODIFIER	silent_mutation	Average:13.262; most accessible tissue: Callus, score: 32.798	N	N	N	N
vg0631229654	G -> T	LOC_Os06g51540.1	intron_variant ; MODIFIER	silent_mutation	Average:13.262; most accessible tissue: Callus, score: 32.798	N	N	N	N
vg0631229654	G -> DEL	N	N	silent_mutation	Average:13.262; most accessible tissue: Callus, score: 32.798	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0631229654	NA	3.08E-09	mr1047	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
vg0631229654	4.76E-06	NA	mr1666	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
vg0631229654	NA	1.46E-21	mr1551_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
vg0631229654	NA	1.11E-15	mr1744_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