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Detailed information for vg1206202617:

Variant ID: vg1206202617 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 6202617
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.88, A: 0.13, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:

CAAAAATACAAAAAAAAAGAGGAAAATGAAAAAAGGAAAAAGAAACTGGATGTAGGGCTATTATCCACCTTGGAGGCCCGAACCAGTATAAAAGCCTTGT[G/A]
TCTTTCGCACTTGTGTGAATGATAATTCGTGGAAAAACCCCAAGGCAAACGCCTGATCAGCGAAAACGCCGGGGGGGGGCGAAACAAATCGGCCGAAGCA

Reverse complement sequence

TGCTTCGGCCGATTTGTTTCGCCCCCCCCCGGCGTTTTCGCTGATCAGGCGTTTGCCTTGGGGTTTTTCCACGAATTATCATTCACACAAGTGCGAAAGA[C/T]
ACAAGGCTTTTATACTGGTTCGGGCCTCCAAGGTGGATAATAGCCCTACATCCAGTTTCTTTTTCCTTTTTTCATTTTCCTCTTTTTTTTTGTATTTTTG

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	39.00%	32.10%	2.39%	26.56%	NA
All Indica	2759	36.70%	52.20%	3.19%	7.97%	NA
All Japonica	1512	35.60%	3.30%	0.93%	60.12%	NA
Aus	269	60.20%	1.90%	2.97%	34.94%	NA
Indica I	595	77.50%	7.70%	3.87%	10.92%	NA
Indica II	465	12.90%	76.80%	1.51%	8.82%	NA
Indica III	913	19.40%	74.50%	2.08%	4.05%	NA
Indica Intermediate	786	39.90%	45.30%	4.96%	9.80%	NA
Temperate Japonica	767	48.20%	3.40%	1.17%	47.20%	NA
Tropical Japonica	504	12.30%	4.20%	0.60%	82.94%	NA
Japonica Intermediate	241	44.40%	1.20%	0.83%	53.53%	NA
VI/Aromatic	96	95.80%	2.10%	0.00%	2.08%	NA
Intermediate	90	40.00%	23.30%	3.33%	33.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1206202617	G -> DEL	N	N	silent_mutation	Average:10.529; most accessible tissue: Callus, score: 35.156	N	N	N	N
vg1206202617	G -> A	LOC_Os12g11470.1	downstream_gene_variant ; 4537.0bp to feature; MODIFIER	silent_mutation	Average:10.529; most accessible tissue: Callus, score: 35.156	N	N	N	N
vg1206202617	G -> A	LOC_Os12g11480.1	downstream_gene_variant ; 312.0bp to feature; MODIFIER	silent_mutation	Average:10.529; most accessible tissue: Callus, score: 35.156	N	N	N	N
vg1206202617	G -> A	LOC_Os12g11490.1	downstream_gene_variant ; 580.0bp to feature; MODIFIER	silent_mutation	Average:10.529; most accessible tissue: Callus, score: 35.156	N	N	N	N
vg1206202617	G -> A	LOC_Os12g11480-LOC_Os12g11490	intergenic_region ; MODIFIER	silent_mutation	Average:10.529; most accessible tissue: Callus, score: 35.156	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1206202617	NA	2.31E-09	mr1565	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
vg1206202617	8.03E-07	NA	mr1845	Jap_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
vg1206202617	1.76E-06	1.76E-06	mr1935	Jap_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
vg1206202617	NA	6.62E-06	mr1508_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
vg1206202617	NA	2.21E-13	mr1565_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
vg1206202617	NA	1.93E-10	mr1565_2	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