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Detailed information for vg1204271026:

Variant ID: vg1204271026 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 4271026
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 30. )

Flanking Sequence (100 bp) in Reference Genome:

TACAACTGGGGAAGAAGTATATCAAAGATCCATCTGTTTAAGAATGTGCCCTTACACTAGATAATTCTCATCAATATAGGGACGAGCGGCTGAGATGAAA[A/G]
CAATTTGGTCACTCACGACCCCCAGCCCATTTGCTATCCGAGTAATCAAAAAAGTGCACTCAACAGGAGCAGAAAATCTTATACTCTCTAACCATTGCCT

Reverse complement sequence

AGGCAATGGTTAGAGAGTATAAGATTTTCTGCTCCTGTTGAGTGCACTTTTTTGATTACTCGGATAGCAAATGGGCTGGGGGTCGTGAGTGACCAAATTG[T/C]
TTTCATCTCAGCCGCTCGTCCCTATATTGATGAGAATTATCTAGTGTAAGGGCACATTCTTAAACAGATGGATCTTTGATATACTTCTTCCCCAGTTGTA

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	26.70%	22.10%	3.13%	48.03%	NA
All Indica	2759	38.60%	4.50%	2.94%	54.01%	NA
All Japonica	1512	8.40%	53.80%	2.78%	35.05%	NA
Aus	269	6.70%	25.30%	7.43%	60.59%	NA
Indica I	595	19.80%	5.00%	2.52%	72.61%	NA
Indica II	465	51.00%	5.60%	1.29%	42.15%	NA
Indica III	913	43.20%	0.80%	3.50%	52.57%	NA
Indica Intermediate	786	40.20%	7.60%	3.56%	48.60%	NA
Temperate Japonica	767	2.20%	77.40%	4.17%	16.17%	NA
Tropical Japonica	504	14.10%	27.20%	0.99%	57.74%	NA
Japonica Intermediate	241	16.20%	34.00%	2.07%	47.72%	NA
VI/Aromatic	96	35.40%	14.60%	1.04%	48.96%	NA
Intermediate	90	22.20%	28.90%	4.44%	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
vg1204271026	A -> DEL	N	N	silent_mutation	Average:14.486; most accessible tissue: Callus, score: 53.081	N	N	N	N
vg1204271026	A -> G	LOC_Os12g08400.1	downstream_gene_variant ; 157.0bp to feature; MODIFIER	silent_mutation	Average:14.486; most accessible tissue: Callus, score: 53.081	N	N	N	N
vg1204271026	A -> G	LOC_Os12g08410.1	downstream_gene_variant ; 1347.0bp to feature; MODIFIER	silent_mutation	Average:14.486; most accessible tissue: Callus, score: 53.081	N	N	N	N
vg1204271026	A -> G	LOC_Os12g08390-LOC_Os12g08400	intergenic_region ; MODIFIER	silent_mutation	Average:14.486; most accessible tissue: Callus, score: 53.081	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1204271026	9.59E-08	2.65E-10	mr1350_2	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