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Detailed information for vg0228079438:

Variant ID: vg0228079438 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 28079438
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.92, G: 0.08, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:

CCTTTTTCGACTTTCTTAAGATCAACAAACCTCATTTCTCGCTTCCGTGCAGCTTCTTTCAAAGCTGTGTTTACTAGCCTCTTTGCAATTCCCTACCAAA[A/G]
TTATGGAAATTAGATTTAGCACCTTTCCAAGTAATCAGCCTAGGCATTGCGGGATAGTCCCACAAACAAAGAAAAACAAGCAACGACACATGTAAGTAAA

Reverse complement sequence

TTTACTTACATGTGTCGTTGCTTGTTTTTCTTTGTTTGTGGGACTATCCCGCAATGCCTAGGCTGATTACTTGGAAAGGTGCTAAATCTAATTTCCATAA[T/C]
TTTGGTAGGGAATTGCAAAGAGGCTAGTAAACACAGCTTTGAAAGAAGCTGCACGGAAGCGAGAAATGAGGTTTGTTGATCTTAAGAAAGTCGAAAAAGG

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	58.50%	41.10%	0.06%	0.34%	NA
All Indica	2759	93.20%	6.30%	0.04%	0.51%	NA
All Japonica	1512	0.70%	99.30%	0.00%	0.00%	NA
Aus	269	55.80%	43.50%	0.37%	0.37%	NA
Indica I	595	97.10%	2.40%	0.17%	0.34%	NA
Indica II	465	97.20%	2.20%	0.00%	0.65%	NA
Indica III	913	88.30%	11.20%	0.00%	0.55%	NA
Indica Intermediate	786	93.50%	6.00%	0.00%	0.51%	NA
Temperate Japonica	767	0.40%	99.60%	0.00%	0.00%	NA
Tropical Japonica	504	1.20%	98.80%	0.00%	0.00%	NA
Japonica Intermediate	241	0.40%	99.60%	0.00%	0.00%	NA
VI/Aromatic	96	1.00%	99.00%	0.00%	0.00%	NA
Intermediate	90	34.40%	63.30%	1.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0228079438	A -> G	LOC_Os02g46070.1	downstream_gene_variant ; 4136.0bp to feature; MODIFIER	silent_mutation	Average:52.018; most accessible tissue: Callus, score: 82.378	N	N	N	N
vg0228079438	A -> G	LOC_Os02g46080.1	intron_variant ; MODIFIER	silent_mutation	Average:52.018; most accessible tissue: Callus, score: 82.378	N	N	N	N
vg0228079438	A -> G	LOC_Os02g46080.2	intron_variant ; MODIFIER	silent_mutation	Average:52.018; most accessible tissue: Callus, score: 82.378	N	N	N	N
vg0228079438	A -> DEL	N	N	silent_mutation	Average:52.018; most accessible tissue: Callus, score: 82.378	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0228079438	NA	1.74E-08	mr1342	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
vg0228079438	NA	1.99E-76	mr1629	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
vg0228079438	NA	2.22E-08	mr1322_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