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Detailed information for vg0228078837:

Variant ID: vg0228078837 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 28078837
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.60, G: 0.40, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:

ACAGGGATACTGTTTTCAGAGCCCTTTGGCCCGTGGGCTATGGACGCAATGAGAACATCGCGTCCGTGAGAAGGCCGGACGCTCTAGATCGGTGGCGTCC[A/G]
ATTGTTTTAATGGGACGCTGCGGAATTACGTTGTCCTGCTTACGAATAAAAATCCAATACCTCAGTGTTTACATAAAAAAATATATTTTTTGTTTTGCTC

Reverse complement sequence

GAGCAAAACAAAAAATATATTTTTTTATGTAAACACTGAGGTATTGGATTTTTATTCGTAAGCAGGACAACGTAATTCCGCAGCGTCCCATTAAAACAAT[T/C]
GGACGCCACCGATCTAGAGCGTCCGGCCTTCTCACGGACGCGATGTTCTCATTGCGTCCATAGCCCACGGGCCAAAGGGCTCTGAAAACAGTATCCCTGT

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	59.90%	39.80%	0.15%	0.15%	NA
All Indica	2759	95.10%	4.80%	0.11%	0.00%	NA
All Japonica	1512	0.70%	98.60%	0.26%	0.46%	NA
Aus	269	61.30%	38.70%	0.00%	0.00%	NA
Indica I	595	98.70%	1.20%	0.17%	0.00%	NA
Indica II	465	97.20%	2.80%	0.00%	0.00%	NA
Indica III	913	91.60%	8.30%	0.11%	0.00%	NA
Indica Intermediate	786	95.20%	4.70%	0.13%	0.00%	NA
Temperate Japonica	767	0.40%	99.60%	0.00%	0.00%	NA
Tropical Japonica	504	1.20%	97.00%	0.60%	1.19%	NA
Japonica Intermediate	241	0.40%	98.80%	0.41%	0.41%	NA
VI/Aromatic	96	1.00%	99.00%	0.00%	0.00%	NA
Intermediate	90	37.80%	62.20%	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
vg0228078837	A -> G	LOC_Os02g46080.2	3_prime_UTR_variant ; 341.0bp to feature; MODIFIER	silent_mutation	Average:57.085; most accessible tissue: Minghui63 root, score: 72.134	N	N	N	N
vg0228078837	A -> G	LOC_Os02g46070.1	downstream_gene_variant ; 3535.0bp to feature; MODIFIER	silent_mutation	Average:57.085; most accessible tissue: Minghui63 root, score: 72.134	N	N	N	N
vg0228078837	A -> G	LOC_Os02g46080.1	downstream_gene_variant ; 158.0bp to feature; MODIFIER	silent_mutation	Average:57.085; most accessible tissue: Minghui63 root, score: 72.134	N	N	N	N
vg0228078837	A -> DEL	N	N	silent_mutation	Average:57.085; most accessible tissue: Minghui63 root, score: 72.134	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0228078837	NA	5.10E-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