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Detailed information for vg0200805132:

Variant ID: vg0200805132 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 805132
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AATTAACTTTTTCTTACACTGTTTAACCACTCGTCTTATTCAAAAATTTATGCAAATATAAAAAATGAAAAGTTGTACTTAAAGTACTTTGGATAATAAA[G/A]
TAAGTCACAAATAAAATAAATAATAATTTTAATTTTTTTTAATAAGACGAATGGTCAAATAGTGCAAGAAAAAGTCAAAATCCCCTATATTATGGGACGG

Reverse complement sequence

CCGTCCCATAATATAGGGGATTTTGACTTTTTCTTGCACTATTTGACCATTCGTCTTATTAAAAAAAATTAAAATTATTATTTATTTTATTTGTGACTTA[C/T]
TTTATTATCCAAAGTACTTTAAGTACAACTTTTCATTTTTTATATTTGCATAAATTTTTGAATAAGACGAGTGGTTAAACAGTGTAAGAAAAAGTTAATT

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	94.10%	5.90%	0.02%	0.00%	NA
All Indica	2759	93.80%	6.10%	0.04%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	60.60%	39.40%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	92.50%	7.50%	0.00%	0.00%	NA
Indica III	913	91.10%	8.90%	0.00%	0.00%	NA
Indica Intermediate	786	93.10%	6.70%	0.13%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	4.40%	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
vg0200805132	G -> A	LOC_Os02g02380-LOC_Os02g02390	intergenic_region ; MODIFIER	silent_mutation	Average:83.318; most accessible tissue: Minghui63 flag leaf, score: 94.221	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0200805132	6.34E-06	NA	mr1994_2	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