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Detailed information for vg0232881115:

Variant ID: vg0232881115 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 32881115
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAAAAAAGTCAACGGCGTCAAATATTTTGGGATGCAGGGAGTACTTTTTATCAGAAAACTATAGCTTTATTTTGACAGGTTCTAGACTCTCTCATCATAT[A/G]
CACATGAAATACTTATATCGGTGTAAGTTTACCCCACATATTGTGCACCCGTAGTAGATAAAATTATAATTTTGTAAAAAATCAATTGTTATTGTTGTTG

Reverse complement sequence

CAACAACAATAACAATTGATTTTTTACAAAATTATAATTTTATCTACTACGGGTGCACAATATGTGGGGTAAACTTACACCGATATAAGTATTTCATGTG[T/C]
ATATGATGAGAGAGTCTAGAACCTGTCAAAATAAAGCTATAGTTTTCTGATAAAAAGTACTCCCTGCATCCCAAAATATTTGACGCCGTTGACTTTTTTA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	97.70%	1.30%	1.08%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	92.90%	3.90%	3.24%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	86.70%	7.20%	6.13%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	97.50%	1.70%	0.83%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	0.00%	2.22%	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
vg0232881115	A -> G	LOC_Os02g53710-LOC_Os02g53720	intergenic_region ; MODIFIER	silent_mutation	Average:46.405; most accessible tissue: Minghui63 panicle, score: 71.773	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0232881115	NA	6.65E-06	mr1210	Jap_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
vg0232881115	2.27E-06	NA	mr1682	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