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Detailed information for vg0207291958:

Variant ID: vg0207291958 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 7291958
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGCAATTTCACAACAGCACCATATGCTCTCTATTGGTATTCTACTACTATTATTATCGTCAACTAGGAAGTAGCCCGCGCGACGGGTCGTATGATAATAG[A/G]
TTTGAGATACTTATAAGAGCGAAGTATTAACCGGAGAACATCTGCCATAATTTCTCCCAAATTGTTTTCGTCGGCATTAATTGCTTTTACAATTTTCTAA

Reverse complement sequence

TTAGAAAATTGTAAAAGCAATTAATGCCGACGAAAACAATTTGGGAGAAATTATGGCAGATGTTCTCCGGTTAATACTTCGCTCTTATAAGTATCTCAAA[T/C]
CTATTATCATACGACCCGTCGCGCGGGCTACTTCCTAGTTGACGATAATAATAGTAGTAGAATACCAATAGAGAGCATATGGTGCTGTTGTGAAATTGCT

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	91.60%	8.40%	0.02%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	74.50%	25.50%	0.00%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	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	72.80%	27.20%	0.00%	0.00%	NA
Tropical Japonica	504	84.30%	15.70%	0.00%	0.00%	NA
Japonica Intermediate	241	59.30%	40.70%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	8.90%	1.11%	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
vg0207291958	A -> G	LOC_Os02g13580-LOC_Os02g13590	intergenic_region ; MODIFIER	silent_mutation	Average:38.7; most accessible tissue: Callus, score: 50.488	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0207291958	NA	1.49E-06	mr1201_2	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
vg0207291958	7.82E-06	NA	mr1219_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
vg0207291958	NA	3.64E-06	mr1219_2	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
vg0207291958	1.23E-06	NA	mr1274_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
vg0207291958	NA	7.87E-06	mr1274_2	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