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Detailed information for vg0724211615:

Variant ID: vg0724211615 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 24211615
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:

TTTAACAAGTTTCTCCTGTTACTAACTAATTCTTATTTTCTTTTCATGATTTAGACGAGAACCGGGGTGCAAGGGTGATGCTGATGGTTCGTTTTATTGG[A/G]
TCAATCGATCTATCATCTTTTGTCTTGTTGATTTTCGTTTTGCCCTTATTTCTTCGTTCCCTGATAATGGTTGTTTCTTGTTTCTTTTTTCCATTTTAGG

Reverse complement sequence

CCTAAAATGGAAAAAAGAAACAAGAAACAACCATTATCAGGGAACGAAGAAATAAGGGCAAAACGAAAATCAACAAGACAAAAGATGATAGATCGATTGA[T/C]
CCAATAAAACGAACCATCAGCATCACCCTTGCACCCCGGTTCTCGTCTAAATCATGAAAAGAAAATAAGAATTAGTTAGTAACAGGAGAAACTTGTTAAA

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	97.10%	2.90%	0.02%	0.00%	NA
All Indica	2759	99.50%	0.50%	0.00%	0.00%	NA
All Japonica	1512	99.10%	0.80%	0.07%	0.00%	NA
Aus	269	58.70%	41.30%	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	99.50%	0.50%	0.00%	0.00%	NA
Indica Intermediate	786	99.00%	1.00%	0.00%	0.00%	NA
Temperate Japonica	767	98.70%	1.20%	0.13%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	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
vg0724211615	A -> G	LOC_Os07g40370.1	upstream_gene_variant ; 3650.0bp to feature; MODIFIER	silent_mutation	Average:47.051; most accessible tissue: Callus, score: 67.615	N	N	N	N
vg0724211615	A -> G	LOC_Os07g40390.1	downstream_gene_variant ; 4263.0bp to feature; MODIFIER	silent_mutation	Average:47.051; most accessible tissue: Callus, score: 67.615	N	N	N	N
vg0724211615	A -> G	LOC_Os07g40380.1	intron_variant ; MODIFIER	silent_mutation	Average:47.051; most accessible tissue: Callus, score: 67.615	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0724211615	1.44E-06	NA	mr1829_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