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Detailed information for vg0103247262:

Variant ID: vg0103247262 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 3247262
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.73, A: 0.29, others allele: 0.00, population size: 59. )

Flanking Sequence (100 bp) in Reference Genome:

TAGTTAGTGGGAATCTCTGAACGACCCTGAATCTGTATAAGGCAAATAATAATCAGTAGCACTAATAAGAGAGTCTCTTTTGCCAAGTGTGTGTGTGTGT[G/A]
TATTTTGAATCTACTGACCTGCATCATGGTGTATGGCAGTGATGGTGTTACCACCTCTGCTTGTACTGGACACTTTGATGTGTTTGAATCACTCTTTTTC

Reverse complement sequence

GAAAAAGAGTGATTCAAACACATCAAAGTGTCCAGTACAAGCAGAGGTGGTAACACCATCACTGCCATACACCATGATGCAGGTCAGTAGATTCAAAATA[C/T]
ACACACACACACACTTGGCAAAAGAGACTCTCTTATTAGTGCTACTGATTATTATTTGCCTTATACAGATTCAGGGTCGTTCAGAGATTCCCACTAACTA

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	66.30%	7.00%	16.53%	10.14%	NA
All Indica	2759	72.70%	3.40%	18.81%	5.00%	NA
All Japonica	1512	46.10%	15.00%	16.34%	22.55%	NA
Aus	269	98.50%	0.40%	1.12%	0.00%	NA
Indica I	595	75.60%	0.80%	18.82%	4.71%	NA
Indica II	465	67.70%	4.10%	21.94%	6.24%	NA
Indica III	913	71.60%	5.50%	18.18%	4.71%	NA
Indica Intermediate	786	74.80%	2.70%	17.68%	4.83%	NA
Temperate Japonica	767	51.40%	4.60%	9.26%	34.81%	NA
Tropical Japonica	504	36.10%	32.90%	25.79%	5.16%	NA
Japonica Intermediate	241	50.20%	10.80%	19.09%	19.92%	NA
VI/Aromatic	96	97.90%	0.00%	2.08%	0.00%	NA
Intermediate	90	80.00%	8.90%	11.11%	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
vg0103247262	G -> A	LOC_Os01g06870.1	upstream_gene_variant ; 3942.0bp to feature; MODIFIER	silent_mutation	Average:45.463; most accessible tissue: Minghui63 flag leaf, score: 69.182	N	N	N	N
vg0103247262	G -> A	LOC_Os01g06836.1	downstream_gene_variant ; 3947.0bp to feature; MODIFIER	silent_mutation	Average:45.463; most accessible tissue: Minghui63 flag leaf, score: 69.182	N	N	N	N
vg0103247262	G -> A	LOC_Os01g06852.1	intron_variant ; MODIFIER	silent_mutation	Average:45.463; most accessible tissue: Minghui63 flag leaf, score: 69.182	N	N	N	N
vg0103247262	G -> DEL	N	N	silent_mutation	Average:45.463; most accessible tissue: Minghui63 flag leaf, score: 69.182	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0103247262	NA	4.04E-06	mr1518	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