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Detailed information for vg0220758243:

Variant ID: vg0220758243 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 20758243
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, A: 0.08, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

CGATCCTCATACTATGCAAATACCGGAATCGCGACATCAAATGTCGACAGTTGCGCGCCAGGTAGGGGATCTTTTGGTGCTTCAAGGTTTCGATGAGATG[G/A]
GTTTAAGAGATGGATTCTCCGACAACGAGCTACTCGACGACTTCAGCTGAGGGGGAGATCCAACCTAACCAGATCGGAACCATCATCGTCATTGACAACT

Reverse complement sequence

AGTTGTCAATGACGATGATGGTTCCGATCTGGTTAGGTTGGATCTCCCCCTCAGCTGAAGTCGTCGAGTAGCTCGTTGTCGGAGAATCCATCTCTTAAAC[C/T]
CATCTCATCGAAACCTTGAAGCACCAAAAGATCCCCTACCTGGCGCGCAACTGTCGACATTTGATGTCGCGATTCCGGTATTTGCATAGTATGAGGATCG

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	67.70%	31.80%	0.42%	0.08%	NA
All Indica	2759	49.30%	50.50%	0.18%	0.07%	NA
All Japonica	1512	96.60%	2.60%	0.73%	0.00%	NA
Aus	269	77.30%	21.90%	0.00%	0.74%	NA
Indica I	595	72.90%	26.90%	0.17%	0.00%	NA
Indica II	465	64.90%	34.80%	0.22%	0.00%	NA
Indica III	913	29.40%	70.50%	0.11%	0.00%	NA
Indica Intermediate	786	45.30%	54.20%	0.25%	0.25%	NA
Temperate Japonica	767	99.50%	0.40%	0.13%	0.00%	NA
Tropical Japonica	504	93.30%	5.80%	0.99%	0.00%	NA
Japonica Intermediate	241	94.60%	3.30%	2.07%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	83.30%	13.30%	3.33%	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
vg0220758243	G -> A	LOC_Os02g34610.1	upstream_gene_variant ; 4823.0bp to feature; MODIFIER	silent_mutation	Average:31.918; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N
vg0220758243	G -> A	LOC_Os02g34620.1	upstream_gene_variant ; 10.0bp to feature; MODIFIER	silent_mutation	Average:31.918; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N
vg0220758243	G -> A	LOC_Os02g34610-LOC_Os02g34620	intergenic_region ; MODIFIER	silent_mutation	Average:31.918; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N
vg0220758243	G -> DEL	N	N	silent_mutation	Average:31.918; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0220758243	4.00E-06	NA	mr1099_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
vg0220758243	4.27E-06	4.52E-06	mr1099_2	Ind_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