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Detailed information for vg0421809064:

Variant ID: vg0421809064 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 21809064
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:

GAGAGTGAGTTAAGCCAATCCAAGTGCATTGCTTCATTGTTATAGCTAGTGTGGCACTTGATCATCCTCGGCAAGTATCCTAGACTTGTTACTCTTGGAG[G/A]
TTGCCGCCTCCTAGACGGCTTGTGGAGGTGTTGCCCGGTGACCTCTCCGAGGAGATTGTGGAGGAGGCCCGGCACCGTTTGTGAGTGGTTTGGAGTTCAC

Reverse complement sequence

GTGAACTCCAAACCACTCACAAACGGTGCCGGGCCTCCTCCACAATCTCCTCGGAGAGGTCACCGGGCAACACCTCCACAAGCCGTCTAGGAGGCGGCAA[C/T]
CTCCAAGAGTAACAAGTCTAGGATACTTGCCGAGGATGATCAAGTGCCACACTAGCTATAACAATGAAGCAATGCACTTGGATTGGCTTAACTCACTCTC

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	88.20%	11.80%	0.04%	0.00%	NA
All Indica	2759	81.70%	18.30%	0.04%	0.00%	NA
All Japonica	1512	98.10%	1.90%	0.00%	0.00%	NA
Aus	269	98.90%	0.70%	0.37%	0.00%	NA
Indica I	595	72.40%	27.40%	0.17%	0.00%	NA
Indica II	465	82.20%	17.80%	0.00%	0.00%	NA
Indica III	913	87.50%	12.50%	0.00%	0.00%	NA
Indica Intermediate	786	81.70%	18.30%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	94.60%	5.40%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	84.40%	15.60%	0.00%	0.00%	NA
Intermediate	90	92.20%	7.80%	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
vg0421809064	G -> A	LOC_Os04g35790.3	downstream_gene_variant ; 3093.0bp to feature; MODIFIER	silent_mutation	Average:35.117; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0421809064	G -> A	LOC_Os04g35790.1	downstream_gene_variant ; 3093.0bp to feature; MODIFIER	silent_mutation	Average:35.117; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0421809064	G -> A	LOC_Os04g35790.2	downstream_gene_variant ; 3093.0bp to feature; MODIFIER	silent_mutation	Average:35.117; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0421809064	G -> A	LOC_Os04g35780-LOC_Os04g35790	intergenic_region ; MODIFIER	silent_mutation	Average:35.117; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0421809064	3.90E-06	NA	mr1456	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
vg0421809064	2.78E-06	NA	mr1456	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