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Detailed information for vg0127297735:

Variant ID: vg0127297735 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 27297735
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:

AAGGAACAAACAGGATCGTGATTCATGAGTAGCCGCGTGCGCCTACAAGAGACCCTTTCAGATAAACGAGCCAATAGCCGGATTTTATAAATTAACATAC[G/A]
AGAAAACGGCCCTTTCAAACACAATAGTTAATCAATTTGAATCACATATAGAATTTGTTCAATATACCATTTGAATAAAAGATTGCGCGTCTATGGAATA

Reverse complement sequence

TATTCCATAGACGCGCAATCTTTTATTCAAATGGTATATTGAACAAATTCTATATGTGATTCAAATTGATTAACTATTGTGTTTGAAAGGGCCGTTTTCT[C/T]
GTATGTTAATTTATAAAATCCGGCTATTGGCTCGTTTATCTGAAAGGGTCTCTTGTAGGCGCACGCGGCTACTCATGAATCACGATCCTGTTTGTTCCTT

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	96.50%	3.30%	0.13%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	89.30%	10.30%	0.40%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	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	79.10%	20.10%	0.78%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg0127297735	G -> A	LOC_Os01g47730.1	upstream_gene_variant ; 3692.0bp to feature; MODIFIER	silent_mutation	Average:47.476; most accessible tissue: Callus, score: 81.776	N	N	N	N
vg0127297735	G -> A	LOC_Os01g47720.1	downstream_gene_variant ; 2287.0bp to feature; MODIFIER	silent_mutation	Average:47.476; most accessible tissue: Callus, score: 81.776	N	N	N	N
vg0127297735	G -> A	LOC_Os01g47710-LOC_Os01g47720	intergenic_region ; MODIFIER	silent_mutation	Average:47.476; most accessible tissue: Callus, score: 81.776	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0127297735	2.91E-06	NA	mr1920	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