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Detailed information for vg1002797270:

Variant ID: vg1002797270 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 2797270
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, A: 0.01, others allele: 0.00, population size: 123. )

Flanking Sequence (100 bp) in Reference Genome:

ATTTTATATTATGGGGTTGTTCAGATTATAGTCAAAATAAACCTCACTAAATTTTGGCAATACAAAAAATTTAGTAAGTTGACAATATTACCAAAATTTT[G/A]
GCATTATTTCTTACACATTTATGAAAGTTTGGCAAAAAGATTTTGGCATTATTTCTTACGCATTTATGAAAGTTTGGCAAAAAGTTAAATGTATGTACAT

Reverse complement sequence

ATGTACATACATTTAACTTTTTGCCAAACTTTCATAAATGCGTAAGAAATAATGCCAAAATCTTTTTGCCAAACTTTCATAAATGTGTAAGAAATAATGC[C/T]
AAAATTTTGGTAATATTGTCAACTTACTAAATTTTTTGTATTGCCAAAATTTAGTGAGGTTTATTTTGACTATAATCTGAACAACCCCATAATATAAAAT

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	99.80%	0.20%	0.06%	0.00%	NA
All Indica	2759	99.60%	0.30%	0.11%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.30%	0.30%	0.34%	0.00%	NA
Indica II	465	99.10%	0.90%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.60%	0.30%	0.13%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	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
vg1002797270	G -> A	LOC_Os10g05600.1	upstream_gene_variant ; 592.0bp to feature; MODIFIER	N	Average:32.564; most accessible tissue: Callus, score: 66.454	N	N	N	N
vg1002797270	G -> A	LOC_Os10g05610.1	upstream_gene_variant ; 4658.0bp to feature; MODIFIER	N	Average:32.564; most accessible tissue: Callus, score: 66.454	N	N	N	N
vg1002797270	G -> A	LOC_Os10g05600-LOC_Os10g05610	intergenic_region ; MODIFIER	N	Average:32.564; most accessible tissue: Callus, score: 66.454	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1002797270	NA	3.66E-06	mr1165	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