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Detailed information for vg0609264829:

Variant ID: vg0609264829 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 9264829
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 313. )

Flanking Sequence (100 bp) in Reference Genome:

TAAAAAGTATGATATTTGTGCCTTCAATCAGTACACTGGAACAGTTCTGATCGAGTATCTGAAACAGTTTAAATACATATAACTGGGAAAAGAAATTGCT[G/A]
GGTTTGGGAGTTCCTGAGGCTTTTGCCTTTTTCGTTGAATTCCTGACATAAACAAGATCGTACTATCAACATATCTACCTGCTTTTGTACATAGTCCTTA

Reverse complement sequence

TAAGGACTATGTACAAAAGCAGGTAGATATGTTGATAGTACGATCTTGTTTATGTCAGGAATTCAACGAAAAAGGCAAAAGCCTCAGGAACTCCCAAACC[C/T]
AGCAATTTCTTTTCCCAGTTATATGTATTTAAACTGTTTCAGATACTCGATCAGAACTGTTCCAGTGTACTGATTGAAGGCACAAATATCATACTTTTTA

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	99.30%	0.60%	0.08%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	97.90%	1.80%	0.26%	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	100.00%	0.00%	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	96.10%	3.50%	0.39%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	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
vg0609264829	G -> A	LOC_Os06g16260.1	upstream_gene_variant ; 2578.0bp to feature; MODIFIER	silent_mutation	Average:72.527; most accessible tissue: Zhenshan97 flower, score: 80.613	N	N	N	N
vg0609264829	G -> A	LOC_Os06g16260.2	upstream_gene_variant ; 2589.0bp to feature; MODIFIER	silent_mutation	Average:72.527; most accessible tissue: Zhenshan97 flower, score: 80.613	N	N	N	N
vg0609264829	G -> A	LOC_Os06g16280.1	downstream_gene_variant ; 2239.0bp to feature; MODIFIER	silent_mutation	Average:72.527; most accessible tissue: Zhenshan97 flower, score: 80.613	N	N	N	N
vg0609264829	G -> A	LOC_Os06g16270.1	intron_variant ; MODIFIER	silent_mutation	Average:72.527; most accessible tissue: Zhenshan97 flower, score: 80.613	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0609264829	2.70E-06	2.70E-06	mr1577	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