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Detailed information for vg0909046504:

Variant ID: vg0909046504 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 9046504
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: 124. )

Flanking Sequence (100 bp) in Reference Genome:

ATGGAAAAATTTCCGATGAAATCCTTTGAAACAAAGGATTGAATCCTATACTATCCTTTAAAATTCCTATGAAATGAGTAATCCTATAGAGATTTTAGAG[G/A]
AAAGTTAGCAAGAGGTCCAACCTCTTGAAAAATTCCTTTGAGTCTCTCTCTCATCCGATTCCTACATTTTTCCTGTGGTCCAATCAAATAGTCATTCATG

Reverse complement sequence

CATGAATGACTATTTGATTGGACCACAGGAAAAATGTAGGAATCGGATGAGAGAGAGACTCAAAGGAATTTTTCAAGAGGTTGGACCTCTTGCTAACTTT[C/T]
CTCTAAAATCTCTATAGGATTACTCATTTCATAGGAATTTTAAAGGATAGTATAGGATTCAATCCTTTGTTTCAAAGGATTTCATCGGAAATTTTTCCAT

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	91.00%	5.90%	2.77%	0.36%	NA
All Indica	2759	85.30%	10.10%	4.60%	0.00%	NA
All Japonica	1512	98.70%	0.00%	0.20%	1.12%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	53.60%	32.80%	13.61%	0.00%	NA
Indica II	465	95.90%	3.70%	0.43%	0.00%	NA
Indica III	913	98.70%	0.40%	0.88%	0.00%	NA
Indica Intermediate	786	87.40%	8.00%	4.58%	0.00%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	96.60%	0.00%	0.20%	3.17%	NA
Japonica Intermediate	241	99.20%	0.00%	0.41%	0.41%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	0.00%	1.11%	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
vg0909046504	G -> DEL	N	N	silent_mutation	Average:40.408; most accessible tissue: Minghui63 young leaf, score: 59.171	N	N	N	N
vg0909046504	G -> A	LOC_Os09g15010-LOC_Os09g15020	intergenic_region ; MODIFIER	silent_mutation	Average:40.408; most accessible tissue: Minghui63 young leaf, score: 59.171	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0909046504	1.19E-08	6.71E-12	mr1172_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
vg0909046504	4.88E-07	1.71E-07	mr1172_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