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Detailed information for vg0912998506:

Variant ID: vg0912998506 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 12998506
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.89, T: 0.11, others allele: 0.00, population size: 186. )

Flanking Sequence (100 bp) in Reference Genome:

GGGCGGAGCAAGGGCATTTCCATCTCTCATCATCCGGCGGATGAGCGAAAATCATTTCAGAAATGAATAAAACTGTGAAAATGGCAATGTGGTAGTAAGC[T/G]
CGTGCTCCATATTGACATTTTATCGAATCCCGTTTTGAGAATGGCATACGTATACTAGTGAAACCCTGGTTTGAACGCGGCTAAATATCCATTTTCTCGC

Reverse complement sequence

GCGAGAAAATGGATATTTAGCCGCGTTCAAACCAGGGTTTCACTAGTATACGTATGCCATTCTCAAAACGGGATTCGATAAAATGTCAATATGGAGCACG[A/C]
GCTTACTACCACATTGCCATTTTCACAGTTTTATTCATTTCTGAAATGATTTTCGCTCATCCGCCGGATGATGAGAGATGGAAATGCCCTTGCTCCGCCC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	90.80%	9.10%	0.04%	0.00%	NA
All Indica	2759	94.60%	5.40%	0.04%	0.00%	NA
All Japonica	1512	99.30%	0.70%	0.00%	0.00%	NA
Aus	269	38.30%	61.70%	0.00%	0.00%	NA
Indica I	595	89.90%	10.10%	0.00%	0.00%	NA
Indica II	465	98.90%	1.10%	0.00%	0.00%	NA
Indica III	913	95.00%	4.90%	0.11%	0.00%	NA
Indica Intermediate	786	95.00%	5.00%	0.00%	0.00%	NA
Temperate Japonica	767	99.20%	0.80%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	7.30%	91.70%	1.04%	0.00%	NA
Intermediate	90	81.10%	18.90%	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
vg0912998506	T -> G	LOC_Os09g21500-LOC_Os09g21510	intergenic_region ; MODIFIER	silent_mutation	Average:53.438; most accessible tissue: Callus, score: 95.57	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0912998506	NA	7.11E-06	mr1029	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0912998506	NA	3.85E-06	mr1815_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0912998506	NA	1.96E-08	mr1834_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0912998506	1.33E-07	1.29E-09	mr1834_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