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Detailed information for vg1207839557:

Variant ID: vg1207839557 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 7839557
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, T: 0.01, others allele: 0.00, population size: 120. )

Flanking Sequence (100 bp) in Reference Genome:

TAGCTCTTACATATTCATCTTACGACTTTGATTATCCATTGATCCCCAATTTACTGATCACCATGACTCACATAAAAAAATATGTACTACTTAGGGTTTA[G/T]
GACAACTGAAATTGATGAATTATCTGATTTATGTGATAGCTATTTGAGGGTATAAATGAATGAATTGACTTCTAAAAAGTTAAAATGTTGTTTAAAAAAA

Reverse complement sequence

TTTTTTTAAACAACATTTTAACTTTTTAGAAGTCAATTCATTCATTTATACCCTCAAATAGCTATCACATAAATCAGATAATTCATCAATTTCAGTTGTC[C/A]
TAAACCCTAAGTAGTACATATTTTTTTATGTGAGTCATGGTGATCAGTAAATTGGGGATCAATGGATAATCAAAGTCGTAAGATGAATATGTAAGAGCTA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	57.10%	20.40%	21.90%	0.53%	NA
All Indica	2759	35.00%	32.60%	32.29%	0.11%	NA
All Japonica	1512	96.10%	0.50%	2.18%	1.26%	NA
Aus	269	50.60%	19.30%	30.11%	0.00%	NA
Indica I	595	37.80%	19.50%	42.69%	0.00%	NA
Indica II	465	38.50%	21.10%	40.00%	0.43%	NA
Indica III	913	31.40%	46.20%	22.34%	0.00%	NA
Indica Intermediate	786	35.00%	33.50%	31.42%	0.13%	NA
Temperate Japonica	767	96.90%	0.10%	2.61%	0.39%	NA
Tropical Japonica	504	96.20%	1.00%	1.98%	0.79%	NA
Japonica Intermediate	241	93.40%	0.40%	1.24%	4.98%	NA
VI/Aromatic	96	74.00%	2.10%	22.92%	1.04%	NA
Intermediate	90	82.20%	6.70%	8.89%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1207839557	G -> DEL	N	N	silent_mutation	Average:7.093; most accessible tissue: Callus, score: 16.06	N	N	N	N
vg1207839557	G -> T	LOC_Os12g13850.1	downstream_gene_variant ; 4414.0bp to feature; MODIFIER	silent_mutation	Average:7.093; most accessible tissue: Callus, score: 16.06	N	N	N	N
vg1207839557	G -> T	LOC_Os12g13850-LOC_Os12g13860	intergenic_region ; MODIFIER	silent_mutation	Average:7.093; most accessible tissue: Callus, score: 16.06	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1207839557	2.54E-06	2.54E-06	mr1466	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
vg1207839557	NA	6.59E-08	mr1659_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