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Detailed information for vg1214119279:

Variant ID: vg1214119279 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 14119279
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:

ATGATCATAGAGCACTATATATATTGTTCCCCATTGGTTTATACAATACATTAGTAGTTTAGACTTGGAAAATTATTATTATCCCATGACGGTTGCAATA[G/T]
GTTGTGGAGTTTAGGATATAAAGATATCATAAATTTAGACTTGGATATATAATATACAACACGTTGATTGGATGCAGTTTATTCTAATATAACAGTTGCA

Reverse complement sequence

TGCAACTGTTATATTAGAATAAACTGCATCCAATCAACGTGTTGTATATTATATATCCAAGTCTAAATTTATGATATCTTTATATCCTAAACTCCACAAC[C/A]
TATTGCAACCGTCATGGGATAATAATAATTTTCCAAGTCTAAACTACTAATGTATTGTATAAACCAATGGGGAACAATATATATAGTGCTCTATGATCAT

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	91.30%	7.00%	1.69%	0.00%	NA
All Indica	2759	97.90%	1.90%	0.25%	0.00%	NA
All Japonica	1512	77.60%	17.80%	4.56%	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	90.50%	8.60%	0.86%	0.00%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	98.30%	1.30%	0.38%	0.00%	NA
Temperate Japonica	767	94.80%	1.40%	3.78%	0.00%	NA
Tropical Japonica	504	46.40%	47.20%	6.35%	0.00%	NA
Japonica Intermediate	241	88.40%	8.30%	3.32%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	86.70%	8.90%	4.44%	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
vg1214119279	G -> T	LOC_Os12g24650.1	downstream_gene_variant ; 4771.0bp to feature; MODIFIER	silent_mutation	Average:30.458; most accessible tissue: Callus, score: 62.565	N	N	N	N
vg1214119279	G -> T	LOC_Os12g24659.1	downstream_gene_variant ; 3610.0bp to feature; MODIFIER	silent_mutation	Average:30.458; most accessible tissue: Callus, score: 62.565	N	N	N	N
vg1214119279	G -> T	LOC_Os12g24650-LOC_Os12g24659	intergenic_region ; MODIFIER	silent_mutation	Average:30.458; most accessible tissue: Callus, score: 62.565	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1214119279	NA	4.59E-06	mr1044	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
vg1214119279	NA	2.16E-07	mr1408	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
vg1214119279	7.97E-07	NA	mr1546	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
vg1214119279	NA	1.14E-06	mr1583	Jap_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
vg1214119279	NA	4.33E-06	mr1602	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
vg1214119279	NA	3.63E-06	mr1697	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