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Detailed information for vg1215279207:

Variant ID: vg1215279207 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 15279207
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 120. )

Flanking Sequence (100 bp) in Reference Genome:

TAACAATAACTGCAGTTACACGATATGAGTACTTAGTCCGAACACTCATCACGATAACATTATGATACAACACCGAAGAGTTCACAATACTACTAGTACA[A/G]
CAATAGTCGGAGGTACTCATTACAACAACATTCATTGAAATTACACAATAGAAGTACTTAGTCCAAATACTCATCACAACACAATAGCATTTTATTTCCT

Reverse complement sequence

AGGAAATAAAATGCTATTGTGTTGTGATGAGTATTTGGACTAAGTACTTCTATTGTGTAATTTCAATGAATGTTGTTGTAATGAGTACCTCCGACTATTG[T/C]
TGTACTAGTAGTATTGTGAACTCTTCGGTGTTGTATCATAATGTTATCGTGATGAGTGTTCGGACTAAGTACTCATATCGTGTAACTGCAGTTATTGTTA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	83.40%	16.20%	0.44%	0.00%	NA
All Indica	2759	74.40%	25.40%	0.18%	0.00%	NA
All Japonica	1512	95.80%	3.70%	0.53%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	92.30%	7.70%	0.00%	0.00%	NA
Indica II	465	45.20%	54.00%	0.86%	0.00%	NA
Indica III	913	80.30%	19.60%	0.11%	0.00%	NA
Indica Intermediate	786	71.50%	28.50%	0.00%	0.00%	NA
Temperate Japonica	767	99.10%	0.80%	0.13%	0.00%	NA
Tropical Japonica	504	89.50%	9.30%	1.19%	0.00%	NA
Japonica Intermediate	241	98.30%	1.20%	0.41%	0.00%	NA
VI/Aromatic	96	92.70%	1.00%	6.25%	0.00%	NA
Intermediate	90	90.00%	7.80%	2.22%	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
vg1215279207	A -> G	LOC_Os12g26204.1	intron_variant ; MODIFIER	silent_mutation	Average:17.264; most accessible tissue: Callus, score: 25.798	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1215279207	NA	2.32E-06	mr1030	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
vg1215279207	NA	1.19E-06	mr1723	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
vg1215279207	8.52E-06	8.52E-06	mr1938	Ind_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
vg1215279207	1.71E-07	NA	mr1490_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