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Detailed information for vg1215048510:

Variant ID: vg1215048510 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 15048510
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.02, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

CAGTATAACATGAACAGATCAAATATGCGCAACATATTGAATACGTACCGAGGTAGCGGAAAGACCGGCTGCTCGGTCGAAACTTTTCGCAGGCGTCTAC[G/A]
AAGGCACGCAGCACGCGAGCGAAGAGGAAGACGAGCCGTCGCGGACAAACAGGGAGCAGTCGCGCAAAGCGCTTCCCAAAAATCTTATTGCCGCCTTCTC

Reverse complement sequence

GAGAAGGCGGCAATAAGATTTTTGGGAAGCGCTTTGCGCGACTGCTCCCTGTTTGTCCGCGACGGCTCGTCTTCCTCTTCGCTCGCGTGCTGCGTGCCTT[C/T]
GTAGACGCCTGCGAAAAGTTTCGACCGAGCAGCCGGTCTTTCCGCTACCTCGGTACGTATTCAATATGTTGCGCATATTTGATCTGTTCATGTTATACTG

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	91.50%	6.70%	1.78%	0.00%	NA
All Indica	2759	86.10%	11.10%	2.83%	0.00%	NA
All Japonica	1512	99.30%	0.50%	0.26%	0.00%	NA
Aus	269	99.30%	0.40%	0.37%	0.00%	NA
Indica I	595	57.30%	34.10%	8.57%	0.00%	NA
Indica II	465	95.90%	3.20%	0.86%	0.00%	NA
Indica III	913	99.00%	0.40%	0.55%	0.00%	NA
Indica Intermediate	786	87.00%	10.70%	2.29%	0.00%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	98.60%	0.60%	0.79%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	94.40%	5.60%	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
vg1215048510	G -> A	LOC_Os12g25920-LOC_Os12g25940	intergenic_region ; MODIFIER	silent_mutation	Average:40.88; most accessible tissue: Minghui63 young leaf, score: 68.07	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1215048510	NA	3.36E-06	mr1170_2	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
vg1215048510	NA	2.54E-06	mr1308_2	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
vg1215048510	2.81E-06	NA	mr1361_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
vg1215048510	8.56E-07	1.04E-08	mr1361_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