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Detailed information for vg1206532904:

Variant ID: vg1206532904 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 6532904
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGCTCTGCTACGATTGCATTGTCGTGTGGGAAATACGGACCTCACAGATGATGCGTCACCTTCTTACCCTACATGTACATGTTATTTCTCGGTTTGTTTT[G/A]
TTTTAATTTTTTTAAAAGAAGTATACTACATGGTCTTGTTATATTAGGAGTAGGTAGTAAGTTTTGTTTCTTTATGTCTTTTCATATAAATAACTAAATT

Reverse complement sequence

AATTTAGTTATTTATATGAAAAGACATAAAGAAACAAAACTTACTACCTACTCCTAATATAACAAGACCATGTAGTATACTTCTTTTAAAAAAATTAAAA[C/T]
AAAACAAACCGAGAAATAACATGTACATGTAGGGTAAGAAGGTGACGCATCATCTGTGAGGTCCGTATTTCCCACACGACAATGCAATCGTAGCAGAGCT

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	81.20%	3.70%	0.78%	14.37%	NA
All Indica	2759	74.70%	3.60%	1.20%	20.51%	NA
All Japonica	1512	97.40%	0.20%	0.20%	2.18%	NA
Aus	269	74.30%	24.50%	0.00%	1.12%	NA
Indica I	595	46.90%	7.60%	2.18%	43.36%	NA
Indica II	465	87.70%	0.20%	1.29%	10.75%	NA
Indica III	913	88.90%	1.00%	0.77%	9.31%	NA
Indica Intermediate	786	71.50%	5.60%	0.89%	22.01%	NA
Temperate Japonica	767	95.80%	0.00%	0.39%	3.78%	NA
Tropical Japonica	504	99.40%	0.20%	0.00%	0.40%	NA
Japonica Intermediate	241	98.30%	0.80%	0.00%	0.83%	NA
VI/Aromatic	96	29.20%	1.00%	1.04%	68.75%	NA
Intermediate	90	82.20%	5.60%	0.00%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1206532904	G -> DEL	N	N	silent_mutation	Average:12.878; most accessible tissue: Callus, score: 68.376	N	N	N	N
vg1206532904	G -> A	LOC_Os12g11950-LOC_Os12g11970	intergenic_region ; MODIFIER	silent_mutation	Average:12.878; most accessible tissue: Callus, score: 68.376	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1206532904	8.36E-07	8.36E-07	mr1349	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