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Detailed information for vg1219817262:

Variant ID: vg1219817262 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 19817262
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAGATTTTACAACCTTTCTTTTTATTTATTTATTCATTCAATCATGTTGCAACATAATTTAGCACGTTGATTTTCTAACTCTCTCTTTTATTTTATTTTT[G/A]
AAACCTGTTATTCAAAAGTGCAAAAAAAATTTGTGATCCCGTTTTCAACTGTTTCAACTTATCTTGCAAAGATTGGTTTACTTTATTTATTTACCTTTTA

Reverse complement sequence

TAAAAGGTAAATAAATAAAGTAAACCAATCTTTGCAAGATAAGTTGAAACAGTTGAAAACGGGATCACAAATTTTTTTTGCACTTTTGAATAACAGGTTT[C/T]
AAAAATAAAATAAAAGAGAGAGTTAGAAAATCAACGTGCTAAATTATGTTGCAACATGATTGAATGAATAAATAAATAAAAAGAAAGGTTGTAAAATCTC

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	44.30%	0.20%	10.45%	45.07%	NA
All Indica	2759	18.70%	0.30%	17.22%	63.86%	NA
All Japonica	1512	87.20%	0.00%	0.26%	12.50%	NA
Aus	269	40.50%	0.40%	3.35%	55.76%	NA
Indica I	595	13.30%	0.20%	12.77%	73.78%	NA
Indica II	465	12.00%	0.20%	10.54%	77.20%	NA
Indica III	913	20.60%	0.40%	23.88%	55.09%	NA
Indica Intermediate	786	24.40%	0.10%	16.79%	58.65%	NA
Temperate Japonica	767	83.80%	0.00%	0.26%	15.91%	NA
Tropical Japonica	504	96.20%	0.00%	0.40%	3.37%	NA
Japonica Intermediate	241	79.30%	0.00%	0.00%	20.75%	NA
VI/Aromatic	96	90.60%	0.00%	1.04%	8.33%	NA
Intermediate	90	71.10%	0.00%	5.56%	23.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1219817262	G -> DEL	N	N	silent_mutation	Average:12.347; most accessible tissue: Callus, score: 18.363	N	N	N	N
vg1219817262	G -> A	LOC_Os12g32800.1	intron_variant ; MODIFIER	silent_mutation	Average:12.347; most accessible tissue: Callus, score: 18.363	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1219817262	2.03E-08	2.03E-08	mr1542	Jap_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
vg1219817262	5.60E-06	5.60E-06	mr1750	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