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Detailed information for vg1216723758:

Variant ID: vg1216723758 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 16723758
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCAGTATTTCAAACTTAGCTTCTGATTTCTTAAAAGCTTTTGTCAAACCTTATTGAGCCTAAAACCCGCAAAAGCTATTAAAAAACTTTCAGTCCTCATT[A/G]
ACTAAGCCAAAAAATCAAGCAAGGCAATGGTAAATCAAGTAAGTAAATTGAATTGATAAAGATCACACTCCATTATTATTATAGTAGCCCCCGACTGGTA

Reverse complement sequence

TACCAGTCGGGGGCTACTATAATAATAATGGAGTGTGATCTTTATCAATTCAATTTACTTACTTGATTTACCATTGCCTTGCTTGATTTTTTGGCTTAGT[T/C]
AATGAGGACTGAAAGTTTTTTAATAGCTTTTGCGGGTTTTAGGCTCAATAAGGTTTGACAAAAGCTTTTAAGAAATCAGAAGCTAAGTTTGAAATACTGA

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	25.60%	0.10%	19.04%	55.25%	NA
All Indica	2759	3.80%	0.10%	24.21%	71.87%	NA
All Japonica	1512	69.30%	0.10%	3.04%	27.58%	NA
Aus	269	9.70%	0.40%	37.92%	52.04%	NA
Indica I	595	3.90%	0.20%	10.42%	85.55%	NA
Indica II	465	3.70%	0.00%	19.78%	76.56%	NA
Indica III	913	2.20%	0.20%	33.73%	63.86%	NA
Indica Intermediate	786	5.70%	0.00%	26.21%	68.07%	NA
Temperate Japonica	767	92.30%	0.10%	0.52%	7.04%	NA
Tropical Japonica	504	30.80%	0.00%	6.75%	62.50%	NA
Japonica Intermediate	241	76.80%	0.00%	3.32%	19.92%	NA
VI/Aromatic	96	0.00%	0.00%	68.75%	31.25%	NA
Intermediate	90	34.40%	0.00%	20.00%	45.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1216723758	A -> DEL	N	N	silent_mutation	Average:6.096; most accessible tissue: Callus, score: 14.841	N	N	N	N
vg1216723758	A -> G	LOC_Os12g28280.1	downstream_gene_variant ; 177.0bp to feature; MODIFIER	silent_mutation	Average:6.096; most accessible tissue: Callus, score: 14.841	N	N	N	N
vg1216723758	A -> G	LOC_Os12g28290.1	downstream_gene_variant ; 4547.0bp to feature; MODIFIER	silent_mutation	Average:6.096; most accessible tissue: Callus, score: 14.841	N	N	N	N
vg1216723758	A -> G	LOC_Os12g28280-LOC_Os12g28290	intergenic_region ; MODIFIER	silent_mutation	Average:6.096; most accessible tissue: Callus, score: 14.841	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1216723758	NA	9.61E-08	mr1030_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
vg1216723758	NA	8.94E-07	mr1045_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
vg1216723758	2.39E-06	NA	mr1571_2	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
vg1216723758	NA	2.26E-07	mr1749_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
vg1216723758	NA	4.57E-07	mr1754_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
vg1216723758	NA	3.31E-06	mr1792_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
vg1216723758	NA	1.28E-07	mr1821_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