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Detailed information for vg1204019821:

Variant ID: vg1204019821 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 4019821
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGAGTGACATTTTTGCCCCGCGGAGAGTCGGGGCCAGGGCCCAGCATTTGGGCGAGTGAGAGGCCGGGGGAGACATTCCTCCTGCGGGTGACCCGCAGGG[A/T]
CTCGGGGGTATATTACCCCTCAATATGTAGCCCATTATAGATTTGCAGGCCCAAAAAGCCCATCTAAAAATAGTGGGAATCCAAGGTATATAAGAAAACA

Reverse complement sequence

TGTTTTCTTATATACCTTGGATTCCCACTATTTTTAGATGGGCTTTTTGGGCCTGCAAATCTATAATGGGCTACATATTGAGGGGTAATATACCCCCGAG[T/A]
CCCTGCGGGTCACCCGCAGGAGGAATGTCTCCCCCGGCCTCTCACTCGCCCAAATGCTGGGCCCTGGCCCCGACTCTCCGCGGGGCAAAAATGTCACTCG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	27.50%	6.50%	0.25%	65.76%	NA
All Indica	2759	7.00%	0.40%	0.33%	92.28%	NA
All Japonica	1512	62.80%	19.00%	0.07%	18.12%	NA
Aus	269	10.00%	0.00%	0.74%	89.22%	NA
Indica I	595	1.30%	0.20%	0.17%	98.32%	NA
Indica II	465	17.20%	0.90%	1.08%	80.86%	NA
Indica III	913	4.40%	0.10%	0.00%	95.51%	NA
Indica Intermediate	786	8.10%	0.80%	0.38%	90.71%	NA
Temperate Japonica	767	83.30%	11.90%	0.13%	4.69%	NA
Tropical Japonica	504	42.30%	26.40%	0.00%	31.35%	NA
Japonica Intermediate	241	40.20%	26.60%	0.00%	33.20%	NA
VI/Aromatic	96	85.40%	0.00%	0.00%	14.58%	NA
Intermediate	90	53.30%	8.90%	0.00%	37.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1204019821	A -> DEL	N	N	silent_mutation	Average:12.408; most accessible tissue: Callus, score: 77.042	N	N	N	N
vg1204019821	A -> T	LOC_Os12g07920.1	upstream_gene_variant ; 383.0bp to feature; MODIFIER	silent_mutation	Average:12.408; most accessible tissue: Callus, score: 77.042	N	N	N	N
vg1204019821	A -> T	LOC_Os12g07910.1	downstream_gene_variant ; 354.0bp to feature; MODIFIER	silent_mutation	Average:12.408; most accessible tissue: Callus, score: 77.042	N	N	N	N
vg1204019821	A -> T	LOC_Os12g07930.1	downstream_gene_variant ; 2863.0bp to feature; MODIFIER	silent_mutation	Average:12.408; most accessible tissue: Callus, score: 77.042	N	N	N	N
vg1204019821	A -> T	LOC_Os12g07910-LOC_Os12g07920	intergenic_region ; MODIFIER	silent_mutation	Average:12.408; most accessible tissue: Callus, score: 77.042	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1204019821	1.69E-08	NA	mr1083	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
vg1204019821	9.67E-06	NA	mr1203	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
vg1204019821	8.97E-06	NA	mr1204	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
vg1204019821	6.00E-06	NA	mr1264	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
vg1204019821	NA	5.06E-07	mr1345	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
vg1204019821	NA	7.16E-09	mr1554	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
vg1204019821	7.45E-06	NA	mr1831	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