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Detailed information for vg0412619214:

Variant ID: vg0412619214 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 12619214
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCATGTTTGCAATAGAATCATTTAGCCCAATAAAACATAGGATCAATGTGGTCAAAGGAGGGGCAAACTTGCCTTCGTTTGCAAACTCCTGAACCTGGTC[G/A]
TCAACAAACTCACCCTCTTCTCCTTCGACGTATTCTTCCTCTATACAAAATATGCGTATACGATAAATACAAAAATGCATAAAAACCAAAATGCATGAAA

Reverse complement sequence

TTTCATGCATTTTGGTTTTTATGCATTTTTGTATTTATCGTATACGCATATTTTGTATAGAGGAAGAATACGTCGAAGGAGAAGAGGGTGAGTTTGTTGA[C/T]
GACCAGGTTCAGGAGTTTGCAAACGAAGGCAAGTTTGCCCCTCCTTTGACCACATTGATCCTATGTTTTATTGGGCTAAATGATTCTATTGCAAACATGC

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	65.40%	0.50%	2.81%	31.29%	NA
All Indica	2759	49.00%	0.80%	3.88%	46.28%	NA
All Japonica	1512	96.40%	0.00%	0.26%	3.31%	NA
Aus	269	47.60%	0.00%	6.69%	45.72%	NA
Indica I	595	35.00%	0.70%	2.35%	62.02%	NA
Indica II	465	57.60%	0.60%	2.37%	39.35%	NA
Indica III	913	53.90%	0.50%	6.68%	38.88%	NA
Indica Intermediate	786	48.90%	1.40%	2.67%	47.07%	NA
Temperate Japonica	767	97.30%	0.00%	0.26%	2.48%	NA
Tropical Japonica	504	99.20%	0.00%	0.00%	0.79%	NA
Japonica Intermediate	241	88.00%	0.00%	0.83%	11.20%	NA
VI/Aromatic	96	94.80%	0.00%	0.00%	5.21%	NA
Intermediate	90	68.90%	0.00%	4.44%	26.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0412619214	G -> DEL	N	N	silent_mutation	Average:7.381; most accessible tissue: Callus, score: 30.725	N	N	N	N
vg0412619214	G -> A	LOC_Os04g22290.1	upstream_gene_variant ; 771.0bp to feature; MODIFIER	silent_mutation	Average:7.381; most accessible tissue: Callus, score: 30.725	N	N	N	N
vg0412619214	G -> A	LOC_Os04g22280-LOC_Os04g22290	intergenic_region ; MODIFIER	silent_mutation	Average:7.381; most accessible tissue: Callus, score: 30.725	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0412619214	4.78E-06	6.18E-06	mr1063	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
vg0412619214	3.24E-06	3.24E-06	mr1602	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
vg0412619214	4.27E-06	NA	mr1637	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