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Detailed information for vg0406883410:

Variant ID: vg0406883410 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 6883410
Reference Allele: A	Alternative Allele: G,T
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, A: 0.08, others allele: 0.00, population size: 66. )

Flanking Sequence (100 bp) in Reference Genome:

CTTCTCTTTCCCGGGAGCGCCAGAACTCCTCTCACTGCTAGAAACATGGACGCCTAGAGTGCATGAGGATTTGAGTTCATGGAGCGGGTACTGCCAATGC[A/G,T]
AGGTTATCGAAAAGCTTTGCCGTGACGCGTCTCATGTGTTGAGACGAGGCTTATGTGTTGGGCAGTCGCGGAGTGCGGGTAAAGTGTACATCCACTGCAG

Reverse complement sequence

CTGCAGTGGATGTACACTTTACCCGCACTCCGCGACTGCCCAACACATAAGCCTCGTCTCAACACATGAGACGCGTCACGGCAAAGCTTTTCGATAACCT[T/C,A]
GCATTGGCAGTACCCGCTCCATGAACTCAAATCCTCATGCACTCTAGGCGTCCATGTTTCTAGCAGTGAGAGGAGTTCTGGCGCTCCCGGGAAAGAGAAG

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	33.50%	12.50%	18.83%	35.06%	T: 0.04%
All Indica	2759	3.20%	20.40%	24.79%	51.61%	T: 0.04%
All Japonica	1512	94.60%	0.70%	0.60%	4.10%	NA
Aus	269	0.70%	1.10%	49.07%	48.70%	T: 0.37%
Indica I	595	1.80%	8.40%	18.49%	71.26%	NA
Indica II	465	6.50%	17.40%	18.06%	58.06%	NA
Indica III	913	1.40%	26.70%	32.53%	39.21%	T: 0.11%
Indica Intermediate	786	4.30%	23.80%	24.55%	47.33%	NA
Temperate Japonica	767	96.00%	0.70%	0.39%	3.00%	NA
Tropical Japonica	504	94.80%	0.80%	0.20%	4.17%	NA
Japonica Intermediate	241	90.00%	0.40%	2.07%	7.47%	NA
VI/Aromatic	96	20.80%	6.20%	48.96%	23.96%	NA
Intermediate	90	48.90%	12.20%	20.00%	18.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0406883410	A -> DEL	N	N	silent_mutation	Average:25.354; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0406883410	A -> G	LOC_Os04g12450.1	upstream_gene_variant ; 3251.0bp to feature; MODIFIER	silent_mutation	Average:25.354; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0406883410	A -> G	LOC_Os04g12450-LOC_Os04g12460	intergenic_region ; MODIFIER	silent_mutation	Average:25.354; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0406883410	A -> T	LOC_Os04g12450.1	upstream_gene_variant ; 3251.0bp to feature; MODIFIER	silent_mutation	Average:25.354; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0406883410	A -> T	LOC_Os04g12450-LOC_Os04g12460	intergenic_region ; MODIFIER	silent_mutation	Average:25.354; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0406883410	6.52E-06	6.52E-06	mr1276	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
vg0406883410	NA	3.26E-06	mr1649	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