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Detailed information for vg0403407500:

Variant ID: vg0403407500 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 3407500
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:

ACGATACTATTTCTTGCGCTTATTCTCGTGATTCTCCTGTGGCCATCTCCAGTTATGTATCAATAAGACAGTTATACTTTTCCCCTAAACAAAAGGACAA[A/T]
CCATGTTCATCTATGAGGAGATTGATCATTCTCTTGATTGGTGAACAACGGACAATATTATTATCAATTCTTTACAATTACAGGCTTGATAAGCTGATCA

Reverse complement sequence

TGATCAGCTTATCAAGCCTGTAATTGTAAAGAATTGATAATAATATTGTCCGTTGTTCACCAATCAAGAGAATGATCAATCTCCTCATAGATGAACATGG[T/A]
TTGTCCTTTTGTTTAGGGGAAAAGTATAACTGTCTTATTGATACATAACTGGAGATGGCCACAGGAGAATCACGAGAATAAGCGCAAGAAATAGTATCGT

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	51.60%	10.20%	4.19%	33.96%	NA
All Indica	2759	26.20%	10.20%	6.71%	56.87%	NA
All Japonica	1512	89.20%	9.90%	0.46%	0.46%	NA
Aus	269	97.80%	1.50%	0.37%	0.37%	NA
Indica I	595	10.80%	6.10%	3.70%	79.50%	NA
Indica II	465	38.10%	3.70%	3.87%	54.41%	NA
Indica III	913	26.40%	14.80%	11.61%	47.21%	NA
Indica Intermediate	786	30.70%	12.00%	4.96%	52.42%	NA
Temperate Japonica	767	93.90%	5.50%	0.39%	0.26%	NA
Tropical Japonica	504	88.30%	10.70%	0.40%	0.60%	NA
Japonica Intermediate	241	76.30%	22.00%	0.83%	0.83%	NA
VI/Aromatic	96	57.30%	40.60%	0.00%	2.08%	NA
Intermediate	90	54.40%	11.10%	5.56%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0403407500	A -> DEL	N	N	silent_mutation	Average:27.468; most accessible tissue: Minghui63 flag leaf, score: 51.386	N	N	N	N
vg0403407500	A -> T	LOC_Os04g06490.1	upstream_gene_variant ; 1869.0bp to feature; MODIFIER	silent_mutation	Average:27.468; most accessible tissue: Minghui63 flag leaf, score: 51.386	N	N	N	N
vg0403407500	A -> T	LOC_Os04g06530.1	downstream_gene_variant ; 98.0bp to feature; MODIFIER	silent_mutation	Average:27.468; most accessible tissue: Minghui63 flag leaf, score: 51.386	N	N	N	N
vg0403407500	A -> T	LOC_Os04g06520.1	downstream_gene_variant ; 3228.0bp to feature; MODIFIER	silent_mutation	Average:27.468; most accessible tissue: Minghui63 flag leaf, score: 51.386	N	N	N	N
vg0403407500	A -> T	LOC_Os04g06490-LOC_Os04g06530	intergenic_region ; MODIFIER	silent_mutation	Average:27.468; most accessible tissue: Minghui63 flag leaf, score: 51.386	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0403407500	2.31E-06	NA	mr1364_2	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