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Detailed information for vg0402996309:

Variant ID: vg0402996309 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 2996309
Reference Allele: T	Alternative Allele: A
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.93, T: 0.07, others allele: 0.00, population size: 69. )

Flanking Sequence (100 bp) in Reference Genome:

AGTAACAACCTAGGGTTTTTTGCGGGAGCGGAGAAGACGAGATGCGCTTGGAGGCTGGAAGGTTTTTTCCACAATAGGCGGCCTTCAAAATGAATCCCCA[T/A]
AACTTCCTTAAATAGACGCACTTCCGACGGTGCGAATTCCAAGGAAAGGAGAGAGATGGCCACCGGAAATTTCTGGGTTCGTTACGCGCGGCAGTTTTTC

Reverse complement sequence

GAAAAACTGCCGCGCGTAACGAACCCAGAAATTTCCGGTGGCCATCTCTCTCCTTTCCTTGGAATTCGCACCGTCGGAAGTGCGTCTATTTAAGGAAGTT[A/T]
TGGGGATTCATTTTGAAGGCCGCCTATTGTGGAAAAAACCTTCCAGCCTCCAAGCGCATCTCGTCTTCTCCGCTCCCGCAAAAAACCCTAGGTTGTTACT

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	36.60%	15.80%	0.47%	47.14%	NA
All Indica	2759	31.30%	6.30%	0.43%	62.02%	NA
All Japonica	1512	41.90%	36.80%	0.13%	21.16%	NA
Aus	269	52.80%	0.40%	2.23%	44.61%	NA
Indica I	595	7.20%	11.60%	0.84%	80.34%	NA
Indica II	465	20.00%	11.60%	0.43%	67.96%	NA
Indica III	913	50.20%	0.30%	0.11%	49.40%	NA
Indica Intermediate	786	34.20%	6.00%	0.51%	59.29%	NA
Temperate Japonica	767	15.60%	66.90%	0.26%	17.21%	NA
Tropical Japonica	504	74.60%	2.60%	0.00%	22.82%	NA
Japonica Intermediate	241	56.80%	12.90%	0.00%	30.29%	NA
VI/Aromatic	96	52.10%	0.00%	1.04%	46.88%	NA
Intermediate	90	44.40%	18.90%	1.11%	35.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0402996309	T -> DEL	N	N	silent_mutation	Average:8.085; most accessible tissue: Callus, score: 28.338	N	N	N	N
vg0402996309	T -> A	LOC_Os04g05820.1	upstream_gene_variant ; 2625.0bp to feature; MODIFIER	silent_mutation	Average:8.085; most accessible tissue: Callus, score: 28.338	N	N	N	N
vg0402996309	T -> A	LOC_Os04g05830.1	upstream_gene_variant ; 134.0bp to feature; MODIFIER	silent_mutation	Average:8.085; most accessible tissue: Callus, score: 28.338	N	N	N	N
vg0402996309	T -> A	LOC_Os04g05840.1	downstream_gene_variant ; 2747.0bp to feature; MODIFIER	silent_mutation	Average:8.085; most accessible tissue: Callus, score: 28.338	N	N	N	N
vg0402996309	T -> A	LOC_Os04g05830-LOC_Os04g05840	intergenic_region ; MODIFIER	silent_mutation	Average:8.085; most accessible tissue: Callus, score: 28.338	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0402996309	NA	1.75E-06	mr1576	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
vg0402996309	NA	6.97E-10	mr1864	Jap_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
vg0402996309	NA	3.43E-07	mr1521_2	Jap_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
vg0402996309	NA	2.34E-08	mr1576_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
vg0402996309	3.67E-06	NA	mr1962_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