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Detailed information for vg0414554740:

Variant ID: vg0414554740 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 14554740
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.83, T: 0.18, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:

AGCTAAAACTAGCACCTATAGTGTTTTGCCCACCTCCACAGGCTGAAAATACAAAAAAAAAATCCATCACCTTTAAGTGAATATAGGTGCCGGTTTAATA[T/G]
AAAAACCAATACCTATACTATAAGTGCTATTTTTTTAAAAAAAACCGACAATTATAATATATTAAAAACCGCCAGCTATAATATATTATCGGTGCCGGTA

Reverse complement sequence

TACCGGCACCGATAATATATTATAGCTGGCGGTTTTTAATATATTATAATTGTCGGTTTTTTTTAAAAAAATAGCACTTATAGTATAGGTATTGGTTTTT[A/C]
TATTAAACCGGCACCTATATTCACTTAAAGGTGATGGATTTTTTTTTTGTATTTTCAGCCTGTGGAGGTGGGCAAAACACTATAGGTGCTAGTTTTAGCT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	47.00%	18.80%	10.75%	23.51%	NA
All Indica	2759	51.40%	6.10%	10.58%	31.97%	NA
All Japonica	1512	46.20%	40.70%	0.40%	12.70%	NA
Aus	269	3.00%	30.90%	65.06%	1.12%	NA
Indica I	595	41.20%	1.00%	1.68%	56.13%	NA
Indica II	465	20.40%	9.20%	23.44%	46.88%	NA
Indica III	913	76.50%	7.30%	10.08%	6.13%	NA
Indica Intermediate	786	48.30%	6.50%	10.31%	34.86%	NA
Temperate Japonica	767	59.10%	25.70%	0.13%	15.12%	NA
Tropical Japonica	504	22.60%	68.10%	0.79%	8.53%	NA
Japonica Intermediate	241	54.40%	31.50%	0.41%	13.69%	NA
VI/Aromatic	96	53.10%	1.00%	32.29%	13.54%	NA
Intermediate	90	48.90%	23.30%	4.44%	23.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0414554740	T -> DEL	N	N	silent_mutation	Average:14.594; most accessible tissue: Callus, score: 33.681	N	N	N	N
vg0414554740	T -> G	LOC_Os04g25180.1	upstream_gene_variant ; 934.0bp to feature; MODIFIER	silent_mutation	Average:14.594; most accessible tissue: Callus, score: 33.681	N	N	N	N
vg0414554740	T -> G	LOC_Os04g25190.1	downstream_gene_variant ; 4180.0bp to feature; MODIFIER	silent_mutation	Average:14.594; most accessible tissue: Callus, score: 33.681	N	N	N	N
vg0414554740	T -> G	LOC_Os04g25170-LOC_Os04g25180	intergenic_region ; MODIFIER	silent_mutation	Average:14.594; most accessible tissue: Callus, score: 33.681	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0414554740	NA	7.33E-06	mr1227	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
vg0414554740	NA	6.37E-07	mr1749	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
vg0414554740	NA	2.25E-07	mr1877	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
vg0414554740	NA	6.48E-07	mr1944	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
vg0414554740	NA	1.34E-06	mr1322_2	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
vg0414554740	NA	8.36E-06	mr1338_2	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
vg0414554740	2.74E-06	NA	mr1712_2	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
vg0414554740	NA	3.91E-06	mr1712_2	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