Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0407629504:

Variant ID: vg0407629504 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 7629504
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGCAGCCAGCTCAGCAAGCACCATCAACGCAGCAGCATCTCCAACCAATCCAACAAACACCGCCAAGGCAACGGCTTCAGCCGATCCAACAGACTCCGGT[A/G]
CGACAGCAGATCGTTCAGCCGATTCAGCACCCGGGGTCGGTCAATGCATCGGCTGGGTTTGCAGCACCTGGGGGGCAACCTGCGCAGCAATTTGTGAATC

Reverse complement sequence

GATTCACAAATTGCTGCGCAGGTTGCCCCCCAGGTGCTGCAAACCCAGCCGATGCATTGACCGACCCCGGGTGCTGAATCGGCTGAACGATCTGCTGTCG[T/C]
ACCGGAGTCTGTTGGATCGGCTGAAGCCGTTGCCTTGGCGGTGTTTGTTGGATTGGTTGGAGATGCTGCTGCGTTGATGGTGCTTGCTGAGCTGGCTGCA

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	48.50%	0.30%	2.20%	48.98%	NA
All Indica	2759	25.00%	0.50%	3.62%	70.86%	NA
All Japonica	1512	98.60%	0.00%	0.07%	1.32%	NA
Aus	269	3.30%	0.40%	0.37%	95.91%	NA
Indica I	595	6.40%	0.50%	3.70%	89.41%	NA
Indica II	465	38.70%	0.40%	4.30%	56.56%	NA
Indica III	913	26.40%	0.80%	3.50%	69.33%	NA
Indica Intermediate	786	29.30%	0.40%	3.31%	67.05%	NA
Temperate Japonica	767	99.60%	0.00%	0.00%	0.39%	NA
Tropical Japonica	504	97.40%	0.00%	0.20%	2.38%	NA
Japonica Intermediate	241	97.90%	0.00%	0.00%	2.07%	NA
VI/Aromatic	96	52.10%	0.00%	1.04%	46.88%	NA
Intermediate	90	57.80%	0.00%	1.11%	41.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0407629504	A -> DEL	N	N	silent_mutation	Average:26.27; most accessible tissue: Zhenshan97 flag leaf, score: 47.303	N	N	N	N
vg0407629504	A -> G	LOC_Os04g13670.1	upstream_gene_variant ; 322.0bp to feature; MODIFIER	silent_mutation	Average:26.27; most accessible tissue: Zhenshan97 flag leaf, score: 47.303	N	N	N	N
vg0407629504	A -> G	LOC_Os04g13680.1	upstream_gene_variant ; 3770.0bp to feature; MODIFIER	silent_mutation	Average:26.27; most accessible tissue: Zhenshan97 flag leaf, score: 47.303	N	N	N	N
vg0407629504	A -> G	LOC_Os04g13650.1	downstream_gene_variant ; 2531.0bp to feature; MODIFIER	silent_mutation	Average:26.27; most accessible tissue: Zhenshan97 flag leaf, score: 47.303	N	N	N	N
vg0407629504	A -> G	LOC_Os04g13660.1	downstream_gene_variant ; 372.0bp to feature; MODIFIER	silent_mutation	Average:26.27; most accessible tissue: Zhenshan97 flag leaf, score: 47.303	N	N	N	N
vg0407629504	A -> G	LOC_Os04g13660-LOC_Os04g13670	intergenic_region ; MODIFIER	silent_mutation	Average:26.27; most accessible tissue: Zhenshan97 flag leaf, score: 47.303	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0407629504	1.31E-06	NA	mr1354	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