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Detailed information for vg0220807490:

Variant ID: vg0220807490 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 20807490
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGCAGTGGGTCTTTTGGGTTGGAATGGAGCTATGGAGCAATAAAAACCCAGCTCCACCTCGTAGTCCATATTTAAGGAGTAGCTCTGCTAACTTCACTCC[T/C]
AAAAACATAGGATCTAAACCATTTGGCACAACTCCGGCTTAAAGCTGGAGTTAAGAGCTAGAGTTGTGCCAAACATGCCGAAAATGTGCTCTCTCTCTCT

Reverse complement sequence

AGAGAGAGAGAGCACATTTTCGGCATGTTTGGCACAACTCTAGCTCTTAACTCCAGCTTTAAGCCGGAGTTGTGCCAAATGGTTTAGATCCTATGTTTTT[A/G]
GGAGTGAAGTTAGCAGAGCTACTCCTTAAATATGGACTACGAGGTGGAGCTGGGTTTTTATTGCTCCATAGCTCCATTCCAACCCAAAAGACCCACTGCC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 71.20% 28.80% 0.02% 0.00% NA
All Indica  2759 98.60% 1.40% 0.00% 0.00% NA
All Japonica  1512 21.40% 78.60% 0.07% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 99.50% 0.50% 0.00% 0.00% NA
Indica II  465 98.10% 1.90% 0.00% 0.00% NA
Indica III  913 98.70% 1.30% 0.00% 0.00% NA
Indica Intermediate  786 98.10% 1.90% 0.00% 0.00% NA
Temperate Japonica  767 6.10% 93.90% 0.00% 0.00% NA
Tropical Japonica  504 32.50% 67.30% 0.20% 0.00% NA
Japonica Intermediate  241 46.50% 53.50% 0.00% 0.00% NA
VI/Aromatic  96 6.20% 93.80% 0.00% 0.00% NA
Intermediate  90 51.10% 48.90% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0220807490 T -> C LOC_Os02g34690.1 upstream_gene_variant ; 3850.0bp to feature; MODIFIER silent_mutation Average:56.475; most accessible tissue: Callus, score: 81.2 N N N N
vg0220807490 T -> C LOC_Os02g34680.1 downstream_gene_variant ; 3016.0bp to feature; MODIFIER silent_mutation Average:56.475; most accessible tissue: Callus, score: 81.2 N N N N
vg0220807490 T -> C LOC_Os02g34680-LOC_Os02g34690 intergenic_region ; MODIFIER silent_mutation Average:56.475; most accessible tissue: Callus, score: 81.2 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0220807490 NA 2.77E-43 mr1563 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
vg0220807490 NA 5.11E-14 mr1128_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
vg0220807490 NA 1.16E-08 mr1198_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
vg0220807490 NA 4.01E-13 mr1217_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
vg0220807490 NA 3.54E-06 mr1232_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
vg0220807490 NA 2.84E-08 mr1275_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
vg0220807490 NA 5.20E-07 mr1557_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
vg0220807490 NA 3.82E-15 mr1575_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
vg0220807490 2.53E-06 6.46E-48 mr1670_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
vg0220807490 NA 2.71E-07 mr1885_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
vg0220807490 NA 1.08E-07 mr1909_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
vg0220807490 NA 2.54E-06 mr1944_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