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Detailed information for vg0220005783:

Variant ID: vg0220005783 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 20005783
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCATAAGGATTTAAATTTCTTTGTTTTACCTAGCTCACAGAAAAACTCATAAGAATTTAAATTTCTCTAAAATTCCTTTAATTTTTTTTTCAATCCAAAA[G/T]
ATTTTCCTTACATTTCGCAAGTCGAAGAACAAATTTGAAACCAAAACATGTAAGGAGAACAAAATAAAAAAAAAATCTTAGAACTTGGAAGCGTAAAAGG

Reverse complement sequence

CCTTTTACGCTTCCAAGTTCTAAGATTTTTTTTTTATTTTGTTCTCCTTACATGTTTTGGTTTCAAATTTGTTCTTCGACTTGCGAAATGTAAGGAAAAT[C/A]
TTTTGGATTGAAAAAAAAATTAAAGGAATTTTAGAGAAATTTAAATTCTTATGAGTTTTTCTGTGAGCTAGGTAAAACAAAGAAATTTAAATCCTTATGA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.30% 1.90% 0.78% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 91.50% 6.00% 2.45% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 86.30% 9.10% 4.56% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 90.50% 8.70% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0220005783 G -> T LOC_Os02g33610.1 upstream_gene_variant ; 180.0bp to feature; MODIFIER silent_mutation Average:91.82; most accessible tissue: Callus, score: 95.084 N N N N
vg0220005783 G -> T LOC_Os02g33610.2 upstream_gene_variant ; 170.0bp to feature; MODIFIER silent_mutation Average:91.82; most accessible tissue: Callus, score: 95.084 N N N N
vg0220005783 G -> T LOC_Os02g33600.1 downstream_gene_variant ; 3962.0bp to feature; MODIFIER silent_mutation Average:91.82; most accessible tissue: Callus, score: 95.084 N N N N
vg0220005783 G -> T LOC_Os02g33600-LOC_Os02g33610 intergenic_region ; MODIFIER silent_mutation Average:91.82; most accessible tissue: Callus, score: 95.084 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0220005783 NA 5.61E-06 mr1416_2 Jap_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