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Detailed information for vg0420224812:

Variant ID: vg0420224812 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 20224812
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 331. )

Flanking Sequence (100 bp) in Reference Genome:


CCGTTTGCTGAAATAAGTTGTCCAATAACGGAGAATCACTATATAAAGCTTATACAGAACATAGTAACTGTAAGCACTGCGGTTCCAGCTGATATATATC[C/A]
TGTTTTCTAACAAGCGAAGAGGGTCGTCTGAATCAAATCAGCAACATCATAACTGGTGGCTCTCTTCACTCTCCTGGGGCAGAGACACCTTGCTTCAGTT

Reverse complement sequence

AACTGAAGCAAGGTGTCTCTGCCCCAGGAGAGTGAAGAGAGCCACCAGTTATGATGTTGCTGATTTGATTCAGACGACCCTCTTCGCTTGTTAGAAAACA[G/T]
GATATATATCAGCTGGAACCGCAGTGCTTACAGTTACTATGTTCTGTATAAGCTTTATATAGTGATTCTCCGTTATTGGACAACTTATTTCAGCAAACGG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.10% 3.90% 0.02% 0.00% NA
All Indica  2759 98.90% 1.10% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 50.90% 48.70% 0.37% 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 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 96.30% 3.70% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 77.10% 22.90% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg0420224812 C -> A LOC_Os04g33440.2 3_prime_UTR_variant ; 66.0bp to feature; MODIFIER silent_mutation Average:71.311; most accessible tissue: Zhenshan97 flower, score: 85.963 N N N N
vg0420224812 C -> A LOC_Os04g33450.1 upstream_gene_variant ; 1738.0bp to feature; MODIFIER silent_mutation Average:71.311; most accessible tissue: Zhenshan97 flower, score: 85.963 N N N N
vg0420224812 C -> A LOC_Os04g33450.3 upstream_gene_variant ; 1738.0bp to feature; MODIFIER silent_mutation Average:71.311; most accessible tissue: Zhenshan97 flower, score: 85.963 N N N N
vg0420224812 C -> A LOC_Os04g33450.2 upstream_gene_variant ; 1730.0bp to feature; MODIFIER silent_mutation Average:71.311; most accessible tissue: Zhenshan97 flower, score: 85.963 N N N N
vg0420224812 C -> A LOC_Os04g33430.1 downstream_gene_variant ; 2072.0bp to feature; MODIFIER silent_mutation Average:71.311; most accessible tissue: Zhenshan97 flower, score: 85.963 N N N N
vg0420224812 C -> A LOC_Os04g33420.1 downstream_gene_variant ; 4410.0bp to feature; MODIFIER silent_mutation Average:71.311; most accessible tissue: Zhenshan97 flower, score: 85.963 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0420224812 NA 8.22E-07 mr1320 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