Search for Variation information by Variation ID:

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

Detailed information for vg0224787962:

Variant ID: vg0224787962 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 24787962
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.74, A: 0.27, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:


GGATCAACTCCCTCCATTTGCATCGGCCAATTAGCCGCATTCTAGTTAATTTGCAACCTTAGAACTTAGAAGAACAACACACACATGTATAGACATCCAC[G/A]
TCAAAGCTAGCGCCGCCGACGACGCACGTATAGTATTTGGCCGGTTACATTCCGCTGTTTTCTCCAGCAGACAAAACAATTATTGCATTGCATTGGTACG

Reverse complement sequence

CGTACCAATGCAATGCAATAATTGTTTTGTCTGCTGGAGAAAACAGCGGAATGTAACCGGCCAAATACTATACGTGCGTCGTCGGCGGCGCTAGCTTTGA[C/T]
GTGGATGTCTATACATGTGTGTGTTGTTCTTCTAAGTTCTAAGGTTGCAAATTAACTAGAATGCGGCTAATTGGCCGATGCAAATGGAGGGAGTTGATCC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 55.70% 44.20% 0.15% 0.00% NA
All Indica  2759 82.70% 17.00% 0.25% 0.00% NA
All Japonica  1512 5.60% 94.40% 0.00% 0.00% NA
Aus  269 79.20% 20.80% 0.00% 0.00% NA
Indica I  595 96.00% 3.70% 0.34% 0.00% NA
Indica II  465 91.20% 8.60% 0.22% 0.00% NA
Indica III  913 75.80% 23.90% 0.33% 0.00% NA
Indica Intermediate  786 75.70% 24.20% 0.13% 0.00% NA
Temperate Japonica  767 5.60% 94.40% 0.00% 0.00% NA
Tropical Japonica  504 7.50% 92.50% 0.00% 0.00% NA
Japonica Intermediate  241 1.70% 98.30% 0.00% 0.00% NA
VI/Aromatic  96 16.70% 83.30% 0.00% 0.00% NA
Intermediate  90 38.90% 61.10% 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
vg0224787962 G -> A LOC_Os02g40900.1 upstream_gene_variant ; 1397.0bp to feature; MODIFIER silent_mutation Average:72.81; most accessible tissue: Callus, score: 88.584 N N N N
vg0224787962 G -> A LOC_Os02g40910.1 downstream_gene_variant ; 1569.0bp to feature; MODIFIER silent_mutation Average:72.81; most accessible tissue: Callus, score: 88.584 N N N N
vg0224787962 G -> A LOC_Os02g40900-LOC_Os02g40910 intergenic_region ; MODIFIER silent_mutation Average:72.81; most accessible tissue: Callus, score: 88.584 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0224787962 3.78E-06 NA mr1877 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
vg0224787962 NA 2.67E-17 mr1199_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