Search for Variation information by Variation ID:

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

Detailed information for vg0224013358:

Variant ID: vg0224013358 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 24013358
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGTGAACGTGGTGCCTCCTTTCAAAGCAGTTTTAATAATATAATAGATAGATAATTAGCTCTAAATGCGAGCACCATGTCAAGTATAGAATCGAATAGAC[A/G]
GGCTCCACCACCAGAAACTCAACCAGTTGAGTTCAGGGTTTACGATTCTGACAGGCCCTTCCGTTTCGAGCTCTGGCGGAATTCGGAATTTCGTGAAATC

Reverse complement sequence

GATTTCACGAAATTCCGAATTCCGCCAGAGCTCGAAACGGAAGGGCCTGTCAGAATCGTAAACCCTGAACTCAACTGGTTGAGTTTCTGGTGGTGGAGCC[T/C]
GTCTATTCGATTCTATACTTGACATGGTGCTCGCATTTAGAGCTAATTATCTATCTATTATATTATTAAAACTGCTTTGAAAGGAGGCACCACGTTCACT

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 98.90% 0.60% 0.51% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 96.60% 1.90% 1.59% 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  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 93.60% 3.50% 2.87% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 99.20% 0.40% 0.41% 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
vg0224013358 A -> G LOC_Os02g39750-LOC_Os02g39764 intergenic_region ; MODIFIER silent_mutation Average:24.683; most accessible tissue: Callus, score: 51.401 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0224013358 NA 8.87E-08 mr1210 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
vg0224013358 2.87E-06 8.77E-09 mr1305 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
vg0224013358 NA 2.21E-09 mr1585 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
vg0224013358 NA 5.34E-08 mr1586 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
vg0224013358 5.48E-07 2.23E-09 mr1305_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
vg0224013358 6.82E-06 6.68E-07 mr1559_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
vg0224013358 2.59E-08 4.75E-13 mr1585_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