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Detailed information for vg0224129878:

Variant ID: vg0224129878 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 24129878
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.01, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:


AGGATTTAAAATATAAAACATTAACATCATCATTATTTTTTTCTGATTCTCATCGTGTGTCTACTTAAATAGCTGCCTCTCAGATTATGGTCTATTTGGT[C/T]
GAGCTCGAACTTCAAGGAGGTGGGTCTGGAGTGGAACAGCCTAAACCCAGCTTCACCTCTCTAGTTCATTTTGTGAGAGCGCTACACCTAGCTTCGTTTC

Reverse complement sequence

GAAACGAAGCTAGGTGTAGCGCTCTCACAAAATGAACTAGAGAGGTGAAGCTGGGTTTAGGCTGTTCCACTCCAGACCCACCTCCTTGAAGTTCGAGCTC[G/A]
ACCAAATAGACCATAATCTGAGAGGCAGCTATTTAAGTAGACACACGATGAGAATCAGAAAAAAATAATGATGATGTTAATGTTTTATATTTTAAATCCT

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 80.40% 19.60% 0.02% 0.00% NA
All Indica  2759 70.50% 29.40% 0.04% 0.00% NA
All Japonica  1512 98.80% 1.20% 0.00% 0.00% NA
Aus  269 78.40% 21.60% 0.00% 0.00% NA
Indica I  595 53.80% 46.20% 0.00% 0.00% NA
Indica II  465 86.20% 13.80% 0.00% 0.00% NA
Indica III  913 70.90% 29.10% 0.00% 0.00% NA
Indica Intermediate  786 73.50% 26.30% 0.13% 0.00% NA
Temperate Japonica  767 99.00% 1.00% 0.00% 0.00% NA
Tropical Japonica  504 98.20% 1.80% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 75.00% 25.00% 0.00% 0.00% NA
Intermediate  90 86.70% 13.30% 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
vg0224129878 C -> T LOC_Os02g39910.1 downstream_gene_variant ; 3305.0bp to feature; MODIFIER silent_mutation Average:48.561; most accessible tissue: Minghui63 root, score: 63.193 N N N N
vg0224129878 C -> T LOC_Os02g39900-LOC_Os02g39910 intergenic_region ; MODIFIER silent_mutation Average:48.561; most accessible tissue: Minghui63 root, score: 63.193 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0224129878 NA 1.73E-06 mr1291_2 Ind_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
vg0224129878 8.80E-06 8.82E-06 mr1500_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
vg0224129878 NA 8.62E-06 mr1763_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
vg0224129878 4.60E-06 4.60E-06 mr1956_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
vg0224129878 NA 5.20E-06 mr1971_2 Ind_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