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Detailed information for vg0224143127:

Variant ID: vg0224143127 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 24143127
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, T: 0.01, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:


TTCCTTTATTGAGATAGAACAAACAGTACAACAACCAGTGTGCTAAAAAGCAACTGAATAGATGCTATTAAATTCTATCTGTTTTGAATTAACATCAAAG[A/T]
TAGGATCAAATCACAATTGAACCACACTAAATAACTCCTATATACTCAGTGTTATAGCAAAGTTTACAAGACAATAACAGGATTTGAATCACAAGCAACT

Reverse complement sequence

AGTTGCTTGTGATTCAAATCCTGTTATTGTCTTGTAAACTTTGCTATAACACTGAGTATATAGGAGTTATTTAGTGTGGTTCAATTGTGATTTGATCCTA[T/A]
CTTTGATGTTAATTCAAAACAGATAGAATTTAATAGCATCTATTCAGTTGCTTTTTAGCACACTGGTTGTTGTACTGTTTGTTCTATCTCAATAAAGGAA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 81.80% 18.20% 0.02% 0.02% NA
All Indica  2759 70.40% 29.50% 0.04% 0.04% NA
All Japonica  1512 97.60% 2.40% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 79.70% 20.30% 0.00% 0.00% NA
Indica II  465 65.60% 34.20% 0.22% 0.00% NA
Indica III  913 66.80% 33.10% 0.00% 0.11% NA
Indica Intermediate  786 70.50% 29.50% 0.00% 0.00% NA
Temperate Japonica  767 99.00% 1.00% 0.00% 0.00% NA
Tropical Japonica  504 94.80% 5.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0224143127 A -> T LOC_Os02g39910.1 upstream_gene_variant ; 3754.0bp to feature; MODIFIER silent_mutation Average:48.201; most accessible tissue: Zhenshan97 young leaf, score: 72.747 N N N N
vg0224143127 A -> T LOC_Os02g39920.1 intron_variant ; MODIFIER silent_mutation Average:48.201; most accessible tissue: Zhenshan97 young leaf, score: 72.747 N N N N
vg0224143127 A -> DEL N N silent_mutation Average:48.201; most accessible tissue: Zhenshan97 young leaf, score: 72.747 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0224143127 NA 3.62E-06 mr1347 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
vg0224143127 3.13E-06 NA mr1406 Ind_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