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Detailed information for vg0224702963:

Variant ID: vg0224702963 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 24702963
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


AAAGACCAAACATCAAACAAACAAAAATATCGAAACATTCTTTATAAAACGAGAAACAAATAAAGTATAAAAACTGCAGTATCATCACTGGTGGAGGAAC[C/T]
ATCTTTGGTCGGTCCACCAGATTTCACAATAGTCCCGGTTATATTAAAAACCGGGAATAAAAACATCTTTAGTCCCAGTTTGAAAGCTCTGATGAATTTT

Reverse complement sequence

AAAATTCATCAGAGCTTTCAAACTGGGACTAAAGATGTTTTTATTCCCGGTTTTTAATATAACCGGGACTATTGTGAAATCTGGTGGACCGACCAAAGAT[G/A]
GTTCCTCCACCAGTGATGATACTGCAGTTTTTATACTTTATTTGTTTCTCGTTTTATAAAGAATGTTTCGATATTTTTGTTTGTTTGATGTTTGGTCTTT

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 87.20% 12.80% 0.04% 0.00% NA
All Indica  2759 81.60% 18.30% 0.07% 0.00% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 68.40% 31.60% 0.00% 0.00% NA
Indica I  595 99.50% 0.50% 0.00% 0.00% NA
Indica II  465 71.00% 29.00% 0.00% 0.00% NA
Indica III  913 77.50% 22.50% 0.00% 0.00% NA
Indica Intermediate  786 79.00% 20.70% 0.25% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 90.00% 10.00% 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
vg0224702963 C -> T LOC_Os02g40750.1 upstream_gene_variant ; 4515.0bp to feature; MODIFIER silent_mutation Average:25.573; most accessible tissue: Callus, score: 54.365 N N N N
vg0224702963 C -> T LOC_Os02g40760.1 upstream_gene_variant ; 1285.0bp to feature; MODIFIER silent_mutation Average:25.573; most accessible tissue: Callus, score: 54.365 N N N N
vg0224702963 C -> T LOC_Os02g40760-LOC_Os02g40770 intergenic_region ; MODIFIER silent_mutation Average:25.573; most accessible tissue: Callus, score: 54.365 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0224702963 NA 5.82E-06 mr1080 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
vg0224702963 NA 9.14E-06 mr1148 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
vg0224702963 NA 5.26E-06 mr1795 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
vg0224702963 5.86E-06 1.59E-10 mr1080_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
vg0224702963 NA 4.19E-08 mr1619_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
vg0224702963 4.40E-06 NA mr1795_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
vg0224702963 1.45E-06 5.50E-10 mr1795_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
vg0224702963 NA 9.18E-09 mr1962_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