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Detailed information for vg0211826989:

Variant ID: vg0211826989 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 11826989
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.68, T: 0.34, others allele: 0.00, population size: 59. )

Flanking Sequence (100 bp) in Reference Genome:


AAAATAAACAGCAGCGGACTAGCGGGCCTACGGCTCCATCTTCACAGGCGCTCAACTGGGGTATAAGCCAGGACTCCACCTAAGACTTCTTCTCCAAAGC[A/T]
TCTCTTACTGAAGGGGGGGAAAAGATTGAGCAAGAGTGAGTACAACCACAGTACTCAGCAAGCCACACCGGCGGATGCATGATTAATGCAAGGGGGTACA

Reverse complement sequence

TGTACCCCCTTGCATTAATCATGCATCCGCCGGTGTGGCTTGCTGAGTACTGTGGTTGTACTCACTCTTGCTCAATCTTTTCCCCCCCTTCAGTAAGAGA[T/A]
GCTTTGGAGAAGAAGTCTTAGGTGGAGTCCTGGCTTATACCCCAGTTGAGCGCCTGTGAAGATGGAGCCGTAGGCCCGCTAGTCCGCTGCTGTTTATTTT

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 41.50% 10.10% 37.13% 11.26% NA
All Indica  2759 10.90% 16.70% 56.87% 15.51% NA
All Japonica  1512 98.10% 0.20% 0.66% 0.99% NA
Aus  269 7.80% 4.50% 58.36% 29.37% NA
Indica I  595 19.50% 9.90% 57.14% 13.45% NA
Indica II  465 11.20% 15.50% 52.26% 21.08% NA
Indica III  913 3.00% 23.10% 60.57% 13.36% NA
Indica Intermediate  786 13.50% 15.10% 55.09% 16.28% NA
Temperate Japonica  767 99.00% 0.00% 0.13% 0.91% NA
Tropical Japonica  504 97.20% 0.40% 0.99% 1.39% NA
Japonica Intermediate  241 97.50% 0.40% 1.66% 0.41% NA
VI/Aromatic  96 99.00% 0.00% 0.00% 1.04% NA
Intermediate  90 66.70% 2.20% 21.11% 10.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0211826989 A -> T LOC_Os02g20080.1 intron_variant ; MODIFIER silent_mutation Average:7.068; most accessible tissue: Callus, score: 24.486 N N N N
vg0211826989 A -> DEL N N silent_mutation Average:7.068; most accessible tissue: Callus, score: 24.486 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0211826989 1.59E-06 2.26E-07 mr1083 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
vg0211826989 NA 7.91E-30 mr1085 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
vg0211826989 NA 3.03E-06 mr1103 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
vg0211826989 3.35E-07 1.22E-07 mr1411 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
vg0211826989 NA 9.40E-23 mr1386_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
vg0211826989 NA 8.82E-07 mr1418_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
vg0211826989 NA 7.46E-10 mr1506_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