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Detailed information for vg0233306848:

Variant ID: vg0233306848 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 33306848
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:


TCGAGTTATGGAGTTCCATCTTCCTATGCTTTTCGTTTGGTTTGCTAATTGATAGTTGCCTTTGGGCTGATTCCTAGCACCCGGGGGCTTGTTGGATGGA[T/C]
CGAATAACGCAAGGTGCTAAGTATTATTCGGAATAAATCAAAAGCATAGAGATAAGATAATTTATTTTCTGCTCTTAATAATTGCAAAAGTACCCGAGTA

Reverse complement sequence

TACTCGGGTACTTTTGCAATTATTAAGAGCAGAAAATAAATTATCTTATCTCTATGCTTTTGATTTATTCCGAATAATACTTAGCACCTTGCGTTATTCG[A/G]
TCCATCCAACAAGCCCCCGGGTGCTAGGAATCAGCCCAAAGGCAACTATCAATTAGCAAACCAAACGAAAAGCATAGGAAGATGGAACTCCATAACTCGA

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 90.40% 8.10% 1.48% 0.00% NA
All Indica  2759 98.00% 1.30% 0.69% 0.00% NA
All Japonica  1512 74.90% 21.80% 3.24% 0.00% NA
Aus  269 98.10% 1.90% 0.00% 0.00% NA
Indica I  595 98.00% 0.70% 1.34% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 97.60% 2.00% 0.44% 0.00% NA
Indica Intermediate  786 97.60% 1.50% 0.89% 0.00% NA
Temperate Japonica  767 54.40% 40.30% 5.35% 0.00% NA
Tropical Japonica  504 98.20% 1.60% 0.20% 0.00% NA
Japonica Intermediate  241 91.70% 5.40% 2.90% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 86.70% 11.10% 2.22% 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
vg0233306848 T -> C LOC_Os02g54310.1 downstream_gene_variant ; 3508.0bp to feature; MODIFIER silent_mutation Average:16.741; most accessible tissue: Zhenshan97 flag leaf, score: 32.264 N N N N
vg0233306848 T -> C LOC_Os02g54320.1 intron_variant ; MODIFIER silent_mutation Average:16.741; most accessible tissue: Zhenshan97 flag leaf, score: 32.264 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0233306848 1.62E-06 NA Yield All YES Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0233306848 NA 5.19E-06 mr1576_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
vg0233306848 NA 6.73E-08 mr1627_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
vg0233306848 NA 9.61E-06 mr1768_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
vg0233306848 6.02E-07 2.59E-08 mr1977_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
vg0233306848 2.23E-07 7.47E-08 mr1977_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