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Detailed information for vg0133435968:

Variant ID: vg0133435968 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 33435968
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:


ATTATTGAGATAAGTATCGCTGGATGGCCGATATAGCCTTCTGCCTAATCTGCTCTACTTCTTCTATGGCTTGGGCATCCTGAGCGTCGGTTCCAGGGAT[A/C]
ACTTTCAGAGACTTGGTCAGATCAGCAACATGCTTGATAGCCGATTTGAGTCTTGCTTTCTGTTTTTCAATAGACTTTGGGAGATCGGCTAGTTTTTTGT

Reverse complement sequence

ACAAAAAACTAGCCGATCTCCCAAAGTCTATTGAAAAACAGAAAGCAAGACTCAAATCGGCTATCAAGCATGTTGCTGATCTGACCAAGTCTCTGAAAGT[T/G]
ATCCCTGGAACCGACGCTCAGGATGCCCAAGCCATAGAAGAAGTAGAGCAGATTAGGCAGAAGGCTATATCGGCCATCCAGCGATACTTATCTCAATAAT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.80% 0.10% 0.28% 0.80% NA
All Indica  2759 98.00% 0.10% 0.47% 1.38% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 98.70% 0.00% 0.67% 0.67% NA
Indica II  465 99.80% 0.00% 0.00% 0.22% NA
Indica III  913 96.20% 0.40% 0.77% 2.63% NA
Indica Intermediate  786 98.60% 0.00% 0.25% 1.15% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 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  90 100.00% 0.00% 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
vg0133435968 A -> C LOC_Os01g57810.1 synonymous_variant ; p.Val746Val; LOW N Average:23.017; most accessible tissue: Callus, score: 35.965 N N N N
vg0133435968 A -> C LOC_Os01g57800.1 downstream_gene_variant ; 552.0bp to feature; MODIFIER N Average:23.017; most accessible tissue: Callus, score: 35.965 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0133435968 6.93E-06 NA mr1531 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