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Detailed information for vg0133435988:

Variant ID: vg0133435988 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 33435988
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:


TGGATGGCCGATATAGCCTTCTGCCTAATCTGCTCTACTTCTTCTATGGCTTGGGCATCCTGAGCGTCGGTTCCAGGGATAACTTTCAGAGACTTGGTCA[G/A]
ATCAGCAACATGCTTGATAGCCGATTTGAGTCTTGCTTTCTGTTTTTCAATAGACTTTGGGAGATCGGCTAGTTTTTTGTGTTCCATGTCCAGCTCAGCG

Reverse complement sequence

CGCTGAGCTGGACATGGAACACAAAAAACTAGCCGATCTCCCAAAGTCTATTGAAAAACAGAAAGCAAGACTCAAATCGGCTATCAAGCATGTTGCTGAT[C/T]
TGACCAAGTCTCTGAAAGTTATCCCTGGAACCGACGCTCAGGATGCCCAAGCCATAGAAGAAGTAGAGCAGATTAGGCAGAAGGCTATATCGGCCATCCA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.00% 0.30% 0.68% 0.06% NA
All Indica  2759 98.40% 0.40% 1.09% 0.11% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 98.10% 1.10% 0.74% 0.00% NA
Indica I  595 99.30% 0.00% 0.50% 0.17% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 96.90% 0.90% 2.08% 0.11% NA
Indica Intermediate  786 98.70% 0.10% 1.02% 0.13% 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
vg0133435988 G -> A LOC_Os01g57810.1 synonymous_variant ; p.Leu740Leu; LOW N Average:23.277; most accessible tissue: Zhenshan97 flag leaf, score: 36.135 N N N N
vg0133435988 G -> A LOC_Os01g57800.1 downstream_gene_variant ; 572.0bp to feature; MODIFIER N Average:23.277; most accessible tissue: Zhenshan97 flag leaf, score: 36.135 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0133435988 4.72E-07 1.63E-06 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