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Detailed information for vg0216380020:

Variant ID: vg0216380020 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 16380020
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCAGTAGGCCCCAAAGGGCGTGATGAATGAAGTCTTCAAGCAGTCGGATTCCTTCAGTCGGATCTGATGATATCCCGAGTAGCAATCCAAAAAACTGAGT[A/C]
GCTCGCAGCCGGCGGTCGAGTCGACCACCTGGTCAATGCGAGGGAACCCGAAGGGATCTTTGGGACAAGACTTGTTGAGGTTGGTGTAATCGACACACAT

Reverse complement sequence

ATGTGTGTCGATTACACCAACCTCAACAAGTCTTGTCCCAAAGATCCCTTCGGGTTCCCTCGCATTGACCAGGTGGTCGACTCGACCGCCGGCTGCGAGC[T/G]
ACTCAGTTTTTTGGATTGCTACTCGGGATATCATCAGATCCGACTGAAGGAATCCGACTGCTTGAAGACTTCATTCATCACGCCCTTTGGGGCCTACTGC

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 97.70% 0.40% 1.33% 0.55% NA
All Indica  2759 96.10% 0.70% 2.28% 0.94% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 95.80% 0.50% 2.18% 1.51% NA
Indica II  465 92.90% 0.90% 4.30% 1.94% NA
Indica III  913 98.00% 0.50% 0.99% 0.44% NA
Indica Intermediate  786 96.10% 0.80% 2.67% 0.51% 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
vg0216380020 A -> DEL LOC_Os02g27640.1 N frameshift_variant Average:44.607; most accessible tissue: Minghui63 young leaf, score: 69.4 N N N N
vg0216380020 A -> C LOC_Os02g27640.1 missense_variant ; p.Leu34Arg; MODERATE nonsynonymous_codon ; L34R Average:44.607; most accessible tissue: Minghui63 young leaf, score: 69.4 probably damaging 2.216 DELETERIOUS 0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0216380020 8.09E-07 NA mr1321 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
vg0216380020 3.06E-06 3.06E-06 mr1321 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
vg0216380020 1.92E-06 NA mr1972 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
vg0216380020 4.41E-06 4.41E-06 mr1972 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