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Detailed information for vg0123297322:

Variant ID: vg0123297322 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 23297322
Reference Allele: AAlternative Allele: T
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTTCTATTCATTTGGATTTACACTGTCTTCTTGAGTGGTACTATGTAATAATTGGCTGTAGCTCTTTTGAATAAAGGCCGGGATATTATATTCCATTTTT[A/T]
AAAAAAAATGTGGTACAAGGACAACAGGTTTCGTTGTTTTCTGCTAAGATTATCATGTCCCTTTTTATGCTGTAGGACAATAGGAGACATTTGGCATCCC

Reverse complement sequence

GGGATGCCAAATGTCTCCTATTGTCCTACAGCATAAAAAGGGACATGATAATCTTAGCAGAAAACAACGAAACCTGTTGTCCTTGTACCACATTTTTTTT[T/A]
AAAAATGGAATATAATATCCCGGCCTTTATTCAAAAGAGCTACAGCCAATTATTACATAGTACCACTCAAGAAGACAGTGTAAATCCAAATGAATAGAAC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 80.30% 19.70% 0.00% 0.00% NA
All Indica  2759 99.10% 0.90% 0.00% 0.00% NA
All Japonica  1512 43.30% 56.70% 0.00% 0.00% NA
Aus  269 98.10% 1.90% 0.00% 0.00% NA
Indica I  595 99.50% 0.50% 0.00% 0.00% NA
Indica II  465 98.30% 1.70% 0.00% 0.00% NA
Indica III  913 99.70% 0.30% 0.00% 0.00% NA
Indica Intermediate  786 98.50% 1.50% 0.00% 0.00% NA
Temperate Japonica  767 6.90% 93.10% 0.00% 0.00% NA
Tropical Japonica  504 92.70% 7.30% 0.00% 0.00% NA
Japonica Intermediate  241 56.00% 44.00% 0.00% 0.00% NA
VI/Aromatic  96 71.90% 28.10% 0.00% 0.00% NA
Intermediate  90 80.00% 20.00% 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
vg0123297322 A -> T LOC_Os01g41145.1 3_prime_UTR_variant ; 805.0bp to feature; MODIFIER silent_mutation Average:49.076; most accessible tissue: Minghui63 panicle, score: 75.788 N N N N
vg0123297322 A -> T LOC_Os01g41140.1 upstream_gene_variant ; 4655.0bp to feature; MODIFIER silent_mutation Average:49.076; most accessible tissue: Minghui63 panicle, score: 75.788 N N N N
vg0123297322 A -> T LOC_Os01g41160.1 downstream_gene_variant ; 3544.0bp to feature; MODIFIER silent_mutation Average:49.076; most accessible tissue: Minghui63 panicle, score: 75.788 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0123297322 NA 7.71E-06 mr1097 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
vg0123297322 1.29E-06 NA mr1128 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
vg0123297322 NA 2.04E-08 mr1879_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