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Detailed information for vg0513751374:

Variant ID: vg0513751374 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 13751374
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:


CATCTTAGCTATGTTTATCCAATGATGTTGTATAGTTTACCTTATACTTTACTCAAGATTAATAAAAAATAATTTGTGTGTGATTCCAGTGGTTTACCTT[G/A]
TGTTTCCATCTACCTTTGTATGGACAATAATAAAAAGATTATTGTTTGTTTGATAATTCAATAATAAAACATTCATAAGTTGTATCATTTATTTAGCAAT

Reverse complement sequence

ATTGCTAAATAAATGATACAACTTATGAATGTTTTATTATTGAATTATCAAACAAACAATAATCTTTTTATTATTGTCCATACAAAGGTAGATGGAAACA[C/T]
AAGGTAAACCACTGGAATCACACACAAATTATTTTTTATTAATCTTGAGTAAAGTATAAGGTAAACTATACAACATCATTGGATAAACATAGCTAAGATG

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 95.90% 0.40% 2.41% 1.31% NA
All Indica  2759 95.40% 0.00% 2.32% 2.25% NA
All Japonica  1512 95.80% 1.10% 3.11% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 86.70% 0.00% 5.71% 7.56% NA
Indica II  465 98.70% 0.00% 0.86% 0.43% NA
Indica III  913 99.90% 0.00% 0.11% 0.00% NA
Indica Intermediate  786 94.90% 0.00% 3.18% 1.91% NA
Temperate Japonica  767 93.10% 2.10% 4.82% 0.00% NA
Tropical Japonica  504 98.80% 0.00% 1.19% 0.00% NA
Japonica Intermediate  241 98.30% 0.00% 1.66% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 1.10% 3.33% 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
vg0513751374 G -> DEL N N silent_mutation Average:28.175; most accessible tissue: Callus, score: 43.277 N N N N
vg0513751374 G -> A LOC_Os05g23910.1 3_prime_UTR_variant ; 228.0bp to feature; MODIFIER silent_mutation Average:28.175; most accessible tissue: Callus, score: 43.277 N N N N
vg0513751374 G -> A LOC_Os05g23900.1 upstream_gene_variant ; 4677.0bp to feature; MODIFIER silent_mutation Average:28.175; most accessible tissue: Callus, score: 43.277 N N N N
vg0513751374 G -> A LOC_Os05g23924.1 downstream_gene_variant ; 4153.0bp to feature; MODIFIER silent_mutation Average:28.175; most accessible tissue: Callus, score: 43.277 N N N N
vg0513751374 G -> A LOC_Os05g23924.2 downstream_gene_variant ; 4140.0bp to feature; MODIFIER silent_mutation Average:28.175; most accessible tissue: Callus, score: 43.277 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0513751374 3.15E-07 3.15E-07 mr1173_2 Jap_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
vg0513751374 1.79E-06 1.79E-06 mr1499_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
vg0513751374 3.46E-06 9.77E-07 mr1546_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
vg0513751374 NA 7.22E-06 mr1549_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
vg0513751374 NA 7.73E-06 mr1821_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