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Detailed information for vg0526873682:

Variant ID: vg0526873682 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 26873682
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 345. )

Flanking Sequence (100 bp) in Reference Genome:


CTAAATTTTTTCCTATGTTTTGGGTATGCCAGTGCACACCGACAATCCATGGGTTCACCCTGATATGGGATAATAAGAAGTGGTGTCTTACCATCTATTA[C/A]
TGATGAGAAGAAAATTTATGAGAGGACCGTTCTCACATTGGCATGATACCGTTCTGGTATGCCGCTAATAACAACAATTAATATGTAATTTAGGCTCATA

Reverse complement sequence

TATGAGCCTAAATTACATATTAATTGTTGTTATTAGCGGCATACCAGAACGGTATCATGCCAATGTGAGAACGGTCCTCTCATAAATTTTCTTCTCATCA[G/T]
TAATAGATGGTAAGACACCACTTCTTATTATCCCATATCAGGGTGAACCCATGGATTGTCGGTGTGCACTGGCATACCCAAAACATAGGAAAAAATTTAG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.30% 1.20% 0.42% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 94.80% 3.90% 1.32% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 90.90% 6.80% 2.35% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 96.30% 2.90% 0.83% 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
vg0526873682 C -> A LOC_Os05g46360.1 downstream_gene_variant ; 2529.0bp to feature; MODIFIER silent_mutation Average:65.37; most accessible tissue: Callus, score: 86.623 N N N N
vg0526873682 C -> A LOC_Os05g46360.3 downstream_gene_variant ; 3731.0bp to feature; MODIFIER silent_mutation Average:65.37; most accessible tissue: Callus, score: 86.623 N N N N
vg0526873682 C -> A LOC_Os05g46360.2 downstream_gene_variant ; 2529.0bp to feature; MODIFIER silent_mutation Average:65.37; most accessible tissue: Callus, score: 86.623 N N N N
vg0526873682 C -> A LOC_Os05g46360-LOC_Os05g46370 intergenic_region ; MODIFIER silent_mutation Average:65.37; most accessible tissue: Callus, score: 86.623 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0526873682 NA 4.79E-06 mr1354 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
vg0526873682 1.30E-08 1.30E-08 mr1412 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
vg0526873682 NA 4.24E-09 mr1354_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
vg0526873682 NA 5.14E-06 mr1829_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
vg0526873682 NA 7.41E-06 mr1902_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