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Detailed information for vg0522745101:

Variant ID: vg0522745101 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 22745101
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:


TACGCATGCAAATTCAAAACGGCTGGCAACAAATTATAAGCCCAAGATTTGCACGTGTATAGTAGATTTGCATGTGATAAATTGGGTGTATCCAATTGAT[G/T]
ATCAGAGTGTACAAAGCCATACGTTTTAAACCATTTAGCATGTTCGTTATTATCACAACAAAAAACATTTACTTGTTGAAGCCCCACCCCCCAATTTACA

Reverse complement sequence

TGTAAATTGGGGGGTGGGGCTTCAACAAGTAAATGTTTTTTGTTGTGATAATAACGAACATGCTAAATGGTTTAAAACGTATGGCTTTGTACACTCTGAT[C/A]
ATCAATTGGATACACCCAATTTATCACATGCAAATCTACTATACACGTGCAAATCTTGGGCTTATAATTTGTTGCCAGCCGTTTTGAATTTGCATGCGTA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.20% 3.80% 0.00% 0.00% NA
All Indica  2759 93.50% 6.50% 0.00% 0.00% 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 97.80% 2.20% 0.00% 0.00% NA
Indica II  465 92.90% 7.10% 0.00% 0.00% NA
Indica III  913 88.80% 11.20% 0.00% 0.00% NA
Indica Intermediate  786 95.90% 4.10% 0.00% 0.00% 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
vg0522745101 G -> T LOC_Os05g38770.1 3_prime_UTR_variant ; 264.0bp to feature; MODIFIER silent_mutation Average:34.587; most accessible tissue: Zhenshan97 young leaf, score: 53.314 N N N N
vg0522745101 G -> T LOC_Os05g38760.1 upstream_gene_variant ; 649.0bp to feature; MODIFIER silent_mutation Average:34.587; most accessible tissue: Zhenshan97 young leaf, score: 53.314 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0522745101 NA 7.77E-06 mr1671 Ind_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