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Detailed information for vg0522746463:

Variant ID: vg0522746463 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 22746463
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


CTTGTCCGCCGGCAAATCTGCCGACGACGACGATGCAACAATAACAGAACAATGGACAATCTCATTATCGTCGTCTTAGAGTATTCGTTCGCGTTGCGGC[G/A]
TGTGGTGGGTGTGCGTACCGAACAAGTGTTCTTCCAAGTTGCCGGCGGACATGAACTCGTAGACGAGGAGCCGCTGGTCGCCGTCGGCGCAGTAGCCGAT

Reverse complement sequence

ATCGGCTACTGCGCCGACGGCGACCAGCGGCTCCTCGTCTACGAGTTCATGTCCGCCGGCAACTTGGAAGAACACTTGTTCGGTACGCACACCCACCACA[C/T]
GCCGCAACGCGAACGAATACTCTAAGACGACGATAATGAGATTGTCCATTGTTCTGTTATTGTTGCATCGTCGTCGTCGGCAGATTTGCCGGCGGACAAG

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 97.60% 2.40% 0.00% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 67.70% 32.30% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.40% 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 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 80.20% 19.80% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0522746463 G -> A LOC_Os05g38760.1 upstream_gene_variant ; 2011.0bp to feature; MODIFIER silent_mutation Average:64.45; most accessible tissue: Zhenshan97 young leaf, score: 82.763 N N N N
vg0522746463 G -> A LOC_Os05g38770.1 intron_variant ; MODIFIER silent_mutation Average:64.45; most accessible tissue: Zhenshan97 young leaf, score: 82.763 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0522746463 NA 5.67E-06 mr1052 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
vg0522746463 NA 6.52E-11 mr1499 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
vg0522746463 NA 4.84E-06 mr1633 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
vg0522746463 NA 1.31E-08 mr1989 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
vg0522746463 NA 1.64E-06 mr1465_2 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
vg0522746463 NA 3.01E-10 mr1612_2 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