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Detailed information for vg0627801213:

Variant ID: vg0627801213 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 27801213
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 313. )

Flanking Sequence (100 bp) in Reference Genome:


ATATATATATCTCATCTCAAATGCTATTTTCCCTACATATATAGATTGATCCAACCACCTATGGTGACAGCAAAACCCACTTCTTTGTATCTTGGACGGT[A/G]
TGTGTCCACTTATATTCATTGTTTGTGCACTTGAAATACATTGCTTAATTACCATGCATATGTCTTTAATTACAAGGTTTTGATATGGATGCATGACATA

Reverse complement sequence

TATGTCATGCATCCATATCAAAACCTTGTAATTAAAGACATATGCATGGTAATTAAGCAATGTATTTCAAGTGCACAAACAATGAATATAAGTGGACACA[T/C]
ACCGTCCAAGATACAAAGAAGTGGGTTTTGCTGTCACCATAGGTGGTTGGATCAATCTATATATGTAGGGAAAATAGCATTTGAGATGAGATATATATAT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.40% 5.60% 0.00% 0.00% NA
All Indica  2759 90.50% 9.50% 0.00% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 95.30% 4.70% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 88.00% 12.00% 0.00% 0.00% NA
Indica Intermediate  786 84.40% 15.60% 0.00% 0.00% NA
Temperate Japonica  767 99.50% 0.50% 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 98.90% 1.10% 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
vg0627801213 A -> G LOC_Os06g45920.1 splice_region_variant&intron_variant ; LOW silent_mutation Average:56.084; most accessible tissue: Callus, score: 84.596 N N N N
vg0627801213 A -> G LOC_Os06g45910.1 downstream_gene_variant ; 2633.0bp to feature; MODIFIER silent_mutation Average:56.084; most accessible tissue: Callus, score: 84.596 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0627801213 NA 7.56E-06 mr1442_2 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
vg0627801213 NA 3.10E-07 mr1533_2 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
vg0627801213 NA 9.11E-07 mr1980_2 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