Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0130805560:

Variant ID: vg0130805560 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 30805560
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.04, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:


AAAAGTGAAATCCAACATACAACTAGAATATTCCACATCATCAAATAAATACTTCATCCGTTCTAAAATATAAACATTTTTAGCATAGTGACAAGTCAAA[T/C]
ATTTTTAACTTTAACTATTAATAGAAAAAAAACTGAAGTGTAGTGAAAAACACAGGGTGTTCCAGACCCTTCTAGCAGGCAAGAATAACTACATGTTTGA

Reverse complement sequence

TCAAACATGTAGTTATTCTTGCCTGCTAGAAGGGTCTGGAACACCCTGTGTTTTTCACTACACTTCAGTTTTTTTTCTATTAATAGTTAAAGTTAAAAAT[A/G]
TTTGACTTGTCACTATGCTAAAAATGTTTATATTTTAGAACGGATGAAGTATTTATTTGATGATGTGGAATATTCTAGTTGTATGTTGGATTTCACTTTT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 55.20% 44.70% 0.04% 0.00% NA
All Indica  2759 83.60% 16.30% 0.04% 0.00% NA
All Japonica  1512 0.90% 99.10% 0.00% 0.00% NA
Aus  269 95.50% 4.50% 0.00% 0.00% NA
Indica I  595 92.90% 7.10% 0.00% 0.00% NA
Indica II  465 97.80% 2.20% 0.00% 0.00% NA
Indica III  913 70.00% 30.00% 0.00% 0.00% NA
Indica Intermediate  786 84.00% 15.90% 0.13% 0.00% NA
Temperate Japonica  767 0.40% 99.60% 0.00% 0.00% NA
Tropical Japonica  504 1.20% 98.80% 0.00% 0.00% NA
Japonica Intermediate  241 1.70% 98.30% 0.00% 0.00% NA
VI/Aromatic  96 9.40% 90.60% 0.00% 0.00% NA
Intermediate  90 27.80% 71.10% 1.11% 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
vg0130805560 T -> C LOC_Os01g53630-LOC_Os01g53640 intergenic_region ; MODIFIER silent_mutation Average:40.33; most accessible tissue: Callus, score: 79.695 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0130805560 5.13E-06 NA mr1097 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
vg0130805560 5.94E-08 2.22E-09 mr1097 Ind_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
vg0130805560 NA 1.11E-11 mr1553 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
vg0130805560 NA 1.80E-13 mr1553_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