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Detailed information for vg0133266800:

Variant ID: vg0133266800 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 33266800
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.84, A: 0.16, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:


CCGTTGGCACTGGTCAAGCTAATTTTTGCCTCCACTAAAATGTTTAAAATAGTACTCCCTCCGTTTTTTAATAAATAACGCCGTTGACTTTTTTTCACAT[G/A]
TTTAACCATTCGTCTTATTCAAAAAAATTTACGTAATTATAATTTATTTTGTTATGAGTTGTTTTATCACGCATAGTACTTTAAATGTGATTTATATCAT

Reverse complement sequence

ATGATATAAATCACATTTAAAGTACTATGCGTGATAAAACAACTCATAACAAAATAAATTATAATTACGTAAATTTTTTTGAATAAGACGAATGGTTAAA[C/T]
ATGTGAAAAAAAGTCAACGGCGTTATTTATTAAAAAACGGAGGGAGTACTATTTTAAACATTTTAGTGGAGGCAAAAATTAGCTTGACCAGTGCCAACGG

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 54.00% 45.40% 0.47% 0.15% NA
All Indica  2759 84.80% 14.30% 0.69% 0.25% NA
All Japonica  1512 1.30% 98.70% 0.00% 0.00% NA
Aus  269 63.90% 36.10% 0.00% 0.00% NA
Indica I  595 92.90% 6.40% 0.50% 0.17% NA
Indica II  465 78.30% 19.40% 1.72% 0.65% NA
Indica III  913 84.80% 15.10% 0.00% 0.11% NA
Indica Intermediate  786 82.40% 16.30% 1.02% 0.25% NA
Temperate Japonica  767 1.00% 99.00% 0.00% 0.00% NA
Tropical Japonica  504 1.00% 99.00% 0.00% 0.00% NA
Japonica Intermediate  241 2.50% 97.50% 0.00% 0.00% NA
VI/Aromatic  96 2.10% 96.90% 1.04% 0.00% NA
Intermediate  90 22.20% 75.60% 2.22% 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
vg0133266800 G -> A LOC_Os01g57570.1 intron_variant ; MODIFIER silent_mutation Average:50.262; most accessible tissue: Minghui63 root, score: 76.721 N N N N
vg0133266800 G -> A LOC_Os01g57570.2 intron_variant ; MODIFIER silent_mutation Average:50.262; most accessible tissue: Minghui63 root, score: 76.721 N N N N
vg0133266800 G -> DEL N N silent_mutation Average:50.262; most accessible tissue: Minghui63 root, score: 76.721 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0133266800 1.29E-08 NA mr1008 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
vg0133266800 2.34E-08 8.08E-10 mr1008 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
vg0133266800 6.15E-08 NA mr1009 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
vg0133266800 9.44E-08 5.81E-09 mr1009 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
vg0133266800 8.88E-06 NA mr1014 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
vg0133266800 NA 4.72E-06 mr1193 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
vg0133266800 2.55E-07 NA mr1008_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
vg0133266800 3.41E-09 8.61E-10 mr1008_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