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Detailed information for vg0133007467:

Variant ID: vg0133007467 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 33007467
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTCAGGATTACCATTCCTTGAATTTTCCAAAAAATCTGTGGAGCAAAACCAAAATTAAAATCATATAATACATAATAAAATAAAAATGTTTTTTTTCCAG[A/C]
TTGAAGCCTTTCTTGTGTTTCTCACCATTGCTAAGCAATCTATAAGAGGTATCCTCTGAGTGATCAAAAGATTCTCCACCATTGTTAAGTTCCACCATTA

Reverse complement sequence

TAATGGTGGAACTTAACAATGGTGGAGAATCTTTTGATCACTCAGAGGATACCTCTTATAGATTGCTTAGCAATGGTGAGAAACACAAGAAAGGCTTCAA[T/G]
CTGGAAAAAAAACATTTTTATTTTATTATGTATTATATGATTTTAATTTTGGTTTTGCTCCACAGATTTTTTGGAAAATTCAAGGAATGGTAATCCTGAG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.50% 1.30% 0.23% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 95.90% 3.50% 0.60% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 88.50% 9.90% 1.59% 0.00% NA
Japonica Intermediate  241 98.30% 1.20% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 91.10% 6.70% 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
vg0133007467 A -> C LOC_Os01g57110.1 intron_variant ; MODIFIER silent_mutation Average:54.11; most accessible tissue: Callus, score: 82.788 N N N N
vg0133007467 A -> C LOC_Os01g57110.2 intron_variant ; MODIFIER silent_mutation Average:54.11; most accessible tissue: Callus, score: 82.788 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0133007467 NA 9.86E-06 mr1218 Jap_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
vg0133007467 NA 6.65E-06 mr1448 Jap_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
vg0133007467 NA 3.17E-08 mr1583 Jap_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
vg0133007467 7.28E-06 1.06E-09 mr1830 Jap_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
vg0133007467 NA 1.81E-06 mr1188_2 Jap_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
vg0133007467 NA 8.40E-07 mr1850_2 Jap_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