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Detailed information for vg0125055790:

Variant ID: vg0125055790 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 25055790
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TATAAGACTTTCTGGTATTGCCCACATTCACATATGCTAGAAAGTCTTATAACCTGGAATGGAGGTAGTACAATTTTGATGAAGTTGCAAAATATTCGTT[T/C]
TGCTATATTTTTAAAGTGTCGATTCAATCAAACCAAATATTTGACAATACCTTTTCTTTACAAACTAAATGGAGAATTAATTTATTGATATGGCTAAATT

Reverse complement sequence

AATTTAGCCATATCAATAAATTAATTCTCCATTTAGTTTGTAAAGAAAAGGTATTGTCAAATATTTGGTTTGATTGAATCGACACTTTAAAAATATAGCA[A/G]
AACGAATATTTTGCAACTTCATCAAAATTGTACTACCTCCATTCCAGGTTATAAGACTTTCTAGCATATGTGAATGTGGGCAATACCAGAAAGTCTTATA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.30% 6.70% 0.02% 0.00% NA
All Indica  2759 97.10% 2.80% 0.04% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 19.00% 81.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 95.10% 4.90% 0.00% 0.00% NA
Indica Intermediate  786 95.80% 4.10% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 88.50% 11.50% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg0125055790 T -> C LOC_Os01g43720.1 3_prime_UTR_variant ; 758.0bp to feature; MODIFIER silent_mutation Average:66.533; most accessible tissue: Callus, score: 92.843 N N N N
vg0125055790 T -> C LOC_Os01g43740.1 upstream_gene_variant ; 4974.0bp to feature; MODIFIER silent_mutation Average:66.533; most accessible tissue: Callus, score: 92.843 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0125055790 NA 5.36E-20 mr1305_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
vg0125055790 NA 1.95E-07 mr1582_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
vg0125055790 NA 5.89E-08 mr1808_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
vg0125055790 NA 3.20E-06 mr1815_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