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Detailed information for vg0705425288:

Variant ID: vg0705425288 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 5425288
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.76, C: 0.25, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:


TTCTTTAGATCTTGCAGGTAAGAACATAAATGCCTTATCTCCTGAAATGGATTTGAATTGTTTTGATCAGTTACATTTGCAGGCACTTTGACGACCTATC[T/C]
GGAGTCAAGCTAAAACACATAGAATTTGCTTTATACTGCATTCTTCAAAATGGCGTTATATTCAAACCAAAGCATTTCTTAACCTCTTATTCCGATTTGC

Reverse complement sequence

GCAAATCGGAATAAGAGGTTAAGAAATGCTTTGGTTTGAATATAACGCCATTTTGAAGAATGCAGTATAAAGCAAATTCTATGTGTTTTAGCTTGACTCC[A/G]
GATAGGTCGTCAAAGTGCCTGCAAATGTAACTGATCAAAACAATTCAAATCCATTTCAGGAGATAAGGCATTTATGTTCTTACCTGCAAGATCTAAAGAA

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 98.70% 1.30% 0.00% 0.00% NA
All Indica  2759 99.70% 0.30% 0.00% 0.00% NA
All Japonica  1512 96.60% 3.40% 0.00% 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 99.70% 0.30% 0.00% 0.00% NA
Indica Intermediate  786 99.40% 0.60% 0.00% 0.00% NA
Temperate Japonica  767 94.50% 5.50% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 96.30% 3.70% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 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
vg0705425288 T -> C LOC_Os07g10110.1 intron_variant ; MODIFIER silent_mutation Average:46.833; most accessible tissue: Callus, score: 82.803 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0705425288 2.89E-11 2.70E-12 mr1549_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
vg0705425288 4.88E-10 2.04E-10 mr1550_2 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
vg0705425288 2.06E-09 1.11E-10 mr1757_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